Date: 2021-07-22 20:59:15 CEST, cola version: 1.9.4
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First the variable is renamed to res_rh.
res_rh = rh
The partition hierarchy and all available functions which can be applied to res_rh object.
res_rh
#> A 'HierarchicalPartition' object with 4 combinations of top-value methods and partitioning methods.
#> On a matrix with 375878 rows and 888 columns.
#> Performed in total 135800 partitions.
#> There are 66 groups under the following parameters:
#> - min_samples: 9
#> - mean_silhouette_cutoff: 0.9
#> - min_n_signatures: 1000 (signatures are selected based on:)
#> - fdr_cutoff: 0.05
#> - group_diff: 0.25
#>
#> Hierarchy of the partition:
#> 0, 888 cols
#> |-- 01, 155 cols, 22951 signatures
#> | |-- 011, 50 cols, 2144 signatures
#> | | |-- 0111, 10 cols (b)
#> | | |-- 0112, 15 cols (b)
#> | | |-- 0113, 12 cols (b)
#> | | |-- 0114, 5 cols (b)
#> | | `-- 0115, 8 cols (b)
#> | |-- 012, 29 cols, 15450 signatures
#> | | |-- 0121, 2 cols (b)
#> | | |-- 0122, 17 cols (b)
#> | | `-- 0123, 10 cols (b)
#> | |-- 013, 25 cols, 12745 signatures
#> | | |-- 0131, 9 cols (b)
#> | | |-- 0132, 6 cols (b)
#> | | |-- 0133, 6 cols (b)
#> | | `-- 0134, 4 cols (b)
#> | |-- 014, 27 cols, 0 signatures (c)
#> | `-- 015, 24 cols, 21454 signatures
#> | |-- 0151, 2 cols (b)
#> | |-- 0152, 11 cols (b)
#> | |-- 0153, 3 cols (b)
#> | `-- 0154, 8 cols (b)
#> |-- 02, 311 cols, 23761 signatures
#> | |-- 021, 76 cols, 14822 signatures
#> | | |-- 0211, 27 cols, 708 signatures (c)
#> | | |-- 0212, 18 cols, 1222 signatures
#> | | | |-- 02121, 8 cols (b)
#> | | | `-- 02122, 10 cols (b)
#> | | `-- 0213, 31 cols, 1414 signatures
#> | | |-- 02131, 20 cols, 54 signatures (c)
#> | | `-- 02132, 11 cols (b)
#> | |-- 022, 55 cols, 1749 signatures
#> | | |-- 0221, 23 cols, 6990 signatures
#> | | | |-- 02211, 8 cols (b)
#> | | | |-- 02212, 4 cols (b)
#> | | | |-- 02213, 6 cols (b)
#> | | | `-- 02214, 5 cols (b)
#> | | `-- 0222, 32 cols, 3920 signatures
#> | | |-- 02221, 10 cols (b)
#> | | |-- 02222, 10 cols (b)
#> | | `-- 02223, 12 cols (b)
#> | |-- 023, 95 cols, 7407 signatures
#> | | |-- 0231, 39 cols, 613 signatures (c)
#> | | |-- 0232, 27 cols, 1863 signatures
#> | | | |-- 02321, 19 cols, 424 signatures (c)
#> | | | `-- 02322, 8 cols (b)
#> | | `-- 0233, 29 cols, 845 signatures (c)
#> | `-- 024, 85 cols, 1823 signatures
#> | |-- 0241, 44 cols, 826 signatures (c)
#> | `-- 0242, 41 cols, 8366 signatures
#> | |-- 02421, 12 cols (b)
#> | |-- 02422, 19 cols, 70 signatures (c)
#> | `-- 02423, 10 cols (b)
#> |-- 03, 134 cols, 20697 signatures
#> | |-- 031, 44 cols, 8878 signatures
#> | | |-- 0311, 18 cols, 511 signatures (c)
#> | | |-- 0312, 6 cols (b)
#> | | |-- 0313, 12 cols (b)
#> | | `-- 0314, 8 cols (b)
#> | |-- 032, 27 cols, 1257 signatures
#> | | |-- 0321, 12 cols (b)
#> | | `-- 0322, 15 cols (b)
#> | |-- 033, 44 cols, 2288 signatures
#> | | |-- 0331, 17 cols (b)
#> | | `-- 0332, 27 cols, 555 signatures (c)
#> | `-- 034, 19 cols, 9552 signatures
#> | |-- 0341, 11 cols (b)
#> | |-- 0342, 6 cols (b)
#> | `-- 0343, 2 cols (b)
#> `-- 04, 288 cols, 4517 signatures
#> |-- 041, 117 cols, 12308 signatures
#> | |-- 0411, 54 cols, 1859 signatures
#> | | |-- 04111, 22 cols, 73 signatures (c)
#> | | |-- 04112, 8 cols (b)
#> | | `-- 04113, 24 cols, 1170 signatures
#> | | |-- 041131, 6 cols (b)
#> | | |-- 041132, 14 cols (b)
#> | | `-- 041133, 4 cols (b)
#> | |-- 0412, 45 cols, 159 signatures (c)
#> | `-- 0413, 18 cols, 3775 signatures
#> | |-- 04131, 9 cols (b)
#> | |-- 04132, 5 cols (b)
#> | `-- 04133, 4 cols (b)
#> |-- 042, 67 cols, 8036 signatures
#> | |-- 0421, 40 cols, 987 signatures (c)
#> | |-- 0422, 19 cols, 5436 signatures
#> | | |-- 04221, 5 cols (b)
#> | | `-- 04222, 14 cols (b)
#> | `-- 0423, 8 cols (b)
#> `-- 043, 104 cols, 3086 signatures
#> |-- 0431, 55 cols, 52 signatures (c)
#> |-- 0432, 14 cols (b)
#> `-- 0433, 35 cols, 7632 signatures
#> |-- 04331, 4 cols (b)
#> |-- 04332, 25 cols, 485 signatures (c)
#> `-- 04333, 6 cols (b)
#> Stop reason:
#> b) Subgroup had too few columns.
#> c) There were too few signatures.
#>
#> Following methods can be applied to this 'HierarchicalPartition' object:
#> [1] "all_leaves" "all_nodes" "cola_report" "collect_classes"
#> [5] "colnames" "compare_signatures" "dimension_reduction" "functional_enrichment"
#> [9] "get_anno_col" "get_anno" "get_children_nodes" "get_classes"
#> [13] "get_matrix" "get_signatures" "is_leaf_node" "max_depth"
#> [17] "merge_node" "ncol" "node_info" "node_level"
#> [21] "nrow" "rownames" "show" "split_node"
#> [25] "suggest_best_k" "test_to_known_factors" "top_rows_heatmap" "top_rows_overlap"
#>
#> You can get result for a single node by e.g. object["01"]
The call of hierarchical_partition() was:
#> hierarchical_partition(data = mat, top_n = 1000, top_value_method = c("SD", "ATC"),
#> partition_method = c("kmeans", "skmeans"), subset = 500, group_diff = 0.25, min_n_signatures = 1000,
#> filter_fun = function(mat) {
#> s = rowSds(mat)
#> order(-s)[1:30000]
#> }, max_k = 8, scale_rows = FALSE, cores = 4)
Dimension of the input matrix:
mat = get_matrix(res_rh)
dim(mat)
#> [1] 375878 888
All the methods that were tried:
res_rh@param$combination_method
#> [[1]]
#> [1] "SD" "kmeans"
#>
#> [[2]]
#> [1] "ATC" "kmeans"
#>
#> [[3]]
#> [1] "SD" "skmeans"
#>
#> [[4]]
#> [1] "ATC" "skmeans"
The density distribution for each sample is visualized as one column in the following heatmap. The clustering is based on the distance which is the Kolmogorov-Smirnov statistic between two distributions.
library(ComplexHeatmap)
densityHeatmap(mat, ylab = "value", cluster_columns = TRUE, show_column_names = FALSE,
mc.cores = 1)
Some values about the hierarchy:
all_nodes(res_rh)
#> [1] "0" "01" "011" "0111" "0112" "0113" "0114" "0115" "012" "0121"
#> [11] "0122" "0123" "013" "0131" "0132" "0133" "0134" "014" "015" "0151"
#> [21] "0152" "0153" "0154" "02" "021" "0211" "0212" "02121" "02122" "0213"
#> [31] "02131" "02132" "022" "0221" "02211" "02212" "02213" "02214" "0222" "02221"
#> [41] "02222" "02223" "023" "0231" "0232" "02321" "02322" "0233" "024" "0241"
#> [51] "0242" "02421" "02422" "02423" "03" "031" "0311" "0312" "0313" "0314"
#> [61] "032" "0321" "0322" "033" "0331" "0332" "034" "0341" "0342" "0343"
#> [71] "04" "041" "0411" "04111" "04112" "04113" "041131" "041132" "041133" "0412"
#> [81] "0413" "04131" "04132" "04133" "042" "0421" "0422" "04221" "04222" "0423"
#> [91] "043" "0431" "0432" "0433" "04331" "04332" "04333"
all_leaves(res_rh)
#> [1] "0111" "0112" "0113" "0114" "0115" "0121" "0122" "0123" "0131" "0132"
#> [11] "0133" "0134" "014" "0151" "0152" "0153" "0154" "0211" "02121" "02122"
#> [21] "02131" "02132" "02211" "02212" "02213" "02214" "02221" "02222" "02223" "0231"
#> [31] "02321" "02322" "0233" "0241" "02421" "02422" "02423" "0311" "0312" "0313"
#> [41] "0314" "0321" "0322" "0331" "0332" "0341" "0342" "0343" "04111" "04112"
#> [51] "041131" "041132" "041133" "0412" "04131" "04132" "04133" "0421" "04221" "04222"
#> [61] "0423" "0431" "0432" "04331" "04332" "04333"
node_info(res_rh)
#> id best_method depth best_k n_columns n_signatures p_signatures is_leaf
#> 1 0 SD:skmeans 1 4 888 32783 0.087217 FALSE
#> 2 01 SD:skmeans 2 5 155 22951 0.061060 FALSE
#> 3 011 ATC:skmeans 3 5 50 2144 0.005704 FALSE
#> 4 0111 not applied 4 NA 10 NA NA TRUE
#> 5 0112 not applied 4 NA 15 NA NA TRUE
#> 6 0113 not applied 4 NA 12 NA NA TRUE
#> 7 0114 not applied 4 NA 5 NA NA TRUE
#> 8 0115 not applied 4 NA 8 NA NA TRUE
#> 9 012 ATC:kmeans 3 3 29 15450 0.041104 FALSE
#> 10 0121 not applied 4 NA 2 NA NA TRUE
#> 11 0122 not applied 4 NA 17 NA NA TRUE
#> 12 0123 not applied 4 NA 10 NA NA TRUE
#> 13 013 ATC:skmeans 3 4 25 12745 0.033907 FALSE
#> 14 0131 not applied 4 NA 9 NA NA TRUE
#> 15 0132 not applied 4 NA 6 NA NA TRUE
#> 16 0133 not applied 4 NA 6 NA NA TRUE
#> 17 0134 not applied 4 NA 4 NA NA TRUE
#> 18 014 ATC:kmeans 3 2 27 0 0.000000 TRUE
#> 19 015 ATC:skmeans 3 4 24 21454 0.057077 FALSE
#> 20 0151 not applied 4 NA 2 NA NA TRUE
#> 21 0152 not applied 4 NA 11 NA NA TRUE
#> 22 0153 not applied 4 NA 3 NA NA TRUE
#> 23 0154 not applied 4 NA 8 NA NA TRUE
#> 24 02 ATC:kmeans 2 4 311 23761 0.063215 FALSE
#> 25 021 ATC:kmeans 3 3 76 14822 0.039433 FALSE
#> 26 0211 ATC:kmeans 4 2 27 708 0.001884 TRUE
#> 27 0212 ATC:skmeans 4 2 18 1222 0.003251 FALSE
#> 28 02121 not applied 5 NA 8 NA NA TRUE
#> 29 02122 not applied 5 NA 10 NA NA TRUE
#> 30 0213 ATC:kmeans 4 2 31 1414 0.003762 FALSE
#> 31 02131 ATC:skmeans 5 2 20 54 0.000144 TRUE
#> 32 02132 not applied 5 NA 11 NA NA TRUE
#> 33 022 ATC:kmeans 3 2 55 1749 0.004653 FALSE
#> 34 0221 ATC:kmeans 4 4 23 6990 0.018596 FALSE
#> 35 02211 not applied 5 NA 8 NA NA TRUE
#> 36 02212 not applied 5 NA 4 NA NA TRUE
#> 37 02213 not applied 5 NA 6 NA NA TRUE
#> 38 02214 not applied 5 NA 5 NA NA TRUE
#> 39 0222 ATC:kmeans 4 3 32 3920 0.010429 FALSE
#> 40 02221 not applied 5 NA 10 NA NA TRUE
#> 41 02222 not applied 5 NA 10 NA NA TRUE
#> 42 02223 not applied 5 NA 12 NA NA TRUE
#> 43 023 ATC:kmeans 3 3 95 7407 0.019706 FALSE
#> 44 0231 SD:kmeans 4 2 39 613 0.001631 TRUE
#> 45 0232 ATC:kmeans 4 2 27 1863 0.004956 FALSE
#> 46 02321 ATC:kmeans 5 2 19 424 0.001128 TRUE
#> 47 02322 not applied 5 NA 8 NA NA TRUE
#> 48 0233 ATC:kmeans 4 2 29 845 0.002248 TRUE
#> 49 024 ATC:kmeans 3 2 85 1823 0.004850 FALSE
#> 50 0241 ATC:skmeans 4 2 44 826 0.002198 TRUE
#> 51 0242 ATC:skmeans 4 3 41 8366 0.022257 FALSE
#> 52 02421 not applied 5 NA 12 NA NA TRUE
#> 53 02422 ATC:skmeans 5 2 19 70 0.000186 TRUE
#> 54 02423 not applied 5 NA 10 NA NA TRUE
#> 55 03 ATC:skmeans 2 4 134 20697 0.055063 FALSE
#> 56 031 ATC:kmeans 3 4 44 8878 0.023619 FALSE
#> 57 0311 ATC:skmeans 4 3 18 511 0.001359 TRUE
#> 58 0312 not applied 4 NA 6 NA NA TRUE
#> 59 0313 not applied 4 NA 12 NA NA TRUE
#> 60 0314 not applied 4 NA 8 NA NA TRUE
#> 61 032 ATC:skmeans 3 2 27 1257 0.003344 FALSE
#> 62 0321 not applied 4 NA 12 NA NA TRUE
#> 63 0322 not applied 4 NA 15 NA NA TRUE
#> 64 033 SD:kmeans 3 2 44 2288 0.006087 FALSE
#> 65 0331 not applied 4 NA 17 NA NA TRUE
#> 66 0332 ATC:kmeans 4 2 27 555 0.001477 TRUE
#> 67 034 ATC:kmeans 3 3 19 9552 0.025413 FALSE
#> 68 0341 not applied 4 NA 11 NA NA TRUE
#> 69 0342 not applied 4 NA 6 NA NA TRUE
#> 70 0343 not applied 4 NA 2 NA NA TRUE
#> 71 04 ATC:kmeans 2 3 288 4517 0.012017 FALSE
#> 72 041 ATC:kmeans 3 3 117 12308 0.032745 FALSE
#> 73 0411 ATC:kmeans 4 3 54 1859 0.004946 FALSE
#> 74 04111 ATC:kmeans 5 2 22 73 0.000194 TRUE
#> 75 04112 not applied 5 NA 8 NA NA TRUE
#> 76 04113 ATC:skmeans 5 3 24 1170 0.003113 FALSE
#> 77 041131 not applied 6 NA 6 NA NA TRUE
#> 78 041132 not applied 6 NA 14 NA NA TRUE
#> 79 041133 not applied 6 NA 4 NA NA TRUE
#> 80 0412 ATC:skmeans 4 2 45 159 0.000423 TRUE
#> 81 0413 ATC:skmeans 4 3 18 3775 0.010043 FALSE
#> 82 04131 not applied 5 NA 9 NA NA TRUE
#> 83 04132 not applied 5 NA 5 NA NA TRUE
#> 84 04133 not applied 5 NA 4 NA NA TRUE
#> 85 042 ATC:skmeans 3 3 67 8036 0.021379 FALSE
#> 86 0421 ATC:kmeans 4 3 40 987 0.002626 TRUE
#> 87 0422 ATC:kmeans 4 2 19 5436 0.014462 FALSE
#> 88 04221 not applied 5 NA 5 NA NA TRUE
#> 89 04222 not applied 5 NA 14 NA NA TRUE
#> 90 0423 not applied 4 NA 8 NA NA TRUE
#> 91 043 ATC:skmeans 3 3 104 3086 0.008210 FALSE
#> 92 0431 SD:kmeans 4 2 55 52 0.000138 TRUE
#> 93 0432 not applied 4 NA 14 NA NA TRUE
#> 94 0433 ATC:skmeans 4 3 35 7632 0.020304 FALSE
#> 95 04331 not applied 5 NA 4 NA NA TRUE
#> 96 04332 ATC:skmeans 5 3 25 485 0.001290 TRUE
#> 97 04333 not applied 5 NA 6 NA NA TRUE
In the output from node_info(), there are the following columns:
id: The node id.best_method: The best method selected.depth: Depth of the node in the hierarchy.best_k: Best number of groups of the partition on that node.n_columns: Number of columns in the submatrix.n_signatures: Number of signatures with the best_k.p_signatures: Proportion of hte signatures in total number of rows in the matrix.is_leaf: Whether the node is a leaf.Labels of nodes are encoded in a special way. The number of digits correspond to the depth of the node in the hierarchy and the value of the digits correspond to the index of the subgroup in the current node, E.g. a label of “012” means the node is the second subgroup of the partition which is the first subgroup of the root node.
Following table shows the best k (number of partitions) for each node in the
partition hierarchy. Clicking on the node name in the table goes to the
corresponding section for the partitioning on that node.
The cola vignette explains the definition of the metrics used for determining the best number of partitions.
suggest_best_k(res_rh)
| Node | Best method | Is leaf | Best k | 1-PAC | Mean silhouette | Concordance | #samples | |
|---|---|---|---|---|---|---|---|---|
| Node0 | SD:skmeans | 4 | 1.00 | 0.98 | 0.99 | 888 | ** | |
| Node01 | SD:skmeans | 5 | 1.00 | 0.97 | 0.99 | 155 | ** | |
| Node011 | ATC:skmeans | 8 | 0.92 | 0.81 | 0.87 | 50 | * | |
| Node0111-leaf | not applied | ✓ (b) | 10 | |||||
| Node0112-leaf | not applied | ✓ (b) | 15 | |||||
| Node0113-leaf | not applied | ✓ (b) | 12 | |||||
| Node0114-leaf | not applied | ✓ (b) | 5 | |||||
| Node0115-leaf | not applied | ✓ (b) | 8 | |||||
| Node012 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 29 | ** | |
| Node0121-leaf | not applied | ✓ (b) | 2 | |||||
| Node0122-leaf | not applied | ✓ (b) | 17 | |||||
| Node0123-leaf | not applied | ✓ (b) | 10 | |||||
| Node013 | ATC:skmeans | 4 | 1.00 | 0.96 | 0.98 | 25 | ** | |
| Node0131-leaf | not applied | ✓ (b) | 9 | |||||
| Node0132-leaf | not applied | ✓ (b) | 6 | |||||
| Node0133-leaf | not applied | ✓ (b) | 6 | |||||
| Node0134-leaf | not applied | ✓ (b) | 4 | |||||
| Node014-leaf | ATC:kmeans | ✓ (c) | 3 | 1.00 | 0.95 | 1.00 | 27 | ** |
| Node015 | ATC:skmeans | 4 | 1.00 | 0.99 | 0.99 | 24 | ** | |
| Node0151-leaf | not applied | ✓ (b) | 2 | |||||
| Node0152-leaf | not applied | ✓ (b) | 11 | |||||
| Node0153-leaf | not applied | ✓ (b) | 3 | |||||
| Node0154-leaf | not applied | ✓ (b) | 8 | |||||
| Node02 | ATC:kmeans | 4 | 1.00 | 0.97 | 0.99 | 311 | ** | |
| Node021 | ATC:kmeans | 3 | 1.00 | 0.98 | 0.99 | 76 | ** | |
| Node0211-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 0.99 | 0.99 | 27 | ** |
| Node0212 | ATC:skmeans | 5 | 0.90 | 0.84 | 0.95 | 18 | * | |
| Node02121-leaf | not applied | ✓ (b) | 8 | |||||
| Node02122-leaf | not applied | ✓ (b) | 10 | |||||
| Node0213 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 31 | ** | |
| Node02131-leaf | ATC:skmeans | ✓ (c) | 2 | 0.90 | 0.98 | 0.99 | 20 | |
| Node02132-leaf | not applied | ✓ (b) | 11 | |||||
| Node022 | ATC:kmeans | 2 | 1.00 | 0.99 | 0.99 | 55 | ** | |
| Node0221 | ATC:kmeans | 4 | 0.90 | 0.96 | 0.95 | 23 | * | |
| Node02211-leaf | not applied | ✓ (b) | 8 | |||||
| Node02212-leaf | not applied | ✓ (b) | 4 | |||||
| Node02213-leaf | not applied | ✓ (b) | 6 | |||||
| Node02214-leaf | not applied | ✓ (b) | 5 | |||||
| Node0222 | ATC:kmeans | 3 | 1.00 | 1.00 | 1.00 | 32 | ** | |
| Node02221-leaf | not applied | ✓ (b) | 10 | |||||
| Node02222-leaf | not applied | ✓ (b) | 10 | |||||
| Node02223-leaf | not applied | ✓ (b) | 12 | |||||
| Node023 | ATC:kmeans | 3 | 1.00 | 0.96 | 0.98 | 95 | ** | |
| Node0231-leaf | SD:kmeans | ✓ (c) | 2 | 0.95 | 0.97 | 0.99 | 39 | * |
| Node0232 | ATC:kmeans | 2 | 1.00 | 0.97 | 0.99 | 27 | ** | |
| Node02321-leaf | ATC:kmeans | ✓ (c) | 7 | 0.90 | 0.87 | 0.92 | 19 | * |
| Node02322-leaf | not applied | ✓ (b) | 8 | |||||
| Node0233-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 29 | ** |
| Node024 | ATC:kmeans | 4 | 0.91 | 0.89 | 0.94 | 85 | * | |
| Node0241-leaf | ATC:skmeans | ✓ (c) | 3 | 0.90 | 0.85 | 0.95 | 44 | * |
| Node0242 | ATC:skmeans | 3 | 1.00 | 0.96 | 0.98 | 41 | ** | |
| Node02421-leaf | not applied | ✓ (b) | 12 | |||||
| Node02422-leaf | ATC:skmeans | ✓ (c) | 8 | 0.91 | 0.81 | 0.91 | 19 | * |
| Node02423-leaf | not applied | ✓ (b) | 10 | |||||
| Node03 | ATC:skmeans | 4 | 1.00 | 0.97 | 0.99 | 134 | ** | |
| Node031 | ATC:kmeans | 4 | 0.91 | 0.97 | 0.97 | 44 | * | |
| Node0311-leaf | ATC:skmeans | ✓ (c) | 8 | 0.93 | 0.61 | 0.89 | 18 | * |
| Node0312-leaf | not applied | ✓ (b) | 6 | |||||
| Node0313-leaf | not applied | ✓ (b) | 12 | |||||
| Node0314-leaf | not applied | ✓ (b) | 8 | |||||
| Node032 | ATC:skmeans | 3 | 0.91 | 0.92 | 0.95 | 27 | * | |
| Node0321-leaf | not applied | ✓ (b) | 12 | |||||
| Node0322-leaf | not applied | ✓ (b) | 15 | |||||
| Node033 | SD:kmeans | 2 | 1.00 | 0.98 | 0.99 | 44 | ** | |
| Node0331-leaf | not applied | ✓ (b) | 17 | |||||
| Node0332-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 0.95 | 0.98 | 27 | ** |
| Node034 | ATC:kmeans | 3 | 1.00 | 1.00 | 0.99 | 19 | ** | |
| Node0341-leaf | not applied | ✓ (b) | 11 | |||||
| Node0342-leaf | not applied | ✓ (b) | 6 | |||||
| Node0343-leaf | not applied | ✓ (b) | 2 | |||||
| Node04 | ATC:kmeans | 4 | 0.92 | 0.88 | 0.95 | 288 | * | |
| Node041 | ATC:kmeans | 4 | 0.99 | 0.94 | 0.98 | 117 | ** | |
| Node0411 | ATC:kmeans | 3 | 0.90 | 0.96 | 0.97 | 54 | * | |
| Node04111-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 22 | ** |
| Node04112-leaf | not applied | ✓ (b) | 8 | |||||
| Node04113 | ATC:skmeans | 3 | 1.00 | 1.00 | 1.00 | 24 | ** | |
| Node041131-leaf | not applied | ✓ (b) | 6 | |||||
| Node041132-leaf | not applied | ✓ (b) | 14 | |||||
| Node041133-leaf | not applied | ✓ (b) | 4 | |||||
| Node0412-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 0.98 | 0.99 | 45 | ** |
| Node0413 | ATC:skmeans | 7 | 0.92 | 0.64 | 0.92 | 18 | * | |
| Node04131-leaf | not applied | ✓ (b) | 9 | |||||
| Node04132-leaf | not applied | ✓ (b) | 5 | |||||
| Node04133-leaf | not applied | ✓ (b) | 4 | |||||
| Node042 | ATC:skmeans | 3 | 1.00 | 1.00 | 1.00 | 67 | ** | |
| Node0421-leaf | ATC:kmeans | ✓ (c) | 3 | 0.97 | 0.98 | 0.99 | 40 | ** |
| Node0422 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 19 | ** | |
| Node04221-leaf | not applied | ✓ (b) | 5 | |||||
| Node04222-leaf | not applied | ✓ (b) | 14 | |||||
| Node0423-leaf | not applied | ✓ (b) | 8 | |||||
| Node043 | ATC:skmeans | 3 | 1.00 | 0.97 | 0.99 | 104 | ** | |
| Node0431-leaf | SD:kmeans | ✓ (c) | 2 | 1.00 | 0.98 | 0.99 | 55 | ** |
| Node0432-leaf | not applied | ✓ (b) | 14 | |||||
| Node0433 | ATC:skmeans | 3 | 1.00 | 0.96 | 0.98 | 35 | ** | |
| Node04331-leaf | not applied | ✓ (b) | 4 | |||||
| Node04332-leaf | ATC:skmeans | ✓ (c) | 3 | 1.00 | 1.00 | 1.00 | 25 | ** |
| Node04333-leaf | not applied | ✓ (b) | 6 |
Stop reason: b) Subgroup had too few columns. c) There were too few signatures.
**: 1-PAC > 0.95, *: 1-PAC > 0.9
The nodes of the hierarchy can be merged by setting the merge_node parameters. Here we
control the hierarchy with the min_n_signatures parameter. The value of min_n_signatures is
from node_info().
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1170))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1222))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1257))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1414))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1749))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1823))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1859))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1863))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2144))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2288))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3086))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3775))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3920))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4517))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5436))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6990))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7407))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7632))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8036))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8366))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8878))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 9552))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 12308))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 12745))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 14822))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 15450))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 20697))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 21454))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 22951))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 23761))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 32783))
Following shows the table of the partitions (You need to click the show/hide code output link to see it).
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1170))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "0412" "0421" "04132" "02122" "0412" "0313"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04112" "0122" "0431" "0431" "04222" "0431"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "0112" "04131" "02131" "02321" "0211" "0421"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "02132" "0233" "04112" "0241" "04111"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "0311" "0231" "0431" "0313" "0431" "02223"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "02122" "0241" "0231" "02213" "0311" "0311"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "0115" "02131" "0332" "0123" "041132" "0113"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "0233" "04111" "0241" "02223" "04132" "0421"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "0231" "04333" "04332" "0412" "0332" "0421"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04332" "0432" "0241" "041132" "0421" "041131"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04111" "0421" "0231" "0311" "04332" "04112"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04222" "02122" "02421" "0231" "04131" "0431"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "0314" "0431" "02214" "0133" "02222"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "0342" "0321" "04111" "0412" "0233" "0421"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "0412" "0113" "02423" "0241" "0152" "0421"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "0114" "0331" "02223" "02321" "0233" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "0432" "014" "02422" "02423" "02322" "02321"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "0412" "0211" "0133" "02131" "0241" "02321"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04222" "0332" "0122" "0412" "02122" "0313"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "0233" "04221" "0233" "0342" "0233" "04131"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "0241" "0431" "0241" "0115" "0412" "0421"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "02222" "0122" "0322" "0231" "0314" "0241"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04331" "0311" "0322" "0241" "0331" "02132"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "0112" "0332" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "0423" "0113" "02421" "0132" "0112" "041132"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "0412" "0112" "0241" "04331" "0431" "02211"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "0421" "02131" "014" "041132" "0114" "02131"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "02421" "041131" "0113" "0332" "0341" "02221"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "0421" "04332" "0152" "041133" "04131" "04222"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "02422" "0412" "0431" "0412" "0151" "0113"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "0331" "02321" "0122" "041132" "04332" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04133" "041133" "0322" "0241" "0115" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "02321" "0112" "0412" "0332" "0431"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "0431" "0241" "02211" "0431" "04222" "0421"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "0322" "02421" "0132" "04221" "0431" "0231"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "0231" "02122" "0342" "0423" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "02131" "0314" "0131" "04222" "0311"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "02222" "0123" "0233" "0412" "0231" "0312"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "0231" "014" "0322" "02131" "041132" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "0233" "0231" "04111" "0312" "0231" "02122"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "041133" "0233" "0311" "0412" "0431" "0421"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "0313" "0412" "02321" "0322" "0421" "0423"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "0421" "0321" "0431" "014" "0233"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "0313" "02421" "04133" "0322" "0431" "02422"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "0231" "0431" "0423" "04111" "0332" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "02423" "0211" "0122" "014" "04132"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "0233" "0131" "02321" "0211" "014" "04111"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "0412" "0112" "041132" "0154" "02223" "0432"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "04332" "0241" "0432" "02131" "02422"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "0241" "0241" "0412" "0431" "0153" "04332"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "0431" "04111" "04333" "0421" "02322" "0231"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "0421" "0123" "0341" "014" "0432" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04112" "0332" "0331" "04131" "0241" "0332"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04112" "0112" "0421" "0233" "02131" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "0332" "0231" "0331" "04221" "0423" "04332"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "0332" "0313" "0421" "02321" "0241" "02131"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "02211" "0233" "0154" "02132" "0241" "04111"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "0412" "0211" "0231" "02222" "0113" "0431"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "0432" "0431" "04111" "0233" "0241" "0233"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "02213" "0431" "0332" "0133" "0322" "0112"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "0321" "0431" "0231" "02422" "0115" "02322"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "02422" "0123" "0312" "0111" "0231" "02421"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "02423" "02321" "0322" "0431" "0115"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "02422" "02422" "0313" "0311" "0431" "0115"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "0113" "02212" "041132" "0431" "02121" "0233"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "0312" "0152" "0421" "0115" "02221" "0111"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04333" "04331" "02321" "0412" "02221" "0431"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "0313" "0332" "0211" "02321" "0241" "0314"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "02422" "0412" "02223" "02122" "0412" "0113"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "0421" "02422" "0111" "0241" "0113" "0321"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "0233" "0152" "0241" "02132" "0314"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "02222" "02321" "0421" "0341" "0241" "02131"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "02222" "014" "0211" "04332" "0132" "04131"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "0341" "0233" "0431" "0341" "04332" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "0431" "0241" "0211" "0211" "0412" "02214"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "02223" "0412" "0431" "0423" "02212" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "02121" "02211" "02422" "0341" "0233" "0112"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04111" "0332" "02422" "0211" "02122" "04222"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04333" "0412" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "02131" "0111" "0343" "04333" "02422" "0111"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "02322" "02214" "02421" "02131" "02121" "0412"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "0231" "02121" "0311" "0423" "0111" "0321"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "04133" "0412" "0122" "0321" "0431"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "0431" "02322" "02322" "0241" "0331" "02213"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "0421" "04112" "0152" "02214" "0332" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "0332" "0112" "0154" "0241" "0241" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "0314" "04332" "0412" "0431" "0231" "04132"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04222" "04111" "0122" "02212" "02221" "02421"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "0314" "0241" "0412" "0332" "0412" "04332"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "0231" "0122" "02223" "0211" "04111" "0432"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "0111" "0342" "04332" "0412" "04132" "02423"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "02321" "0311" "0331" "0431" "02223" "02421"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "0421" "02423" "0241" "0152" "02421" "0322"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "0412" "0412" "0331" "02322" "0313" "041132"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "0432" "041131" "04332" "0421" "02422" "0321"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "0231" "0112" "0134" "0412" "0431" "02131"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04111" "04332" "0123" "04333" "04111" "02211"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "0431" "0122" "0241" "0321"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "0412" "0241" "0112" "0231" "0321" "04332"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "0342" "02122" "0421" "0134" "02421" "02222"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "0432" "0233" "0331" "0233" "02421" "04222"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04222" "02423" "014" "02131" "0322" "04222"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "0332" "04222" "0431" "0114" "0111"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "0233" "0233" "0313" "02222" "0332" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "0332" "0332" "0113" "0431" "02131" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "041131" "0132" "0311" "0311" "0421" "0233"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "02132" "0421" "0311" "02213" "04131" "02211"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "04332" "02321" "0112" "04331" "0331"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "02132" "0421" "0131" "0115" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "0231" "0112" "04111" "02211" "0231" "0241"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "0231" "0432" "02223" "0241" "02422" "0111"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "0231" "041133" "0341" "0331" "04131" "0431"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "02221" "02423" "04131" "02422" "02221" "0412"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "0314" "0341" "0421" "04222" "04111" "0432"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "0343" "04112" "04332" "0431" "0412" "0241"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "02221" "0431" "0152" "0421" "014" "0313"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "0331" "02423" "014" "0412" "02132" "0421"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "0432" "0341" "041132" "04332" "02132" "0431"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "02121" "02321" "0122" "0231" "0332"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "0342" "04111" "0211" "0431" "02423" "0331"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "0432" "0322" "0311" "0412" "0241" "0431"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "0421" "02214" "0421" "04332" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "0233" "0133" "0114" "0231" "0431" "0312"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "0412" "0431" "02422" "02321" "0211" "0431"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "0111" "0431" "02121" "0412" "02221" "02131"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "0332" "0432" "04111" "0112" "04332" "0231"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04332" "0211" "04332" "0133" "04332" "02131"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "0313" "02321" "0421" "0421" "02132" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "02132" "0154" "02322" "0431" "02222" "0233"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "0231" "0152" "0211" "0423" "0331" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "0431" "04221" "0231" "0331" "0332" "0233"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04222" "014" "0412" "041131" "02422" "0311"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "04111" "02211" "041132" "0421" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "0241" "041132" "0154" "0241" "0231" "0341"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "0241" "0322" "0322" "02131" "0231"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "0241" "0431" "02212" "041131" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "0114" "02422" "0231" "0241" "02213"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "041132" "0331" "0332" "0151" "02223" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "02122" "0321" "0231" "0332" "0231" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "0241" "02223" "0412" "0412" "0421" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04221" "0233" "0431" "02221" "02213" "02223"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04111" "02221" "0412" "0123" "0412" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "0322" "0421" "014" "0431" "0241" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "02132" "04133" "0331" "0241" "02131" "02121"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "0113" "02222" "0312" "0113" "0311" "02121"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "041132" "0231" "0123" "0211" "04332" "0321"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "0341" "0321" "0421" "02321" "0431" "04111"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "0231" "04112" "0332" "0311" "0132" "0311"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1222))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "0412" "0421" "04132" "02122" "0412" "0313"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04112" "0122" "0431" "0431" "04222" "0431"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "0112" "04131" "02131" "02321" "0211" "0421"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "02132" "0233" "04112" "0241" "04111"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "0311" "0231" "0431" "0313" "0431" "02223"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "02122" "0241" "0231" "02213" "0311" "0311"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "0115" "02131" "0332" "0123" "04113" "0113"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "0233" "04111" "0241" "02223" "04132" "0421"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "0231" "04333" "04332" "0412" "0332" "0421"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04332" "0432" "0241" "04113" "0421" "04113"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04111" "0421" "0231" "0311" "04332" "04112"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04222" "02122" "02421" "0231" "04131" "0431"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "0314" "0431" "02214" "0133" "02222"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "0342" "0321" "04111" "0412" "0233" "0421"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "0412" "0113" "02423" "0241" "0152" "0421"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "0114" "0331" "02223" "02321" "0233" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "0432" "014" "02422" "02423" "02322" "02321"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "0412" "0211" "0133" "02131" "0241" "02321"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04222" "0332" "0122" "0412" "02122" "0313"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "0233" "04221" "0233" "0342" "0233" "04131"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "0241" "0431" "0241" "0115" "0412" "0421"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "02222" "0122" "0322" "0231" "0314" "0241"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04331" "0311" "0322" "0241" "0331" "02132"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "0112" "0332" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "0423" "0113" "02421" "0132" "0112" "04113"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "0412" "0112" "0241" "04331" "0431" "02211"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "0421" "02131" "014" "04113" "0114" "02131"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "02421" "04113" "0113" "0332" "0341" "02221"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "0421" "04332" "0152" "04113" "04131" "04222"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "02422" "0412" "0431" "0412" "0151" "0113"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "0331" "02321" "0122" "04113" "04332" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04133" "04113" "0322" "0241" "0115" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "02321" "0112" "0412" "0332" "0431"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "0431" "0241" "02211" "0431" "04222" "0421"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "0322" "02421" "0132" "04221" "0431" "0231"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "0231" "02122" "0342" "0423" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "02131" "0314" "0131" "04222" "0311"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "02222" "0123" "0233" "0412" "0231" "0312"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "0231" "014" "0322" "02131" "04113" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "0233" "0231" "04111" "0312" "0231" "02122"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "04113" "0233" "0311" "0412" "0431" "0421"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "0313" "0412" "02321" "0322" "0421" "0423"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "0421" "0321" "0431" "014" "0233"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "0313" "02421" "04133" "0322" "0431" "02422"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "0231" "0431" "0423" "04111" "0332" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "02423" "0211" "0122" "014" "04132"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "0233" "0131" "02321" "0211" "014" "04111"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "0412" "0112" "04113" "0154" "02223" "0432"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "04332" "0241" "0432" "02131" "02422"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "0241" "0241" "0412" "0431" "0153" "04332"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "0431" "04111" "04333" "0421" "02322" "0231"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "0421" "0123" "0341" "014" "0432" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04112" "0332" "0331" "04131" "0241" "0332"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04112" "0112" "0421" "0233" "02131" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "0332" "0231" "0331" "04221" "0423" "04332"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "0332" "0313" "0421" "02321" "0241" "02131"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "02211" "0233" "0154" "02132" "0241" "04111"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "0412" "0211" "0231" "02222" "0113" "0431"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "0432" "0431" "04111" "0233" "0241" "0233"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "02213" "0431" "0332" "0133" "0322" "0112"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "0321" "0431" "0231" "02422" "0115" "02322"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "02422" "0123" "0312" "0111" "0231" "02421"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "02423" "02321" "0322" "0431" "0115"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "02422" "02422" "0313" "0311" "0431" "0115"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "0113" "02212" "04113" "0431" "02121" "0233"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "0312" "0152" "0421" "0115" "02221" "0111"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04333" "04331" "02321" "0412" "02221" "0431"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "0313" "0332" "0211" "02321" "0241" "0314"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "02422" "0412" "02223" "02122" "0412" "0113"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "0421" "02422" "0111" "0241" "0113" "0321"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "0233" "0152" "0241" "02132" "0314"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "02222" "02321" "0421" "0341" "0241" "02131"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "02222" "014" "0211" "04332" "0132" "04131"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "0341" "0233" "0431" "0341" "04332" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "0431" "0241" "0211" "0211" "0412" "02214"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "02223" "0412" "0431" "0423" "02212" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "02121" "02211" "02422" "0341" "0233" "0112"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04111" "0332" "02422" "0211" "02122" "04222"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04333" "0412" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "02131" "0111" "0343" "04333" "02422" "0111"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "02322" "02214" "02421" "02131" "02121" "0412"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "0231" "02121" "0311" "0423" "0111" "0321"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "04133" "0412" "0122" "0321" "0431"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "0431" "02322" "02322" "0241" "0331" "02213"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "0421" "04112" "0152" "02214" "0332" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "0332" "0112" "0154" "0241" "0241" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "0314" "04332" "0412" "0431" "0231" "04132"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04222" "04111" "0122" "02212" "02221" "02421"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "0314" "0241" "0412" "0332" "0412" "04332"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "0231" "0122" "02223" "0211" "04111" "0432"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "0111" "0342" "04332" "0412" "04132" "02423"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "02321" "0311" "0331" "0431" "02223" "02421"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "0421" "02423" "0241" "0152" "02421" "0322"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "0412" "0412" "0331" "02322" "0313" "04113"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "0432" "04113" "04332" "0421" "02422" "0321"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "0231" "0112" "0134" "0412" "0431" "02131"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04111" "04332" "0123" "04333" "04111" "02211"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "0431" "0122" "0241" "0321"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "0412" "0241" "0112" "0231" "0321" "04332"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "0342" "02122" "0421" "0134" "02421" "02222"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "0432" "0233" "0331" "0233" "02421" "04222"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04222" "02423" "014" "02131" "0322" "04222"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "0332" "04222" "0431" "0114" "0111"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "0233" "0233" "0313" "02222" "0332" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "0332" "0332" "0113" "0431" "02131" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "04113" "0132" "0311" "0311" "0421" "0233"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "02132" "0421" "0311" "02213" "04131" "02211"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "04332" "02321" "0112" "04331" "0331"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "02132" "0421" "0131" "0115" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "0231" "0112" "04111" "02211" "0231" "0241"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "0231" "0432" "02223" "0241" "02422" "0111"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "0231" "04113" "0341" "0331" "04131" "0431"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "02221" "02423" "04131" "02422" "02221" "0412"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "0314" "0341" "0421" "04222" "04111" "0432"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "0343" "04112" "04332" "0431" "0412" "0241"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "02221" "0431" "0152" "0421" "014" "0313"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "0331" "02423" "014" "0412" "02132" "0421"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "0432" "0341" "04113" "04332" "02132" "0431"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "02121" "02321" "0122" "0231" "0332"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "0342" "04111" "0211" "0431" "02423" "0331"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "0432" "0322" "0311" "0412" "0241" "0431"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "0421" "02214" "0421" "04332" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "0233" "0133" "0114" "0231" "0431" "0312"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "0412" "0431" "02422" "02321" "0211" "0431"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "0111" "0431" "02121" "0412" "02221" "02131"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "0332" "0432" "04111" "0112" "04332" "0231"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04332" "0211" "04332" "0133" "04332" "02131"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "0313" "02321" "0421" "0421" "02132" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "02132" "0154" "02322" "0431" "02222" "0233"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "0231" "0152" "0211" "0423" "0331" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "0431" "04221" "0231" "0331" "0332" "0233"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04222" "014" "0412" "04113" "02422" "0311"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "04111" "02211" "04113" "0421" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "0241" "04113" "0154" "0241" "0231" "0341"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "0241" "0322" "0322" "02131" "0231"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "0241" "0431" "02212" "04113" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "0114" "02422" "0231" "0241" "02213"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "04113" "0331" "0332" "0151" "02223" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "02122" "0321" "0231" "0332" "0231" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "0241" "02223" "0412" "0412" "0421" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04221" "0233" "0431" "02221" "02213" "02223"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04111" "02221" "0412" "0123" "0412" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "0322" "0421" "014" "0431" "0241" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "02132" "04133" "0331" "0241" "02131" "02121"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "0113" "02222" "0312" "0113" "0311" "02121"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "04113" "0231" "0123" "0211" "04332" "0321"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "0341" "0321" "0421" "02321" "0431" "04111"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "0231" "04112" "0332" "0311" "0132" "0311"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1257))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "0412" "0421" "04132" "0212" "0412" "0313"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04112" "0122" "0431" "0431" "04222" "0431"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "0112" "04131" "02131" "02321" "0211" "0421"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "02132" "0233" "04112" "0241" "04111"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "0311" "0231" "0431" "0313" "0431" "02223"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "0212" "0241" "0231" "02213" "0311" "0311"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "0115" "02131" "0332" "0123" "04113" "0113"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "0233" "04111" "0241" "02223" "04132" "0421"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "0231" "04333" "04332" "0412" "0332" "0421"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04332" "0432" "0241" "04113" "0421" "04113"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04111" "0421" "0231" "0311" "04332" "04112"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04222" "0212" "02421" "0231" "04131" "0431"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "0314" "0431" "02214" "0133" "02222"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "0342" "0321" "04111" "0412" "0233" "0421"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "0412" "0113" "02423" "0241" "0152" "0421"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "0114" "0331" "02223" "02321" "0233" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "0432" "014" "02422" "02423" "02322" "02321"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "0412" "0211" "0133" "02131" "0241" "02321"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04222" "0332" "0122" "0412" "0212" "0313"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "0233" "04221" "0233" "0342" "0233" "04131"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "0241" "0431" "0241" "0115" "0412" "0421"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "02222" "0122" "0322" "0231" "0314" "0241"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04331" "0311" "0322" "0241" "0331" "02132"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "0112" "0332" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "0423" "0113" "02421" "0132" "0112" "04113"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "0412" "0112" "0241" "04331" "0431" "02211"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "0421" "02131" "014" "04113" "0114" "02131"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "02421" "04113" "0113" "0332" "0341" "02221"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "0421" "04332" "0152" "04113" "04131" "04222"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "02422" "0412" "0431" "0412" "0151" "0113"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "0331" "02321" "0122" "04113" "04332" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04133" "04113" "0322" "0241" "0115" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "02321" "0112" "0412" "0332" "0431"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "0431" "0241" "02211" "0431" "04222" "0421"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "0322" "02421" "0132" "04221" "0431" "0231"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "0231" "0212" "0342" "0423" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "02131" "0314" "0131" "04222" "0311"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "02222" "0123" "0233" "0412" "0231" "0312"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "0231" "014" "0322" "02131" "04113" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "0233" "0231" "04111" "0312" "0231" "0212"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "04113" "0233" "0311" "0412" "0431" "0421"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "0313" "0412" "02321" "0322" "0421" "0423"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "0421" "0321" "0431" "014" "0233"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "0313" "02421" "04133" "0322" "0431" "02422"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "0231" "0431" "0423" "04111" "0332" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "02423" "0211" "0122" "014" "04132"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "0233" "0131" "02321" "0211" "014" "04111"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "0412" "0112" "04113" "0154" "02223" "0432"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "04332" "0241" "0432" "02131" "02422"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "0241" "0241" "0412" "0431" "0153" "04332"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "0431" "04111" "04333" "0421" "02322" "0231"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "0421" "0123" "0341" "014" "0432" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04112" "0332" "0331" "04131" "0241" "0332"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04112" "0112" "0421" "0233" "02131" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "0332" "0231" "0331" "04221" "0423" "04332"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "0332" "0313" "0421" "02321" "0241" "02131"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "02211" "0233" "0154" "02132" "0241" "04111"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "0412" "0211" "0231" "02222" "0113" "0431"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "0432" "0431" "04111" "0233" "0241" "0233"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "02213" "0431" "0332" "0133" "0322" "0112"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "0321" "0431" "0231" "02422" "0115" "02322"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "02422" "0123" "0312" "0111" "0231" "02421"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "02423" "02321" "0322" "0431" "0115"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "02422" "02422" "0313" "0311" "0431" "0115"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "0113" "02212" "04113" "0431" "0212" "0233"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "0312" "0152" "0421" "0115" "02221" "0111"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04333" "04331" "02321" "0412" "02221" "0431"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "0313" "0332" "0211" "02321" "0241" "0314"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "02422" "0412" "02223" "0212" "0412" "0113"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "0421" "02422" "0111" "0241" "0113" "0321"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "0233" "0152" "0241" "02132" "0314"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "02222" "02321" "0421" "0341" "0241" "02131"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "02222" "014" "0211" "04332" "0132" "04131"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "0341" "0233" "0431" "0341" "04332" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "0431" "0241" "0211" "0211" "0412" "02214"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "02223" "0412" "0431" "0423" "02212" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "0212" "02211" "02422" "0341" "0233" "0112"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04111" "0332" "02422" "0211" "0212" "04222"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04333" "0412" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "02131" "0111" "0343" "04333" "02422" "0111"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "02322" "02214" "02421" "02131" "0212" "0412"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "0231" "0212" "0311" "0423" "0111" "0321"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "04133" "0412" "0122" "0321" "0431"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "0431" "02322" "02322" "0241" "0331" "02213"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "0421" "04112" "0152" "02214" "0332" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "0332" "0112" "0154" "0241" "0241" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "0314" "04332" "0412" "0431" "0231" "04132"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04222" "04111" "0122" "02212" "02221" "02421"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "0314" "0241" "0412" "0332" "0412" "04332"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "0231" "0122" "02223" "0211" "04111" "0432"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "0111" "0342" "04332" "0412" "04132" "02423"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "02321" "0311" "0331" "0431" "02223" "02421"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "0421" "02423" "0241" "0152" "02421" "0322"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "0412" "0412" "0331" "02322" "0313" "04113"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "0432" "04113" "04332" "0421" "02422" "0321"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "0231" "0112" "0134" "0412" "0431" "02131"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04111" "04332" "0123" "04333" "04111" "02211"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "0431" "0122" "0241" "0321"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "0412" "0241" "0112" "0231" "0321" "04332"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "0342" "0212" "0421" "0134" "02421" "02222"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "0432" "0233" "0331" "0233" "02421" "04222"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04222" "02423" "014" "02131" "0322" "04222"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "0332" "04222" "0431" "0114" "0111"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "0233" "0233" "0313" "02222" "0332" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "0332" "0332" "0113" "0431" "02131" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "04113" "0132" "0311" "0311" "0421" "0233"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "02132" "0421" "0311" "02213" "04131" "02211"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "04332" "02321" "0112" "04331" "0331"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "02132" "0421" "0131" "0115" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "0231" "0112" "04111" "02211" "0231" "0241"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "0231" "0432" "02223" "0241" "02422" "0111"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "0231" "04113" "0341" "0331" "04131" "0431"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "02221" "02423" "04131" "02422" "02221" "0412"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "0314" "0341" "0421" "04222" "04111" "0432"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "0343" "04112" "04332" "0431" "0412" "0241"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "02221" "0431" "0152" "0421" "014" "0313"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "0331" "02423" "014" "0412" "02132" "0421"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "0432" "0341" "04113" "04332" "02132" "0431"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "0212" "02321" "0122" "0231" "0332"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "0342" "04111" "0211" "0431" "02423" "0331"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "0432" "0322" "0311" "0412" "0241" "0431"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "0421" "02214" "0421" "04332" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "0233" "0133" "0114" "0231" "0431" "0312"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "0412" "0431" "02422" "02321" "0211" "0431"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "0111" "0431" "0212" "0412" "02221" "02131"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "0332" "0432" "04111" "0112" "04332" "0231"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04332" "0211" "04332" "0133" "04332" "02131"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "0313" "02321" "0421" "0421" "02132" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "02132" "0154" "02322" "0431" "02222" "0233"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "0231" "0152" "0211" "0423" "0331" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "0431" "04221" "0231" "0331" "0332" "0233"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04222" "014" "0412" "04113" "02422" "0311"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "04111" "02211" "04113" "0421" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "0241" "04113" "0154" "0241" "0231" "0341"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "0241" "0322" "0322" "02131" "0231"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "0241" "0431" "02212" "04113" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "0114" "02422" "0231" "0241" "02213"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "04113" "0331" "0332" "0151" "02223" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "0212" "0321" "0231" "0332" "0231" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "0241" "02223" "0412" "0412" "0421" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04221" "0233" "0431" "02221" "02213" "02223"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04111" "02221" "0412" "0123" "0412" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "0322" "0421" "014" "0431" "0241" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "02132" "04133" "0331" "0241" "02131" "0212"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "0113" "02222" "0312" "0113" "0311" "0212"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "04113" "0231" "0123" "0211" "04332" "0321"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "0341" "0321" "0421" "02321" "0431" "04111"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "0231" "04112" "0332" "0311" "0132" "0311"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1414))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "0412" "0421" "04132" "0212" "0412" "0313"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04112" "0122" "0431" "0431" "04222" "0431"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "0112" "04131" "02131" "02321" "0211" "0421"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "02132" "0233" "04112" "0241" "04111"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "0311" "0231" "0431" "0313" "0431" "02223"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "0212" "0241" "0231" "02213" "0311" "0311"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "0115" "02131" "0332" "0123" "04113" "0113"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "0233" "04111" "0241" "02223" "04132" "0421"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "0231" "04333" "04332" "0412" "0332" "0421"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04332" "0432" "0241" "04113" "0421" "04113"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04111" "0421" "0231" "0311" "04332" "04112"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04222" "0212" "02421" "0231" "04131" "0431"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "0314" "0431" "02214" "0133" "02222"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "0342" "032" "04111" "0412" "0233" "0421"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "0412" "0113" "02423" "0241" "0152" "0421"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "0114" "0331" "02223" "02321" "0233" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "0432" "014" "02422" "02423" "02322" "02321"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "0412" "0211" "0133" "02131" "0241" "02321"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04222" "0332" "0122" "0412" "0212" "0313"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "0233" "04221" "0233" "0342" "0233" "04131"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "0241" "0431" "0241" "0115" "0412" "0421"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "02222" "0122" "032" "0231" "0314" "0241"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04331" "0311" "032" "0241" "0331" "02132"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "0112" "0332" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "0423" "0113" "02421" "0132" "0112" "04113"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "0412" "0112" "0241" "04331" "0431" "02211"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "0421" "02131" "014" "04113" "0114" "02131"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "02421" "04113" "0113" "0332" "0341" "02221"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "0421" "04332" "0152" "04113" "04131" "04222"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "02422" "0412" "0431" "0412" "0151" "0113"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "0331" "02321" "0122" "04113" "04332" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04133" "04113" "032" "0241" "0115" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "02321" "0112" "0412" "0332" "0431"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "0431" "0241" "02211" "0431" "04222" "0421"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "02421" "0132" "04221" "0431" "0231"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "0231" "0212" "0342" "0423" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "02131" "0314" "0131" "04222" "0311"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "02222" "0123" "0233" "0412" "0231" "0312"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "0231" "014" "032" "02131" "04113" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "0233" "0231" "04111" "0312" "0231" "0212"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "04113" "0233" "0311" "0412" "0431" "0421"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "0313" "0412" "02321" "032" "0421" "0423"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "0421" "032" "0431" "014" "0233"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "0313" "02421" "04133" "032" "0431" "02422"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "0231" "0431" "0423" "04111" "0332" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "02423" "0211" "0122" "014" "04132"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "0233" "0131" "02321" "0211" "014" "04111"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "0412" "0112" "04113" "0154" "02223" "0432"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "04332" "0241" "0432" "02131" "02422"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "0241" "0241" "0412" "0431" "0153" "04332"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "0431" "04111" "04333" "0421" "02322" "0231"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "0421" "0123" "0341" "014" "0432" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04112" "0332" "0331" "04131" "0241" "0332"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04112" "0112" "0421" "0233" "02131" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "0332" "0231" "0331" "04221" "0423" "04332"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "0332" "0313" "0421" "02321" "0241" "02131"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "02211" "0233" "0154" "02132" "0241" "04111"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "0412" "0211" "0231" "02222" "0113" "0431"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "0432" "0431" "04111" "0233" "0241" "0233"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "02213" "0431" "0332" "0133" "032" "0112"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "0431" "0231" "02422" "0115" "02322"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "02422" "0123" "0312" "0111" "0231" "02421"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "02423" "02321" "032" "0431" "0115"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "02422" "02422" "0313" "0311" "0431" "0115"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "0113" "02212" "04113" "0431" "0212" "0233"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "0312" "0152" "0421" "0115" "02221" "0111"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04333" "04331" "02321" "0412" "02221" "0431"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "0313" "0332" "0211" "02321" "0241" "0314"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "02422" "0412" "02223" "0212" "0412" "0113"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "0421" "02422" "0111" "0241" "0113" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "0233" "0152" "0241" "02132" "0314"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "02222" "02321" "0421" "0341" "0241" "02131"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "02222" "014" "0211" "04332" "0132" "04131"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "0341" "0233" "0431" "0341" "04332" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "0431" "0241" "0211" "0211" "0412" "02214"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "02223" "0412" "0431" "0423" "02212" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "0212" "02211" "02422" "0341" "0233" "0112"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04111" "0332" "02422" "0211" "0212" "04222"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04333" "0412" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "02131" "0111" "0343" "04333" "02422" "0111"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "02322" "02214" "02421" "02131" "0212" "0412"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "0231" "0212" "0311" "0423" "0111" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "04133" "0412" "0122" "032" "0431"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "0431" "02322" "02322" "0241" "0331" "02213"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "0421" "04112" "0152" "02214" "0332" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "0332" "0112" "0154" "0241" "0241" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "0314" "04332" "0412" "0431" "0231" "04132"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04222" "04111" "0122" "02212" "02221" "02421"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "0314" "0241" "0412" "0332" "0412" "04332"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "0231" "0122" "02223" "0211" "04111" "0432"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "0111" "0342" "04332" "0412" "04132" "02423"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "02321" "0311" "0331" "0431" "02223" "02421"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "0421" "02423" "0241" "0152" "02421" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "0412" "0412" "0331" "02322" "0313" "04113"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "0432" "04113" "04332" "0421" "02422" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "0231" "0112" "0134" "0412" "0431" "02131"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04111" "04332" "0123" "04333" "04111" "02211"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "0431" "0122" "0241" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "0412" "0241" "0112" "0231" "032" "04332"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "0342" "0212" "0421" "0134" "02421" "02222"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "0432" "0233" "0331" "0233" "02421" "04222"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04222" "02423" "014" "02131" "032" "04222"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "0332" "04222" "0431" "0114" "0111"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "0233" "0233" "0313" "02222" "0332" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "0332" "0332" "0113" "0431" "02131" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "04113" "0132" "0311" "0311" "0421" "0233"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "02132" "0421" "0311" "02213" "04131" "02211"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "04332" "02321" "0112" "04331" "0331"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "02132" "0421" "0131" "0115" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "0231" "0112" "04111" "02211" "0231" "0241"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "0231" "0432" "02223" "0241" "02422" "0111"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "0231" "04113" "0341" "0331" "04131" "0431"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "02221" "02423" "04131" "02422" "02221" "0412"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "0314" "0341" "0421" "04222" "04111" "0432"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "0343" "04112" "04332" "0431" "0412" "0241"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "02221" "0431" "0152" "0421" "014" "0313"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "0331" "02423" "014" "0412" "02132" "0421"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "0432" "0341" "04113" "04332" "02132" "0431"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "0212" "02321" "0122" "0231" "0332"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "0342" "04111" "0211" "0431" "02423" "0331"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "0432" "032" "0311" "0412" "0241" "0431"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "0421" "02214" "0421" "04332" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "0233" "0133" "0114" "0231" "0431" "0312"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "0412" "0431" "02422" "02321" "0211" "0431"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "0111" "0431" "0212" "0412" "02221" "02131"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "0332" "0432" "04111" "0112" "04332" "0231"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04332" "0211" "04332" "0133" "04332" "02131"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "0313" "02321" "0421" "0421" "02132" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "02132" "0154" "02322" "0431" "02222" "0233"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "0231" "0152" "0211" "0423" "0331" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "0431" "04221" "0231" "0331" "0332" "0233"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04222" "014" "0412" "04113" "02422" "0311"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "04111" "02211" "04113" "0421" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "0241" "04113" "0154" "0241" "0231" "0341"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "0241" "032" "032" "02131" "0231"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "0241" "0431" "02212" "04113" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "0114" "02422" "0231" "0241" "02213"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "04113" "0331" "0332" "0151" "02223" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "0212" "032" "0231" "0332" "0231" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "0241" "02223" "0412" "0412" "0421" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04221" "0233" "0431" "02221" "02213" "02223"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04111" "02221" "0412" "0123" "0412" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "0421" "014" "0431" "0241" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "02132" "04133" "0331" "0241" "02131" "0212"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "0113" "02222" "0312" "0113" "0311" "0212"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "04113" "0231" "0123" "0211" "04332" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "0341" "032" "0421" "02321" "0431" "04111"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "0231" "04112" "0332" "0311" "0132" "0311"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1749))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "0412" "0421" "04132" "0212" "0412" "0313"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04112" "0122" "0431" "0431" "04222" "0431"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "0112" "04131" "0213" "02321" "0211" "0421"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "0213" "0233" "04112" "0241" "04111"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "0311" "0231" "0431" "0313" "0431" "02223"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "0212" "0241" "0231" "02213" "0311" "0311"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "0115" "0213" "0332" "0123" "04113" "0113"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "0233" "04111" "0241" "02223" "04132" "0421"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "0231" "04333" "04332" "0412" "0332" "0421"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04332" "0432" "0241" "04113" "0421" "04113"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04111" "0421" "0231" "0311" "04332" "04112"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04222" "0212" "02421" "0231" "04131" "0431"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "0314" "0431" "02214" "0133" "02222"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "0342" "032" "04111" "0412" "0233" "0421"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "0412" "0113" "02423" "0241" "0152" "0421"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "0114" "0331" "02223" "02321" "0233" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "0432" "014" "02422" "02423" "02322" "02321"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "0412" "0211" "0133" "0213" "0241" "02321"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04222" "0332" "0122" "0412" "0212" "0313"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "0233" "04221" "0233" "0342" "0233" "04131"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "0241" "0431" "0241" "0115" "0412" "0421"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "02222" "0122" "032" "0231" "0314" "0241"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04331" "0311" "032" "0241" "0331" "0213"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "0112" "0332" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "0423" "0113" "02421" "0132" "0112" "04113"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "0412" "0112" "0241" "04331" "0431" "02211"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "0421" "0213" "014" "04113" "0114" "0213"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "02421" "04113" "0113" "0332" "0341" "02221"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "0421" "04332" "0152" "04113" "04131" "04222"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "02422" "0412" "0431" "0412" "0151" "0113"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "0331" "02321" "0122" "04113" "04332" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04133" "04113" "032" "0241" "0115" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "02321" "0112" "0412" "0332" "0431"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "0431" "0241" "02211" "0431" "04222" "0421"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "02421" "0132" "04221" "0431" "0231"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "0231" "0212" "0342" "0423" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "0213" "0314" "0131" "04222" "0311"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "02222" "0123" "0233" "0412" "0231" "0312"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "0231" "014" "032" "0213" "04113" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "0233" "0231" "04111" "0312" "0231" "0212"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "04113" "0233" "0311" "0412" "0431" "0421"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "0313" "0412" "02321" "032" "0421" "0423"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "0421" "032" "0431" "014" "0233"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "0313" "02421" "04133" "032" "0431" "02422"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "0231" "0431" "0423" "04111" "0332" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "02423" "0211" "0122" "014" "04132"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "0233" "0131" "02321" "0211" "014" "04111"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "0412" "0112" "04113" "0154" "02223" "0432"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "04332" "0241" "0432" "0213" "02422"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "0241" "0241" "0412" "0431" "0153" "04332"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "0431" "04111" "04333" "0421" "02322" "0231"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "0421" "0123" "0341" "014" "0432" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04112" "0332" "0331" "04131" "0241" "0332"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04112" "0112" "0421" "0233" "0213" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "0332" "0231" "0331" "04221" "0423" "04332"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "0332" "0313" "0421" "02321" "0241" "0213"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "02211" "0233" "0154" "0213" "0241" "04111"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "0412" "0211" "0231" "02222" "0113" "0431"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "0432" "0431" "04111" "0233" "0241" "0233"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "02213" "0431" "0332" "0133" "032" "0112"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "0431" "0231" "02422" "0115" "02322"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "02422" "0123" "0312" "0111" "0231" "02421"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "02423" "02321" "032" "0431" "0115"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "02422" "02422" "0313" "0311" "0431" "0115"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "0113" "02212" "04113" "0431" "0212" "0233"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "0312" "0152" "0421" "0115" "02221" "0111"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04333" "04331" "02321" "0412" "02221" "0431"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "0313" "0332" "0211" "02321" "0241" "0314"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "02422" "0412" "02223" "0212" "0412" "0113"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "0421" "02422" "0111" "0241" "0113" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "0233" "0152" "0241" "0213" "0314"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "02222" "02321" "0421" "0341" "0241" "0213"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "02222" "014" "0211" "04332" "0132" "04131"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "0341" "0233" "0431" "0341" "04332" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "0431" "0241" "0211" "0211" "0412" "02214"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "02223" "0412" "0431" "0423" "02212" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "0212" "02211" "02422" "0341" "0233" "0112"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04111" "0332" "02422" "0211" "0212" "04222"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04333" "0412" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "0213" "0111" "0343" "04333" "02422" "0111"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "02322" "02214" "02421" "0213" "0212" "0412"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "0231" "0212" "0311" "0423" "0111" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "04133" "0412" "0122" "032" "0431"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "0431" "02322" "02322" "0241" "0331" "02213"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "0421" "04112" "0152" "02214" "0332" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "0332" "0112" "0154" "0241" "0241" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "0314" "04332" "0412" "0431" "0231" "04132"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04222" "04111" "0122" "02212" "02221" "02421"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "0314" "0241" "0412" "0332" "0412" "04332"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "0231" "0122" "02223" "0211" "04111" "0432"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "0111" "0342" "04332" "0412" "04132" "02423"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "02321" "0311" "0331" "0431" "02223" "02421"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "0421" "02423" "0241" "0152" "02421" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "0412" "0412" "0331" "02322" "0313" "04113"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "0432" "04113" "04332" "0421" "02422" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "0231" "0112" "0134" "0412" "0431" "0213"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04111" "04332" "0123" "04333" "04111" "02211"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "0431" "0122" "0241" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "0412" "0241" "0112" "0231" "032" "04332"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "0342" "0212" "0421" "0134" "02421" "02222"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "0432" "0233" "0331" "0233" "02421" "04222"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04222" "02423" "014" "0213" "032" "04222"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "0332" "04222" "0431" "0114" "0111"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "0233" "0233" "0313" "02222" "0332" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "0332" "0332" "0113" "0431" "0213" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "04113" "0132" "0311" "0311" "0421" "0233"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "0213" "0421" "0311" "02213" "04131" "02211"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "04332" "02321" "0112" "04331" "0331"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "0213" "0421" "0131" "0115" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "0231" "0112" "04111" "02211" "0231" "0241"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "0231" "0432" "02223" "0241" "02422" "0111"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "0231" "04113" "0341" "0331" "04131" "0431"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "02221" "02423" "04131" "02422" "02221" "0412"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "0314" "0341" "0421" "04222" "04111" "0432"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "0343" "04112" "04332" "0431" "0412" "0241"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "02221" "0431" "0152" "0421" "014" "0313"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "0331" "02423" "014" "0412" "0213" "0421"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "0432" "0341" "04113" "04332" "0213" "0431"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "0212" "02321" "0122" "0231" "0332"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "0342" "04111" "0211" "0431" "02423" "0331"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "0432" "032" "0311" "0412" "0241" "0431"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "0421" "02214" "0421" "04332" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "0233" "0133" "0114" "0231" "0431" "0312"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "0412" "0431" "02422" "02321" "0211" "0431"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "0111" "0431" "0212" "0412" "02221" "0213"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "0332" "0432" "04111" "0112" "04332" "0231"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04332" "0211" "04332" "0133" "04332" "0213"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "0313" "02321" "0421" "0421" "0213" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "0213" "0154" "02322" "0431" "02222" "0233"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "0231" "0152" "0211" "0423" "0331" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "0431" "04221" "0231" "0331" "0332" "0233"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04222" "014" "0412" "04113" "02422" "0311"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "04111" "02211" "04113" "0421" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "0241" "04113" "0154" "0241" "0231" "0341"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "0241" "032" "032" "0213" "0231"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "0241" "0431" "02212" "04113" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "0114" "02422" "0231" "0241" "02213"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "04113" "0331" "0332" "0151" "02223" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "0212" "032" "0231" "0332" "0231" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "0241" "02223" "0412" "0412" "0421" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04221" "0233" "0431" "02221" "02213" "02223"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04111" "02221" "0412" "0123" "0412" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "0421" "014" "0431" "0241" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "0213" "04133" "0331" "0241" "0213" "0212"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "0113" "02222" "0312" "0113" "0311" "0212"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "04113" "0231" "0123" "0211" "04332" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "0341" "032" "0421" "02321" "0431" "04111"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "0231" "04112" "0332" "0311" "0132" "0311"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1823))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "0412" "0421" "04132" "0212" "0412" "0313"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04112" "0122" "0431" "0431" "04222" "0431"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "0112" "04131" "0213" "02321" "0211" "0421"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "0213" "0233" "04112" "0241" "04111"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "0311" "0231" "0431" "0313" "0431" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "0212" "0241" "0231" "022" "0311" "0311"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "0115" "0213" "0332" "0123" "04113" "0113"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "0233" "04111" "0241" "022" "04132" "0421"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "0231" "04333" "04332" "0412" "0332" "0421"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04332" "0432" "0241" "04113" "0421" "04113"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04111" "0421" "0231" "0311" "04332" "04112"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04222" "0212" "02421" "0231" "04131" "0431"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "0314" "0431" "022" "0133" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "0342" "032" "04111" "0412" "0233" "0421"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "0412" "0113" "02423" "0241" "0152" "0421"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "0114" "0331" "022" "02321" "0233" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "0432" "014" "02422" "02423" "02322" "02321"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "0412" "0211" "0133" "0213" "0241" "02321"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04222" "0332" "0122" "0412" "0212" "0313"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "0233" "04221" "0233" "0342" "0233" "04131"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "0241" "0431" "0241" "0115" "0412" "0421"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "0122" "032" "0231" "0314" "0241"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04331" "0311" "032" "0241" "0331" "0213"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "0112" "0332" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "0423" "0113" "02421" "0132" "0112" "04113"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "0412" "0112" "0241" "04331" "0431" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "0421" "0213" "014" "04113" "0114" "0213"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "02421" "04113" "0113" "0332" "0341" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "0421" "04332" "0152" "04113" "04131" "04222"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "02422" "0412" "0431" "0412" "0151" "0113"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "0331" "02321" "0122" "04113" "04332" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04133" "04113" "032" "0241" "0115" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "02321" "0112" "0412" "0332" "0431"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "0431" "0241" "022" "0431" "04222" "0421"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "02421" "0132" "04221" "0431" "0231"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "0231" "0212" "0342" "0423" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "0213" "0314" "0131" "04222" "0311"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "0123" "0233" "0412" "0231" "0312"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "0231" "014" "032" "0213" "04113" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "0233" "0231" "04111" "0312" "0231" "0212"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "04113" "0233" "0311" "0412" "0431" "0421"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "0313" "0412" "02321" "032" "0421" "0423"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "0421" "032" "0431" "014" "0233"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "0313" "02421" "04133" "032" "0431" "02422"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "0231" "0431" "0423" "04111" "0332" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "02423" "0211" "0122" "014" "04132"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "0233" "0131" "02321" "0211" "014" "04111"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "0412" "0112" "04113" "0154" "022" "0432"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "04332" "0241" "0432" "0213" "02422"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "0241" "0241" "0412" "0431" "0153" "04332"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "0431" "04111" "04333" "0421" "02322" "0231"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "0421" "0123" "0341" "014" "0432" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04112" "0332" "0331" "04131" "0241" "0332"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04112" "0112" "0421" "0233" "0213" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "0332" "0231" "0331" "04221" "0423" "04332"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "0332" "0313" "0421" "02321" "0241" "0213"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "0233" "0154" "0213" "0241" "04111"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "0412" "0211" "0231" "022" "0113" "0431"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "0432" "0431" "04111" "0233" "0241" "0233"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "0431" "0332" "0133" "032" "0112"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "0431" "0231" "02422" "0115" "02322"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "02422" "0123" "0312" "0111" "0231" "02421"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "02423" "02321" "032" "0431" "0115"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "02422" "02422" "0313" "0311" "0431" "0115"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "0113" "022" "04113" "0431" "0212" "0233"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "0312" "0152" "0421" "0115" "022" "0111"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04333" "04331" "02321" "0412" "022" "0431"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "0313" "0332" "0211" "02321" "0241" "0314"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "02422" "0412" "022" "0212" "0412" "0113"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "0421" "02422" "0111" "0241" "0113" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "0233" "0152" "0241" "0213" "0314"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "02321" "0421" "0341" "0241" "0213"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "0211" "04332" "0132" "04131"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "0341" "0233" "0431" "0341" "04332" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "0431" "0241" "0211" "0211" "0412" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "0412" "0431" "0423" "022" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "0212" "022" "02422" "0341" "0233" "0112"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04111" "0332" "02422" "0211" "0212" "04222"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04333" "0412" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "0213" "0111" "0343" "04333" "02422" "0111"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "02322" "022" "02421" "0213" "0212" "0412"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "0231" "0212" "0311" "0423" "0111" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "04133" "0412" "0122" "032" "0431"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "0431" "02322" "02322" "0241" "0331" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "0421" "04112" "0152" "022" "0332" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "0332" "0112" "0154" "0241" "0241" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "0314" "04332" "0412" "0431" "0231" "04132"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04222" "04111" "0122" "022" "022" "02421"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "0314" "0241" "0412" "0332" "0412" "04332"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "0231" "0122" "022" "0211" "04111" "0432"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "0111" "0342" "04332" "0412" "04132" "02423"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "02321" "0311" "0331" "0431" "022" "02421"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "0421" "02423" "0241" "0152" "02421" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "0412" "0412" "0331" "02322" "0313" "04113"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "0432" "04113" "04332" "0421" "02422" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "0231" "0112" "0134" "0412" "0431" "0213"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04111" "04332" "0123" "04333" "04111" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "0431" "0122" "0241" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "0412" "0241" "0112" "0231" "032" "04332"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "0342" "0212" "0421" "0134" "02421" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "0432" "0233" "0331" "0233" "02421" "04222"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04222" "02423" "014" "0213" "032" "04222"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "0332" "04222" "0431" "0114" "0111"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "0233" "0233" "0313" "022" "0332" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "0332" "0332" "0113" "0431" "0213" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "04113" "0132" "0311" "0311" "0421" "0233"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "0213" "0421" "0311" "022" "04131" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "04332" "02321" "0112" "04331" "0331"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "0213" "0421" "0131" "0115" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "0231" "0112" "04111" "022" "0231" "0241"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "0231" "0432" "022" "0241" "02422" "0111"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "0231" "04113" "0341" "0331" "04131" "0431"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "02423" "04131" "02422" "022" "0412"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "0314" "0341" "0421" "04222" "04111" "0432"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "0343" "04112" "04332" "0431" "0412" "0241"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "0431" "0152" "0421" "014" "0313"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "0331" "02423" "014" "0412" "0213" "0421"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "0432" "0341" "04113" "04332" "0213" "0431"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "0212" "02321" "0122" "0231" "0332"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "0342" "04111" "0211" "0431" "02423" "0331"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "0432" "032" "0311" "0412" "0241" "0431"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "0421" "022" "0421" "04332" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "0233" "0133" "0114" "0231" "0431" "0312"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "0412" "0431" "02422" "02321" "0211" "0431"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "0111" "0431" "0212" "0412" "022" "0213"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "0332" "0432" "04111" "0112" "04332" "0231"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04332" "0211" "04332" "0133" "04332" "0213"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "0313" "02321" "0421" "0421" "0213" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "0213" "0154" "02322" "0431" "022" "0233"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "0231" "0152" "0211" "0423" "0331" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "0431" "04221" "0231" "0331" "0332" "0233"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04222" "014" "0412" "04113" "02422" "0311"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "04111" "022" "04113" "0421" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "0241" "04113" "0154" "0241" "0231" "0341"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "0241" "032" "032" "0213" "0231"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "0241" "0431" "022" "04113" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "0114" "02422" "0231" "0241" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "04113" "0331" "0332" "0151" "022" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "0212" "032" "0231" "0332" "0231" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "0241" "022" "0412" "0412" "0421" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04221" "0233" "0431" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04111" "022" "0412" "0123" "0412" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "0421" "014" "0431" "0241" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "0213" "04133" "0331" "0241" "0213" "0212"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "0113" "022" "0312" "0113" "0311" "0212"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "04113" "0231" "0123" "0211" "04332" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "0341" "032" "0421" "02321" "0431" "04111"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "0231" "04112" "0332" "0311" "0132" "0311"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1859))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "0412" "0421" "04132" "0212" "0412" "0313"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04112" "0122" "0431" "0431" "04222" "0431"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "0112" "04131" "0213" "02321" "0211" "0421"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "0213" "0233" "04112" "024" "04111"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "0311" "0231" "0431" "0313" "0431" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "0212" "024" "0231" "022" "0311" "0311"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "0115" "0213" "0332" "0123" "04113" "0113"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "0233" "04111" "024" "022" "04132" "0421"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "0231" "04333" "04332" "0412" "0332" "0421"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04332" "0432" "024" "04113" "0421" "04113"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04111" "0421" "0231" "0311" "04332" "04112"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04222" "0212" "024" "0231" "04131" "0431"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "0314" "0431" "022" "0133" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "0342" "032" "04111" "0412" "0233" "0421"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "0412" "0113" "024" "024" "0152" "0421"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "0114" "0331" "022" "02321" "0233" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "0432" "014" "024" "024" "02322" "02321"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "0412" "0211" "0133" "0213" "024" "02321"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04222" "0332" "0122" "0412" "0212" "0313"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "0233" "04221" "0233" "0342" "0233" "04131"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "0431" "024" "0115" "0412" "0421"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "0122" "032" "0231" "0314" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04331" "0311" "032" "024" "0331" "0213"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "0112" "0332" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "0423" "0113" "024" "0132" "0112" "04113"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "0412" "0112" "024" "04331" "0431" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "0421" "0213" "014" "04113" "0114" "0213"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "04113" "0113" "0332" "0341" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "0421" "04332" "0152" "04113" "04131" "04222"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "0412" "0431" "0412" "0151" "0113"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "0331" "02321" "0122" "04113" "04332" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04133" "04113" "032" "024" "0115" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "02321" "0112" "0412" "0332" "0431"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "0431" "024" "022" "0431" "04222" "0421"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "024" "0132" "04221" "0431" "0231"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "0231" "0212" "0342" "0423" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "0213" "0314" "0131" "04222" "0311"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "0123" "0233" "0412" "0231" "0312"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "0231" "014" "032" "0213" "04113" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "0233" "0231" "04111" "0312" "0231" "0212"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "04113" "0233" "0311" "0412" "0431" "0421"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "0313" "0412" "02321" "032" "0421" "0423"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "0421" "032" "0431" "014" "0233"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "0313" "024" "04133" "032" "0431" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "0231" "0431" "0423" "04111" "0332" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "024" "0211" "0122" "014" "04132"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "0233" "0131" "02321" "0211" "014" "04111"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "0412" "0112" "04113" "0154" "022" "0432"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "04332" "024" "0432" "0213" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "0412" "0431" "0153" "04332"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "0431" "04111" "04333" "0421" "02322" "0231"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "0421" "0123" "0341" "014" "0432" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04112" "0332" "0331" "04131" "024" "0332"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04112" "0112" "0421" "0233" "0213" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "0332" "0231" "0331" "04221" "0423" "04332"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "0332" "0313" "0421" "02321" "024" "0213"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "0233" "0154" "0213" "024" "04111"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "0412" "0211" "0231" "022" "0113" "0431"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "0432" "0431" "04111" "0233" "024" "0233"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "0431" "0332" "0133" "032" "0112"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "0431" "0231" "024" "0115" "02322"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "0123" "0312" "0111" "0231" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "024" "02321" "032" "0431" "0115"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "0313" "0311" "0431" "0115"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "0113" "022" "04113" "0431" "0212" "0233"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "0312" "0152" "0421" "0115" "022" "0111"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04333" "04331" "02321" "0412" "022" "0431"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "0313" "0332" "0211" "02321" "024" "0314"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "0412" "022" "0212" "0412" "0113"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "0421" "024" "0111" "024" "0113" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "0233" "0152" "024" "0213" "0314"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "02321" "0421" "0341" "024" "0213"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "0211" "04332" "0132" "04131"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "0341" "0233" "0431" "0341" "04332" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "0431" "024" "0211" "0211" "0412" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "0412" "0431" "0423" "022" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "0212" "022" "024" "0341" "0233" "0112"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04111" "0332" "024" "0211" "0212" "04222"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04333" "0412" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "0213" "0111" "0343" "04333" "024" "0111"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "02322" "022" "024" "0213" "0212" "0412"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "0231" "0212" "0311" "0423" "0111" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "04133" "0412" "0122" "032" "0431"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "0431" "02322" "02322" "024" "0331" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "0421" "04112" "0152" "022" "0332" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "0332" "0112" "0154" "024" "024" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "0314" "04332" "0412" "0431" "0231" "04132"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04222" "04111" "0122" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "0314" "024" "0412" "0332" "0412" "04332"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "0231" "0122" "022" "0211" "04111" "0432"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "0111" "0342" "04332" "0412" "04132" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "02321" "0311" "0331" "0431" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "0421" "024" "024" "0152" "024" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "0412" "0412" "0331" "02322" "0313" "04113"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "0432" "04113" "04332" "0421" "024" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "0231" "0112" "0134" "0412" "0431" "0213"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04111" "04332" "0123" "04333" "04111" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "0431" "0122" "024" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "0412" "024" "0112" "0231" "032" "04332"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "0342" "0212" "0421" "0134" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "0432" "0233" "0331" "0233" "024" "04222"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04222" "024" "014" "0213" "032" "04222"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "0332" "04222" "0431" "0114" "0111"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "0233" "0233" "0313" "022" "0332" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "0332" "0332" "0113" "0431" "0213" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "04113" "0132" "0311" "0311" "0421" "0233"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "0213" "0421" "0311" "022" "04131" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "04332" "02321" "0112" "04331" "0331"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "0213" "0421" "0131" "0115" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "0231" "0112" "04111" "022" "0231" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "0231" "0432" "022" "024" "024" "0111"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "0231" "04113" "0341" "0331" "04131" "0431"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "04131" "024" "022" "0412"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "0314" "0341" "0421" "04222" "04111" "0432"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "0343" "04112" "04332" "0431" "0412" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "0431" "0152" "0421" "014" "0313"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "0331" "024" "014" "0412" "0213" "0421"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "0432" "0341" "04113" "04332" "0213" "0431"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "0212" "02321" "0122" "0231" "0332"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "0342" "04111" "0211" "0431" "024" "0331"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "0432" "032" "0311" "0412" "024" "0431"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "0421" "022" "0421" "04332" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "0233" "0133" "0114" "0231" "0431" "0312"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "0412" "0431" "024" "02321" "0211" "0431"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "0111" "0431" "0212" "0412" "022" "0213"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "0332" "0432" "04111" "0112" "04332" "0231"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04332" "0211" "04332" "0133" "04332" "0213"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "0313" "02321" "0421" "0421" "0213" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "0213" "0154" "02322" "0431" "022" "0233"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "0231" "0152" "0211" "0423" "0331" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "0431" "04221" "0231" "0331" "0332" "0233"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04222" "014" "0412" "04113" "024" "0311"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "04111" "022" "04113" "0421" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "04113" "0154" "024" "0231" "0341"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "024" "032" "032" "0213" "0231"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "0431" "022" "04113" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "0114" "024" "0231" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "04113" "0331" "0332" "0151" "022" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "0212" "032" "0231" "0332" "0231" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "0412" "0412" "0421" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04221" "0233" "0431" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04111" "022" "0412" "0123" "0412" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "0421" "014" "0431" "024" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "0213" "04133" "0331" "024" "0213" "0212"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "0113" "022" "0312" "0113" "0311" "0212"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "04113" "0231" "0123" "0211" "04332" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "0341" "032" "0421" "02321" "0431" "04111"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "0231" "04112" "0332" "0311" "0132" "0311"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1863))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "0412" "0421" "04132" "0212" "0412" "0313"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "0411" "0122" "0431" "0431" "04222" "0431"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "0112" "04131" "0213" "02321" "0211" "0421"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "0213" "0233" "0411" "024" "0411"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "0311" "0231" "0431" "0313" "0431" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "0212" "024" "0231" "022" "0311" "0311"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "0115" "0213" "0332" "0123" "0411" "0113"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "0233" "0411" "024" "022" "04132" "0421"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "0231" "04333" "04332" "0412" "0332" "0421"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04332" "0432" "024" "0411" "0421" "0411"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "0411" "0421" "0231" "0311" "04332" "0411"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04222" "0212" "024" "0231" "04131" "0431"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "0314" "0431" "022" "0133" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "0342" "032" "0411" "0412" "0233" "0421"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "0412" "0113" "024" "024" "0152" "0421"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "0114" "0331" "022" "02321" "0233" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "0432" "014" "024" "024" "02322" "02321"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "0412" "0211" "0133" "0213" "024" "02321"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04222" "0332" "0122" "0412" "0212" "0313"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "0233" "04221" "0233" "0342" "0233" "04131"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "0431" "024" "0115" "0412" "0421"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "0122" "032" "0231" "0314" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04331" "0311" "032" "024" "0331" "0213"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "0112" "0332" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "0423" "0113" "024" "0132" "0112" "0411"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "0412" "0112" "024" "04331" "0431" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "0421" "0213" "014" "0411" "0114" "0213"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "0411" "0113" "0332" "0341" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "0421" "04332" "0152" "0411" "04131" "04222"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "0412" "0431" "0412" "0151" "0113"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "0331" "02321" "0122" "0411" "04332" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04133" "0411" "032" "024" "0115" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "02321" "0112" "0412" "0332" "0431"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "0431" "024" "022" "0431" "04222" "0421"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "024" "0132" "04221" "0431" "0231"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "0231" "0212" "0342" "0423" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "0213" "0314" "0131" "04222" "0311"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "0123" "0233" "0412" "0231" "0312"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "0231" "014" "032" "0213" "0411" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "0233" "0231" "0411" "0312" "0231" "0212"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "0411" "0233" "0311" "0412" "0431" "0421"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "0313" "0412" "02321" "032" "0421" "0423"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "0421" "032" "0431" "014" "0233"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "0313" "024" "04133" "032" "0431" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "0231" "0431" "0423" "0411" "0332" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "024" "0211" "0122" "014" "04132"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "0233" "0131" "02321" "0211" "014" "0411"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "0412" "0112" "0411" "0154" "022" "0432"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "04332" "024" "0432" "0213" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "0412" "0431" "0153" "04332"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "0431" "0411" "04333" "0421" "02322" "0231"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "0421" "0123" "0341" "014" "0432" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "0411" "0332" "0331" "04131" "024" "0332"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "0411" "0112" "0421" "0233" "0213" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "0332" "0231" "0331" "04221" "0423" "04332"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "0332" "0313" "0421" "02321" "024" "0213"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "0233" "0154" "0213" "024" "0411"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "0412" "0211" "0231" "022" "0113" "0431"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "0432" "0431" "0411" "0233" "024" "0233"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "0431" "0332" "0133" "032" "0112"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "0431" "0231" "024" "0115" "02322"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "0123" "0312" "0111" "0231" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "024" "02321" "032" "0431" "0115"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "0313" "0311" "0431" "0115"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "0113" "022" "0411" "0431" "0212" "0233"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "0312" "0152" "0421" "0115" "022" "0111"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04333" "04331" "02321" "0412" "022" "0431"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "0313" "0332" "0211" "02321" "024" "0314"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "0412" "022" "0212" "0412" "0113"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "0421" "024" "0111" "024" "0113" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "0233" "0152" "024" "0213" "0314"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "02321" "0421" "0341" "024" "0213"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "0211" "04332" "0132" "04131"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "0341" "0233" "0431" "0341" "04332" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "0431" "024" "0211" "0211" "0412" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "0412" "0431" "0423" "022" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "0212" "022" "024" "0341" "0233" "0112"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "0411" "0332" "024" "0211" "0212" "04222"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04333" "0412" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "0213" "0111" "0343" "04333" "024" "0111"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "02322" "022" "024" "0213" "0212" "0412"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "0231" "0212" "0311" "0423" "0111" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "04133" "0412" "0122" "032" "0431"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "0431" "02322" "02322" "024" "0331" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "0421" "0411" "0152" "022" "0332" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "0332" "0112" "0154" "024" "024" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "0314" "04332" "0412" "0431" "0231" "04132"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04222" "0411" "0122" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "0314" "024" "0412" "0332" "0412" "04332"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "0231" "0122" "022" "0211" "0411" "0432"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "0111" "0342" "04332" "0412" "04132" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "02321" "0311" "0331" "0431" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "0421" "024" "024" "0152" "024" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "0412" "0412" "0331" "02322" "0313" "0411"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "0432" "0411" "04332" "0421" "024" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "0231" "0112" "0134" "0412" "0431" "0213"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "0411" "04332" "0123" "04333" "0411" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "0431" "0122" "024" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "0412" "024" "0112" "0231" "032" "04332"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "0342" "0212" "0421" "0134" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "0432" "0233" "0331" "0233" "024" "04222"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04222" "024" "014" "0213" "032" "04222"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "0332" "04222" "0431" "0114" "0111"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "0233" "0233" "0313" "022" "0332" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "0332" "0332" "0113" "0431" "0213" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "0411" "0132" "0311" "0311" "0421" "0233"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "0213" "0421" "0311" "022" "04131" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "04332" "02321" "0112" "04331" "0331"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "0213" "0421" "0131" "0115" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "0231" "0112" "0411" "022" "0231" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "0231" "0432" "022" "024" "024" "0111"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "0231" "0411" "0341" "0331" "04131" "0431"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "04131" "024" "022" "0412"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "0314" "0341" "0421" "04222" "0411" "0432"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "0343" "0411" "04332" "0431" "0412" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "0431" "0152" "0421" "014" "0313"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "0331" "024" "014" "0412" "0213" "0421"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "0432" "0341" "0411" "04332" "0213" "0431"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "0212" "02321" "0122" "0231" "0332"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "0342" "0411" "0211" "0431" "024" "0331"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "0432" "032" "0311" "0412" "024" "0431"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "0421" "022" "0421" "04332" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "0233" "0133" "0114" "0231" "0431" "0312"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "0412" "0431" "024" "02321" "0211" "0431"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "0111" "0431" "0212" "0412" "022" "0213"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "0332" "0432" "0411" "0112" "04332" "0231"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04332" "0211" "04332" "0133" "04332" "0213"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "0313" "02321" "0421" "0421" "0213" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "0213" "0154" "02322" "0431" "022" "0233"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "0231" "0152" "0211" "0423" "0331" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "0431" "04221" "0231" "0331" "0332" "0233"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04222" "014" "0412" "0411" "024" "0311"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "0411" "022" "0411" "0421" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "0411" "0154" "024" "0231" "0341"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "024" "032" "032" "0213" "0231"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "0431" "022" "0411" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "0114" "024" "0231" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "0411" "0331" "0332" "0151" "022" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "0212" "032" "0231" "0332" "0231" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "0412" "0412" "0421" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04221" "0233" "0431" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "0411" "022" "0412" "0123" "0412" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "0421" "014" "0431" "024" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "0213" "04133" "0331" "024" "0213" "0212"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "0113" "022" "0312" "0113" "0311" "0212"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "0411" "0231" "0123" "0211" "04332" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "0341" "032" "0421" "02321" "0431" "0411"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "0231" "0411" "0332" "0311" "0132" "0311"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2144))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "0412" "0421" "04132" "0212" "0412" "0313"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "0411" "0122" "0431" "0431" "04222" "0431"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "0112" "04131" "0213" "0232" "0211" "0421"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "0213" "0233" "0411" "024" "0411"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "0311" "0231" "0431" "0313" "0431" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "0212" "024" "0231" "022" "0311" "0311"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "0115" "0213" "0332" "0123" "0411" "0113"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "0233" "0411" "024" "022" "04132" "0421"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "0231" "04333" "04332" "0412" "0332" "0421"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04332" "0432" "024" "0411" "0421" "0411"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "0411" "0421" "0231" "0311" "04332" "0411"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04222" "0212" "024" "0231" "04131" "0431"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "0314" "0431" "022" "0133" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "0342" "032" "0411" "0412" "0233" "0421"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "0412" "0113" "024" "024" "0152" "0421"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "0114" "0331" "022" "0232" "0233" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "0432" "014" "024" "024" "0232" "0232"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "0412" "0211" "0133" "0213" "024" "0232"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04222" "0332" "0122" "0412" "0212" "0313"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "0233" "04221" "0233" "0342" "0233" "04131"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "0431" "024" "0115" "0412" "0421"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "0122" "032" "0231" "0314" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04331" "0311" "032" "024" "0331" "0213"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "0112" "0332" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "0423" "0113" "024" "0132" "0112" "0411"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "0412" "0112" "024" "04331" "0431" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "0421" "0213" "014" "0411" "0114" "0213"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "0411" "0113" "0332" "0341" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "0421" "04332" "0152" "0411" "04131" "04222"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "0412" "0431" "0412" "0151" "0113"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "0331" "0232" "0122" "0411" "04332" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04133" "0411" "032" "024" "0115" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "0232" "0112" "0412" "0332" "0431"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "0431" "024" "022" "0431" "04222" "0421"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "024" "0132" "04221" "0431" "0231"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "0231" "0212" "0342" "0423" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "0213" "0314" "0131" "04222" "0311"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "0123" "0233" "0412" "0231" "0312"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "0231" "014" "032" "0213" "0411" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "0233" "0231" "0411" "0312" "0231" "0212"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "0411" "0233" "0311" "0412" "0431" "0421"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "0313" "0412" "0232" "032" "0421" "0423"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "0421" "032" "0431" "014" "0233"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "0313" "024" "04133" "032" "0431" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "0231" "0431" "0423" "0411" "0332" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "024" "0211" "0122" "014" "04132"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "0233" "0131" "0232" "0211" "014" "0411"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "0412" "0112" "0411" "0154" "022" "0432"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "04332" "024" "0432" "0213" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "0412" "0431" "0153" "04332"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "0431" "0411" "04333" "0421" "0232" "0231"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "0421" "0123" "0341" "014" "0432" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "0411" "0332" "0331" "04131" "024" "0332"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "0411" "0112" "0421" "0233" "0213" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "0332" "0231" "0331" "04221" "0423" "04332"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "0332" "0313" "0421" "0232" "024" "0213"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "0233" "0154" "0213" "024" "0411"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "0412" "0211" "0231" "022" "0113" "0431"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "0432" "0431" "0411" "0233" "024" "0233"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "0431" "0332" "0133" "032" "0112"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "0431" "0231" "024" "0115" "0232"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "0123" "0312" "0111" "0231" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "024" "0232" "032" "0431" "0115"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "0313" "0311" "0431" "0115"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "0113" "022" "0411" "0431" "0212" "0233"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "0312" "0152" "0421" "0115" "022" "0111"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04333" "04331" "0232" "0412" "022" "0431"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "0313" "0332" "0211" "0232" "024" "0314"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "0412" "022" "0212" "0412" "0113"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "0421" "024" "0111" "024" "0113" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "0233" "0152" "024" "0213" "0314"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "0232" "0421" "0341" "024" "0213"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "0211" "04332" "0132" "04131"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "0341" "0233" "0431" "0341" "04332" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "0431" "024" "0211" "0211" "0412" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "0412" "0431" "0423" "022" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "0212" "022" "024" "0341" "0233" "0112"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "0411" "0332" "024" "0211" "0212" "04222"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04333" "0412" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "0213" "0111" "0343" "04333" "024" "0111"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "0232" "022" "024" "0213" "0212" "0412"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "0231" "0212" "0311" "0423" "0111" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "04133" "0412" "0122" "032" "0431"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "0431" "0232" "0232" "024" "0331" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "0421" "0411" "0152" "022" "0332" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "0332" "0112" "0154" "024" "024" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "0314" "04332" "0412" "0431" "0231" "04132"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04222" "0411" "0122" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "0314" "024" "0412" "0332" "0412" "04332"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "0231" "0122" "022" "0211" "0411" "0432"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "0111" "0342" "04332" "0412" "04132" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "0232" "0311" "0331" "0431" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "0421" "024" "024" "0152" "024" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "0412" "0412" "0331" "0232" "0313" "0411"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "0432" "0411" "04332" "0421" "024" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "0231" "0112" "0134" "0412" "0431" "0213"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "0411" "04332" "0123" "04333" "0411" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "0431" "0122" "024" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "0412" "024" "0112" "0231" "032" "04332"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "0342" "0212" "0421" "0134" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "0432" "0233" "0331" "0233" "024" "04222"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04222" "024" "014" "0213" "032" "04222"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "0332" "04222" "0431" "0114" "0111"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "0233" "0233" "0313" "022" "0332" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "0332" "0332" "0113" "0431" "0213" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "0411" "0132" "0311" "0311" "0421" "0233"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "0213" "0421" "0311" "022" "04131" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "04332" "0232" "0112" "04331" "0331"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "0213" "0421" "0131" "0115" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "0231" "0112" "0411" "022" "0231" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "0231" "0432" "022" "024" "024" "0111"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "0231" "0411" "0341" "0331" "04131" "0431"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "04131" "024" "022" "0412"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "0314" "0341" "0421" "04222" "0411" "0432"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "0343" "0411" "04332" "0431" "0412" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "0431" "0152" "0421" "014" "0313"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "0331" "024" "014" "0412" "0213" "0421"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "0432" "0341" "0411" "04332" "0213" "0431"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "0212" "0232" "0122" "0231" "0332"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "0342" "0411" "0211" "0431" "024" "0331"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "0432" "032" "0311" "0412" "024" "0431"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "0421" "022" "0421" "04332" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "0233" "0133" "0114" "0231" "0431" "0312"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "0412" "0431" "024" "0232" "0211" "0431"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "0111" "0431" "0212" "0412" "022" "0213"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "0332" "0432" "0411" "0112" "04332" "0231"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04332" "0211" "04332" "0133" "04332" "0213"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "0313" "0232" "0421" "0421" "0213" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "0213" "0154" "0232" "0431" "022" "0233"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "0231" "0152" "0211" "0423" "0331" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "0431" "04221" "0231" "0331" "0332" "0233"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04222" "014" "0412" "0411" "024" "0311"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "0411" "022" "0411" "0421" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "0411" "0154" "024" "0231" "0341"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "024" "032" "032" "0213" "0231"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "0431" "022" "0411" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "0114" "024" "0231" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "0411" "0331" "0332" "0151" "022" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "0212" "032" "0231" "0332" "0231" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "0412" "0412" "0421" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04221" "0233" "0431" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "0411" "022" "0412" "0123" "0412" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "0421" "014" "0431" "024" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "0213" "04133" "0331" "024" "0213" "0212"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "0113" "022" "0312" "0113" "0311" "0212"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "0411" "0231" "0123" "0211" "04332" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "0341" "032" "0421" "0232" "0431" "0411"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "0231" "0411" "0332" "0311" "0132" "0311"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2288))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "0412" "0421" "04132" "0212" "0412" "0313"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "0411" "0122" "0431" "0431" "04222" "0431"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "011" "04131" "0213" "0232" "0211" "0421"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "0213" "0233" "0411" "024" "0411"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "0311" "0231" "0431" "0313" "0431" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "0212" "024" "0231" "022" "0311" "0311"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "011" "0213" "0332" "0123" "0411" "011"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "0233" "0411" "024" "022" "04132" "0421"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "0231" "04333" "04332" "0412" "0332" "0421"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04332" "0432" "024" "0411" "0421" "0411"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "0411" "0421" "0231" "0311" "04332" "0411"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04222" "0212" "024" "0231" "04131" "0431"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "0314" "0431" "022" "0133" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "0342" "032" "0411" "0412" "0233" "0421"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "0412" "011" "024" "024" "0152" "0421"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "011" "0331" "022" "0232" "0233" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "0432" "014" "024" "024" "0232" "0232"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "0412" "0211" "0133" "0213" "024" "0232"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04222" "0332" "0122" "0412" "0212" "0313"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "0233" "04221" "0233" "0342" "0233" "04131"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "0431" "024" "011" "0412" "0421"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "0122" "032" "0231" "0314" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04331" "0311" "032" "024" "0331" "0213"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "011" "0332" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "0423" "011" "024" "0132" "011" "0411"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "0412" "011" "024" "04331" "0431" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "0421" "0213" "014" "0411" "011" "0213"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "0411" "011" "0332" "0341" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "0421" "04332" "0152" "0411" "04131" "04222"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "0412" "0431" "0412" "0151" "011"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "0331" "0232" "0122" "0411" "04332" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04133" "0411" "032" "024" "011" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "0232" "011" "0412" "0332" "0431"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "0431" "024" "022" "0431" "04222" "0421"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "024" "0132" "04221" "0431" "0231"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "0231" "0212" "0342" "0423" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "0213" "0314" "0131" "04222" "0311"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "0123" "0233" "0412" "0231" "0312"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "0231" "014" "032" "0213" "0411" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "0233" "0231" "0411" "0312" "0231" "0212"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "0411" "0233" "0311" "0412" "0431" "0421"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "0313" "0412" "0232" "032" "0421" "0423"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "0421" "032" "0431" "014" "0233"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "0313" "024" "04133" "032" "0431" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "0231" "0431" "0423" "0411" "0332" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "024" "0211" "0122" "014" "04132"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "0233" "0131" "0232" "0211" "014" "0411"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "0412" "011" "0411" "0154" "022" "0432"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "04332" "024" "0432" "0213" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "0412" "0431" "0153" "04332"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "0431" "0411" "04333" "0421" "0232" "0231"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "0421" "0123" "0341" "014" "0432" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "0411" "0332" "0331" "04131" "024" "0332"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "0411" "011" "0421" "0233" "0213" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "0332" "0231" "0331" "04221" "0423" "04332"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "0332" "0313" "0421" "0232" "024" "0213"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "0233" "0154" "0213" "024" "0411"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "0412" "0211" "0231" "022" "011" "0431"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "0432" "0431" "0411" "0233" "024" "0233"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "0431" "0332" "0133" "032" "011"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "0431" "0231" "024" "011" "0232"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "0123" "0312" "011" "0231" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "024" "0232" "032" "0431" "011"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "0313" "0311" "0431" "011"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "011" "022" "0411" "0431" "0212" "0233"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "0312" "0152" "0421" "011" "022" "011"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04333" "04331" "0232" "0412" "022" "0431"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "0313" "0332" "0211" "0232" "024" "0314"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "0412" "022" "0212" "0412" "011"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "0421" "024" "011" "024" "011" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "0233" "0152" "024" "0213" "0314"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "0232" "0421" "0341" "024" "0213"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "0211" "04332" "0132" "04131"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "0341" "0233" "0431" "0341" "04332" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "0431" "024" "0211" "0211" "0412" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "0412" "0431" "0423" "022" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "0212" "022" "024" "0341" "0233" "011"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "0411" "0332" "024" "0211" "0212" "04222"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04333" "0412" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "0213" "011" "0343" "04333" "024" "011"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "0232" "022" "024" "0213" "0212" "0412"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "0231" "0212" "0311" "0423" "011" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "04133" "0412" "0122" "032" "0431"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "0431" "0232" "0232" "024" "0331" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "0421" "0411" "0152" "022" "0332" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "0332" "011" "0154" "024" "024" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "0314" "04332" "0412" "0431" "0231" "04132"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04222" "0411" "0122" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "0314" "024" "0412" "0332" "0412" "04332"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "0231" "0122" "022" "0211" "0411" "0432"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "011" "0342" "04332" "0412" "04132" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "0232" "0311" "0331" "0431" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "0421" "024" "024" "0152" "024" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "0412" "0412" "0331" "0232" "0313" "0411"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "0432" "0411" "04332" "0421" "024" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "0231" "011" "0134" "0412" "0431" "0213"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "0411" "04332" "0123" "04333" "0411" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "0431" "0122" "024" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "0412" "024" "011" "0231" "032" "04332"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "0342" "0212" "0421" "0134" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "0432" "0233" "0331" "0233" "024" "04222"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04222" "024" "014" "0213" "032" "04222"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "0332" "04222" "0431" "011" "011"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "0233" "0233" "0313" "022" "0332" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "0332" "0332" "011" "0431" "0213" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "0411" "0132" "0311" "0311" "0421" "0233"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "0213" "0421" "0311" "022" "04131" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "04332" "0232" "011" "04331" "0331"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "0213" "0421" "0131" "011" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "0231" "011" "0411" "022" "0231" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "0231" "0432" "022" "024" "024" "011"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "0231" "0411" "0341" "0331" "04131" "0431"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "04131" "024" "022" "0412"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "0314" "0341" "0421" "04222" "0411" "0432"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "0343" "0411" "04332" "0431" "0412" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "0431" "0152" "0421" "014" "0313"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "0331" "024" "014" "0412" "0213" "0421"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "0432" "0341" "0411" "04332" "0213" "0431"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "0212" "0232" "0122" "0231" "0332"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "0342" "0411" "0211" "0431" "024" "0331"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "0432" "032" "0311" "0412" "024" "0431"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "0421" "022" "0421" "04332" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "0233" "0133" "011" "0231" "0431" "0312"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "0412" "0431" "024" "0232" "0211" "0431"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "011" "0431" "0212" "0412" "022" "0213"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "0332" "0432" "0411" "011" "04332" "0231"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04332" "0211" "04332" "0133" "04332" "0213"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "0313" "0232" "0421" "0421" "0213" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "0213" "0154" "0232" "0431" "022" "0233"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "0231" "0152" "0211" "0423" "0331" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "0431" "04221" "0231" "0331" "0332" "0233"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04222" "014" "0412" "0411" "024" "0311"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "0411" "022" "0411" "0421" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "0411" "0154" "024" "0231" "0341"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "024" "032" "032" "0213" "0231"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "0431" "022" "0411" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "011" "024" "0231" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "0411" "0331" "0332" "0151" "022" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "0212" "032" "0231" "0332" "0231" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "0412" "0412" "0421" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04221" "0233" "0431" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "0411" "022" "0412" "0123" "0412" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "0421" "014" "0431" "024" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "0213" "04133" "0331" "024" "0213" "0212"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "011" "022" "0312" "011" "0311" "0212"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "0411" "0231" "0123" "0211" "04332" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "0341" "032" "0421" "0232" "0431" "0411"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "0231" "0411" "0332" "0311" "0132" "0311"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3086))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "0412" "0421" "04132" "0212" "0412" "0313"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "0411" "0122" "0431" "0431" "04222" "0431"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "011" "04131" "0213" "0232" "0211" "0421"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "0213" "0233" "0411" "024" "0411"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "0311" "0231" "0431" "0313" "0431" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "0212" "024" "0231" "022" "0311" "0311"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "011" "0213" "033" "0123" "0411" "011"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "0233" "0411" "024" "022" "04132" "0421"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "0231" "04333" "04332" "0412" "033" "0421"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04332" "0432" "024" "0411" "0421" "0411"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "0411" "0421" "0231" "0311" "04332" "0411"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04222" "0212" "024" "0231" "04131" "0431"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "0314" "0431" "022" "0133" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "0342" "032" "0411" "0412" "0233" "0421"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "0412" "011" "024" "024" "0152" "0421"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "011" "033" "022" "0232" "0233" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "0432" "014" "024" "024" "0232" "0232"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "0412" "0211" "0133" "0213" "024" "0232"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04222" "033" "0122" "0412" "0212" "0313"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "0233" "04221" "0233" "0342" "0233" "04131"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "0431" "024" "011" "0412" "0421"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "0122" "032" "0231" "0314" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04331" "0311" "032" "024" "033" "0213"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "011" "033" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "0423" "011" "024" "0132" "011" "0411"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "0412" "011" "024" "04331" "0431" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "0421" "0213" "014" "0411" "011" "0213"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "0411" "011" "033" "0341" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "0421" "04332" "0152" "0411" "04131" "04222"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "0412" "0431" "0412" "0151" "011"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "033" "0232" "0122" "0411" "04332" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04133" "0411" "032" "024" "011" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "0232" "011" "0412" "033" "0431"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "0431" "024" "022" "0431" "04222" "0421"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "024" "0132" "04221" "0431" "0231"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "0231" "0212" "0342" "0423" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "0213" "0314" "0131" "04222" "0311"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "0123" "0233" "0412" "0231" "0312"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "0231" "014" "032" "0213" "0411" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "0233" "0231" "0411" "0312" "0231" "0212"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "0411" "0233" "0311" "0412" "0431" "0421"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "0313" "0412" "0232" "032" "0421" "0423"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "0421" "032" "0431" "014" "0233"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "0313" "024" "04133" "032" "0431" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "0231" "0431" "0423" "0411" "033" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "024" "0211" "0122" "014" "04132"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "0233" "0131" "0232" "0211" "014" "0411"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "0412" "011" "0411" "0154" "022" "0432"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "04332" "024" "0432" "0213" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "0412" "0431" "0153" "04332"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "0431" "0411" "04333" "0421" "0232" "0231"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "0421" "0123" "0341" "014" "0432" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "0411" "033" "033" "04131" "024" "033"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "0411" "011" "0421" "0233" "0213" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "033" "0231" "033" "04221" "0423" "04332"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "033" "0313" "0421" "0232" "024" "0213"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "0233" "0154" "0213" "024" "0411"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "0412" "0211" "0231" "022" "011" "0431"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "0432" "0431" "0411" "0233" "024" "0233"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "0431" "033" "0133" "032" "011"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "0431" "0231" "024" "011" "0232"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "0123" "0312" "011" "0231" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "024" "0232" "032" "0431" "011"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "0313" "0311" "0431" "011"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "011" "022" "0411" "0431" "0212" "0233"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "0312" "0152" "0421" "011" "022" "011"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04333" "04331" "0232" "0412" "022" "0431"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "0313" "033" "0211" "0232" "024" "0314"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "0412" "022" "0212" "0412" "011"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "0421" "024" "011" "024" "011" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "0233" "0152" "024" "0213" "0314"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "0232" "0421" "0341" "024" "0213"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "0211" "04332" "0132" "04131"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "0341" "0233" "0431" "0341" "04332" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "0431" "024" "0211" "0211" "0412" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "0412" "0431" "0423" "022" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "0212" "022" "024" "0341" "0233" "011"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "0411" "033" "024" "0211" "0212" "04222"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04333" "0412" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "0213" "011" "0343" "04333" "024" "011"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "0232" "022" "024" "0213" "0212" "0412"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "0231" "0212" "0311" "0423" "011" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "04133" "0412" "0122" "032" "0431"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "0431" "0232" "0232" "024" "033" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "0421" "0411" "0152" "022" "033" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "033" "011" "0154" "024" "024" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "0314" "04332" "0412" "0431" "0231" "04132"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04222" "0411" "0122" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "0314" "024" "0412" "033" "0412" "04332"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "0231" "0122" "022" "0211" "0411" "0432"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "011" "0342" "04332" "0412" "04132" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "0232" "0311" "033" "0431" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "0421" "024" "024" "0152" "024" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "0412" "0412" "033" "0232" "0313" "0411"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "0432" "0411" "04332" "0421" "024" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "0231" "011" "0134" "0412" "0431" "0213"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "0411" "04332" "0123" "04333" "0411" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "0431" "0122" "024" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "0412" "024" "011" "0231" "032" "04332"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "0342" "0212" "0421" "0134" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "0432" "0233" "033" "0233" "024" "04222"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04222" "024" "014" "0213" "032" "04222"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "033" "04222" "0431" "011" "011"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "0233" "0233" "0313" "022" "033" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "033" "033" "011" "0431" "0213" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "0411" "0132" "0311" "0311" "0421" "0233"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "0213" "0421" "0311" "022" "04131" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "04332" "0232" "011" "04331" "033"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "0213" "0421" "0131" "011" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "0231" "011" "0411" "022" "0231" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "0231" "0432" "022" "024" "024" "011"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "0231" "0411" "0341" "033" "04131" "0431"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "04131" "024" "022" "0412"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "0314" "0341" "0421" "04222" "0411" "0432"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "0343" "0411" "04332" "0431" "0412" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "0431" "0152" "0421" "014" "0313"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "033" "024" "014" "0412" "0213" "0421"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "0432" "0341" "0411" "04332" "0213" "0431"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "0212" "0232" "0122" "0231" "033"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "0342" "0411" "0211" "0431" "024" "033"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "0432" "032" "0311" "0412" "024" "0431"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "0421" "022" "0421" "04332" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "0233" "0133" "011" "0231" "0431" "0312"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "0412" "0431" "024" "0232" "0211" "0431"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "011" "0431" "0212" "0412" "022" "0213"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "033" "0432" "0411" "011" "04332" "0231"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04332" "0211" "04332" "0133" "04332" "0213"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "0313" "0232" "0421" "0421" "0213" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "0213" "0154" "0232" "0431" "022" "0233"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "0231" "0152" "0211" "0423" "033" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "0431" "04221" "0231" "033" "033" "0233"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04222" "014" "0412" "0411" "024" "0311"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "0411" "022" "0411" "0421" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "0411" "0154" "024" "0231" "0341"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "024" "032" "032" "0213" "0231"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "0431" "022" "0411" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "011" "024" "0231" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "0411" "033" "033" "0151" "022" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "0212" "032" "0231" "033" "0231" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "0412" "0412" "0421" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04221" "0233" "0431" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "0411" "022" "0412" "0123" "0412" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "0421" "014" "0431" "024" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "0213" "04133" "033" "024" "0213" "0212"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "011" "022" "0312" "011" "0311" "0212"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "0411" "0231" "0123" "0211" "04332" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "0341" "032" "0421" "0232" "0431" "0411"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "0231" "0411" "033" "0311" "0132" "0311"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3775))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "0412" "0421" "04132" "0212" "0412" "0313"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "0411" "0122" "043" "043" "04222" "043"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "011" "04131" "0213" "0232" "0211" "0421"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "0213" "0233" "0411" "024" "0411"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "0311" "0231" "043" "0313" "043" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "0212" "024" "0231" "022" "0311" "0311"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "011" "0213" "033" "0123" "0411" "011"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "0233" "0411" "024" "022" "04132" "0421"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "0231" "043" "043" "0412" "033" "0421"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "043" "043" "024" "0411" "0421" "0411"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "0411" "0421" "0231" "0311" "043" "0411"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04222" "0212" "024" "0231" "04131" "043"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "0314" "043" "022" "0133" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "0342" "032" "0411" "0412" "0233" "0421"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "0412" "011" "024" "024" "0152" "0421"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "011" "033" "022" "0232" "0233" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "043" "014" "024" "024" "0232" "0232"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "0412" "0211" "0133" "0213" "024" "0232"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04222" "033" "0122" "0412" "0212" "0313"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "0233" "04221" "0233" "0342" "0233" "04131"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "043" "024" "011" "0412" "0421"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "0122" "032" "0231" "0314" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "043" "0311" "032" "024" "033" "0213"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "011" "033" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "0423" "011" "024" "0132" "011" "0411"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "0412" "011" "024" "043" "043" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "0421" "0213" "014" "0411" "011" "0213"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "0411" "011" "033" "0341" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "0421" "043" "0152" "0411" "04131" "04222"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "0412" "043" "0412" "0151" "011"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "033" "0232" "0122" "0411" "043" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04133" "0411" "032" "024" "011" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "0232" "011" "0412" "033" "043"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "043" "024" "022" "043" "04222" "0421"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "024" "0132" "04221" "043" "0231"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "0231" "0212" "0342" "0423" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "0213" "0314" "0131" "04222" "0311"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "0123" "0233" "0412" "0231" "0312"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "0231" "014" "032" "0213" "0411" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "0233" "0231" "0411" "0312" "0231" "0212"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "0411" "0233" "0311" "0412" "043" "0421"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "0313" "0412" "0232" "032" "0421" "0423"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "0421" "032" "043" "014" "0233"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "0313" "024" "04133" "032" "043" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "0231" "043" "0423" "0411" "033" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "024" "0211" "0122" "014" "04132"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "0233" "0131" "0232" "0211" "014" "0411"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "0412" "011" "0411" "0154" "022" "043"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "043" "024" "043" "0213" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "0412" "043" "0153" "043"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "043" "0411" "043" "0421" "0232" "0231"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "0421" "0123" "0341" "014" "043" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "0411" "033" "033" "04131" "024" "033"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "0411" "011" "0421" "0233" "0213" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "033" "0231" "033" "04221" "0423" "043"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "033" "0313" "0421" "0232" "024" "0213"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "0233" "0154" "0213" "024" "0411"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "0412" "0211" "0231" "022" "011" "043"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "043" "043" "0411" "0233" "024" "0233"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "043" "033" "0133" "032" "011"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "043" "0231" "024" "011" "0232"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "0123" "0312" "011" "0231" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "024" "0232" "032" "043" "011"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "0313" "0311" "043" "011"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "011" "022" "0411" "043" "0212" "0233"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "0312" "0152" "0421" "011" "022" "011"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "043" "043" "0232" "0412" "022" "043"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "0313" "033" "0211" "0232" "024" "0314"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "0412" "022" "0212" "0412" "011"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "0421" "024" "011" "024" "011" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "0233" "0152" "024" "0213" "0314"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "0232" "0421" "0341" "024" "0213"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "0211" "043" "0132" "04131"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "0341" "0233" "043" "0341" "043" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "043" "024" "0211" "0211" "0412" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "0412" "043" "0423" "022" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "0212" "022" "024" "0341" "0233" "011"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "0411" "033" "024" "0211" "0212" "04222"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "043" "0412" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "0213" "011" "0343" "043" "024" "011"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "0232" "022" "024" "0213" "0212" "0412"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "0231" "0212" "0311" "0423" "011" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "04133" "0412" "0122" "032" "043"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "043" "0232" "0232" "024" "033" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "0421" "0411" "0152" "022" "033" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "033" "011" "0154" "024" "024" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "0314" "043" "0412" "043" "0231" "04132"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04222" "0411" "0122" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "0314" "024" "0412" "033" "0412" "043"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "0231" "0122" "022" "0211" "0411" "043"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "011" "0342" "043" "0412" "04132" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "0232" "0311" "033" "043" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "0421" "024" "024" "0152" "024" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "0412" "0412" "033" "0232" "0313" "0411"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "043" "0411" "043" "0421" "024" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "0231" "011" "0134" "0412" "043" "0213"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "0411" "043" "0123" "043" "0411" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "043" "0122" "024" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "0412" "024" "011" "0231" "032" "043"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "0342" "0212" "0421" "0134" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "043" "0233" "033" "0233" "024" "04222"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04222" "024" "014" "0213" "032" "04222"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "033" "04222" "043" "011" "011"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "0233" "0233" "0313" "022" "033" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "033" "033" "011" "043" "0213" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "0411" "0132" "0311" "0311" "0421" "0233"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "0213" "0421" "0311" "022" "04131" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "043" "0232" "011" "043" "033"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "0213" "0421" "0131" "011" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "0231" "011" "0411" "022" "0231" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "0231" "043" "022" "024" "024" "011"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "0231" "0411" "0341" "033" "04131" "043"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "04131" "024" "022" "0412"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "0314" "0341" "0421" "04222" "0411" "043"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "0343" "0411" "043" "043" "0412" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "043" "0152" "0421" "014" "0313"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "033" "024" "014" "0412" "0213" "0421"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "043" "0341" "0411" "043" "0213" "043"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "0212" "0232" "0122" "0231" "033"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "0342" "0411" "0211" "043" "024" "033"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "043" "032" "0311" "0412" "024" "043"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "0421" "022" "0421" "043" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "0233" "0133" "011" "0231" "043" "0312"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "0412" "043" "024" "0232" "0211" "043"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "011" "043" "0212" "0412" "022" "0213"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "033" "043" "0411" "011" "043" "0231"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "043" "0211" "043" "0133" "043" "0213"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "0313" "0232" "0421" "0421" "0213" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "0213" "0154" "0232" "043" "022" "0233"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "0231" "0152" "0211" "0423" "033" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "043" "04221" "0231" "033" "033" "0233"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04222" "014" "0412" "0411" "024" "0311"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "0411" "022" "0411" "0421" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "0411" "0154" "024" "0231" "0341"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "024" "032" "032" "0213" "0231"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "043" "022" "0411" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "011" "024" "0231" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "0411" "033" "033" "0151" "022" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "0212" "032" "0231" "033" "0231" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "0412" "0412" "0421" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04221" "0233" "043" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "0411" "022" "0412" "0123" "0412" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "0421" "014" "043" "024" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "0213" "04133" "033" "024" "0213" "0212"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "011" "022" "0312" "011" "0311" "0212"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "0411" "0231" "0123" "0211" "043" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "0341" "032" "0421" "0232" "043" "0411"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "0231" "0411" "033" "0311" "0132" "0311"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3920))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "0412" "0421" "0413" "0212" "0412" "0313"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "0411" "0122" "043" "043" "04222" "043"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "011" "0413" "0213" "0232" "0211" "0421"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "0213" "0233" "0411" "024" "0411"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "0311" "0231" "043" "0313" "043" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "0212" "024" "0231" "022" "0311" "0311"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "011" "0213" "033" "0123" "0411" "011"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "0233" "0411" "024" "022" "0413" "0421"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "0231" "043" "043" "0412" "033" "0421"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "043" "043" "024" "0411" "0421" "0411"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "0411" "0421" "0231" "0311" "043" "0411"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04222" "0212" "024" "0231" "0413" "043"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "0314" "043" "022" "0133" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "0342" "032" "0411" "0412" "0233" "0421"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "0412" "011" "024" "024" "0152" "0421"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "011" "033" "022" "0232" "0233" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "043" "014" "024" "024" "0232" "0232"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "0412" "0211" "0133" "0213" "024" "0232"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04222" "033" "0122" "0412" "0212" "0313"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "0233" "04221" "0233" "0342" "0233" "0413"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "043" "024" "011" "0412" "0421"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "0122" "032" "0231" "0314" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "043" "0311" "032" "024" "033" "0213"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "011" "033" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "0423" "011" "024" "0132" "011" "0411"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "0412" "011" "024" "043" "043" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "0421" "0213" "014" "0411" "011" "0213"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "0411" "011" "033" "0341" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "0421" "043" "0152" "0411" "0413" "04222"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "0412" "043" "0412" "0151" "011"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "033" "0232" "0122" "0411" "043" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "0413" "0411" "032" "024" "011" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "0232" "011" "0412" "033" "043"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "043" "024" "022" "043" "04222" "0421"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "024" "0132" "04221" "043" "0231"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "0231" "0212" "0342" "0423" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "0213" "0314" "0131" "04222" "0311"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "0123" "0233" "0412" "0231" "0312"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "0231" "014" "032" "0213" "0411" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "0233" "0231" "0411" "0312" "0231" "0212"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "0411" "0233" "0311" "0412" "043" "0421"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "0313" "0412" "0232" "032" "0421" "0423"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "0421" "032" "043" "014" "0233"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "0313" "024" "0413" "032" "043" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "0231" "043" "0423" "0411" "033" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "024" "0211" "0122" "014" "0413"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "0233" "0131" "0232" "0211" "014" "0411"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "0412" "011" "0411" "0154" "022" "043"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "043" "024" "043" "0213" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "0412" "043" "0153" "043"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "043" "0411" "043" "0421" "0232" "0231"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "0421" "0123" "0341" "014" "043" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "0411" "033" "033" "0413" "024" "033"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "0411" "011" "0421" "0233" "0213" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "033" "0231" "033" "04221" "0423" "043"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "033" "0313" "0421" "0232" "024" "0213"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "0233" "0154" "0213" "024" "0411"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "0412" "0211" "0231" "022" "011" "043"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "043" "043" "0411" "0233" "024" "0233"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "043" "033" "0133" "032" "011"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "043" "0231" "024" "011" "0232"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "0123" "0312" "011" "0231" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "024" "0232" "032" "043" "011"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "0313" "0311" "043" "011"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "011" "022" "0411" "043" "0212" "0233"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "0312" "0152" "0421" "011" "022" "011"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "043" "043" "0232" "0412" "022" "043"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "0313" "033" "0211" "0232" "024" "0314"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "0412" "022" "0212" "0412" "011"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "0421" "024" "011" "024" "011" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "0233" "0152" "024" "0213" "0314"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "0232" "0421" "0341" "024" "0213"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "0211" "043" "0132" "0413"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "0341" "0233" "043" "0341" "043" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "043" "024" "0211" "0211" "0412" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "0412" "043" "0423" "022" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "0212" "022" "024" "0341" "0233" "011"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "0411" "033" "024" "0211" "0212" "04222"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "043" "0412" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "0213" "011" "0343" "043" "024" "011"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "0232" "022" "024" "0213" "0212" "0412"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "0231" "0212" "0311" "0423" "011" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "0413" "0412" "0122" "032" "043"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "043" "0232" "0232" "024" "033" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "0421" "0411" "0152" "022" "033" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "033" "011" "0154" "024" "024" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "0314" "043" "0412" "043" "0231" "0413"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04222" "0411" "0122" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "0314" "024" "0412" "033" "0412" "043"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "0231" "0122" "022" "0211" "0411" "043"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "011" "0342" "043" "0412" "0413" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "0232" "0311" "033" "043" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "0421" "024" "024" "0152" "024" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "0412" "0412" "033" "0232" "0313" "0411"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "043" "0411" "043" "0421" "024" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "0231" "011" "0134" "0412" "043" "0213"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "0411" "043" "0123" "043" "0411" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "043" "0122" "024" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "0412" "024" "011" "0231" "032" "043"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "0342" "0212" "0421" "0134" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "043" "0233" "033" "0233" "024" "04222"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04222" "024" "014" "0213" "032" "04222"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "033" "04222" "043" "011" "011"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "0233" "0233" "0313" "022" "033" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "033" "033" "011" "043" "0213" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "0411" "0132" "0311" "0311" "0421" "0233"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "0213" "0421" "0311" "022" "0413" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "043" "0232" "011" "043" "033"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "0213" "0421" "0131" "011" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "0231" "011" "0411" "022" "0231" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "0231" "043" "022" "024" "024" "011"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "0231" "0411" "0341" "033" "0413" "043"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "0413" "024" "022" "0412"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "0314" "0341" "0421" "04222" "0411" "043"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "0343" "0411" "043" "043" "0412" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "043" "0152" "0421" "014" "0313"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "033" "024" "014" "0412" "0213" "0421"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "043" "0341" "0411" "043" "0213" "043"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "0212" "0232" "0122" "0231" "033"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "0342" "0411" "0211" "043" "024" "033"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "043" "032" "0311" "0412" "024" "043"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "0421" "022" "0421" "043" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "0233" "0133" "011" "0231" "043" "0312"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "0412" "043" "024" "0232" "0211" "043"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "011" "043" "0212" "0412" "022" "0213"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "033" "043" "0411" "011" "043" "0231"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "043" "0211" "043" "0133" "043" "0213"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "0313" "0232" "0421" "0421" "0213" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "0213" "0154" "0232" "043" "022" "0233"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "0231" "0152" "0211" "0423" "033" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "043" "04221" "0231" "033" "033" "0233"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04222" "014" "0412" "0411" "024" "0311"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "0411" "022" "0411" "0421" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "0411" "0154" "024" "0231" "0341"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "024" "032" "032" "0213" "0231"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "043" "022" "0411" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "011" "024" "0231" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "0411" "033" "033" "0151" "022" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "0212" "032" "0231" "033" "0231" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "0412" "0412" "0421" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04221" "0233" "043" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "0411" "022" "0412" "0123" "0412" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "0421" "014" "043" "024" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "0213" "0413" "033" "024" "0213" "0212"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "011" "022" "0312" "011" "0311" "0212"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "0411" "0231" "0123" "0211" "043" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "0341" "032" "0421" "0232" "043" "0411"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "0231" "0411" "033" "0311" "0132" "0311"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4517))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "0412" "0421" "0413" "0212" "0412" "0313"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "0411" "0122" "043" "043" "04222" "043"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "011" "0413" "0213" "0232" "0211" "0421"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "0213" "0233" "0411" "024" "0411"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "0311" "0231" "043" "0313" "043" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "0212" "024" "0231" "022" "0311" "0311"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "011" "0213" "033" "0123" "0411" "011"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "0233" "0411" "024" "022" "0413" "0421"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "0231" "043" "043" "0412" "033" "0421"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "043" "043" "024" "0411" "0421" "0411"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "0411" "0421" "0231" "0311" "043" "0411"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04222" "0212" "024" "0231" "0413" "043"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "0314" "043" "022" "0133" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "0342" "032" "0411" "0412" "0233" "0421"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "0412" "011" "024" "024" "0152" "0421"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "011" "033" "022" "0232" "0233" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "043" "014" "024" "024" "0232" "0232"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "0412" "0211" "0133" "0213" "024" "0232"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04222" "033" "0122" "0412" "0212" "0313"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "0233" "04221" "0233" "0342" "0233" "0413"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "043" "024" "011" "0412" "0421"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "0122" "032" "0231" "0314" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "043" "0311" "032" "024" "033" "0213"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "011" "033" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "0423" "011" "024" "0132" "011" "0411"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "0412" "011" "024" "043" "043" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "0421" "0213" "014" "0411" "011" "0213"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "0411" "011" "033" "0341" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "0421" "043" "0152" "0411" "0413" "04222"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "0412" "043" "0412" "0151" "011"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "033" "0232" "0122" "0411" "043" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "0413" "0411" "032" "024" "011" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "0232" "011" "0412" "033" "043"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "043" "024" "022" "043" "04222" "0421"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "024" "0132" "04221" "043" "0231"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "0231" "0212" "0342" "0423" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "0213" "0314" "0131" "04222" "0311"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "0123" "0233" "0412" "0231" "0312"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "0231" "014" "032" "0213" "0411" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "0233" "0231" "0411" "0312" "0231" "0212"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "0411" "0233" "0311" "0412" "043" "0421"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "0313" "0412" "0232" "032" "0421" "0423"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "0421" "032" "043" "014" "0233"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "0313" "024" "0413" "032" "043" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "0231" "043" "0423" "0411" "033" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "024" "0211" "0122" "014" "0413"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "0233" "0131" "0232" "0211" "014" "0411"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "0412" "011" "0411" "0154" "022" "043"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "043" "024" "043" "0213" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "0412" "043" "0153" "043"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "043" "0411" "043" "0421" "0232" "0231"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "0421" "0123" "0341" "014" "043" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "0411" "033" "033" "0413" "024" "033"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "0411" "011" "0421" "0233" "0213" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "033" "0231" "033" "04221" "0423" "043"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "033" "0313" "0421" "0232" "024" "0213"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "0233" "0154" "0213" "024" "0411"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "0412" "0211" "0231" "022" "011" "043"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "043" "043" "0411" "0233" "024" "0233"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "043" "033" "0133" "032" "011"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "043" "0231" "024" "011" "0232"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "0123" "0312" "011" "0231" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "024" "0232" "032" "043" "011"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "0313" "0311" "043" "011"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "011" "022" "0411" "043" "0212" "0233"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "0312" "0152" "0421" "011" "022" "011"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "043" "043" "0232" "0412" "022" "043"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "0313" "033" "0211" "0232" "024" "0314"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "0412" "022" "0212" "0412" "011"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "0421" "024" "011" "024" "011" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "0233" "0152" "024" "0213" "0314"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "0232" "0421" "0341" "024" "0213"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "0211" "043" "0132" "0413"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "0341" "0233" "043" "0341" "043" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "043" "024" "0211" "0211" "0412" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "0412" "043" "0423" "022" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "0212" "022" "024" "0341" "0233" "011"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "0411" "033" "024" "0211" "0212" "04222"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "043" "0412" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "0213" "011" "0343" "043" "024" "011"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "0232" "022" "024" "0213" "0212" "0412"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "0231" "0212" "0311" "0423" "011" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "0413" "0412" "0122" "032" "043"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "043" "0232" "0232" "024" "033" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "0421" "0411" "0152" "022" "033" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "033" "011" "0154" "024" "024" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "0314" "043" "0412" "043" "0231" "0413"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04222" "0411" "0122" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "0314" "024" "0412" "033" "0412" "043"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "0231" "0122" "022" "0211" "0411" "043"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "011" "0342" "043" "0412" "0413" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "0232" "0311" "033" "043" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "0421" "024" "024" "0152" "024" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "0412" "0412" "033" "0232" "0313" "0411"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "043" "0411" "043" "0421" "024" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "0231" "011" "0134" "0412" "043" "0213"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "0411" "043" "0123" "043" "0411" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "043" "0122" "024" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "0412" "024" "011" "0231" "032" "043"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "0342" "0212" "0421" "0134" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "043" "0233" "033" "0233" "024" "04222"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04222" "024" "014" "0213" "032" "04222"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "033" "04222" "043" "011" "011"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "0233" "0233" "0313" "022" "033" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "033" "033" "011" "043" "0213" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "0411" "0132" "0311" "0311" "0421" "0233"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "0213" "0421" "0311" "022" "0413" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "043" "0232" "011" "043" "033"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "0213" "0421" "0131" "011" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "0231" "011" "0411" "022" "0231" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "0231" "043" "022" "024" "024" "011"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "0231" "0411" "0341" "033" "0413" "043"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "0413" "024" "022" "0412"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "0314" "0341" "0421" "04222" "0411" "043"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "0343" "0411" "043" "043" "0412" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "043" "0152" "0421" "014" "0313"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "033" "024" "014" "0412" "0213" "0421"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "043" "0341" "0411" "043" "0213" "043"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "0212" "0232" "0122" "0231" "033"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "0342" "0411" "0211" "043" "024" "033"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "043" "032" "0311" "0412" "024" "043"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "0421" "022" "0421" "043" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "0233" "0133" "011" "0231" "043" "0312"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "0412" "043" "024" "0232" "0211" "043"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "011" "043" "0212" "0412" "022" "0213"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "033" "043" "0411" "011" "043" "0231"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "043" "0211" "043" "0133" "043" "0213"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "0313" "0232" "0421" "0421" "0213" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "0213" "0154" "0232" "043" "022" "0233"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "0231" "0152" "0211" "0423" "033" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "043" "04221" "0231" "033" "033" "0233"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04222" "014" "0412" "0411" "024" "0311"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "0411" "022" "0411" "0421" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "0411" "0154" "024" "0231" "0341"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "024" "032" "032" "0213" "0231"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "043" "022" "0411" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "011" "024" "0231" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "0411" "033" "033" "0151" "022" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "0212" "032" "0231" "033" "0231" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "0412" "0412" "0421" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04221" "0233" "043" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "0411" "022" "0412" "0123" "0412" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "0421" "014" "043" "024" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "0213" "0413" "033" "024" "0213" "0212"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "011" "022" "0312" "011" "0311" "0212"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "0411" "0231" "0123" "0211" "043" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "0341" "032" "0421" "0232" "043" "0411"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "0231" "0411" "033" "0311" "0132" "0311"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5436))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "04" "04" "04" "0212" "04" "0313"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04" "0122" "04" "04" "04222" "04"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "011" "04" "0213" "0232" "0211" "04"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "0213" "0233" "04" "024" "04"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "0311" "0231" "04" "0313" "04" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "0212" "024" "0231" "022" "0311" "0311"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "011" "0213" "033" "0123" "04" "011"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "0233" "04" "024" "022" "04" "04"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "0231" "04" "04" "04" "033" "04"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04" "04" "024" "04" "04" "04"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04" "04" "0231" "0311" "04" "04"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04222" "0212" "024" "0231" "04" "04"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "0314" "04" "022" "0133" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "0342" "032" "04" "04" "0233" "04"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "04" "011" "024" "024" "0152" "04"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "011" "033" "022" "0232" "0233" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "04" "014" "024" "024" "0232" "0232"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "04" "0211" "0133" "0213" "024" "0232"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04222" "033" "0122" "04" "0212" "0313"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "0233" "04221" "0233" "0342" "0233" "04"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "04" "024" "011" "04" "04"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "0122" "032" "0231" "0314" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04" "0311" "032" "024" "033" "0213"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "011" "033" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "04" "011" "024" "0132" "011" "04"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "04" "011" "024" "04" "04" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "04" "0213" "014" "04" "011" "0213"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "04" "011" "033" "0341" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "04" "04" "0152" "04" "04" "04222"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "04" "04" "04" "0151" "011"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "033" "0232" "0122" "04" "04" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04" "04" "032" "024" "011" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "0232" "011" "04" "033" "04"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "04" "024" "022" "04" "04222" "04"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "024" "0132" "04221" "04" "0231"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "0231" "0212" "0342" "04" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "0213" "0314" "0131" "04222" "0311"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "0123" "0233" "04" "0231" "0312"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "0231" "014" "032" "0213" "04" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "0233" "0231" "04" "0312" "0231" "0212"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "04" "0233" "0311" "04" "04" "04"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "0313" "04" "0232" "032" "04" "04"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "04" "032" "04" "014" "0233"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "0313" "024" "04" "032" "04" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "0231" "04" "04" "04" "033" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "024" "0211" "0122" "014" "04"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "0233" "0131" "0232" "0211" "014" "04"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "04" "011" "04" "0154" "022" "04"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "04" "024" "04" "0213" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "04" "04" "0153" "04"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "04" "04" "04" "04" "0232" "0231"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "04" "0123" "0341" "014" "04" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04" "033" "033" "04" "024" "033"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04" "011" "04" "0233" "0213" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "033" "0231" "033" "04221" "04" "04"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "033" "0313" "04" "0232" "024" "0213"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "0233" "0154" "0213" "024" "04"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "04" "0211" "0231" "022" "011" "04"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "04" "04" "04" "0233" "024" "0233"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "04" "033" "0133" "032" "011"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "04" "0231" "024" "011" "0232"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "0123" "0312" "011" "0231" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "024" "0232" "032" "04" "011"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "0313" "0311" "04" "011"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "011" "022" "04" "04" "0212" "0233"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "0312" "0152" "04" "011" "022" "011"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04" "04" "0232" "04" "022" "04"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "0313" "033" "0211" "0232" "024" "0314"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "04" "022" "0212" "04" "011"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "04" "024" "011" "024" "011" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "0233" "0152" "024" "0213" "0314"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "0232" "04" "0341" "024" "0213"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "0211" "04" "0132" "04"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "0341" "0233" "04" "0341" "04" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "04" "024" "0211" "0211" "04" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "04" "04" "04" "022" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "0212" "022" "024" "0341" "0233" "011"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04" "033" "024" "0211" "0212" "04222"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04" "04" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "0213" "011" "0343" "04" "024" "011"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "0232" "022" "024" "0213" "0212" "04"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "0231" "0212" "0311" "04" "011" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "04" "04" "0122" "032" "04"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "04" "0232" "0232" "024" "033" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "04" "04" "0152" "022" "033" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "033" "011" "0154" "024" "024" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "0314" "04" "04" "04" "0231" "04"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04222" "04" "0122" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "0314" "024" "04" "033" "04" "04"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "0231" "0122" "022" "0211" "04" "04"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "011" "0342" "04" "04" "04" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "0232" "0311" "033" "04" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "04" "024" "024" "0152" "024" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "04" "04" "033" "0232" "0313" "04"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "04" "04" "04" "04" "024" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "0231" "011" "0134" "04" "04" "0213"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04" "04" "0123" "04" "04" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "04" "0122" "024" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "04" "024" "011" "0231" "032" "04"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "0342" "0212" "04" "0134" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "04" "0233" "033" "0233" "024" "04222"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04222" "024" "014" "0213" "032" "04222"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "033" "04222" "04" "011" "011"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "0233" "0233" "0313" "022" "033" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "033" "033" "011" "04" "0213" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "04" "0132" "0311" "0311" "04" "0233"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "0213" "04" "0311" "022" "04" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "04" "0232" "011" "04" "033"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "0213" "04" "0131" "011" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "0231" "011" "04" "022" "0231" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "0231" "04" "022" "024" "024" "011"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "0231" "04" "0341" "033" "04" "04"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "04" "024" "022" "04"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "0314" "0341" "04" "04222" "04" "04"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "0343" "04" "04" "04" "04" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "04" "0152" "04" "014" "0313"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "033" "024" "014" "04" "0213" "04"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "04" "0341" "04" "04" "0213" "04"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "0212" "0232" "0122" "0231" "033"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "0342" "04" "0211" "04" "024" "033"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "04" "032" "0311" "04" "024" "04"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "04" "022" "04" "04" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "0233" "0133" "011" "0231" "04" "0312"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "04" "04" "024" "0232" "0211" "04"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "011" "04" "0212" "04" "022" "0213"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "033" "04" "04" "011" "04" "0231"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04" "0211" "04" "0133" "04" "0213"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "0313" "0232" "04" "04" "0213" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "0213" "0154" "0232" "04" "022" "0233"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "0231" "0152" "0211" "04" "033" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "04" "04221" "0231" "033" "033" "0233"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04222" "014" "04" "04" "024" "0311"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "04" "022" "04" "04" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "04" "0154" "024" "0231" "0341"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "024" "032" "032" "0213" "0231"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "04" "022" "04" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "011" "024" "0231" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "04" "033" "033" "0151" "022" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "0212" "032" "0231" "033" "0231" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "04" "04" "04" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04221" "0233" "04" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04" "022" "04" "0123" "04" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "04" "014" "04" "024" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "0213" "04" "033" "024" "0213" "0212"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "011" "022" "0312" "011" "0311" "0212"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "04" "0231" "0123" "0211" "04" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "0341" "032" "04" "0232" "04" "04"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "0231" "04" "033" "0311" "0132" "0311"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6990))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "04" "04" "04" "0212" "04" "0313"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04" "0122" "04" "04" "04" "04"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "011" "04" "0213" "0232" "0211" "04"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "0213" "0233" "04" "024" "04"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "0311" "0231" "04" "0313" "04" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "0212" "024" "0231" "022" "0311" "0311"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "011" "0213" "033" "0123" "04" "011"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "0233" "04" "024" "022" "04" "04"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "0231" "04" "04" "04" "033" "04"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04" "04" "024" "04" "04" "04"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04" "04" "0231" "0311" "04" "04"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04" "0212" "024" "0231" "04" "04"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "0314" "04" "022" "0133" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "0342" "032" "04" "04" "0233" "04"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "04" "011" "024" "024" "0152" "04"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "011" "033" "022" "0232" "0233" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "04" "014" "024" "024" "0232" "0232"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "04" "0211" "0133" "0213" "024" "0232"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04" "033" "0122" "04" "0212" "0313"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "0233" "04" "0233" "0342" "0233" "04"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "04" "024" "011" "04" "04"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "0122" "032" "0231" "0314" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04" "0311" "032" "024" "033" "0213"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "011" "033" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "04" "011" "024" "0132" "011" "04"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "04" "011" "024" "04" "04" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "04" "0213" "014" "04" "011" "0213"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "04" "011" "033" "0341" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "04" "04" "0152" "04" "04" "04"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "04" "04" "04" "0151" "011"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "033" "0232" "0122" "04" "04" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04" "04" "032" "024" "011" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "0232" "011" "04" "033" "04"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "04" "024" "022" "04" "04" "04"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "024" "0132" "04" "04" "0231"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "0231" "0212" "0342" "04" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "0213" "0314" "0131" "04" "0311"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "0123" "0233" "04" "0231" "0312"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "0231" "014" "032" "0213" "04" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "0233" "0231" "04" "0312" "0231" "0212"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "04" "0233" "0311" "04" "04" "04"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "0313" "04" "0232" "032" "04" "04"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "04" "032" "04" "014" "0233"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "0313" "024" "04" "032" "04" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "0231" "04" "04" "04" "033" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "024" "0211" "0122" "014" "04"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "0233" "0131" "0232" "0211" "014" "04"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "04" "011" "04" "0154" "022" "04"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "04" "024" "04" "0213" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "04" "04" "0153" "04"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "04" "04" "04" "04" "0232" "0231"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "04" "0123" "0341" "014" "04" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04" "033" "033" "04" "024" "033"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04" "011" "04" "0233" "0213" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "033" "0231" "033" "04" "04" "04"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "033" "0313" "04" "0232" "024" "0213"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "0233" "0154" "0213" "024" "04"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "04" "0211" "0231" "022" "011" "04"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "04" "04" "04" "0233" "024" "0233"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "04" "033" "0133" "032" "011"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "04" "0231" "024" "011" "0232"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "0123" "0312" "011" "0231" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "024" "0232" "032" "04" "011"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "0313" "0311" "04" "011"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "011" "022" "04" "04" "0212" "0233"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "0312" "0152" "04" "011" "022" "011"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04" "04" "0232" "04" "022" "04"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "0313" "033" "0211" "0232" "024" "0314"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "04" "022" "0212" "04" "011"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "04" "024" "011" "024" "011" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "0233" "0152" "024" "0213" "0314"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "0232" "04" "0341" "024" "0213"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "0211" "04" "0132" "04"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "0341" "0233" "04" "0341" "04" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "04" "024" "0211" "0211" "04" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "04" "04" "04" "022" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "0212" "022" "024" "0341" "0233" "011"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04" "033" "024" "0211" "0212" "04"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04" "04" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "0213" "011" "0343" "04" "024" "011"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "0232" "022" "024" "0213" "0212" "04"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "0231" "0212" "0311" "04" "011" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "04" "04" "0122" "032" "04"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "04" "0232" "0232" "024" "033" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "04" "04" "0152" "022" "033" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "033" "011" "0154" "024" "024" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "0314" "04" "04" "04" "0231" "04"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04" "04" "0122" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "0314" "024" "04" "033" "04" "04"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "0231" "0122" "022" "0211" "04" "04"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "011" "0342" "04" "04" "04" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "0232" "0311" "033" "04" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "04" "024" "024" "0152" "024" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "04" "04" "033" "0232" "0313" "04"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "04" "04" "04" "04" "024" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "0231" "011" "0134" "04" "04" "0213"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04" "04" "0123" "04" "04" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "04" "0122" "024" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "04" "024" "011" "0231" "032" "04"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "0342" "0212" "04" "0134" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "04" "0233" "033" "0233" "024" "04"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04" "024" "014" "0213" "032" "04"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "033" "04" "04" "011" "011"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "0233" "0233" "0313" "022" "033" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "033" "033" "011" "04" "0213" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "04" "0132" "0311" "0311" "04" "0233"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "0213" "04" "0311" "022" "04" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "04" "0232" "011" "04" "033"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "0213" "04" "0131" "011" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "0231" "011" "04" "022" "0231" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "0231" "04" "022" "024" "024" "011"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "0231" "04" "0341" "033" "04" "04"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "04" "024" "022" "04"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "0314" "0341" "04" "04" "04" "04"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "0343" "04" "04" "04" "04" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "04" "0152" "04" "014" "0313"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "033" "024" "014" "04" "0213" "04"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "04" "0341" "04" "04" "0213" "04"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "0212" "0232" "0122" "0231" "033"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "0342" "04" "0211" "04" "024" "033"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "04" "032" "0311" "04" "024" "04"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "04" "022" "04" "04" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "0233" "0133" "011" "0231" "04" "0312"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "04" "04" "024" "0232" "0211" "04"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "011" "04" "0212" "04" "022" "0213"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "033" "04" "04" "011" "04" "0231"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04" "0211" "04" "0133" "04" "0213"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "0313" "0232" "04" "04" "0213" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "0213" "0154" "0232" "04" "022" "0233"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "0231" "0152" "0211" "04" "033" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "04" "04" "0231" "033" "033" "0233"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04" "014" "04" "04" "024" "0311"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "04" "022" "04" "04" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "04" "0154" "024" "0231" "0341"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "024" "032" "032" "0213" "0231"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "04" "022" "04" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "011" "024" "0231" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "04" "033" "033" "0151" "022" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "0212" "032" "0231" "033" "0231" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "04" "04" "04" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04" "0233" "04" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04" "022" "04" "0123" "04" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "04" "014" "04" "024" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "0213" "04" "033" "024" "0213" "0212"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "011" "022" "0312" "011" "0311" "0212"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "04" "0231" "0123" "0211" "04" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "0341" "032" "04" "0232" "04" "04"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "0231" "04" "033" "0311" "0132" "0311"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7407))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "04" "04" "04" "0212" "04" "0313"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04" "0122" "04" "04" "04" "04"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "011" "04" "0213" "0232" "0211" "04"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "0213" "0233" "04" "024" "04"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "0311" "0231" "04" "0313" "04" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "0212" "024" "0231" "022" "0311" "0311"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "011" "0213" "033" "0123" "04" "011"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "0233" "04" "024" "022" "04" "04"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "0231" "04" "04" "04" "033" "04"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04" "04" "024" "04" "04" "04"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04" "04" "0231" "0311" "04" "04"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04" "0212" "024" "0231" "04" "04"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "0314" "04" "022" "0133" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "0342" "032" "04" "04" "0233" "04"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "04" "011" "024" "024" "0152" "04"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "011" "033" "022" "0232" "0233" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "04" "014" "024" "024" "0232" "0232"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "04" "0211" "0133" "0213" "024" "0232"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04" "033" "0122" "04" "0212" "0313"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "0233" "04" "0233" "0342" "0233" "04"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "04" "024" "011" "04" "04"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "0122" "032" "0231" "0314" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04" "0311" "032" "024" "033" "0213"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "011" "033" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "04" "011" "024" "0132" "011" "04"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "04" "011" "024" "04" "04" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "04" "0213" "014" "04" "011" "0213"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "04" "011" "033" "0341" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "04" "04" "0152" "04" "04" "04"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "04" "04" "04" "0151" "011"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "033" "0232" "0122" "04" "04" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04" "04" "032" "024" "011" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "0232" "011" "04" "033" "04"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "04" "024" "022" "04" "04" "04"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "024" "0132" "04" "04" "0231"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "0231" "0212" "0342" "04" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "0213" "0314" "0131" "04" "0311"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "0123" "0233" "04" "0231" "0312"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "0231" "014" "032" "0213" "04" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "0233" "0231" "04" "0312" "0231" "0212"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "04" "0233" "0311" "04" "04" "04"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "0313" "04" "0232" "032" "04" "04"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "04" "032" "04" "014" "0233"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "0313" "024" "04" "032" "04" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "0231" "04" "04" "04" "033" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "024" "0211" "0122" "014" "04"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "0233" "0131" "0232" "0211" "014" "04"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "04" "011" "04" "0154" "022" "04"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "04" "024" "04" "0213" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "04" "04" "0153" "04"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "04" "04" "04" "04" "0232" "0231"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "04" "0123" "0341" "014" "04" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04" "033" "033" "04" "024" "033"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04" "011" "04" "0233" "0213" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "033" "0231" "033" "04" "04" "04"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "033" "0313" "04" "0232" "024" "0213"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "0233" "0154" "0213" "024" "04"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "04" "0211" "0231" "022" "011" "04"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "04" "04" "04" "0233" "024" "0233"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "04" "033" "0133" "032" "011"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "04" "0231" "024" "011" "0232"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "0123" "0312" "011" "0231" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "024" "0232" "032" "04" "011"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "0313" "0311" "04" "011"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "011" "022" "04" "04" "0212" "0233"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "0312" "0152" "04" "011" "022" "011"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04" "04" "0232" "04" "022" "04"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "0313" "033" "0211" "0232" "024" "0314"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "04" "022" "0212" "04" "011"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "04" "024" "011" "024" "011" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "0233" "0152" "024" "0213" "0314"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "0232" "04" "0341" "024" "0213"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "0211" "04" "0132" "04"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "0341" "0233" "04" "0341" "04" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "04" "024" "0211" "0211" "04" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "04" "04" "04" "022" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "0212" "022" "024" "0341" "0233" "011"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04" "033" "024" "0211" "0212" "04"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04" "04" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "0213" "011" "0343" "04" "024" "011"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "0232" "022" "024" "0213" "0212" "04"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "0231" "0212" "0311" "04" "011" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "04" "04" "0122" "032" "04"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "04" "0232" "0232" "024" "033" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "04" "04" "0152" "022" "033" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "033" "011" "0154" "024" "024" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "0314" "04" "04" "04" "0231" "04"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04" "04" "0122" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "0314" "024" "04" "033" "04" "04"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "0231" "0122" "022" "0211" "04" "04"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "011" "0342" "04" "04" "04" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "0232" "0311" "033" "04" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "04" "024" "024" "0152" "024" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "04" "04" "033" "0232" "0313" "04"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "04" "04" "04" "04" "024" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "0231" "011" "0134" "04" "04" "0213"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04" "04" "0123" "04" "04" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "04" "0122" "024" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "04" "024" "011" "0231" "032" "04"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "0342" "0212" "04" "0134" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "04" "0233" "033" "0233" "024" "04"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04" "024" "014" "0213" "032" "04"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "033" "04" "04" "011" "011"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "0233" "0233" "0313" "022" "033" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "033" "033" "011" "04" "0213" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "04" "0132" "0311" "0311" "04" "0233"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "0213" "04" "0311" "022" "04" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "04" "0232" "011" "04" "033"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "0213" "04" "0131" "011" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "0231" "011" "04" "022" "0231" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "0231" "04" "022" "024" "024" "011"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "0231" "04" "0341" "033" "04" "04"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "04" "024" "022" "04"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "0314" "0341" "04" "04" "04" "04"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "0343" "04" "04" "04" "04" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "04" "0152" "04" "014" "0313"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "033" "024" "014" "04" "0213" "04"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "04" "0341" "04" "04" "0213" "04"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "0212" "0232" "0122" "0231" "033"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "0342" "04" "0211" "04" "024" "033"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "04" "032" "0311" "04" "024" "04"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "04" "022" "04" "04" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "0233" "0133" "011" "0231" "04" "0312"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "04" "04" "024" "0232" "0211" "04"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "011" "04" "0212" "04" "022" "0213"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "033" "04" "04" "011" "04" "0231"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04" "0211" "04" "0133" "04" "0213"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "0313" "0232" "04" "04" "0213" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "0213" "0154" "0232" "04" "022" "0233"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "0231" "0152" "0211" "04" "033" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "04" "04" "0231" "033" "033" "0233"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04" "014" "04" "04" "024" "0311"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "04" "022" "04" "04" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "04" "0154" "024" "0231" "0341"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "024" "032" "032" "0213" "0231"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "04" "022" "04" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "011" "024" "0231" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "04" "033" "033" "0151" "022" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "0212" "032" "0231" "033" "0231" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "04" "04" "04" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04" "0233" "04" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04" "022" "04" "0123" "04" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "04" "014" "04" "024" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "0213" "04" "033" "024" "0213" "0212"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "011" "022" "0312" "011" "0311" "0212"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "04" "0231" "0123" "0211" "04" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "0341" "032" "04" "0232" "04" "04"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "0231" "04" "033" "0311" "0132" "0311"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7632))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "04" "04" "04" "0212" "04" "0313"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04" "0122" "04" "04" "04" "04"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "011" "04" "0213" "023" "0211" "04"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "0213" "023" "04" "024" "04"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "0311" "023" "04" "0313" "04" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "0212" "024" "023" "022" "0311" "0311"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "011" "0213" "033" "0123" "04" "011"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "023" "04" "024" "022" "04" "04"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "023" "04" "04" "04" "033" "04"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04" "04" "024" "04" "04" "04"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04" "04" "023" "0311" "04" "04"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04" "0212" "024" "023" "04" "04"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "0314" "04" "022" "0133" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "0342" "032" "04" "04" "023" "04"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "04" "011" "024" "024" "0152" "04"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "011" "033" "022" "023" "023" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "04" "014" "024" "024" "023" "023"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "04" "0211" "0133" "0213" "024" "023"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04" "033" "0122" "04" "0212" "0313"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "023" "04" "023" "0342" "023" "04"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "04" "024" "011" "04" "04"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "0122" "032" "023" "0314" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04" "0311" "032" "024" "033" "0213"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "011" "033" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "04" "011" "024" "0132" "011" "04"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "04" "011" "024" "04" "04" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "04" "0213" "014" "04" "011" "0213"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "04" "011" "033" "0341" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "04" "04" "0152" "04" "04" "04"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "04" "04" "04" "0151" "011"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "033" "023" "0122" "04" "04" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04" "04" "032" "024" "011" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "023" "011" "04" "033" "04"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "04" "024" "022" "04" "04" "04"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "024" "0132" "04" "04" "023"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "023" "0212" "0342" "04" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "0213" "0314" "0131" "04" "0311"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "0123" "023" "04" "023" "0312"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "023" "014" "032" "0213" "04" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "023" "023" "04" "0312" "023" "0212"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "04" "023" "0311" "04" "04" "04"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "0313" "04" "023" "032" "04" "04"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "04" "032" "04" "014" "023"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "0313" "024" "04" "032" "04" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "023" "04" "04" "04" "033" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "024" "0211" "0122" "014" "04"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "023" "0131" "023" "0211" "014" "04"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "04" "011" "04" "0154" "022" "04"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "04" "024" "04" "0213" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "04" "04" "0153" "04"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "04" "04" "04" "04" "023" "023"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "04" "0123" "0341" "014" "04" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04" "033" "033" "04" "024" "033"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04" "011" "04" "023" "0213" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "033" "023" "033" "04" "04" "04"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "033" "0313" "04" "023" "024" "0213"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "023" "0154" "0213" "024" "04"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "04" "0211" "023" "022" "011" "04"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "04" "04" "04" "023" "024" "023"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "04" "033" "0133" "032" "011"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "04" "023" "024" "011" "023"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "0123" "0312" "011" "023" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "024" "023" "032" "04" "011"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "0313" "0311" "04" "011"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "011" "022" "04" "04" "0212" "023"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "0312" "0152" "04" "011" "022" "011"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04" "04" "023" "04" "022" "04"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "0313" "033" "0211" "023" "024" "0314"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "04" "022" "0212" "04" "011"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "04" "024" "011" "024" "011" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "023" "0152" "024" "0213" "0314"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "023" "04" "0341" "024" "0213"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "0211" "04" "0132" "04"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "0341" "023" "04" "0341" "04" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "04" "024" "0211" "0211" "04" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "04" "04" "04" "022" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "0212" "022" "024" "0341" "023" "011"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04" "033" "024" "0211" "0212" "04"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04" "04" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "0213" "011" "0343" "04" "024" "011"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "023" "022" "024" "0213" "0212" "04"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "023" "0212" "0311" "04" "011" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "04" "04" "0122" "032" "04"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "04" "023" "023" "024" "033" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "04" "04" "0152" "022" "033" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "033" "011" "0154" "024" "024" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "0314" "04" "04" "04" "023" "04"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04" "04" "0122" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "0314" "024" "04" "033" "04" "04"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "023" "0122" "022" "0211" "04" "04"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "011" "0342" "04" "04" "04" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "023" "0311" "033" "04" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "04" "024" "024" "0152" "024" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "04" "04" "033" "023" "0313" "04"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "04" "04" "04" "04" "024" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "023" "011" "0134" "04" "04" "0213"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04" "04" "0123" "04" "04" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "04" "0122" "024" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "04" "024" "011" "023" "032" "04"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "0342" "0212" "04" "0134" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "04" "023" "033" "023" "024" "04"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04" "024" "014" "0213" "032" "04"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "033" "04" "04" "011" "011"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "023" "023" "0313" "022" "033" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "033" "033" "011" "04" "0213" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "04" "0132" "0311" "0311" "04" "023"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "0213" "04" "0311" "022" "04" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "04" "023" "011" "04" "033"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "0213" "04" "0131" "011" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "023" "011" "04" "022" "023" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "023" "04" "022" "024" "024" "011"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "023" "04" "0341" "033" "04" "04"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "04" "024" "022" "04"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "0314" "0341" "04" "04" "04" "04"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "0343" "04" "04" "04" "04" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "04" "0152" "04" "014" "0313"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "033" "024" "014" "04" "0213" "04"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "04" "0341" "04" "04" "0213" "04"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "0212" "023" "0122" "023" "033"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "0342" "04" "0211" "04" "024" "033"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "04" "032" "0311" "04" "024" "04"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "04" "022" "04" "04" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "023" "0133" "011" "023" "04" "0312"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "04" "04" "024" "023" "0211" "04"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "011" "04" "0212" "04" "022" "0213"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "033" "04" "04" "011" "04" "023"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04" "0211" "04" "0133" "04" "0213"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "0313" "023" "04" "04" "0213" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "0213" "0154" "023" "04" "022" "023"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "023" "0152" "0211" "04" "033" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "04" "04" "023" "033" "033" "023"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04" "014" "04" "04" "024" "0311"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "04" "022" "04" "04" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "04" "0154" "024" "023" "0341"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "024" "032" "032" "0213" "023"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "04" "022" "04" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "011" "024" "023" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "04" "033" "033" "0151" "022" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "0212" "032" "023" "033" "023" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "04" "04" "04" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04" "023" "04" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04" "022" "04" "0123" "04" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "04" "014" "04" "024" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "0213" "04" "033" "024" "0213" "0212"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "011" "022" "0312" "011" "0311" "0212"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "04" "023" "0123" "0211" "04" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "0341" "032" "04" "023" "04" "04"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "023" "04" "033" "0311" "0132" "0311"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8036))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "04" "04" "04" "0212" "04" "0313"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04" "0122" "04" "04" "04" "04"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "011" "04" "0213" "023" "0211" "04"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "0213" "023" "04" "024" "04"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "0311" "023" "04" "0313" "04" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "0212" "024" "023" "022" "0311" "0311"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "011" "0213" "033" "0123" "04" "011"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "023" "04" "024" "022" "04" "04"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "023" "04" "04" "04" "033" "04"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04" "04" "024" "04" "04" "04"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04" "04" "023" "0311" "04" "04"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04" "0212" "024" "023" "04" "04"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "0314" "04" "022" "0133" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "0342" "032" "04" "04" "023" "04"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "04" "011" "024" "024" "0152" "04"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "011" "033" "022" "023" "023" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "04" "014" "024" "024" "023" "023"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "04" "0211" "0133" "0213" "024" "023"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04" "033" "0122" "04" "0212" "0313"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "023" "04" "023" "0342" "023" "04"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "04" "024" "011" "04" "04"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "0122" "032" "023" "0314" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04" "0311" "032" "024" "033" "0213"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "011" "033" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "04" "011" "024" "0132" "011" "04"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "04" "011" "024" "04" "04" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "04" "0213" "014" "04" "011" "0213"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "04" "011" "033" "0341" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "04" "04" "0152" "04" "04" "04"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "04" "04" "04" "0151" "011"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "033" "023" "0122" "04" "04" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04" "04" "032" "024" "011" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "023" "011" "04" "033" "04"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "04" "024" "022" "04" "04" "04"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "024" "0132" "04" "04" "023"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "023" "0212" "0342" "04" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "0213" "0314" "0131" "04" "0311"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "0123" "023" "04" "023" "0312"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "023" "014" "032" "0213" "04" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "023" "023" "04" "0312" "023" "0212"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "04" "023" "0311" "04" "04" "04"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "0313" "04" "023" "032" "04" "04"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "04" "032" "04" "014" "023"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "0313" "024" "04" "032" "04" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "023" "04" "04" "04" "033" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "024" "0211" "0122" "014" "04"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "023" "0131" "023" "0211" "014" "04"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "04" "011" "04" "0154" "022" "04"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "04" "024" "04" "0213" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "04" "04" "0153" "04"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "04" "04" "04" "04" "023" "023"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "04" "0123" "0341" "014" "04" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04" "033" "033" "04" "024" "033"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04" "011" "04" "023" "0213" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "033" "023" "033" "04" "04" "04"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "033" "0313" "04" "023" "024" "0213"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "023" "0154" "0213" "024" "04"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "04" "0211" "023" "022" "011" "04"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "04" "04" "04" "023" "024" "023"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "04" "033" "0133" "032" "011"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "04" "023" "024" "011" "023"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "0123" "0312" "011" "023" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "024" "023" "032" "04" "011"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "0313" "0311" "04" "011"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "011" "022" "04" "04" "0212" "023"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "0312" "0152" "04" "011" "022" "011"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04" "04" "023" "04" "022" "04"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "0313" "033" "0211" "023" "024" "0314"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "04" "022" "0212" "04" "011"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "04" "024" "011" "024" "011" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "023" "0152" "024" "0213" "0314"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "023" "04" "0341" "024" "0213"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "0211" "04" "0132" "04"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "0341" "023" "04" "0341" "04" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "04" "024" "0211" "0211" "04" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "04" "04" "04" "022" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "0212" "022" "024" "0341" "023" "011"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04" "033" "024" "0211" "0212" "04"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04" "04" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "0213" "011" "0343" "04" "024" "011"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "023" "022" "024" "0213" "0212" "04"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "023" "0212" "0311" "04" "011" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "04" "04" "0122" "032" "04"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "04" "023" "023" "024" "033" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "04" "04" "0152" "022" "033" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "033" "011" "0154" "024" "024" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "0314" "04" "04" "04" "023" "04"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04" "04" "0122" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "0314" "024" "04" "033" "04" "04"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "023" "0122" "022" "0211" "04" "04"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "011" "0342" "04" "04" "04" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "023" "0311" "033" "04" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "04" "024" "024" "0152" "024" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "04" "04" "033" "023" "0313" "04"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "04" "04" "04" "04" "024" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "023" "011" "0134" "04" "04" "0213"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04" "04" "0123" "04" "04" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "04" "0122" "024" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "04" "024" "011" "023" "032" "04"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "0342" "0212" "04" "0134" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "04" "023" "033" "023" "024" "04"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04" "024" "014" "0213" "032" "04"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "033" "04" "04" "011" "011"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "023" "023" "0313" "022" "033" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "033" "033" "011" "04" "0213" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "04" "0132" "0311" "0311" "04" "023"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "0213" "04" "0311" "022" "04" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "04" "023" "011" "04" "033"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "0213" "04" "0131" "011" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "023" "011" "04" "022" "023" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "023" "04" "022" "024" "024" "011"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "023" "04" "0341" "033" "04" "04"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "04" "024" "022" "04"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "0314" "0341" "04" "04" "04" "04"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "0343" "04" "04" "04" "04" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "04" "0152" "04" "014" "0313"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "033" "024" "014" "04" "0213" "04"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "04" "0341" "04" "04" "0213" "04"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "0212" "023" "0122" "023" "033"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "0342" "04" "0211" "04" "024" "033"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "04" "032" "0311" "04" "024" "04"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "04" "022" "04" "04" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "023" "0133" "011" "023" "04" "0312"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "04" "04" "024" "023" "0211" "04"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "011" "04" "0212" "04" "022" "0213"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "033" "04" "04" "011" "04" "023"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04" "0211" "04" "0133" "04" "0213"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "0313" "023" "04" "04" "0213" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "0213" "0154" "023" "04" "022" "023"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "023" "0152" "0211" "04" "033" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "04" "04" "023" "033" "033" "023"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04" "014" "04" "04" "024" "0311"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "04" "022" "04" "04" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "04" "0154" "024" "023" "0341"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "024" "032" "032" "0213" "023"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "04" "022" "04" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "011" "024" "023" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "04" "033" "033" "0151" "022" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "0212" "032" "023" "033" "023" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "04" "04" "04" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04" "023" "04" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04" "022" "04" "0123" "04" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "04" "014" "04" "024" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "0213" "04" "033" "024" "0213" "0212"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "011" "022" "0312" "011" "0311" "0212"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "04" "023" "0123" "0211" "04" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "0341" "032" "04" "023" "04" "04"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "023" "04" "033" "0311" "0132" "0311"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8366))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "04" "04" "04" "0212" "04" "0313"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04" "0122" "04" "04" "04" "04"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "011" "04" "0213" "023" "0211" "04"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "0213" "023" "04" "024" "04"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "0311" "023" "04" "0313" "04" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "0212" "024" "023" "022" "0311" "0311"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "011" "0213" "033" "0123" "04" "011"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "023" "04" "024" "022" "04" "04"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "023" "04" "04" "04" "033" "04"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04" "04" "024" "04" "04" "04"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04" "04" "023" "0311" "04" "04"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04" "0212" "024" "023" "04" "04"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "0314" "04" "022" "0133" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "0342" "032" "04" "04" "023" "04"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "04" "011" "024" "024" "0152" "04"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "011" "033" "022" "023" "023" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "04" "014" "024" "024" "023" "023"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "04" "0211" "0133" "0213" "024" "023"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04" "033" "0122" "04" "0212" "0313"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "023" "04" "023" "0342" "023" "04"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "04" "024" "011" "04" "04"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "0122" "032" "023" "0314" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04" "0311" "032" "024" "033" "0213"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "011" "033" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "04" "011" "024" "0132" "011" "04"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "04" "011" "024" "04" "04" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "04" "0213" "014" "04" "011" "0213"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "04" "011" "033" "0341" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "04" "04" "0152" "04" "04" "04"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "04" "04" "04" "0151" "011"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "033" "023" "0122" "04" "04" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04" "04" "032" "024" "011" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "023" "011" "04" "033" "04"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "04" "024" "022" "04" "04" "04"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "024" "0132" "04" "04" "023"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "023" "0212" "0342" "04" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "0213" "0314" "0131" "04" "0311"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "0123" "023" "04" "023" "0312"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "023" "014" "032" "0213" "04" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "023" "023" "04" "0312" "023" "0212"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "04" "023" "0311" "04" "04" "04"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "0313" "04" "023" "032" "04" "04"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "04" "032" "04" "014" "023"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "0313" "024" "04" "032" "04" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "023" "04" "04" "04" "033" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "024" "0211" "0122" "014" "04"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "023" "0131" "023" "0211" "014" "04"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "04" "011" "04" "0154" "022" "04"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "04" "024" "04" "0213" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "04" "04" "0153" "04"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "04" "04" "04" "04" "023" "023"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "04" "0123" "0341" "014" "04" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04" "033" "033" "04" "024" "033"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04" "011" "04" "023" "0213" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "033" "023" "033" "04" "04" "04"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "033" "0313" "04" "023" "024" "0213"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "023" "0154" "0213" "024" "04"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "04" "0211" "023" "022" "011" "04"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "04" "04" "04" "023" "024" "023"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "04" "033" "0133" "032" "011"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "04" "023" "024" "011" "023"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "0123" "0312" "011" "023" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "024" "023" "032" "04" "011"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "0313" "0311" "04" "011"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "011" "022" "04" "04" "0212" "023"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "0312" "0152" "04" "011" "022" "011"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04" "04" "023" "04" "022" "04"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "0313" "033" "0211" "023" "024" "0314"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "04" "022" "0212" "04" "011"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "04" "024" "011" "024" "011" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "023" "0152" "024" "0213" "0314"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "023" "04" "0341" "024" "0213"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "0211" "04" "0132" "04"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "0341" "023" "04" "0341" "04" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "04" "024" "0211" "0211" "04" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "04" "04" "04" "022" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "0212" "022" "024" "0341" "023" "011"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04" "033" "024" "0211" "0212" "04"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04" "04" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "0213" "011" "0343" "04" "024" "011"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "023" "022" "024" "0213" "0212" "04"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "023" "0212" "0311" "04" "011" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "04" "04" "0122" "032" "04"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "04" "023" "023" "024" "033" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "04" "04" "0152" "022" "033" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "033" "011" "0154" "024" "024" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "0314" "04" "04" "04" "023" "04"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04" "04" "0122" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "0314" "024" "04" "033" "04" "04"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "023" "0122" "022" "0211" "04" "04"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "011" "0342" "04" "04" "04" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "023" "0311" "033" "04" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "04" "024" "024" "0152" "024" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "04" "04" "033" "023" "0313" "04"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "04" "04" "04" "04" "024" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "023" "011" "0134" "04" "04" "0213"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04" "04" "0123" "04" "04" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "04" "0122" "024" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "04" "024" "011" "023" "032" "04"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "0342" "0212" "04" "0134" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "04" "023" "033" "023" "024" "04"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04" "024" "014" "0213" "032" "04"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "033" "04" "04" "011" "011"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "023" "023" "0313" "022" "033" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "033" "033" "011" "04" "0213" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "04" "0132" "0311" "0311" "04" "023"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "0213" "04" "0311" "022" "04" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "04" "023" "011" "04" "033"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "0213" "04" "0131" "011" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "023" "011" "04" "022" "023" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "023" "04" "022" "024" "024" "011"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "023" "04" "0341" "033" "04" "04"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "04" "024" "022" "04"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "0314" "0341" "04" "04" "04" "04"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "0343" "04" "04" "04" "04" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "04" "0152" "04" "014" "0313"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "033" "024" "014" "04" "0213" "04"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "04" "0341" "04" "04" "0213" "04"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "0212" "023" "0122" "023" "033"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "0342" "04" "0211" "04" "024" "033"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "04" "032" "0311" "04" "024" "04"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "04" "022" "04" "04" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "023" "0133" "011" "023" "04" "0312"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "04" "04" "024" "023" "0211" "04"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "011" "04" "0212" "04" "022" "0213"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "033" "04" "04" "011" "04" "023"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04" "0211" "04" "0133" "04" "0213"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "0313" "023" "04" "04" "0213" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "0213" "0154" "023" "04" "022" "023"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "023" "0152" "0211" "04" "033" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "04" "04" "023" "033" "033" "023"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04" "014" "04" "04" "024" "0311"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "04" "022" "04" "04" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "04" "0154" "024" "023" "0341"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "024" "032" "032" "0213" "023"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "04" "022" "04" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "011" "024" "023" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "04" "033" "033" "0151" "022" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "0212" "032" "023" "033" "023" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "04" "04" "04" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04" "023" "04" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04" "022" "04" "0123" "04" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "04" "014" "04" "024" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "0213" "04" "033" "024" "0213" "0212"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "011" "022" "0312" "011" "0311" "0212"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "04" "023" "0123" "0211" "04" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "0341" "032" "04" "023" "04" "04"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "023" "04" "033" "0311" "0132" "0311"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8878))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "04" "04" "04" "0212" "04" "0313"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04" "0122" "04" "04" "04" "04"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "011" "04" "0213" "023" "0211" "04"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "0213" "023" "04" "024" "04"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "0311" "023" "04" "0313" "04" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "0212" "024" "023" "022" "0311" "0311"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "011" "0213" "033" "0123" "04" "011"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "023" "04" "024" "022" "04" "04"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "023" "04" "04" "04" "033" "04"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04" "04" "024" "04" "04" "04"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04" "04" "023" "0311" "04" "04"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04" "0212" "024" "023" "04" "04"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "0314" "04" "022" "0133" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "0342" "032" "04" "04" "023" "04"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "04" "011" "024" "024" "0152" "04"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "011" "033" "022" "023" "023" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "04" "014" "024" "024" "023" "023"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "04" "0211" "0133" "0213" "024" "023"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04" "033" "0122" "04" "0212" "0313"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "023" "04" "023" "0342" "023" "04"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "04" "024" "011" "04" "04"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "0122" "032" "023" "0314" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04" "0311" "032" "024" "033" "0213"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "011" "033" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "04" "011" "024" "0132" "011" "04"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "04" "011" "024" "04" "04" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "04" "0213" "014" "04" "011" "0213"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "04" "011" "033" "0341" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "04" "04" "0152" "04" "04" "04"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "04" "04" "04" "0151" "011"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "033" "023" "0122" "04" "04" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04" "04" "032" "024" "011" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "023" "011" "04" "033" "04"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "04" "024" "022" "04" "04" "04"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "024" "0132" "04" "04" "023"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "023" "0212" "0342" "04" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "0213" "0314" "0131" "04" "0311"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "0123" "023" "04" "023" "0312"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "023" "014" "032" "0213" "04" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "023" "023" "04" "0312" "023" "0212"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "04" "023" "0311" "04" "04" "04"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "0313" "04" "023" "032" "04" "04"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "04" "032" "04" "014" "023"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "0313" "024" "04" "032" "04" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "023" "04" "04" "04" "033" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "024" "0211" "0122" "014" "04"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "023" "0131" "023" "0211" "014" "04"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "04" "011" "04" "0154" "022" "04"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "04" "024" "04" "0213" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "04" "04" "0153" "04"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "04" "04" "04" "04" "023" "023"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "04" "0123" "0341" "014" "04" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04" "033" "033" "04" "024" "033"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04" "011" "04" "023" "0213" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "033" "023" "033" "04" "04" "04"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "033" "0313" "04" "023" "024" "0213"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "023" "0154" "0213" "024" "04"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "04" "0211" "023" "022" "011" "04"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "04" "04" "04" "023" "024" "023"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "04" "033" "0133" "032" "011"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "04" "023" "024" "011" "023"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "0123" "0312" "011" "023" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "024" "023" "032" "04" "011"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "0313" "0311" "04" "011"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "011" "022" "04" "04" "0212" "023"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "0312" "0152" "04" "011" "022" "011"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04" "04" "023" "04" "022" "04"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "0313" "033" "0211" "023" "024" "0314"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "04" "022" "0212" "04" "011"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "04" "024" "011" "024" "011" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "023" "0152" "024" "0213" "0314"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "023" "04" "0341" "024" "0213"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "0211" "04" "0132" "04"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "0341" "023" "04" "0341" "04" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "04" "024" "0211" "0211" "04" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "04" "04" "04" "022" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "0212" "022" "024" "0341" "023" "011"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04" "033" "024" "0211" "0212" "04"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04" "04" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "0213" "011" "0343" "04" "024" "011"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "023" "022" "024" "0213" "0212" "04"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "023" "0212" "0311" "04" "011" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "04" "04" "0122" "032" "04"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "04" "023" "023" "024" "033" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "04" "04" "0152" "022" "033" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "033" "011" "0154" "024" "024" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "0314" "04" "04" "04" "023" "04"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04" "04" "0122" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "0314" "024" "04" "033" "04" "04"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "023" "0122" "022" "0211" "04" "04"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "011" "0342" "04" "04" "04" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "023" "0311" "033" "04" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "04" "024" "024" "0152" "024" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "04" "04" "033" "023" "0313" "04"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "04" "04" "04" "04" "024" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "023" "011" "0134" "04" "04" "0213"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04" "04" "0123" "04" "04" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "04" "0122" "024" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "04" "024" "011" "023" "032" "04"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "0342" "0212" "04" "0134" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "04" "023" "033" "023" "024" "04"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04" "024" "014" "0213" "032" "04"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "033" "04" "04" "011" "011"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "023" "023" "0313" "022" "033" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "033" "033" "011" "04" "0213" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "04" "0132" "0311" "0311" "04" "023"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "0213" "04" "0311" "022" "04" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "04" "023" "011" "04" "033"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "0213" "04" "0131" "011" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "023" "011" "04" "022" "023" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "023" "04" "022" "024" "024" "011"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "023" "04" "0341" "033" "04" "04"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "04" "024" "022" "04"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "0314" "0341" "04" "04" "04" "04"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "0343" "04" "04" "04" "04" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "04" "0152" "04" "014" "0313"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "033" "024" "014" "04" "0213" "04"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "04" "0341" "04" "04" "0213" "04"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "0212" "023" "0122" "023" "033"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "0342" "04" "0211" "04" "024" "033"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "04" "032" "0311" "04" "024" "04"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "04" "022" "04" "04" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "023" "0133" "011" "023" "04" "0312"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "04" "04" "024" "023" "0211" "04"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "011" "04" "0212" "04" "022" "0213"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "033" "04" "04" "011" "04" "023"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04" "0211" "04" "0133" "04" "0213"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "0313" "023" "04" "04" "0213" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "0213" "0154" "023" "04" "022" "023"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "023" "0152" "0211" "04" "033" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "04" "04" "023" "033" "033" "023"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04" "014" "04" "04" "024" "0311"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "04" "022" "04" "04" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "04" "0154" "024" "023" "0341"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "024" "032" "032" "0213" "023"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "04" "022" "04" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "011" "024" "023" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "04" "033" "033" "0151" "022" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "0212" "032" "023" "033" "023" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "04" "04" "04" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04" "023" "04" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04" "022" "04" "0123" "04" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "04" "014" "04" "024" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "0213" "04" "033" "024" "0213" "0212"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "011" "022" "0312" "011" "0311" "0212"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "04" "023" "0123" "0211" "04" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "0341" "032" "04" "023" "04" "04"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "023" "04" "033" "0311" "0132" "0311"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 9552))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "04" "04" "04" "0212" "04" "031"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04" "0122" "04" "04" "04" "04"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "011" "04" "0213" "023" "0211" "04"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "0213" "023" "04" "024" "04"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "031" "023" "04" "031" "04" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "0212" "024" "023" "022" "031" "031"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "011" "0213" "033" "0123" "04" "011"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "023" "04" "024" "022" "04" "04"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "023" "04" "04" "04" "033" "04"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04" "04" "024" "04" "04" "04"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04" "04" "023" "031" "04" "04"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04" "0212" "024" "023" "04" "04"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "031" "04" "022" "0133" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "0342" "032" "04" "04" "023" "04"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "04" "011" "024" "024" "0152" "04"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "011" "033" "022" "023" "023" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "04" "014" "024" "024" "023" "023"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "04" "0211" "0133" "0213" "024" "023"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04" "033" "0122" "04" "0212" "031"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "023" "04" "023" "0342" "023" "04"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "04" "024" "011" "04" "04"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "0122" "032" "023" "031" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04" "031" "032" "024" "033" "0213"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "011" "033" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "04" "011" "024" "0132" "011" "04"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "04" "011" "024" "04" "04" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "04" "0213" "014" "04" "011" "0213"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "04" "011" "033" "0341" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "04" "04" "0152" "04" "04" "04"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "04" "04" "04" "0151" "011"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "033" "023" "0122" "04" "04" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04" "04" "032" "024" "011" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "023" "011" "04" "033" "04"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "04" "024" "022" "04" "04" "04"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "024" "0132" "04" "04" "023"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "023" "0212" "0342" "04" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "0213" "031" "0131" "04" "031"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "0123" "023" "04" "023" "031"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "023" "014" "032" "0213" "04" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "023" "023" "04" "031" "023" "0212"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "04" "023" "031" "04" "04" "04"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "031" "04" "023" "032" "04" "04"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "04" "032" "04" "014" "023"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "031" "024" "04" "032" "04" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "023" "04" "04" "04" "033" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "024" "0211" "0122" "014" "04"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "023" "0131" "023" "0211" "014" "04"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "04" "011" "04" "0154" "022" "04"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "04" "024" "04" "0213" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "04" "04" "0153" "04"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "04" "04" "04" "04" "023" "023"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "04" "0123" "0341" "014" "04" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04" "033" "033" "04" "024" "033"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04" "011" "04" "023" "0213" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "033" "023" "033" "04" "04" "04"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "033" "031" "04" "023" "024" "0213"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "023" "0154" "0213" "024" "04"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "04" "0211" "023" "022" "011" "04"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "04" "04" "04" "023" "024" "023"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "04" "033" "0133" "032" "011"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "04" "023" "024" "011" "023"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "0123" "031" "011" "023" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "024" "023" "032" "04" "011"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "031" "031" "04" "011"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "011" "022" "04" "04" "0212" "023"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "031" "0152" "04" "011" "022" "011"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04" "04" "023" "04" "022" "04"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "031" "033" "0211" "023" "024" "031"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "04" "022" "0212" "04" "011"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "04" "024" "011" "024" "011" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "023" "0152" "024" "0213" "031"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "023" "04" "0341" "024" "0213"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "0211" "04" "0132" "04"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "0341" "023" "04" "0341" "04" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "04" "024" "0211" "0211" "04" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "04" "04" "04" "022" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "0212" "022" "024" "0341" "023" "011"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04" "033" "024" "0211" "0212" "04"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04" "04" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "0213" "011" "0343" "04" "024" "011"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "023" "022" "024" "0213" "0212" "04"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "023" "0212" "031" "04" "011" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "04" "04" "0122" "032" "04"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "04" "023" "023" "024" "033" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "04" "04" "0152" "022" "033" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "033" "011" "0154" "024" "024" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "031" "04" "04" "04" "023" "04"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04" "04" "0122" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "031" "024" "04" "033" "04" "04"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "023" "0122" "022" "0211" "04" "04"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "011" "0342" "04" "04" "04" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "023" "031" "033" "04" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "04" "024" "024" "0152" "024" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "04" "04" "033" "023" "031" "04"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "04" "04" "04" "04" "024" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "023" "011" "0134" "04" "04" "0213"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04" "04" "0123" "04" "04" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "04" "0122" "024" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "04" "024" "011" "023" "032" "04"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "0342" "0212" "04" "0134" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "04" "023" "033" "023" "024" "04"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04" "024" "014" "0213" "032" "04"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "033" "04" "04" "011" "011"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "023" "023" "031" "022" "033" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "033" "033" "011" "04" "0213" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "04" "0132" "031" "031" "04" "023"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "0213" "04" "031" "022" "04" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "04" "023" "011" "04" "033"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "0213" "04" "0131" "011" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "023" "011" "04" "022" "023" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "023" "04" "022" "024" "024" "011"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "023" "04" "0341" "033" "04" "04"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "04" "024" "022" "04"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "031" "0341" "04" "04" "04" "04"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "0343" "04" "04" "04" "04" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "04" "0152" "04" "014" "031"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "033" "024" "014" "04" "0213" "04"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "04" "0341" "04" "04" "0213" "04"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "0212" "023" "0122" "023" "033"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "0342" "04" "0211" "04" "024" "033"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "04" "032" "031" "04" "024" "04"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "04" "022" "04" "04" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "023" "0133" "011" "023" "04" "031"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "04" "04" "024" "023" "0211" "04"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "011" "04" "0212" "04" "022" "0213"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "033" "04" "04" "011" "04" "023"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04" "0211" "04" "0133" "04" "0213"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "031" "023" "04" "04" "0213" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "0213" "0154" "023" "04" "022" "023"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "023" "0152" "0211" "04" "033" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "04" "04" "023" "033" "033" "023"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04" "014" "04" "04" "024" "031"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "04" "022" "04" "04" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "04" "0154" "024" "023" "0341"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "024" "032" "032" "0213" "023"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "04" "022" "04" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "011" "024" "023" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "04" "033" "033" "0151" "022" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "0212" "032" "023" "033" "023" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "04" "04" "04" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04" "023" "04" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04" "022" "04" "0123" "04" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "04" "014" "04" "024" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "0213" "04" "033" "024" "0213" "0212"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "011" "022" "031" "011" "031" "0212"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "04" "023" "0123" "0211" "04" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "0341" "032" "04" "023" "04" "04"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "023" "04" "033" "031" "0132" "031"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 12308))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "04" "04" "04" "0212" "04" "031"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04" "0122" "04" "04" "04" "04"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "011" "04" "0213" "023" "0211" "04"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "0213" "023" "04" "024" "04"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "031" "023" "04" "031" "04" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "0212" "024" "023" "022" "031" "031"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "011" "0213" "033" "0123" "04" "011"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "023" "04" "024" "022" "04" "04"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "023" "04" "04" "04" "033" "04"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04" "04" "024" "04" "04" "04"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04" "04" "023" "031" "04" "04"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04" "0212" "024" "023" "04" "04"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "031" "04" "022" "0133" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "034" "032" "04" "04" "023" "04"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "04" "011" "024" "024" "0152" "04"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "011" "033" "022" "023" "023" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "04" "014" "024" "024" "023" "023"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "04" "0211" "0133" "0213" "024" "023"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04" "033" "0122" "04" "0212" "031"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "023" "04" "023" "034" "023" "04"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "04" "024" "011" "04" "04"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "0122" "032" "023" "031" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04" "031" "032" "024" "033" "0213"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "011" "033" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "04" "011" "024" "0132" "011" "04"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "04" "011" "024" "04" "04" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "04" "0213" "014" "04" "011" "0213"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "04" "011" "033" "034" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "04" "04" "0152" "04" "04" "04"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "04" "04" "04" "0151" "011"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "033" "023" "0122" "04" "04" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04" "04" "032" "024" "011" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "023" "011" "04" "033" "04"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "04" "024" "022" "04" "04" "04"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "024" "0132" "04" "04" "023"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "023" "0212" "034" "04" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "0213" "031" "0131" "04" "031"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "0123" "023" "04" "023" "031"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "023" "014" "032" "0213" "04" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "023" "023" "04" "031" "023" "0212"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "04" "023" "031" "04" "04" "04"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "031" "04" "023" "032" "04" "04"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "04" "032" "04" "014" "023"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "031" "024" "04" "032" "04" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "023" "04" "04" "04" "033" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "024" "0211" "0122" "014" "04"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "023" "0131" "023" "0211" "014" "04"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "04" "011" "04" "0154" "022" "04"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "04" "024" "04" "0213" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "04" "04" "0153" "04"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "04" "04" "04" "04" "023" "023"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "04" "0123" "034" "014" "04" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04" "033" "033" "04" "024" "033"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04" "011" "04" "023" "0213" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "033" "023" "033" "04" "04" "04"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "033" "031" "04" "023" "024" "0213"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "023" "0154" "0213" "024" "04"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "04" "0211" "023" "022" "011" "04"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "04" "04" "04" "023" "024" "023"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "04" "033" "0133" "032" "011"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "04" "023" "024" "011" "023"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "0123" "031" "011" "023" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "024" "023" "032" "04" "011"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "031" "031" "04" "011"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "011" "022" "04" "04" "0212" "023"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "031" "0152" "04" "011" "022" "011"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04" "04" "023" "04" "022" "04"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "031" "033" "0211" "023" "024" "031"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "04" "022" "0212" "04" "011"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "04" "024" "011" "024" "011" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "023" "0152" "024" "0213" "031"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "023" "04" "034" "024" "0213"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "0211" "04" "0132" "04"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "034" "023" "04" "034" "04" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "04" "024" "0211" "0211" "04" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "04" "04" "04" "022" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "0212" "022" "024" "034" "023" "011"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04" "033" "024" "0211" "0212" "04"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04" "04" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "0213" "011" "034" "04" "024" "011"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "023" "022" "024" "0213" "0212" "04"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "023" "0212" "031" "04" "011" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "04" "04" "0122" "032" "04"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "04" "023" "023" "024" "033" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "04" "04" "0152" "022" "033" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "033" "011" "0154" "024" "024" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "031" "04" "04" "04" "023" "04"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04" "04" "0122" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "031" "024" "04" "033" "04" "04"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "023" "0122" "022" "0211" "04" "04"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "011" "034" "04" "04" "04" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "023" "031" "033" "04" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "04" "024" "024" "0152" "024" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "04" "04" "033" "023" "031" "04"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "04" "04" "04" "04" "024" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "023" "011" "0134" "04" "04" "0213"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04" "04" "0123" "04" "04" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "04" "0122" "024" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "04" "024" "011" "023" "032" "04"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "034" "0212" "04" "0134" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "04" "023" "033" "023" "024" "04"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04" "024" "014" "0213" "032" "04"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "033" "04" "04" "011" "011"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "023" "023" "031" "022" "033" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "033" "033" "011" "04" "0213" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "04" "0132" "031" "031" "04" "023"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "0213" "04" "031" "022" "04" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "04" "023" "011" "04" "033"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "0213" "04" "0131" "011" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "023" "011" "04" "022" "023" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "023" "04" "022" "024" "024" "011"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "023" "04" "034" "033" "04" "04"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "04" "024" "022" "04"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "031" "034" "04" "04" "04" "04"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "034" "04" "04" "04" "04" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "04" "0152" "04" "014" "031"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "033" "024" "014" "04" "0213" "04"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "04" "034" "04" "04" "0213" "04"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "0212" "023" "0122" "023" "033"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "034" "04" "0211" "04" "024" "033"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "04" "032" "031" "04" "024" "04"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "04" "022" "04" "04" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "023" "0133" "011" "023" "04" "031"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "04" "04" "024" "023" "0211" "04"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "011" "04" "0212" "04" "022" "0213"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "033" "04" "04" "011" "04" "023"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04" "0211" "04" "0133" "04" "0213"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "031" "023" "04" "04" "0213" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "0213" "0154" "023" "04" "022" "023"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "023" "0152" "0211" "04" "033" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "04" "04" "023" "033" "033" "023"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04" "014" "04" "04" "024" "031"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "04" "022" "04" "04" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "04" "0154" "024" "023" "034"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "024" "032" "032" "0213" "023"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "04" "022" "04" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "011" "024" "023" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "04" "033" "033" "0151" "022" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "0212" "032" "023" "033" "023" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "04" "04" "04" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04" "023" "04" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04" "022" "04" "0123" "04" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "04" "014" "04" "024" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "0213" "04" "033" "024" "0213" "0212"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "011" "022" "031" "011" "031" "0212"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "04" "023" "0123" "0211" "04" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "034" "032" "04" "023" "04" "04"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "023" "04" "033" "031" "0132" "031"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 12745))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "04" "04" "04" "0212" "04" "031"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04" "0122" "04" "04" "04" "04"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "011" "04" "0213" "023" "0211" "04"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "0213" "023" "04" "024" "04"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "031" "023" "04" "031" "04" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "0212" "024" "023" "022" "031" "031"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "011" "0213" "033" "0123" "04" "011"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "023" "04" "024" "022" "04" "04"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "023" "04" "04" "04" "033" "04"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04" "04" "024" "04" "04" "04"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04" "04" "023" "031" "04" "04"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04" "0212" "024" "023" "04" "04"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "031" "04" "022" "0133" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "034" "032" "04" "04" "023" "04"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "04" "011" "024" "024" "0152" "04"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "011" "033" "022" "023" "023" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "04" "014" "024" "024" "023" "023"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "04" "0211" "0133" "0213" "024" "023"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04" "033" "0122" "04" "0212" "031"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "023" "04" "023" "034" "023" "04"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "04" "024" "011" "04" "04"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "0122" "032" "023" "031" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04" "031" "032" "024" "033" "0213"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "011" "033" "0134" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "04" "011" "024" "0132" "011" "04"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "04" "011" "024" "04" "04" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "04" "0213" "014" "04" "011" "0213"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "04" "011" "033" "034" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "04" "04" "0152" "04" "04" "04"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "04" "04" "04" "0151" "011"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "033" "023" "0122" "04" "04" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04" "04" "032" "024" "011" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "023" "011" "04" "033" "04"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "04" "024" "022" "04" "04" "04"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "024" "0132" "04" "04" "023"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "023" "0212" "034" "04" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "0131" "0213" "031" "0131" "04" "031"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "0123" "023" "04" "023" "031"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "023" "014" "032" "0213" "04" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "023" "023" "04" "031" "023" "0212"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "04" "023" "031" "04" "04" "04"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "031" "04" "023" "032" "04" "04"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "04" "032" "04" "014" "023"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "031" "024" "04" "032" "04" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "023" "04" "04" "04" "033" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "024" "0211" "0122" "014" "04"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "023" "0131" "023" "0211" "014" "04"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "04" "011" "04" "0154" "022" "04"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "0131" "04" "024" "04" "0213" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "04" "04" "0153" "04"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "04" "04" "04" "04" "023" "023"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "04" "0123" "034" "014" "04" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04" "033" "033" "04" "024" "033"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04" "011" "04" "023" "0213" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "033" "023" "033" "04" "04" "04"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "033" "031" "04" "023" "024" "0213"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "023" "0154" "0213" "024" "04"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "04" "0211" "023" "022" "011" "04"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "04" "04" "04" "023" "024" "023"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "04" "033" "0133" "032" "011"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "04" "023" "024" "011" "023"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "0123" "031" "011" "023" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "0134" "024" "023" "032" "04" "011"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "031" "031" "04" "011"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "011" "022" "04" "04" "0212" "023"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "031" "0152" "04" "011" "022" "011"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04" "04" "023" "04" "022" "04"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "031" "033" "0211" "023" "024" "031"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "04" "022" "0212" "04" "011"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "04" "024" "011" "024" "011" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "023" "0152" "024" "0213" "031"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "023" "04" "034" "024" "0213"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "0211" "04" "0132" "04"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "034" "023" "04" "034" "04" "0131"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "04" "024" "0211" "0211" "04" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "04" "04" "04" "022" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "0212" "022" "024" "034" "023" "011"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04" "033" "024" "0211" "0212" "04"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04" "04" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "0213" "011" "034" "04" "024" "011"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "023" "022" "024" "0213" "0212" "04"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "023" "0212" "031" "04" "011" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "04" "04" "0122" "032" "04"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "04" "023" "023" "024" "033" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "04" "04" "0152" "022" "033" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "033" "011" "0154" "024" "024" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "031" "04" "04" "04" "023" "04"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04" "04" "0122" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "031" "024" "04" "033" "04" "04"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "023" "0122" "022" "0211" "04" "04"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "011" "034" "04" "04" "04" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "023" "031" "033" "04" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "04" "024" "024" "0152" "024" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "04" "04" "033" "023" "031" "04"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "04" "04" "04" "04" "024" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "023" "011" "0134" "04" "04" "0213"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04" "04" "0123" "04" "04" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "04" "0122" "024" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "04" "024" "011" "023" "032" "04"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "034" "0212" "04" "0134" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "04" "023" "033" "023" "024" "04"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04" "024" "014" "0213" "032" "04"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "0132" "033" "04" "04" "011" "011"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "023" "023" "031" "022" "033" "0133"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "033" "033" "011" "04" "0213" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "04" "0132" "031" "031" "04" "023"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "0213" "04" "031" "022" "04" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "04" "023" "011" "04" "033"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "0131" "0213" "04" "0131" "011" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "023" "011" "04" "022" "023" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "023" "04" "022" "024" "024" "011"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "023" "04" "034" "033" "04" "04"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "04" "024" "022" "04"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "031" "034" "04" "04" "04" "04"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "034" "04" "04" "04" "04" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "04" "0152" "04" "014" "031"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "033" "024" "014" "04" "0213" "04"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "04" "034" "04" "04" "0213" "04"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "0212" "023" "0122" "023" "033"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "034" "04" "0211" "04" "024" "033"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "04" "032" "031" "04" "024" "04"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "04" "022" "04" "04" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "023" "0133" "011" "023" "04" "031"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "04" "04" "024" "023" "0211" "04"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "011" "04" "0212" "04" "022" "0213"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "033" "04" "04" "011" "04" "023"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04" "0211" "04" "0133" "04" "0213"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "031" "023" "04" "04" "0213" "0131"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "0213" "0154" "023" "04" "022" "023"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "023" "0152" "0211" "04" "033" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "04" "04" "023" "033" "033" "023"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04" "014" "04" "04" "024" "031"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "04" "022" "04" "04" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "04" "0154" "024" "023" "034"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "024" "032" "032" "0213" "023"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "04" "022" "04" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "011" "024" "023" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "04" "033" "033" "0151" "022" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "0212" "032" "023" "033" "023" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "04" "04" "04" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04" "023" "04" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04" "022" "04" "0123" "04" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "04" "014" "04" "024" "0131"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "0213" "04" "033" "024" "0213" "0212"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "011" "022" "031" "011" "031" "0212"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "04" "023" "0123" "0211" "04" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "034" "032" "04" "023" "04" "04"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "023" "04" "033" "031" "0132" "031"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 14822))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "04" "04" "04" "0212" "04" "031"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04" "0122" "04" "04" "04" "04"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "011" "04" "0213" "023" "0211" "04"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "0213" "023" "04" "024" "04"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "031" "023" "04" "031" "04" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "0212" "024" "023" "022" "031" "031"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "011" "0213" "033" "0123" "04" "011"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "023" "04" "024" "022" "04" "04"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "023" "04" "04" "04" "033" "04"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04" "04" "024" "04" "04" "04"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04" "04" "023" "031" "04" "04"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04" "0212" "024" "023" "04" "04"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "031" "04" "022" "013" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "034" "032" "04" "04" "023" "04"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "04" "011" "024" "024" "0152" "04"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "011" "033" "022" "023" "023" "0211"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "04" "014" "024" "024" "023" "023"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "04" "0211" "013" "0213" "024" "023"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04" "033" "0122" "04" "0212" "031"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "023" "04" "023" "034" "023" "04"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "04" "024" "011" "04" "04"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "0122" "032" "023" "031" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04" "031" "032" "024" "033" "0213"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "0211" "0152" "011" "033" "013" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "04" "011" "024" "013" "011" "04"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "04" "011" "024" "04" "04" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "04" "0213" "014" "04" "011" "0213"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "04" "011" "033" "034" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "04" "04" "0152" "04" "04" "04"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "04" "04" "04" "0151" "011"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "033" "023" "0122" "04" "04" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04" "04" "032" "024" "011" "0211"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "0211" "023" "011" "04" "033" "04"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "04" "024" "022" "04" "04" "04"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "024" "013" "04" "04" "023"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "023" "0212" "034" "04" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "013" "0213" "031" "013" "04" "031"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "0123" "023" "04" "023" "031"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "023" "014" "032" "0213" "04" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "023" "023" "04" "031" "023" "0212"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "04" "023" "031" "04" "04" "04"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "031" "04" "023" "032" "04" "04"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "04" "032" "04" "014" "023"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "031" "024" "04" "032" "04" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "023" "04" "04" "04" "033" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "024" "0211" "0122" "014" "04"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "023" "013" "023" "0211" "014" "04"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "04" "011" "04" "0154" "022" "04"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "013" "04" "024" "04" "0213" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "04" "04" "0153" "04"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "04" "04" "04" "04" "023" "023"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "04" "0123" "034" "014" "04" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04" "033" "033" "04" "024" "033"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04" "011" "04" "023" "0213" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "033" "023" "033" "04" "04" "04"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "033" "031" "04" "023" "024" "0213"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "023" "0154" "0213" "024" "04"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "04" "0211" "023" "022" "011" "04"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "04" "04" "04" "023" "024" "023"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "04" "033" "013" "032" "011"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "04" "023" "024" "011" "023"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "0123" "031" "011" "023" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "013" "024" "023" "032" "04" "011"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "031" "031" "04" "011"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "011" "022" "04" "04" "0212" "023"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "031" "0152" "04" "011" "022" "011"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04" "04" "023" "04" "022" "04"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "031" "033" "0211" "023" "024" "031"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "04" "022" "0212" "04" "011"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "04" "024" "011" "024" "011" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "023" "0152" "024" "0213" "031"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "023" "04" "034" "024" "0213"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "0211" "04" "013" "04"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "034" "023" "04" "034" "04" "013"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "04" "024" "0211" "0211" "04" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "04" "04" "04" "022" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "0212" "022" "024" "034" "023" "011"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04" "033" "024" "0211" "0212" "04"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04" "04" "0123" "014" "014" "0211"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "0213" "011" "034" "04" "024" "011"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "023" "022" "024" "0213" "0212" "04"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "023" "0212" "031" "04" "011" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "0211" "04" "04" "0122" "032" "04"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "04" "023" "023" "024" "033" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "04" "04" "0152" "022" "033" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "033" "011" "0154" "024" "024" "0211"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "031" "04" "04" "04" "023" "04"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04" "04" "0122" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "031" "024" "04" "033" "04" "04"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "023" "0122" "022" "0211" "04" "04"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "011" "034" "04" "04" "04" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "023" "031" "033" "04" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "04" "024" "024" "0152" "024" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "04" "04" "033" "023" "031" "04"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "04" "04" "04" "04" "024" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "023" "011" "013" "04" "04" "0213"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04" "04" "0123" "04" "04" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "04" "0122" "024" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "04" "024" "011" "023" "032" "04"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "034" "0212" "04" "013" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "04" "023" "033" "023" "024" "04"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04" "024" "014" "0213" "032" "04"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "013" "033" "04" "04" "011" "011"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "023" "023" "031" "022" "033" "013"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "033" "033" "011" "04" "0213" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "04" "013" "031" "031" "04" "023"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "0213" "04" "031" "022" "04" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "0211" "04" "023" "011" "04" "033"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "013" "0213" "04" "013" "011" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "023" "011" "04" "022" "023" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "023" "04" "022" "024" "024" "011"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "023" "04" "034" "033" "04" "04"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "04" "024" "022" "04"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "031" "034" "04" "04" "04" "04"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "034" "04" "04" "04" "04" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "04" "0152" "04" "014" "031"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "033" "024" "014" "04" "0213" "04"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "04" "034" "04" "04" "0213" "04"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "0211" "0212" "023" "0122" "023" "033"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "034" "04" "0211" "04" "024" "033"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "04" "032" "031" "04" "024" "04"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "04" "022" "04" "04" "0211"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "023" "013" "011" "023" "04" "031"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "04" "04" "024" "023" "0211" "04"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "011" "04" "0212" "04" "022" "0213"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "033" "04" "04" "011" "04" "023"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04" "0211" "04" "013" "04" "0213"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "031" "023" "04" "04" "0213" "013"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "0213" "0154" "023" "04" "022" "023"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "023" "0152" "0211" "04" "033" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "04" "04" "023" "033" "033" "023"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04" "014" "04" "04" "024" "031"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "04" "022" "04" "04" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "04" "0154" "024" "023" "034"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "024" "032" "032" "0213" "023"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "04" "022" "04" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "011" "024" "023" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "04" "033" "033" "0151" "022" "0211"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "0212" "032" "023" "033" "023" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "04" "04" "04" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04" "023" "04" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04" "022" "04" "0123" "04" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "04" "014" "04" "024" "013"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "0213" "04" "033" "024" "0213" "0212"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "011" "022" "031" "011" "031" "0212"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "04" "023" "0123" "0211" "04" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "034" "032" "04" "023" "04" "04"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "023" "04" "033" "031" "013" "031"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 15450))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "04" "04" "04" "021" "04" "031"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04" "0122" "04" "04" "04" "04"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "011" "04" "021" "023" "021" "04"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "021" "023" "04" "024" "04"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "031" "023" "04" "031" "04" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "021" "024" "023" "022" "031" "031"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "011" "021" "033" "0123" "04" "011"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "023" "04" "024" "022" "04" "04"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "023" "04" "04" "04" "033" "04"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04" "04" "024" "04" "04" "04"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04" "04" "023" "031" "04" "04"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04" "021" "024" "023" "04" "04"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "031" "04" "022" "013" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "034" "032" "04" "04" "023" "04"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "04" "011" "024" "024" "0152" "04"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "011" "033" "022" "023" "023" "021"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "04" "014" "024" "024" "023" "023"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "04" "021" "013" "021" "024" "023"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04" "033" "0122" "04" "021" "031"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "023" "04" "023" "034" "023" "04"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "04" "024" "011" "04" "04"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "0122" "032" "023" "031" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04" "031" "032" "024" "033" "021"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "021" "0152" "011" "033" "013" "0122"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "04" "011" "024" "013" "011" "04"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "04" "011" "024" "04" "04" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "04" "021" "014" "04" "011" "021"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "04" "011" "033" "034" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "04" "04" "0152" "04" "04" "04"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "04" "04" "04" "0151" "011"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "033" "023" "0122" "04" "04" "0121"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04" "04" "032" "024" "011" "021"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "021" "023" "011" "04" "033" "04"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "04" "024" "022" "04" "04" "04"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "024" "013" "04" "04" "023"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "023" "021" "034" "04" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "013" "021" "031" "013" "04" "031"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "0123" "023" "04" "023" "031"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "023" "014" "032" "021" "04" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "023" "023" "04" "031" "023" "021"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "04" "023" "031" "04" "04" "04"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "031" "04" "023" "032" "04" "04"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "04" "032" "04" "014" "023"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "031" "024" "04" "032" "04" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "023" "04" "04" "04" "033" "0123"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "0122" "024" "021" "0122" "014" "04"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "023" "013" "023" "021" "014" "04"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "04" "011" "04" "0154" "022" "04"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "013" "04" "024" "04" "021" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "04" "04" "0153" "04"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "04" "04" "04" "04" "023" "023"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "04" "0123" "034" "014" "04" "0122"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04" "033" "033" "04" "024" "033"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04" "011" "04" "023" "021" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "033" "023" "033" "04" "04" "04"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "033" "031" "04" "023" "024" "021"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "023" "0154" "021" "024" "04"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "04" "021" "023" "022" "011" "04"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "04" "04" "04" "023" "024" "023"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "04" "033" "013" "032" "011"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "04" "023" "024" "011" "023"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "0123" "031" "011" "023" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "013" "024" "023" "032" "04" "011"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "031" "031" "04" "011"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "011" "022" "04" "04" "021" "023"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "031" "0152" "04" "011" "022" "011"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04" "04" "023" "04" "022" "04"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "031" "033" "021" "023" "024" "031"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "04" "022" "021" "04" "011"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "04" "024" "011" "024" "011" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "023" "0152" "024" "021" "031"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "023" "04" "034" "024" "021"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "021" "04" "013" "04"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "034" "023" "04" "034" "04" "013"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "04" "024" "021" "021" "04" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "04" "04" "04" "022" "0122"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "021" "022" "024" "034" "023" "011"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04" "033" "024" "021" "021" "04"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04" "04" "0123" "014" "014" "021"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "021" "011" "034" "04" "024" "011"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "023" "022" "024" "021" "021" "04"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "023" "021" "031" "04" "011" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "021" "04" "04" "0122" "032" "04"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "04" "023" "023" "024" "033" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "04" "04" "0152" "022" "033" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "033" "011" "0154" "024" "024" "021"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "031" "04" "04" "04" "023" "04"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04" "04" "0122" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "031" "024" "04" "033" "04" "04"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "023" "0122" "022" "021" "04" "04"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "011" "034" "04" "04" "04" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "023" "031" "033" "04" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "04" "024" "024" "0152" "024" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "04" "04" "033" "023" "031" "04"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "04" "04" "04" "04" "024" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "023" "011" "013" "04" "04" "021"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04" "04" "0123" "04" "04" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "04" "0122" "024" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "04" "024" "011" "023" "032" "04"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "034" "021" "04" "013" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "04" "023" "033" "023" "024" "04"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04" "024" "014" "021" "032" "04"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "013" "033" "04" "04" "011" "011"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "023" "023" "031" "022" "033" "013"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "033" "033" "011" "04" "021" "0122"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "04" "013" "031" "031" "04" "023"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "021" "04" "031" "022" "04" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "021" "04" "023" "011" "04" "033"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "013" "021" "04" "013" "011" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "023" "011" "04" "022" "023" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "023" "04" "022" "024" "024" "011"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "023" "04" "034" "033" "04" "04"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "04" "024" "022" "04"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "031" "034" "04" "04" "04" "04"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "034" "04" "04" "04" "04" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "04" "0152" "04" "014" "031"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "033" "024" "014" "04" "021" "04"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "04" "034" "04" "04" "021" "04"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "021" "021" "023" "0122" "023" "033"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "034" "04" "021" "04" "024" "033"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "04" "032" "031" "04" "024" "04"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "0122" "04" "022" "04" "04" "021"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "023" "013" "011" "023" "04" "031"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "04" "04" "024" "023" "021" "04"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "011" "04" "021" "04" "022" "021"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "033" "04" "04" "011" "04" "023"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04" "021" "04" "013" "04" "021"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "031" "023" "04" "04" "021" "013"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "021" "0154" "023" "04" "022" "023"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "023" "0152" "021" "04" "033" "0121"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "04" "04" "023" "033" "033" "023"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04" "014" "04" "04" "024" "031"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "04" "022" "04" "04" "0123"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "04" "0154" "024" "023" "034"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "024" "032" "032" "021" "023"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "04" "022" "04" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "011" "024" "023" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "04" "033" "033" "0151" "022" "021"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "021" "032" "023" "033" "023" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "04" "04" "04" "0122"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04" "023" "04" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04" "022" "04" "0123" "04" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "04" "014" "04" "024" "013"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "021" "04" "033" "024" "021" "021"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "011" "022" "031" "011" "031" "021"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "04" "023" "0123" "021" "04" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "034" "032" "04" "023" "04" "04"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "023" "04" "033" "031" "013" "031"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 20697))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "04" "04" "04" "021" "04" "031"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04" "012" "04" "04" "04" "04"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "011" "04" "021" "023" "021" "04"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "021" "023" "04" "024" "04"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "031" "023" "04" "031" "04" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "021" "024" "023" "022" "031" "031"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "011" "021" "033" "012" "04" "011"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "023" "04" "024" "022" "04" "04"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "023" "04" "04" "04" "033" "04"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04" "04" "024" "04" "04" "04"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04" "04" "023" "031" "04" "04"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04" "021" "024" "023" "04" "04"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "031" "04" "022" "013" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "034" "032" "04" "04" "023" "04"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "04" "011" "024" "024" "0152" "04"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "011" "033" "022" "023" "023" "021"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "04" "014" "024" "024" "023" "023"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "04" "021" "013" "021" "024" "023"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04" "033" "012" "04" "021" "031"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "023" "04" "023" "034" "023" "04"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "04" "024" "011" "04" "04"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "012" "032" "023" "031" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04" "031" "032" "024" "033" "021"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "021" "0152" "011" "033" "013" "012"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "04" "011" "024" "013" "011" "04"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "04" "011" "024" "04" "04" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "04" "021" "014" "04" "011" "021"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "04" "011" "033" "034" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "04" "04" "0152" "04" "04" "04"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "04" "04" "04" "0151" "011"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "033" "023" "012" "04" "04" "012"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04" "04" "032" "024" "011" "021"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "021" "023" "011" "04" "033" "04"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "04" "024" "022" "04" "04" "04"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "032" "024" "013" "04" "04" "023"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "023" "021" "034" "04" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "013" "021" "031" "013" "04" "031"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "012" "023" "04" "023" "031"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "023" "014" "032" "021" "04" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "023" "023" "04" "031" "023" "021"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "04" "023" "031" "04" "04" "04"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "031" "04" "023" "032" "04" "04"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "04" "032" "04" "014" "023"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "031" "024" "04" "032" "04" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "023" "04" "04" "04" "033" "012"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "012" "024" "021" "012" "014" "04"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "023" "013" "023" "021" "014" "04"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "04" "011" "04" "0154" "022" "04"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "013" "04" "024" "04" "021" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "04" "04" "0153" "04"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "04" "04" "04" "04" "023" "023"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "04" "012" "034" "014" "04" "012"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04" "033" "033" "04" "024" "033"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04" "011" "04" "023" "021" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "033" "023" "033" "04" "04" "04"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "033" "031" "04" "023" "024" "021"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "023" "0154" "021" "024" "04"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "04" "021" "023" "022" "011" "04"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "04" "04" "04" "023" "024" "023"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "04" "033" "013" "032" "011"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "032" "04" "023" "024" "011" "023"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "012" "031" "011" "023" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "013" "024" "023" "032" "04" "011"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "031" "031" "04" "011"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "011" "022" "04" "04" "021" "023"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "031" "0152" "04" "011" "022" "011"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04" "04" "023" "04" "022" "04"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "031" "033" "021" "023" "024" "031"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "04" "022" "021" "04" "011"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "04" "024" "011" "024" "011" "032"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "023" "0152" "024" "021" "031"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "023" "04" "034" "024" "021"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "021" "04" "013" "04"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "034" "023" "04" "034" "04" "013"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "04" "024" "021" "021" "04" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "04" "04" "04" "022" "012"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "021" "022" "024" "034" "023" "011"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04" "033" "024" "021" "021" "04"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04" "04" "012" "014" "014" "021"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "021" "011" "034" "04" "024" "011"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "023" "022" "024" "021" "021" "04"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "023" "021" "031" "04" "011" "032"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "021" "04" "04" "012" "032" "04"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "04" "023" "023" "024" "033" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "04" "04" "0152" "022" "033" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "033" "011" "0154" "024" "024" "021"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "031" "04" "04" "04" "023" "04"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04" "04" "012" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "031" "024" "04" "033" "04" "04"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "023" "012" "022" "021" "04" "04"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "011" "034" "04" "04" "04" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "023" "031" "033" "04" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "04" "024" "024" "0152" "024" "032"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "04" "04" "033" "023" "031" "04"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "04" "04" "04" "04" "024" "032"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "023" "011" "013" "04" "04" "021"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04" "04" "012" "04" "04" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "04" "012" "024" "032"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "04" "024" "011" "023" "032" "04"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "034" "021" "04" "013" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "04" "023" "033" "023" "024" "04"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04" "024" "014" "021" "032" "04"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "013" "033" "04" "04" "011" "011"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "023" "023" "031" "022" "033" "013"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "033" "033" "011" "04" "021" "012"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "04" "013" "031" "031" "04" "023"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "021" "04" "031" "022" "04" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "021" "04" "023" "011" "04" "033"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "013" "021" "04" "013" "011" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "023" "011" "04" "022" "023" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "023" "04" "022" "024" "024" "011"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "023" "04" "034" "033" "04" "04"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "04" "024" "022" "04"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "031" "034" "04" "04" "04" "04"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "034" "04" "04" "04" "04" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "04" "0152" "04" "014" "031"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "033" "024" "014" "04" "021" "04"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "04" "034" "04" "04" "021" "04"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "021" "021" "023" "012" "023" "033"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "034" "04" "021" "04" "024" "033"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "04" "032" "031" "04" "024" "04"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "012" "04" "022" "04" "04" "021"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "023" "013" "011" "023" "04" "031"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "04" "04" "024" "023" "021" "04"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "011" "04" "021" "04" "022" "021"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "033" "04" "04" "011" "04" "023"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04" "021" "04" "013" "04" "021"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "031" "023" "04" "04" "021" "013"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "021" "0154" "023" "04" "022" "023"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "023" "0152" "021" "04" "033" "012"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "04" "04" "023" "033" "033" "023"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04" "014" "04" "04" "024" "031"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "04" "022" "04" "04" "012"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "04" "0154" "024" "023" "034"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "024" "032" "032" "021" "023"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "04" "022" "04" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "011" "024" "023" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "04" "033" "033" "0151" "022" "021"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "021" "032" "023" "033" "023" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "04" "04" "04" "012"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04" "023" "04" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04" "022" "04" "012" "04" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "032" "04" "014" "04" "024" "013"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "021" "04" "033" "024" "021" "021"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "011" "022" "031" "011" "031" "021"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "04" "023" "012" "021" "04" "032"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "034" "032" "04" "023" "04" "04"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "023" "04" "033" "031" "013" "031"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 21454))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "04" "04" "04" "021" "04" "03"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04" "012" "04" "04" "04" "04"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "011" "04" "021" "023" "021" "04"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "021" "023" "04" "024" "04"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "03" "023" "04" "03" "04" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "021" "024" "023" "022" "03" "03"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "011" "021" "03" "012" "04" "011"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "023" "04" "024" "022" "04" "04"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "023" "04" "04" "04" "03" "04"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04" "04" "024" "04" "04" "04"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04" "04" "023" "03" "04" "04"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04" "021" "024" "023" "04" "04"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "0154" "03" "04" "022" "013" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "03" "03" "04" "04" "023" "04"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "04" "011" "024" "024" "0152" "04"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "011" "03" "022" "023" "023" "021"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "04" "014" "024" "024" "023" "023"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "04" "021" "013" "021" "024" "023"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04" "03" "012" "04" "021" "03"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "023" "04" "023" "03" "023" "04"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "04" "024" "011" "04" "04"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "012" "03" "023" "03" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04" "03" "03" "024" "03" "021"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "021" "0152" "011" "03" "013" "012"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "04" "011" "024" "013" "011" "04"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "04" "011" "024" "04" "04" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "04" "021" "014" "04" "011" "021"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "04" "011" "03" "03" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "04" "04" "0152" "04" "04" "04"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "04" "04" "04" "0151" "011"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "03" "023" "012" "04" "04" "012"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04" "04" "03" "024" "011" "021"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "021" "023" "011" "04" "03" "04"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "04" "024" "022" "04" "04" "04"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "03" "024" "013" "04" "04" "023"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "0154" "023" "021" "03" "04" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "013" "021" "03" "013" "04" "03"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "012" "023" "04" "023" "03"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "023" "014" "03" "021" "04" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "023" "023" "04" "03" "023" "021"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "04" "023" "03" "04" "04" "04"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "03" "04" "023" "03" "04" "04"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "04" "03" "04" "014" "023"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "03" "024" "04" "03" "04" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "023" "04" "04" "04" "03" "012"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "012" "024" "021" "012" "014" "04"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "023" "013" "023" "021" "014" "04"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "04" "011" "04" "0154" "022" "04"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "013" "04" "024" "04" "021" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "04" "04" "0153" "04"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "04" "04" "04" "04" "023" "023"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "04" "012" "03" "014" "04" "012"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04" "03" "03" "04" "024" "03"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04" "011" "04" "023" "021" "0153"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "03" "023" "03" "04" "04" "04"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "03" "03" "04" "023" "024" "021"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "023" "0154" "021" "024" "04"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "04" "021" "023" "022" "011" "04"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "04" "04" "04" "023" "024" "023"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "04" "03" "013" "03" "011"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "03" "04" "023" "024" "011" "023"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "012" "03" "011" "023" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "013" "024" "023" "03" "04" "011"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "03" "03" "04" "011"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "011" "022" "04" "04" "021" "023"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "03" "0152" "04" "011" "022" "011"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04" "04" "023" "04" "022" "04"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "03" "03" "021" "023" "024" "03"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "04" "022" "021" "04" "011"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "04" "024" "011" "024" "011" "03"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "023" "0152" "024" "021" "03"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "023" "04" "03" "024" "021"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "021" "04" "013" "04"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "03" "023" "04" "03" "04" "013"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "04" "024" "021" "021" "04" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "04" "04" "04" "022" "012"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "021" "022" "024" "03" "023" "011"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04" "03" "024" "021" "021" "04"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04" "04" "012" "014" "014" "021"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "021" "011" "03" "04" "024" "011"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "023" "022" "024" "021" "021" "04"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "023" "021" "03" "04" "011" "03"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "021" "04" "04" "012" "03" "04"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "04" "023" "023" "024" "03" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "04" "04" "0152" "022" "03" "0154"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "03" "011" "0154" "024" "024" "021"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "03" "04" "04" "04" "023" "04"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04" "04" "012" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "03" "024" "04" "03" "04" "04"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "023" "012" "022" "021" "04" "04"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "011" "03" "04" "04" "04" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "023" "03" "03" "04" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "04" "024" "024" "0152" "024" "03"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "04" "04" "03" "023" "03" "04"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "04" "04" "04" "04" "024" "03"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "023" "011" "013" "04" "04" "021"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04" "04" "012" "04" "04" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "0152" "0153" "04" "012" "024" "03"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "04" "024" "011" "023" "03" "04"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "03" "021" "04" "013" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "04" "023" "03" "023" "024" "04"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04" "024" "014" "021" "03" "04"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "013" "03" "04" "04" "011" "011"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "023" "023" "03" "022" "03" "013"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "03" "03" "011" "04" "021" "012"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "04" "013" "03" "03" "04" "023"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "021" "04" "03" "022" "04" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "021" "04" "023" "011" "04" "03"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "013" "021" "04" "013" "011" "0152"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "023" "011" "04" "022" "023" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "023" "04" "022" "024" "024" "011"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "023" "04" "03" "03" "04" "04"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "04" "024" "022" "04"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "03" "03" "04" "04" "04" "04"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "03" "04" "04" "04" "04" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "04" "0152" "04" "014" "03"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "03" "024" "014" "04" "021" "04"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "04" "03" "04" "04" "021" "04"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "021" "021" "023" "012" "023" "03"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "03" "04" "021" "04" "024" "03"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "04" "03" "03" "04" "024" "04"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "012" "04" "022" "04" "04" "021"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "023" "013" "011" "023" "04" "03"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "04" "04" "024" "023" "021" "04"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "011" "04" "021" "04" "022" "021"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "03" "04" "04" "011" "04" "023"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04" "021" "04" "013" "04" "021"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "03" "023" "04" "04" "021" "013"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "021" "0154" "023" "04" "022" "023"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "023" "0152" "021" "04" "03" "012"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "04" "04" "023" "03" "03" "023"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04" "014" "04" "04" "024" "03"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "04" "022" "04" "04" "012"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "04" "0154" "024" "023" "03"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "024" "03" "03" "021" "023"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "04" "022" "04" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "011" "024" "023" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "04" "03" "03" "0151" "022" "021"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "021" "03" "023" "03" "023" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "04" "04" "04" "012"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04" "023" "04" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04" "022" "04" "012" "04" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "03" "04" "014" "04" "024" "013"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "021" "04" "03" "024" "021" "021"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "011" "022" "03" "011" "03" "021"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "04" "023" "012" "021" "04" "03"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "03" "03" "04" "023" "04" "04"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "023" "04" "03" "03" "013" "03"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 22951))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "04" "04" "04" "021" "04" "03"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04" "012" "04" "04" "04" "04"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "011" "04" "021" "023" "021" "04"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "014" "021" "023" "04" "024" "04"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "03" "023" "04" "03" "04" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "021" "024" "023" "022" "03" "03"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "011" "021" "03" "012" "04" "011"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "023" "04" "024" "022" "04" "04"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "023" "04" "04" "04" "03" "04"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04" "04" "024" "04" "04" "04"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04" "04" "023" "03" "04" "04"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04" "021" "024" "023" "04" "04"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "015" "03" "04" "022" "013" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "03" "03" "04" "04" "023" "04"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "04" "011" "024" "024" "015" "04"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "011" "03" "022" "023" "023" "021"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "04" "014" "024" "024" "023" "023"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "04" "021" "013" "021" "024" "023"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04" "03" "012" "04" "021" "03"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "023" "04" "023" "03" "023" "04"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "04" "024" "011" "04" "04"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "012" "03" "023" "03" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04" "03" "03" "024" "03" "021"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "021" "015" "011" "03" "013" "012"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "04" "011" "024" "013" "011" "04"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "04" "011" "024" "04" "04" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "04" "021" "014" "04" "011" "021"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "04" "011" "03" "03" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "04" "04" "015" "04" "04" "04"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "04" "04" "04" "015" "011"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "03" "023" "012" "04" "04" "012"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04" "04" "03" "024" "011" "021"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "021" "023" "011" "04" "03" "04"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "04" "024" "022" "04" "04" "04"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "03" "024" "013" "04" "04" "023"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "015" "023" "021" "03" "04" "014"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "013" "021" "03" "013" "04" "03"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "012" "023" "04" "023" "03"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "023" "014" "03" "021" "04" "014"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "023" "023" "04" "03" "023" "021"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "04" "023" "03" "04" "04" "04"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "03" "04" "023" "03" "04" "04"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "014" "04" "03" "04" "014" "023"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "03" "024" "04" "03" "04" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "023" "04" "04" "04" "03" "012"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "012" "024" "021" "012" "014" "04"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "023" "013" "023" "021" "014" "04"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "04" "011" "04" "015" "022" "04"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "013" "04" "024" "04" "021" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "04" "04" "015" "04"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "04" "04" "04" "04" "023" "023"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "04" "012" "03" "014" "04" "012"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04" "03" "03" "04" "024" "03"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04" "011" "04" "023" "021" "015"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "03" "023" "03" "04" "04" "04"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "03" "03" "04" "023" "024" "021"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "023" "015" "021" "024" "04"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "04" "021" "023" "022" "011" "04"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "04" "04" "04" "023" "024" "023"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "04" "03" "013" "03" "011"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "03" "04" "023" "024" "011" "023"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "012" "03" "011" "023" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "013" "024" "023" "03" "04" "011"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "03" "03" "04" "011"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "011" "022" "04" "04" "021" "023"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "03" "015" "04" "011" "022" "011"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04" "04" "023" "04" "022" "04"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "03" "03" "021" "023" "024" "03"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "04" "022" "021" "04" "011"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "04" "024" "011" "024" "011" "03"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "014" "023" "015" "024" "021" "03"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "023" "04" "03" "024" "021"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "014" "021" "04" "013" "04"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "03" "023" "04" "03" "04" "013"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "04" "024" "021" "021" "04" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "04" "04" "04" "022" "012"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "021" "022" "024" "03" "023" "011"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04" "03" "024" "021" "021" "04"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04" "04" "012" "014" "014" "021"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "021" "011" "03" "04" "024" "011"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "023" "022" "024" "021" "021" "04"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "023" "021" "03" "04" "011" "03"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "021" "04" "04" "012" "03" "04"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "04" "023" "023" "024" "03" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "04" "04" "015" "022" "03" "015"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "03" "011" "015" "024" "024" "021"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "03" "04" "04" "04" "023" "04"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04" "04" "012" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "03" "024" "04" "03" "04" "04"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "023" "012" "022" "021" "04" "04"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "011" "03" "04" "04" "04" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "023" "03" "03" "04" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "04" "024" "024" "015" "024" "03"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "04" "04" "03" "023" "03" "04"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "04" "04" "04" "04" "024" "03"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "023" "011" "013" "04" "04" "021"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04" "04" "012" "04" "04" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "015" "015" "04" "012" "024" "03"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "04" "024" "011" "023" "03" "04"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "03" "021" "04" "013" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "04" "023" "03" "023" "024" "04"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04" "024" "014" "021" "03" "04"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "013" "03" "04" "04" "011" "011"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "023" "023" "03" "022" "03" "013"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "03" "03" "011" "04" "021" "012"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "04" "013" "03" "03" "04" "023"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "021" "04" "03" "022" "04" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "021" "04" "023" "011" "04" "03"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "013" "021" "04" "013" "011" "015"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "023" "011" "04" "022" "023" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "023" "04" "022" "024" "024" "011"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "023" "04" "03" "03" "04" "04"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "04" "024" "022" "04"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "03" "03" "04" "04" "04" "04"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "03" "04" "04" "04" "04" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "04" "015" "04" "014" "03"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "03" "024" "014" "04" "021" "04"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "04" "03" "04" "04" "021" "04"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "021" "021" "023" "012" "023" "03"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "03" "04" "021" "04" "024" "03"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "04" "03" "03" "04" "024" "04"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "012" "04" "022" "04" "04" "021"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "023" "013" "011" "023" "04" "03"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "04" "04" "024" "023" "021" "04"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "011" "04" "021" "04" "022" "021"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "03" "04" "04" "011" "04" "023"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04" "021" "04" "013" "04" "021"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "03" "023" "04" "04" "021" "013"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "021" "015" "023" "04" "022" "023"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "023" "015" "021" "04" "03" "012"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "04" "04" "023" "03" "03" "023"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04" "014" "04" "04" "024" "03"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "014" "04" "022" "04" "04" "012"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "04" "015" "024" "023" "03"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "014" "024" "03" "03" "021" "023"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "04" "022" "04" "014" "014"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "014" "011" "024" "023" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "04" "03" "03" "015" "022" "021"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "021" "03" "023" "03" "023" "014"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "04" "04" "04" "012"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04" "023" "04" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04" "022" "04" "012" "04" "014"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "03" "04" "014" "04" "024" "013"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "021" "04" "03" "024" "021" "021"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "011" "022" "03" "011" "03" "021"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "04" "023" "012" "021" "04" "03"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "03" "03" "04" "023" "04" "04"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "023" "04" "03" "03" "013" "03"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 23761))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "04" "04" "04" "021" "04" "03"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04" "01" "04" "04" "04" "04"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "01" "04" "021" "023" "021" "04"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "01" "021" "023" "04" "024" "04"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "03" "023" "04" "03" "04" "022"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "021" "024" "023" "022" "03" "03"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "01" "021" "03" "01" "04" "01"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "023" "04" "024" "022" "04" "04"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "023" "04" "04" "04" "03" "04"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04" "04" "024" "04" "04" "04"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04" "04" "023" "03" "04" "04"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04" "021" "024" "023" "04" "04"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "01" "03" "04" "022" "01" "022"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "03" "03" "04" "04" "023" "04"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "04" "01" "024" "024" "01" "04"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "01" "03" "022" "023" "023" "021"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "04" "01" "024" "024" "023" "023"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "04" "021" "01" "021" "024" "023"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04" "03" "01" "04" "021" "03"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "023" "04" "023" "03" "023" "04"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "024" "04" "024" "01" "04" "04"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "022" "01" "03" "023" "03" "024"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04" "03" "03" "024" "03" "021"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "021" "01" "01" "03" "01" "01"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "04" "01" "024" "01" "01" "04"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "04" "01" "024" "04" "04" "022"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "04" "021" "01" "04" "01" "021"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "024" "04" "01" "03" "03" "022"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "04" "04" "01" "04" "04" "04"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "024" "04" "04" "04" "01" "01"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "03" "023" "01" "04" "04" "01"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04" "04" "03" "024" "01" "021"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "021" "023" "01" "04" "03" "04"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "04" "024" "022" "04" "04" "04"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "03" "024" "01" "04" "04" "023"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "01" "023" "021" "03" "04" "01"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "01" "021" "03" "01" "04" "03"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "022" "01" "023" "04" "023" "03"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "023" "01" "03" "021" "04" "01"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "023" "023" "04" "03" "023" "021"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "04" "023" "03" "04" "04" "04"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "03" "04" "023" "03" "04" "04"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "01" "04" "03" "04" "01" "023"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "03" "024" "04" "03" "04" "024"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "023" "04" "04" "04" "03" "01"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "01" "024" "021" "01" "01" "04"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "023" "01" "023" "021" "01" "04"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "04" "01" "04" "01" "022" "04"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "01" "04" "024" "04" "021" "024"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "024" "024" "04" "04" "01" "04"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "04" "04" "04" "04" "023" "023"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "04" "01" "03" "01" "04" "01"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04" "03" "03" "04" "024" "03"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04" "01" "04" "023" "021" "01"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "03" "023" "03" "04" "04" "04"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "03" "03" "04" "023" "024" "021"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "022" "023" "01" "021" "024" "04"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "04" "021" "023" "022" "01" "04"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "04" "04" "04" "023" "024" "023"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "022" "04" "03" "01" "03" "01"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "03" "04" "023" "024" "01" "023"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "024" "01" "03" "01" "023" "024"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "01" "024" "023" "03" "04" "01"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "024" "024" "03" "03" "04" "01"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "01" "022" "04" "04" "021" "023"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "03" "01" "04" "01" "022" "01"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04" "04" "023" "04" "022" "04"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "03" "03" "021" "023" "024" "03"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "024" "04" "022" "021" "04" "01"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "04" "024" "01" "024" "01" "03"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "01" "023" "01" "024" "021" "03"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "022" "023" "04" "03" "024" "021"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "022" "01" "021" "04" "01" "04"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "03" "023" "04" "03" "04" "01"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "04" "024" "021" "021" "04" "022"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "022" "04" "04" "04" "022" "01"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "021" "022" "024" "03" "023" "01"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04" "03" "024" "021" "021" "04"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04" "04" "01" "01" "01" "021"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "021" "01" "03" "04" "024" "01"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "023" "022" "024" "021" "021" "04"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "023" "021" "03" "04" "01" "03"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "021" "04" "04" "01" "03" "04"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "04" "023" "023" "024" "03" "022"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "04" "04" "01" "022" "03" "01"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "03" "01" "01" "024" "024" "021"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "03" "04" "04" "04" "023" "04"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04" "04" "01" "022" "022" "024"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "03" "024" "04" "03" "04" "04"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "023" "01" "022" "021" "04" "04"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "01" "03" "04" "04" "04" "024"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "023" "03" "03" "04" "022" "024"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "04" "024" "024" "01" "024" "03"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "04" "04" "03" "023" "03" "04"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "04" "04" "04" "04" "024" "03"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "023" "01" "01" "04" "04" "021"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04" "04" "01" "04" "04" "022"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "01" "01" "04" "01" "024" "03"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "04" "024" "01" "023" "03" "04"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "03" "021" "04" "01" "024" "022"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "04" "023" "03" "023" "024" "04"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04" "024" "01" "021" "03" "04"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "01" "03" "04" "04" "01" "01"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "023" "023" "03" "022" "03" "01"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "03" "03" "01" "04" "021" "01"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "04" "01" "03" "03" "04" "023"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "021" "04" "03" "022" "04" "022"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "021" "04" "023" "01" "04" "03"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "01" "021" "04" "01" "01" "01"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "023" "01" "04" "022" "023" "024"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "023" "04" "022" "024" "024" "01"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "023" "04" "03" "03" "04" "04"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "022" "024" "04" "024" "022" "04"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "03" "03" "04" "04" "04" "04"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "03" "04" "04" "04" "04" "024"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "022" "04" "01" "04" "01" "03"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "03" "024" "01" "04" "021" "04"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "04" "03" "04" "04" "021" "04"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "021" "021" "023" "01" "023" "03"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "03" "04" "021" "04" "024" "03"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "04" "03" "03" "04" "024" "04"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "01" "04" "022" "04" "04" "021"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "023" "01" "01" "023" "04" "03"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "04" "04" "024" "023" "021" "04"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "01" "04" "021" "04" "022" "021"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "03" "04" "04" "01" "04" "023"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04" "021" "04" "01" "04" "021"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "03" "023" "04" "04" "021" "01"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "021" "01" "023" "04" "022" "023"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "023" "01" "021" "04" "03" "01"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "04" "04" "023" "03" "03" "023"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04" "01" "04" "04" "024" "03"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "01" "04" "022" "04" "04" "01"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "024" "04" "01" "024" "023" "03"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "01" "024" "03" "03" "021" "023"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "024" "04" "022" "04" "01" "01"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "01" "01" "024" "023" "024" "022"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "04" "03" "03" "01" "022" "021"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "021" "03" "023" "03" "023" "01"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "024" "022" "04" "04" "04" "01"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04" "023" "04" "022" "022" "022"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04" "022" "04" "01" "04" "01"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "03" "04" "01" "04" "024" "01"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "021" "04" "03" "024" "021" "021"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "01" "022" "03" "01" "03" "021"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "04" "023" "01" "021" "04" "03"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "03" "03" "04" "023" "04" "04"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "023" "04" "03" "03" "01" "03"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 32783))
#> TCGA.OL.A66H.01 TCGA.3C.AALK.01 TCGA.AC.A5EH.01 TCGA.EW.A2FW.01 TCGA.E9.A1R0.01 TCGA.AR.A1AJ.01
#> "04" "04" "04" "02" "04" "03"
#> TCGA.AC.A62Y.01 TCGA.E9.A1QZ.01 TCGA.E9.A1R2.01 TCGA.E9.A3X8.01 TCGA.AR.A255.01 TCGA.E2.A10B.01
#> "04" "01" "04" "04" "04" "04"
#> TCGA.E9.A1N4.11 TCGA.AO.A0JD.01 TCGA.D8.A1JD.01 TCGA.D8.A1XA.01 TCGA.AO.A1KQ.01 TCGA.A8.A0A6.01
#> "01" "04" "02" "02" "02" "04"
#> TCGA.BH.A1F2.11 TCGA.A7.A3RF.01 TCGA.A2.A0SW.01 TCGA.A7.A3IY.01 TCGA.GM.A2D9.01 TCGA.D8.A3Z5.01
#> "01" "02" "02" "04" "02" "04"
#> TCGA.E9.A1ND.01 TCGA.EW.A1P5.01 TCGA.E9.A1RD.01 TCGA.AR.A1AQ.01 TCGA.LD.A66U.01 TCGA.BH.A1EN.01
#> "03" "02" "04" "03" "04" "02"
#> TCGA.BH.A1FN.01 TCGA.EW.A1PD.01 TCGA.E9.A1N5.01 TCGA.D8.A1J8.01 TCGA.E9.A3QA.01 TCGA.S3.AA15.01
#> "02" "02" "02" "02" "03" "03"
#> TCGA.BH.A0DP.11 TCGA.BH.A0H0.01 TCGA.A2.A3XX.01 TCGA.AC.A2FB.01 TCGA.AC.A3QP.01 TCGA.BH.A0BF.11
#> "01" "02" "03" "01" "04" "01"
#> TCGA.A2.A0YC.01 TCGA.GM.A2DK.01 TCGA.GM.A2DC.01 TCGA.AR.A24N.01 TCGA.E2.A1B0.01 TCGA.BH.A1EY.01
#> "02" "04" "02" "02" "04" "04"
#> TCGA.EW.A6S9.01 TCGA.AC.A8OS.01 TCGA.GM.A2DN.01 TCGA.AO.A03M.01 TCGA.A2.A3XT.01 TCGA.A2.A4RW.01
#> "02" "04" "04" "04" "03" "04"
#> TCGA.AC.A6IV.01 TCGA.LL.A7SZ.01 TCGA.A1.A0SJ.01 TCGA.AR.A2LJ.01 TCGA.AQ.A1H3.01 TCGA.D8.A1JB.01
#> "04" "04" "02" "04" "04" "04"
#> TCGA.BH.A0BC.01 TCGA.BH.A1EW.01 TCGA.BH.A1FG.01 TCGA.EW.A1P7.01 TCGA.GM.A2DH.01 TCGA.D8.A27P.01
#> "04" "04" "02" "03" "04" "04"
#> TCGA.EW.A2FS.01 TCGA.E2.A1IL.01 TCGA.A7.A3IZ.01 TCGA.E2.A570.01 TCGA.OL.A66J.01 TCGA.AR.A2LO.01
#> "04" "02" "02" "02" "04" "04"
#> TCGA.BH.A1FC.11 TCGA.E9.A5FL.01 TCGA.BH.A201.01 TCGA.LL.A5YM.01 TCGA.BH.A0H9.11 TCGA.AC.A4ZE.01
#> "01" "03" "04" "02" "01" "02"
#> TCGA.A2.A0T2.01 TCGA.AR.A0TP.01 TCGA.S3.AA14.01 TCGA.B6.A0RS.01 TCGA.EW.A1P0.01 TCGA.AR.A1AT.01
#> "03" "03" "04" "04" "02" "04"
#> TCGA.A2.A1G0.01 TCGA.BH.A208.11 TCGA.AR.A24H.01 TCGA.D8.A1XV.01 TCGA.AR.A2LQ.01 TCGA.AC.A3OD.01
#> "04" "01" "02" "02" "01" "04"
#> TCGA.BH.A0DI.11 TCGA.AR.A0TU.01 TCGA.AN.A0XV.01 TCGA.A2.A0YT.01 TCGA.BH.A0B5.01 TCGA.D8.A1JI.01
#> "01" "03" "02" "02" "02" "02"
#> TCGA.UU.A93S.01 TCGA.E9.A1N6.11 TCGA.E9.A1R6.01 TCGA.D8.A1XZ.01 TCGA.BH.A0B8.01 TCGA.LL.A6FQ.01
#> "04" "01" "02" "02" "02" "02"
#> TCGA.XX.A89A.01 TCGA.EW.A1OY.01 TCGA.A7.A13G.11 TCGA.B6.A0RP.01 TCGA.LL.A9Q3.01 TCGA.A1.A0SQ.01
#> "04" "02" "01" "02" "02" "02"
#> TCGA.AR.A5QM.01 TCGA.A7.A26I.01 TCGA.E2.A1B6.01 TCGA.PE.A5DE.01 TCGA.E9.A1RB.01 TCGA.A2.A0ST.01
#> "04" "03" "01" "04" "02" "03"
#> TCGA.B6.A0RO.01 TCGA.AC.A23H.01 TCGA.AC.A2BM.01 TCGA.BH.A0WA.01 TCGA.EW.A1J6.01 TCGA.D8.A27V.01
#> "02" "04" "02" "03" "02" "04"
#> TCGA.B6.A40C.01 TCGA.A2.A1FZ.01 TCGA.A7.A26H.01 TCGA.BH.A0H7.11 TCGA.BH.A0BA.01 TCGA.BH.AB28.01
#> "02" "04" "02" "01" "04" "04"
#> TCGA.E2.A2P6.01 TCGA.B6.A0RT.01 TCGA.AR.A1AY.01 TCGA.A2.A25C.01 TCGA.S3.AA10.01 TCGA.OL.A5DA.01
#> "02" "01" "03" "02" "03" "02"
#> TCGA.D8.A27R.01 TCGA.EW.A6SB.01 TCGA.A7.A5ZV.01 TCGA.LL.A50Y.01 TCGA.B6.A0WX.01 TCGA.LL.A442.01
#> "04" "03" "03" "02" "03" "02"
#> TCGA.C8.A26Z.01 TCGA.BH.A1FU.01 TCGA.AO.A1KO.01 TCGA.BH.A0E0.01 TCGA.A7.A0DB.11 TCGA.E9.A2JT.01
#> "02" "01" "01" "03" "01" "01"
#> TCGA.OL.A5D6.01 TCGA.BH.A0AU.11 TCGA.BH.A1FJ.01 TCGA.E9.A1RC.11 TCGA.E9.A1NE.11 TCGA.E2.A3DX.01
#> "04" "01" "02" "01" "01" "04"
#> TCGA.A1.A0SE.01 TCGA.BH.A1FM.11 TCGA.E9.A3HO.01 TCGA.D8.A1XT.01 TCGA.C8.A1HI.01 TCGA.E9.A1NA.01
#> "04" "01" "02" "04" "04" "02"
#> TCGA.A2.A0T4.01 TCGA.BH.A0BS.01 TCGA.BH.A203.11 TCGA.MS.A51U.01 TCGA.E2.A1B5.11 TCGA.B6.A0WT.01
#> "04" "02" "01" "04" "01" "02"
#> TCGA.B6.A0RN.01 TCGA.D8.A1Y2.01 TCGA.PL.A8LY.01 TCGA.B6.A0RU.01 TCGA.EW.A1PH.01 TCGA.D8.A1XJ.01
#> "02" "04" "01" "03" "03" "02"
#> TCGA.BH.A0DG.01 TCGA.C8.A3M7.01 TCGA.BH.A1EW.11 TCGA.E2.A1L6.01 TCGA.D8.A1XY.01 TCGA.D8.A27G.01
#> "04" "04" "01" "04" "04" "04"
#> TCGA.E2.A109.01 TCGA.AR.A1AM.01 TCGA.4H.AAAK.01 TCGA.AC.A5XS.01 TCGA.AC.A5EI.01 TCGA.BH.A1EU.11
#> "02" "04" "04" "04" "01" "01"
#> TCGA.A2.A3XS.01 TCGA.3C.AALI.01 TCGA.OL.A5RY.01 TCGA.E2.A1IF.01 TCGA.AC.A2FO.01 TCGA.BH.A209.01
#> "03" "02" "01" "04" "04" "01"
#> TCGA.AR.A24S.01 TCGA.A2.A3KD.01 TCGA.B6.A1KF.01 TCGA.BH.A1FL.01 TCGA.BH.A0B3.11 TCGA.E2.A15K.01
#> "04" "04" "03" "02" "01" "02"
#> TCGA.E2.A15K.06 TCGA.E9.A1NI.01 TCGA.AC.A2FK.01 TCGA.E9.A226.01 TCGA.E2.A1AZ.01 TCGA.D8.A1X8.01
#> "02" "02" "01" "04" "03" "04"
#> TCGA.A2.A0T5.01 TCGA.AO.A12G.01 TCGA.C8.A1HO.01 TCGA.LD.A74U.01 TCGA.AR.A0TQ.01 TCGA.AO.A0JE.01
#> "04" "02" "02" "04" "04" "04"
#> TCGA.AC.A62X.01 TCGA.AN.A0XR.01 TCGA.E9.A1RF.11 TCGA.E9.A228.01 TCGA.E9.A1RA.01 TCGA.BH.A0HA.01
#> "03" "02" "01" "04" "04" "02"
#> TCGA.E2.A1L7.11 TCGA.D8.A1XS.01 TCGA.OL.A6VR.01 TCGA.E9.A22G.01 TCGA.LL.A740.01 TCGA.AC.A2FG.11
#> "01" "02" "02" "03" "04" "01"
#> TCGA.E9.A1RI.11 TCGA.AR.A1AS.01 TCGA.D8.A27M.01 TCGA.E9.A1N8.11 TCGA.BH.A0BZ.01 TCGA.BH.A0RX.01
#> "01" "02" "03" "01" "04" "03"
#> TCGA.S3.A6ZG.01 TCGA.AR.A1AW.01 TCGA.AN.A0XP.01 TCGA.EW.A2FV.01 TCGA.D8.A1XD.01 TCGA.A2.A4S1.01
#> "02" "01" "02" "04" "02" "03"
#> TCGA.AR.A24M.01 TCGA.BH.A1FH.01 TCGA.D8.A1JM.01 TCGA.AC.A6NO.01 TCGA.BH.A0DV.01 TCGA.BH.A0AY.11
#> "02" "01" "03" "02" "04" "01"
#> TCGA.E2.A572.01 TCGA.BH.A1ES.01 TCGA.A2.A0YI.01 TCGA.AC.A2QJ.01 TCGA.EW.A1PE.01 TCGA.BH.A0H6.01
#> "02" "02" "04" "03" "02" "02"
#> TCGA.BH.A0BM.01 TCGA.A7.A2KD.01 TCGA.E2.A1II.01 TCGA.D8.A27I.01 TCGA.A2.A0YD.01 TCGA.BH.A0C0.01
#> "04" "02" "03" "04" "04" "04"
#> TCGA.B6.A3ZX.01 TCGA.E9.A1NG.01 TCGA.S3.A6ZH.01 TCGA.HN.A2NL.01 TCGA.EW.A1IW.01 TCGA.JL.A3YW.01
#> "03" "04" "02" "03" "04" "04"
#> TCGA.BH.A1F0.11 TCGA.AN.A0XN.01 TCGA.A1.A0SK.01 TCGA.E9.A6HE.01 TCGA.BH.A1FR.11 TCGA.BH.A1EX.01
#> "01" "04" "03" "04" "01" "02"
#> TCGA.LL.A441.01 TCGA.AO.A125.01 TCGA.C8.A26W.01 TCGA.A2.A0YM.01 TCGA.BH.A0DP.01 TCGA.UL.AAZ6.01
#> "03" "02" "04" "03" "04" "02"
#> TCGA.A2.A0CK.01 TCGA.AR.A2LN.01 TCGA.D8.A1JF.01 TCGA.OL.A6VQ.01 TCGA.LL.A5YP.01 TCGA.AR.A252.01
#> "02" "04" "04" "04" "03" "01"
#> TCGA.A2.A25F.01 TCGA.PE.A5DC.01 TCGA.EW.A6SC.01 TCGA.GM.A2DO.01 TCGA.E9.A1ND.11 TCGA.E2.A1LL.01
#> "01" "02" "02" "01" "01" "04"
#> TCGA.C8.A273.01 TCGA.E9.A1RD.11 TCGA.AR.A0U2.01 TCGA.C8.A1HL.01 TCGA.BH.A1FN.11 TCGA.BH.A0AU.01
#> "02" "01" "02" "02" "01" "04"
#> TCGA.A2.A0T1.01 TCGA.BH.A28O.01 TCGA.AR.A24W.01 TCGA.EW.A1P1.01 TCGA.E2.A9RU.01 TCGA.AR.A0TT.01
#> "04" "01" "04" "01" "02" "04"
#> TCGA.E2.A1IO.11 TCGA.AC.A3W6.01 TCGA.D8.A1JJ.01 TCGA.OL.A66P.01 TCGA.E2.A1B4.01 TCGA.B6.A1KC.01
#> "01" "04" "02" "04" "02" "02"
#> TCGA.E9.A5UP.01 TCGA.A2.A1G4.01 TCGA.AR.A24L.01 TCGA.BH.A0H3.01 TCGA.LL.A73Z.01 TCGA.EW.A1IZ.01
#> "02" "02" "04" "04" "01" "04"
#> TCGA.AO.A0JA.01 TCGA.AR.A0TX.01 TCGA.AO.A0JG.01 TCGA.OL.A66N.01 TCGA.A2.A1FV.01 TCGA.D8.A1XC.01
#> "04" "04" "04" "04" "02" "02"
#> TCGA.A7.A4SC.01 TCGA.AR.A2LH.01 TCGA.LL.A6FR.01 TCGA.A7.A13F.11 TCGA.GM.A2DB.01 TCGA.LL.A5YO.01
#> "04" "01" "03" "01" "04" "01"
#> TCGA.E9.A1N3.01 TCGA.PL.A8LV.01 TCGA.AO.A1KR.01 TCGA.AN.A0XL.01 TCGA.E2.A15J.01 TCGA.E9.A244.01
#> "04" "03" "03" "04" "02" "03"
#> TCGA.E9.A24A.01 TCGA.BH.A1EV.11 TCGA.GM.A2DL.01 TCGA.S3.AA11.01 TCGA.AC.A3QQ.01 TCGA.Z7.A8R5.01
#> "04" "01" "04" "02" "02" "01"
#> TCGA.B6.A400.01 TCGA.AQ.A54O.01 TCGA.BH.A1FC.01 TCGA.E9.A22B.01 TCGA.A2.A3XV.01 TCGA.AC.A6IX.06
#> "03" "02" "03" "04" "04" "04"
#> TCGA.BH.A0B9.01 TCGA.BH.A18V.06 TCGA.AC.A6IX.01 TCGA.D8.A1JT.01 TCGA.AR.A2LL.01 TCGA.D8.A1X7.01
#> "03" "03" "04" "02" "02" "02"
#> TCGA.E9.A247.01 TCGA.D8.A1X5.01 TCGA.AO.A03U.01 TCGA.A8.A075.01 TCGA.D8.A73X.01 TCGA.B6.A0WY.01
#> "02" "02" "01" "02" "02" "04"
#> TCGA.E9.A1R4.01 TCGA.E9.A3Q9.01 TCGA.BH.A0E1.01 TCGA.EW.A423.01 TCGA.BH.A1ES.11 TCGA.EW.A1J2.01
#> "04" "02" "02" "02" "01" "04"
#> TCGA.BH.A0GY.01 TCGA.W8.A86G.01 TCGA.A7.A5ZW.01 TCGA.E2.A106.01 TCGA.AR.A0TV.01 TCGA.E2.A56Z.01
#> "04" "04" "04" "02" "02" "02"
#> TCGA.AC.A2FM.01 TCGA.C8.A1HF.01 TCGA.C8.A27B.01 TCGA.E2.A15I.11 TCGA.A7.A13E.01 TCGA.A2.A1G6.01
#> "02" "04" "03" "01" "03" "01"
#> TCGA.B6.A402.01 TCGA.A2.A0T7.01 TCGA.A7.A0D9.01 TCGA.AC.A5XU.01 TCGA.BH.A0DH.11 TCGA.BH.A204.01
#> "03" "04" "02" "02" "01" "02"
#> TCGA.B6.A0WW.01 TCGA.A2.A3XZ.01 TCGA.AR.A1AI.01 TCGA.BH.A0BC.11 TCGA.D8.A1XL.01 TCGA.E9.A5UO.01
#> "02" "01" "03" "01" "02" "02"
#> TCGA.A7.A13E.11 TCGA.A2.A0SV.01 TCGA.OL.A5RZ.01 TCGA.E2.A1LS.01 TCGA.AO.A0JJ.01 TCGA.BH.A0BA.11
#> "01" "02" "02" "03" "04" "01"
#> TCGA.AR.A24R.01 TCGA.AO.A1KP.01 TCGA.D8.A1JL.01 TCGA.E2.A1LH.01 TCGA.B6.A0X7.01 TCGA.BH.A0DK.11
#> "02" "02" "03" "03" "04" "01"
#> TCGA.D8.A4Z1.01 TCGA.E9.A1RE.01 TCGA.OL.A5RV.01 TCGA.E2.A1BC.01 TCGA.GM.A2DM.01 TCGA.A2.A0YF.01
#> "01" "02" "04" "04" "02" "02"
#> TCGA.A2.A3Y0.01 TCGA.AC.A3YI.01 TCGA.E9.A22D.01 TCGA.BH.A0E0.11 TCGA.C8.A274.01 TCGA.BH.A0B2.11
#> "03" "01" "04" "01" "02" "01"
#> TCGA.A1.A0SF.01 TCGA.EW.A6SD.01 TCGA.C8.A1HM.01 TCGA.A7.A426.01 TCGA.E9.A1RC.01 TCGA.AR.A1AU.01
#> "04" "04" "02" "04" "02" "04"
#> TCGA.AO.A129.01 TCGA.A2.A4RX.01 TCGA.BH.A6R8.01 TCGA.BH.A1FM.01 TCGA.D8.A1JP.01 TCGA.E2.A1IP.01
#> "03" "03" "02" "02" "02" "03"
#> TCGA.AO.A0JM.01 TCGA.E9.A1N6.01 TCGA.BH.A0DS.01 TCGA.V7.A7HQ.01 TCGA.D8.A27L.01 TCGA.A2.A4RY.01
#> "02" "04" "02" "02" "04" "01"
#> TCGA.E9.A1NF.01 TCGA.EW.A1PA.01 TCGA.BH.A0BV.11 TCGA.AC.A3TM.01 TCGA.BH.A0DG.11 TCGA.D8.A27H.01
#> "04" "02" "01" "02" "01" "03"
#> TCGA.AC.A23H.11 TCGA.AR.A2LE.01 TCGA.EW.A1PG.01 TCGA.GM.A3NY.01 TCGA.BH.A5J0.01 TCGA.E9.A1NC.01
#> "01" "02" "01" "02" "02" "03"
#> TCGA.BH.A0HK.01 TCGA.AR.A24Z.01 TCGA.A1.A0SM.01 TCGA.AO.A124.01 TCGA.S3.A6ZF.01 TCGA.Z7.A8R6.01
#> "02" "02" "04" "03" "02" "02"
#> TCGA.OL.A66K.01 TCGA.E2.A1IF.11 TCGA.D8.A1JC.01 TCGA.LD.A7W5.01 TCGA.BH.A209.11 TCGA.E2.A1LA.01
#> "02" "01" "02" "04" "01" "04"
#> TCGA.AR.A256.01 TCGA.JL.A3YX.01 TCGA.BH.A42V.01 TCGA.EW.A1OW.01 TCGA.E9.A5FK.01 TCGA.E9.A1R7.11
#> "03" "02" "04" "03" "04" "01"
#> TCGA.D8.A1XB.01 TCGA.AN.A0XO.01 TCGA.BH.A0DQ.01 TCGA.B6.A2IU.01 TCGA.E9.A227.01 TCGA.AR.A250.01
#> "04" "02" "02" "02" "04" "02"
#> TCGA.OL.A5D8.01 TCGA.A2.A0YL.01 TCGA.A7.A5ZX.01 TCGA.D8.A1JG.01 TCGA.AQ.A04H.01 TCGA.AR.A5QQ.01
#> "02" "04" "04" "04" "02" "01"
#> TCGA.D8.A1XG.01 TCGA.AR.A0TZ.01 TCGA.AR.A0U3.01 TCGA.A2.A0YE.01 TCGA.BH.A0HN.01 TCGA.E2.A1LB.11
#> "02" "02" "02" "03" "02" "01"
#> TCGA.AO.A0JF.01 TCGA.A2.A0T0.01 TCGA.EW.A1OX.01 TCGA.AR.A24V.01 TCGA.AN.A0XS.01 TCGA.C8.A8HQ.01
#> "04" "03" "02" "02" "02" "04"
#> TCGA.AC.A2B8.01 TCGA.A2.A4S3.01 TCGA.A2.A0CR.01 TCGA.BH.A1FH.11 TCGA.BH.A1FJ.11 TCGA.LL.A6FP.01
#> "04" "04" "01" "01" "01" "02"
#> TCGA.E2.A1L8.01 TCGA.BH.A0HK.11 TCGA.AC.A2QH.01 TCGA.A2.A0CO.01 TCGA.A2.A1FW.01 TCGA.BH.A0BM.11
#> "02" "01" "03" "04" "02" "01"
#> TCGA.AC.A62V.01 TCGA.E2.A576.01 TCGA.GM.A3NW.01 TCGA.A7.A4SB.01 TCGA.E9.A245.01 TCGA.BH.A0AZ.01
#> "02" "02" "02" "02" "02" "04"
#> TCGA.AO.A126.01 TCGA.AC.A8OR.01 TCGA.E2.A573.01 TCGA.E2.A1LE.01 TCGA.BH.A0E1.11 TCGA.OL.A6VO.01
#> "02" "02" "03" "04" "01" "03"
#> TCGA.A7.A4SF.01 TCGA.A2.A0YH.01 TCGA.LL.A5YN.01 TCGA.AR.A1AO.01 TCGA.A2.A3XU.01 TCGA.AC.A23G.01
#> "02" "04" "04" "01" "03" "04"
#> TCGA.GM.A3XN.01 TCGA.A7.A26J.01 TCGA.A2.A25B.01 TCGA.D8.A27W.01 TCGA.GM.A3XL.01 TCGA.E9.A2JS.01
#> "04" "02" "02" "02" "03" "02"
#> TCGA.C8.A275.01 TCGA.E2.A1IK.01 TCGA.BH.A1FB.01 TCGA.C8.A3M8.01 TCGA.AN.A0XU.01 TCGA.A2.A3XW.01
#> "04" "04" "01" "02" "03" "01"
#> TCGA.A7.A6VV.01 TCGA.BH.A1FE.11 TCGA.A7.A0DC.11 TCGA.D8.A1XU.01 TCGA.BH.A1ES.06 TCGA.D8.A1X6.01
#> "03" "01" "01" "02" "02" "02"
#> TCGA.EW.A3U0.01 TCGA.AQ.A7U7.01 TCGA.A1.A0SI.01 TCGA.A2.A25A.01 TCGA.PL.A8LX.01 TCGA.E9.A1RH.01
#> "03" "04" "04" "04" "02" "04"
#> TCGA.AO.A12E.01 TCGA.A7.A13H.01 TCGA.AO.A0JC.01 TCGA.EW.A6SA.01 TCGA.E9.A1R5.01 TCGA.E9.A54Y.01
#> "04" "04" "01" "02" "02" "02"
#> TCGA.E9.A243.01 TCGA.AC.A3TN.01 TCGA.E2.A1IO.01 TCGA.OL.A5S0.01 TCGA.C8.A26Y.01 TCGA.A2.A25D.01
#> "03" "02" "04" "03" "04" "04"
#> TCGA.EW.A1J3.01 TCGA.A2.A0EP.01 TCGA.BH.A1F8.01 TCGA.B6.A0X5.01 TCGA.AN.A0XW.01 TCGA.BH.A0AW.01
#> "02" "01" "02" "02" "04" "04"
#> TCGA.BH.A0BJ.11 TCGA.D8.A27F.01 TCGA.BH.A0B6.01 TCGA.E9.A229.01 TCGA.D8.A1JK.01 TCGA.AQ.A04L.01
#> "01" "03" "04" "04" "04" "02"
#> TCGA.B6.A0WV.01 TCGA.E2.A1LI.01 TCGA.A7.A26F.01 TCGA.GM.A5PX.01 TCGA.BH.A1FD.01 TCGA.A7.A13F.01
#> "02" "03" "03" "04" "02" "02"
#> TCGA.AR.A5QN.01 TCGA.E2.A2P5.01 TCGA.AO.A1KS.01 TCGA.BH.A42U.01 TCGA.BH.A0DD.01 TCGA.B6.A0RE.01
#> "04" "02" "02" "01" "02" "03"
#> TCGA.BH.A208.01 TCGA.EW.A1IX.01 TCGA.BH.A1F6.01 TCGA.BH.A0HX.01 TCGA.E2.A14N.01 TCGA.A2.A259.01
#> "04" "04" "03" "02" "03" "04"
#> TCGA.GM.A2DD.01 TCGA.E2.A1B1.01 TCGA.D8.A73U.01 TCGA.D8.A27N.01 TCGA.D8.A1X9.01 TCGA.OL.A5RW.01
#> "04" "04" "04" "04" "02" "03"
#> TCGA.AR.A0TR.01 TCGA.BH.A1F5.11 TCGA.BH.A1EO.11 TCGA.E9.A22E.01 TCGA.OL.A5RX.01 TCGA.A7.A0DC.01
#> "02" "01" "01" "04" "04" "02"
#> TCGA.D8.A1XO.01 TCGA.AC.A23C.01 TCGA.E9.A1NE.01 TCGA.A7.A56D.01 TCGA.A1.A0SH.01 TCGA.C8.A9FZ.01
#> "04" "04" "01" "04" "04" "02"
#> TCGA.C8.A8HR.01 TCGA.BH.A6R9.01 TCGA.AR.A5QP.01 TCGA.C8.A8HP.01 TCGA.AR.A24X.01 TCGA.A1.A0SB.01
#> "01" "01" "04" "01" "02" "03"
#> TCGA.D8.A1Y0.01 TCGA.BH.A0GZ.01 TCGA.AC.A2FM.11 TCGA.B6.A0RM.01 TCGA.AR.A2LR.01 TCGA.BH.A2L8.01
#> "04" "02" "01" "02" "03" "04"
#> TCGA.AR.A251.01 TCGA.AO.A12B.01 TCGA.BH.A202.01 TCGA.A7.A0D9.11 TCGA.BH.A0DH.01 TCGA.D8.A1JN.01
#> "03" "02" "04" "01" "02" "02"
#> TCGA.EW.A1OV.01 TCGA.E2.A1IE.01 TCGA.AR.A1AR.01 TCGA.EW.A1P3.01 TCGA.BH.A8FY.01 TCGA.A1.A0SN.01
#> "04" "02" "03" "02" "02" "04"
#> TCGA.E9.A295.01 TCGA.AO.A1KT.01 TCGA.AC.A2FB.11 TCGA.E2.A1IU.01 TCGA.AO.A0JL.01 TCGA.AC.A8OP.01
#> "04" "02" "01" "02" "03" "04"
#> TCGA.E2.A1LS.11 TCGA.EW.A1P8.01 TCGA.GI.A2C8.01 TCGA.AR.A24P.01 TCGA.BH.A0BT.11 TCGA.BH.A0C0.11
#> "01" "03" "04" "04" "01" "01"
#> TCGA.E9.A22H.01 TCGA.D8.A3Z6.01 TCGA.AR.A0U4.01 TCGA.AR.A2LK.01 TCGA.B6.A409.01 TCGA.E2.A1BC.11
#> "02" "02" "03" "02" "03" "01"
#> TCGA.B6.A0X1.01 TCGA.A2.A0SX.01 TCGA.BH.A0C3.11 TCGA.BH.A0B2.01 TCGA.B6.A0RI.01 TCGA.E9.A248.01
#> "03" "03" "01" "04" "02" "01"
#> TCGA.A2.A0SU.01 TCGA.BH.A204.11 TCGA.EW.A1P4.01 TCGA.AO.A128.01 TCGA.AR.A24T.01 TCGA.A8.A08O.01
#> "04" "01" "03" "03" "04" "02"
#> TCGA.EW.A1P6.01 TCGA.AC.A2FE.01 TCGA.GM.A2DF.01 TCGA.D8.A1XF.01 TCGA.E9.A1N4.01 TCGA.A2.A0CT.01
#> "02" "04" "03" "02" "04" "02"
#> TCGA.E9.A1RG.01 TCGA.XX.A899.01 TCGA.BH.A1F2.01 TCGA.GM.A3XG.01 TCGA.E9.A1N9.01 TCGA.A1.A0SP.01
#> "02" "04" "02" "01" "04" "03"
#> TCGA.E9.A1NF.11 TCGA.AN.A0XT.01 TCGA.S3.AA17.01 TCGA.BH.A1EN.11 TCGA.BH.A0DZ.11 TCGA.AC.A2FF.01
#> "01" "02" "04" "01" "01" "01"
#> TCGA.BH.A0HI.01 TCGA.E9.A1N5.11 TCGA.EW.A1PF.01 TCGA.B6.A0RL.01 TCGA.E2.A1L9.01 TCGA.A7.A26E.01
#> "02" "01" "04" "02" "02" "02"
#> TCGA.BH.A0W3.01 TCGA.AO.A03L.01 TCGA.D8.A1J9.01 TCGA.LL.A7T0.01 TCGA.OL.A66O.01 TCGA.A7.A0CE.11
#> "02" "04" "02" "02" "02" "01"
#> TCGA.AO.A03N.01 TCGA.BH.A0HF.01 TCGA.E2.A1LG.01 TCGA.A7.A6VY.01 TCGA.AC.A2QI.01 TCGA.A2.A4S2.01
#> "02" "04" "03" "03" "04" "04"
#> TCGA.AR.A1AP.01 TCGA.EW.A1PC.01 TCGA.GM.A2DA.01 TCGA.3C.AALJ.01 TCGA.BH.A42T.01 TCGA.A7.A4SA.01
#> "02" "02" "04" "02" "02" "04"
#> TCGA.A7.A26G.01 TCGA.A2.A0YJ.01 TCGA.A2.A3KC.01 TCGA.OL.A66L.01 TCGA.AR.A2LM.01 TCGA.E2.A10C.01
#> "03" "03" "04" "04" "04" "04"
#> TCGA.AC.A7VC.01 TCGA.AR.A1AN.01 TCGA.5L.AAT1.01 TCGA.HN.A2OB.01 TCGA.GM.A5PV.01 TCGA.C8.A26V.01
#> "03" "04" "04" "04" "04" "02"
#> TCGA.BH.A1EV.01 TCGA.E2.A1IJ.01 TCGA.LL.A440.01 TCGA.OK.A5Q2.01 TCGA.BH.A1FG.11 TCGA.OL.A66I.01
#> "02" "04" "01" "04" "01" "03"
#> TCGA.A7.A6VW.01 TCGA.D8.A1JA.01 TCGA.AC.A2FF.11 TCGA.E9.A1R3.01 TCGA.E2.A1IN.01 TCGA.AR.A254.01
#> "03" "02" "01" "04" "02" "04"
#> TCGA.AR.A0TW.01 TCGA.B6.A0I1.01 TCGA.BH.A8G0.01 TCGA.B6.A401.01 TCGA.BH.A0H9.01 TCGA.E2.A1LB.01
#> "04" "03" "04" "04" "02" "04"
#> TCGA.B6.A0RG.01 TCGA.E9.A54X.01 TCGA.C8.A1HN.01 TCGA.LD.A9QF.01 TCGA.BH.A0HB.01 TCGA.LL.A73Y.01
#> "02" "02" "02" "01" "02" "03"
#> TCGA.C8.A1HJ.01 TCGA.BH.A0W5.01 TCGA.A2.A25E.01 TCGA.AC.A3W7.01 TCGA.B6.A1KN.01 TCGA.A2.A1G1.01
#> "03" "04" "02" "04" "02" "03"
#> TCGA.AC.A3W5.01 TCGA.A7.A13D.01 TCGA.A2.A3XY.01 TCGA.B6.A1KI.01 TCGA.AR.A24K.01 TCGA.E9.A1RI.01
#> "04" "03" "03" "04" "02" "04"
#> TCGA.GM.A2DI.01 TCGA.A2.A0T6.01 TCGA.EW.A1OZ.01 TCGA.EW.A3E8.01 TCGA.OL.A5RU.01 TCGA.S3.AA12.01
#> "01" "04" "02" "04" "04" "02"
#> TCGA.A2.A1FX.01 TCGA.BH.A0B8.11 TCGA.BH.A0AZ.11 TCGA.A7.A13G.01 TCGA.E2.A10F.01 TCGA.A7.A4SD.01
#> "02" "01" "01" "02" "04" "03"
#> TCGA.BH.A0C3.01 TCGA.B6.A0RV.01 TCGA.LQ.A4E4.01 TCGA.AQ.A1H2.01 TCGA.D8.A27T.01 TCGA.E2.A1IH.01
#> "04" "04" "02" "02" "02" "04"
#> TCGA.BH.A0DQ.11 TCGA.EW.A1IY.01 TCGA.B6.A0X4.01 TCGA.AR.A24O.01 TCGA.BH.A0HY.01 TCGA.E2.A15I.01
#> "01" "04" "02" "04" "02" "02"
#> TCGA.D8.A1XQ.01 TCGA.C8.A278.01 TCGA.AC.A3HN.01 TCGA.BH.A1FB.11 TCGA.AC.A3BB.01 TCGA.A2.A0EU.01
#> "03" "04" "04" "01" "04" "02"
#> TCGA.BH.A1FE.01 TCGA.BH.A0H7.01 TCGA.A2.A0EN.01 TCGA.BH.A1FE.06 TCGA.BH.A0BF.01 TCGA.A1.A0SG.01
#> "04" "02" "04" "01" "04" "02"
#> TCGA.AC.A6IW.01 TCGA.EW.A1J5.01 TCGA.WT.AB41.01 TCGA.LL.A5YL.01 TCGA.D8.A1XR.01 TCGA.E9.A1RH.11
#> "03" "02" "04" "04" "02" "01"
#> TCGA.AO.A0JB.01 TCGA.A7.A0CH.11 TCGA.C8.A27A.01 TCGA.AR.A1AK.01 TCGA.AC.A3EH.01 TCGA.C8.A1HK.01
#> "02" "01" "02" "04" "02" "02"
#> TCGA.B6.A0WZ.01 TCGA.GM.A4E0.01 TCGA.A8.A0AD.01 TCGA.C8.A26X.01 TCGA.BH.A5IZ.01 TCGA.E9.A22A.01
#> "02" "01" "02" "04" "03" "01"
#> TCGA.A7.A3J1.01 TCGA.D8.A1Y3.01 TCGA.AC.A3YJ.01 TCGA.LL.A8F5.01 TCGA.D8.A1XW.01 TCGA.D8.A1Y1.01
#> "04" "04" "02" "03" "03" "02"
#> TCGA.BH.A0DK.01 TCGA.BH.A1F8.11 TCGA.D8.A1JE.01 TCGA.EW.A2FR.01 TCGA.E2.A105.01 TCGA.PL.A8LZ.01
#> "04" "01" "04" "04" "02" "03"
#> TCGA.E9.A1NA.11 TCGA.BH.A0W4.01 TCGA.BH.A0E2.01 TCGA.BH.A0BJ.01 TCGA.BH.A203.01 TCGA.E2.A1B5.01
#> "01" "04" "02" "04" "04" "01"
#> TCGA.E9.A1R7.01 TCGA.E2.A14U.01 TCGA.E2.A1LI.11 TCGA.E2.A10E.01 TCGA.E9.A249.01 TCGA.AC.A2BK.01
#> "02" "04" "01" "02" "02" "03"
#> TCGA.BH.A1FD.11 TCGA.E2.A1BD.01 TCGA.GI.A2C9.01 TCGA.E2.A1LK.01 TCGA.BH.A1ET.01 TCGA.LD.A7W6.01
#> "01" "02" "03" "03" "02" "02"
#> TCGA.C8.A1HE.01 TCGA.D8.A1XM.01 TCGA.AC.A7VB.01 TCGA.D8.A1JH.01 TCGA.BH.A1F6.11 TCGA.BH.A1ET.11
#> "02" "04" "02" "04" "01" "01"
#> TCGA.E2.A1II.11 TCGA.BH.A0HA.11 TCGA.AO.A12C.01 TCGA.D8.A73W.01 TCGA.B6.A40B.01 TCGA.AO.A0JI.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.BH.A1EU.01 TCGA.OL.A5D7.01 TCGA.A7.A4SE.01 TCGA.OL.A97C.01 TCGA.PE.A5DD.01 TCGA.A2.A04R.01
#> "04" "03" "03" "01" "02" "02"
#> TCGA.BH.A1F5.01 TCGA.S3.AA0Z.01 TCGA.AC.A23E.01 TCGA.BH.A0B3.01 TCGA.D8.A1JS.01 TCGA.E2.A15K.11
#> "02" "03" "02" "03" "02" "01"
#> TCGA.WT.AB44.01 TCGA.EW.A424.01 TCGA.BH.A1FR.01 TCGA.A7.A425.01 TCGA.B6.A0IK.01 TCGA.AR.A24U.01
#> "02" "02" "04" "04" "04" "01"
#> TCGA.E9.A1RF.01 TCGA.B6.A408.01 TCGA.BH.A0HP.01 TCGA.E2.A1L7.01 TCGA.5T.A9QA.01 TCGA.A2.A0SY.01
#> "04" "02" "04" "02" "02" "02"
#> TCGA.BH.A8FZ.01 TCGA.A2.A0YG.01 TCGA.AC.A2FG.01 TCGA.AR.A1AX.01 TCGA.AR.A1AL.01 TCGA.BH.A1EY.11
#> "04" "02" "04" "01" "04" "01"
#> TCGA.AQ.A54N.01 TCGA.BH.A1EO.01 TCGA.BH.A0BZ.11 TCGA.D8.A27K.01 TCGA.BH.A28Q.01 TCGA.E9.A1NG.11
#> "03" "04" "01" "04" "02" "01"
#> TCGA.EW.A1J1.01 TCGA.C8.A1HG.01 TCGA.D8.A1XK.01 TCGA.AQ.A0Y5.01 TCGA.3C.AAAU.01 TCGA.A2.A4S0.01
#> "02" "04" "03" "02" "02" "02"
#> TCGA.BH.A0DV.11 TCGA.AR.A1AV.01 TCGA.AC.A8OQ.01 TCGA.BH.A0BS.11 TCGA.EW.A1PB.01 TCGA.A7.A3J0.01
#> "01" "02" "03" "01" "03" "02"
#> TCGA.D8.A1JU.01 TCGA.A7.A6VX.01 TCGA.E2.A108.01 TCGA.BH.A0BT.01 TCGA.A2.A0YK.01 TCGA.E9.A1N8.01
#> "04" "02" "01" "02" "04" "03"
#> TCGA.E2.A574.01 TCGA.A1.A0SO.01 TCGA.BH.A0DI.01 TCGA.E2.A1IG.01 TCGA.E2.A107.01 TCGA.5L.AAT0.01
#> "03" "03" "04" "02" "04" "04"
#> TCGA.E9.A1NH.01 TCGA.D8.A27E.01 TCGA.AR.A24Q.01 TCGA.BH.A1F0.01 TCGA.E9.A1RB.11 TCGA.AR.A0U0.01
#> "02" "04" "03" "03" "01" "03"
Heatmaps of the top rows:
top_rows_heatmap(res_rh)
#> Error in h(simpleError(msg, call)) :
#> error in evaluating the argument 'object' in selecting a method for function 'draw': no applicable method for 'height' applied to an object of class "list"
Top rows on each node:
top_rows_overlap(res_rh, method = "upset")
UMAP plot which shows how samples are separated.
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1170),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1170),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1222),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1222),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1257),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1257),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1414),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1414),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1749),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1749),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1823),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1823),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1859),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1859),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1863),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1863),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2144),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2144),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2288),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2288),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3086),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3086),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3775),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3775),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3920),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3920),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4517),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4517),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5436),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5436),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 6990),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 6990),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 7407),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 7407),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 7632),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 7632),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 8036),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 8036),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 8366),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 8366),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 8878),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 8878),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 9552),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 9552),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 12308),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 12308),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 12745),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 12745),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 14822),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 14822),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 15450),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 15450),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 20697),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 20697),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 21454),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 21454),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 22951),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 22951),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 23761),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 23761),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 32783),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 32783),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
Signatures on the heatmap are the union of all signatures found on every node on the hierarchy. The number of k-means on rows are automatically selected by the function.
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1170))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1222))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1257))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1414))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1749))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1823))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1859))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1863))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2144))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2288))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3086))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3775))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3920))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4517))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5436))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 6990))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 7407))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 7632))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 8036))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 8366))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 8878))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 9552))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 12308))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 12745))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 14822))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 15450))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 20697))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 21454))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 22951))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 23761))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 32783))
Compare signatures from different nodes:
compare_signatures(res_rh, verbose = FALSE)
If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs. Note it only works on every node and the final signatures
are the union of all signatures of all nodes.
# code only for demonstration
# e.g. to show the top 500 most significant rows on each node.
tb = get_signature(res_rh, top_signatures = 500)
Child nodes: Node01 , Node02 , Node03 , Node04 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0"]
A summary of res and all the functions that can be applied to it:
res
#> A 'DownSamplingConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 375878 rows and 500 columns, randomly sampled from 888 columns.
#> Top rows (1000) are extracted by 'SD' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'DownSamplingConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.991 0.996 0.4668 0.535 0.535
#> 3 3 0.726 0.918 0.927 0.1979 0.912 0.838
#> 4 4 1.000 0.984 0.993 0.2894 0.772 0.529
#> 5 5 0.799 0.738 0.884 0.0978 0.856 0.546
#> 6 6 0.829 0.784 0.895 0.0408 0.847 0.432
#> 7 7 0.812 0.728 0.834 0.0250 0.893 0.515
#> 8 8 0.804 0.542 0.735 0.0184 0.873 0.405
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
get_classes(res, k = 2)
#> class p
#> TCGA.OL.A66H.01 2 0.000
#> TCGA.3C.AALK.01 2 0.000
#> TCGA.AC.A5EH.01 2 0.000
#> TCGA.EW.A2FW.01 2 0.000
#> TCGA.E9.A1R0.01 2 0.000
#> TCGA.AR.A1AJ.01 1 0.000
#> TCGA.AC.A62Y.01 2 0.000
#> TCGA.E9.A1QZ.01 1 0.000
#> TCGA.E9.A1R2.01 2 0.000
#> TCGA.E9.A3X8.01 1 1.000
#> TCGA.AR.A255.01 2 0.000
#> TCGA.E2.A10B.01 2 0.000
#> TCGA.E9.A1N4.11 1 0.000
#> TCGA.AO.A0JD.01 2 0.000
#> TCGA.D8.A1JD.01 2 0.000
#> TCGA.D8.A1XA.01 2 0.000
#> TCGA.AO.A1KQ.01 2 0.000
#> TCGA.A8.A0A6.01 2 0.000
#> TCGA.BH.A1F2.11 1 0.000
#> TCGA.A7.A3RF.01 2 0.000
#> TCGA.A2.A0SW.01 2 0.000
#> TCGA.A7.A3IY.01 1 0.000
#> TCGA.GM.A2D9.01 2 0.000
#> TCGA.D8.A3Z5.01 2 0.000
#> TCGA.E9.A1ND.01 1 0.000
#> TCGA.EW.A1P5.01 2 0.000
#> TCGA.E9.A1RD.01 2 0.000
#> TCGA.AR.A1AQ.01 1 0.000
#> TCGA.LD.A66U.01 2 0.000
#> TCGA.BH.A1EN.01 2 0.000
#> TCGA.BH.A1FN.01 2 0.000
#> TCGA.EW.A1PD.01 2 0.000
#> TCGA.E9.A1N5.01 2 0.000
#> TCGA.D8.A1J8.01 2 0.000
#> TCGA.E9.A3QA.01 1 0.000
#> TCGA.S3.AA15.01 1 0.000
#> TCGA.BH.A0DP.11 1 0.000
#> TCGA.BH.A0H0.01 2 0.000
#> TCGA.A2.A3XX.01 1 0.000
#> TCGA.AC.A2FB.01 1 0.000
#> TCGA.AC.A3QP.01 2 0.502
#> TCGA.BH.A0BF.11 1 0.000
#> TCGA.A2.A0YC.01 2 0.000
#> TCGA.GM.A2DK.01 2 0.000
#> TCGA.GM.A2DC.01 2 0.000
#> TCGA.AR.A24N.01 2 0.000
#> TCGA.E2.A1B0.01 2 1.000
#> TCGA.BH.A1EY.01 2 0.000
#> TCGA.EW.A6S9.01 2 0.000
#> TCGA.AC.A8OS.01 2 0.000
#> TCGA.GM.A2DN.01 2 1.000
#> TCGA.AO.A03M.01 2 0.000
#> TCGA.A2.A3XT.01 1 0.000
#> TCGA.A2.A4RW.01 2 0.000
#> TCGA.AC.A6IV.01 1 1.000
#> TCGA.LL.A7SZ.01 2 0.000
#> TCGA.A1.A0SJ.01 2 0.000
#> TCGA.AR.A2LJ.01 2 1.000
#> TCGA.AQ.A1H3.01 2 0.000
#> TCGA.D8.A1JB.01 1 0.000
#> TCGA.BH.A0BC.01 2 0.000
#> TCGA.BH.A1EW.01 2 0.000
#> TCGA.BH.A1FG.01 2 0.000
#> TCGA.EW.A1P7.01 1 0.000
#> TCGA.GM.A2DH.01 2 0.000
#> TCGA.D8.A27P.01 2 0.000
#> TCGA.EW.A2FS.01 2 0.000
#> TCGA.E2.A1IL.01 2 0.000
#> TCGA.A7.A3IZ.01 2 0.000
#> TCGA.E2.A570.01 2 0.000
#> TCGA.OL.A66J.01 2 0.000
#> TCGA.AR.A2LO.01 1 0.498
#> TCGA.BH.A1FC.11 1 0.000
#> TCGA.E9.A5FL.01 1 0.000
#> TCGA.BH.A201.01 2 0.000
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#> TCGA.BH.A1FE.11 1 0.000
#> TCGA.A7.A0DC.11 1 0.000
#> TCGA.D8.A1XU.01 2 0.000
#> TCGA.BH.A1ES.06 2 0.000
#> TCGA.D8.A1X6.01 2 0.000
#> TCGA.EW.A3U0.01 1 0.000
#> TCGA.AQ.A7U7.01 1 0.751
#> TCGA.A1.A0SI.01 2 0.000
#> TCGA.A2.A25A.01 2 1.000
#> TCGA.PL.A8LX.01 2 0.000
#> TCGA.E9.A1RH.01 2 0.751
#> TCGA.AO.A12E.01 2 0.000
#> TCGA.A7.A13H.01 2 0.000
#> TCGA.AO.A0JC.01 1 0.000
#> TCGA.EW.A6SA.01 2 0.000
#> TCGA.E9.A1R5.01 2 0.000
#> TCGA.E9.A54Y.01 2 0.000
#> TCGA.E9.A243.01 1 0.000
#> TCGA.AC.A3TN.01 2 0.000
#> TCGA.E2.A1IO.01 2 0.000
#> TCGA.OL.A5S0.01 1 0.000
#> TCGA.C8.A26Y.01 2 1.000
#> TCGA.A2.A25D.01 2 0.000
#> TCGA.EW.A1J3.01 2 0.000
#> TCGA.A2.A0EP.01 1 0.000
#> TCGA.BH.A1F8.01 2 0.000
#> TCGA.B6.A0X5.01 2 0.000
#> TCGA.AN.A0XW.01 2 0.000
#> TCGA.BH.A0AW.01 2 0.000
#> TCGA.BH.A0BJ.11 1 0.000
#> TCGA.D8.A27F.01 1 0.000
#> TCGA.BH.A0B6.01 2 0.000
#> TCGA.E9.A229.01 2 0.000
#> TCGA.D8.A1JK.01 2 0.000
#> TCGA.AQ.A04L.01 2 0.000
#> TCGA.B6.A0WV.01 2 0.000
#> TCGA.E2.A1LI.01 1 0.000
#> TCGA.A7.A26F.01 1 0.000
#> TCGA.GM.A5PX.01 2 0.000
#> TCGA.BH.A1FD.01 2 0.000
#> TCGA.A7.A13F.01 2 0.000
#> TCGA.AR.A5QN.01 2 0.000
#> TCGA.E2.A2P5.01 2 0.000
#> TCGA.AO.A1KS.01 2 0.000
#> TCGA.BH.A42U.01 1 0.000
#> TCGA.BH.A0DD.01 2 0.000
#> TCGA.B6.A0RE.01 1 0.000
#> TCGA.BH.A208.01 1 0.498
#> TCGA.EW.A1IX.01 2 0.000
#> TCGA.BH.A1F6.01 1 0.000
#> TCGA.BH.A0HX.01 2 0.000
#> TCGA.E2.A14N.01 1 0.000
#> TCGA.A2.A259.01 2 0.000
#> TCGA.GM.A2DD.01 1 0.000
#> TCGA.E2.A1B1.01 1 0.000
#> TCGA.D8.A73U.01 1 1.000
#> TCGA.D8.A27N.01 2 0.000
#> TCGA.D8.A1X9.01 2 0.000
#> TCGA.OL.A5RW.01 1 0.000
#> TCGA.AR.A0TR.01 2 0.000
#> TCGA.BH.A1F5.11 1 0.000
#> TCGA.BH.A1EO.11 1 0.000
#> TCGA.E9.A22E.01 2 0.498
#> TCGA.OL.A5RX.01 2 0.000
#> TCGA.A7.A0DC.01 2 0.000
#> TCGA.D8.A1XO.01 2 0.000
#> TCGA.AC.A23C.01 2 0.000
#> TCGA.E9.A1NE.01 1 0.000
#> TCGA.A7.A56D.01 2 0.000
#> TCGA.A1.A0SH.01 2 0.000
#> TCGA.C8.A9FZ.01 2 0.000
#> TCGA.C8.A8HR.01 1 0.000
#> TCGA.BH.A6R9.01 1 0.000
#> TCGA.AR.A5QP.01 2 0.498
#> TCGA.C8.A8HP.01 1 0.000
#> TCGA.AR.A24X.01 2 0.000
#> TCGA.A1.A0SB.01 1 0.000
#> TCGA.D8.A1Y0.01 2 0.000
#> TCGA.BH.A0GZ.01 2 0.000
#> TCGA.AC.A2FM.11 1 0.000
#> TCGA.B6.A0RM.01 2 0.000
#> TCGA.AR.A2LR.01 1 0.000
#> TCGA.BH.A2L8.01 2 1.000
#> TCGA.AR.A251.01 1 0.000
#> TCGA.AO.A12B.01 2 0.000
#> TCGA.BH.A202.01 2 0.000
#> TCGA.A7.A0D9.11 1 0.000
#> TCGA.BH.A0DH.01 2 0.000
#> TCGA.D8.A1JN.01 2 0.000
#> TCGA.EW.A1OV.01 2 0.000
#> TCGA.E2.A1IE.01 2 0.000
#> TCGA.AR.A1AR.01 1 0.000
#> TCGA.EW.A1P3.01 2 0.000
#> TCGA.BH.A8FY.01 2 0.000
#> TCGA.A1.A0SN.01 2 0.000
#> TCGA.E9.A295.01 2 0.000
#> TCGA.AO.A1KT.01 2 0.000
#> TCGA.AC.A2FB.11 1 0.000
#> TCGA.E2.A1IU.01 2 0.000
#> TCGA.AO.A0JL.01 1 0.000
#> TCGA.AC.A8OP.01 2 0.000
#> TCGA.E2.A1LS.11 1 0.000
#> TCGA.EW.A1P8.01 1 0.000
#> TCGA.GI.A2C8.01 2 0.000
#> TCGA.AR.A24P.01 2 0.000
#> TCGA.BH.A0BT.11 1 0.000
#> TCGA.BH.A0C0.11 1 0.000
#> TCGA.E9.A22H.01 2 0.000
#> TCGA.D8.A3Z6.01 2 0.000
#> TCGA.AR.A0U4.01 1 0.000
#> TCGA.AR.A2LK.01 2 0.000
#> TCGA.B6.A409.01 1 0.000
#> TCGA.E2.A1BC.11 1 0.000
#> TCGA.B6.A0X1.01 1 0.000
#> TCGA.A2.A0SX.01 1 0.000
#> TCGA.BH.A0C3.11 1 0.000
#> TCGA.BH.A0B2.01 2 0.000
#> TCGA.B6.A0RI.01 2 0.000
#> TCGA.E9.A248.01 1 0.000
#> TCGA.A2.A0SU.01 2 0.000
#> TCGA.BH.A204.11 1 0.000
#> TCGA.EW.A1P4.01 1 0.000
#> TCGA.AO.A128.01 1 0.000
#> TCGA.AR.A24T.01 2 0.000
#> TCGA.A8.A08O.01 2 0.000
#> TCGA.EW.A1P6.01 2 0.000
#> TCGA.AC.A2FE.01 2 0.751
#> TCGA.GM.A2DF.01 1 0.000
#> TCGA.D8.A1XF.01 2 0.000
#> TCGA.E9.A1N4.01 2 0.000
#> TCGA.A2.A0CT.01 2 0.000
#> TCGA.E9.A1RG.01 2 0.000
#> TCGA.XX.A899.01 2 0.751
#> TCGA.BH.A1F2.01 2 0.000
#> TCGA.GM.A3XG.01 1 0.000
#> TCGA.E9.A1N9.01 2 0.000
#> TCGA.A1.A0SP.01 1 0.000
#> TCGA.E9.A1NF.11 1 0.000
#> TCGA.AN.A0XT.01 2 0.000
#> TCGA.S3.AA17.01 2 0.000
#> TCGA.BH.A1EN.11 1 0.000
#> TCGA.BH.A0DZ.11 1 0.000
#> TCGA.AC.A2FF.01 1 0.000
#> TCGA.BH.A0HI.01 2 0.000
#> TCGA.E9.A1N5.11 1 0.000
#> TCGA.EW.A1PF.01 2 0.000
#> TCGA.B6.A0RL.01 2 0.000
#> TCGA.E2.A1L9.01 2 0.000
#> TCGA.A7.A26E.01 2 0.000
#> TCGA.BH.A0W3.01 2 0.000
#> TCGA.AO.A03L.01 2 0.000
#> TCGA.D8.A1J9.01 2 0.000
#> TCGA.LL.A7T0.01 2 0.000
#> TCGA.OL.A66O.01 2 0.000
#> TCGA.A7.A0CE.11 1 0.000
#> TCGA.AO.A03N.01 2 0.000
#> TCGA.BH.A0HF.01 2 0.000
#> TCGA.E2.A1LG.01 1 0.000
#> TCGA.A7.A6VY.01 1 0.000
#> TCGA.AC.A2QI.01 2 0.000
#> TCGA.A2.A4S2.01 2 0.000
#> TCGA.AR.A1AP.01 2 0.000
#> TCGA.EW.A1PC.01 2 0.000
#> TCGA.GM.A2DA.01 2 0.000
#> TCGA.3C.AALJ.01 2 0.000
#> TCGA.BH.A42T.01 2 0.000
#> TCGA.A7.A4SA.01 2 1.000
#> TCGA.A7.A26G.01 1 0.000
#> TCGA.A2.A0YJ.01 1 0.000
#> TCGA.A2.A3KC.01 2 0.000
#> TCGA.OL.A66L.01 2 0.000
#> TCGA.AR.A2LM.01 2 0.000
#> TCGA.E2.A10C.01 2 0.000
#> TCGA.AC.A7VC.01 1 0.000
#> TCGA.AR.A1AN.01 2 0.000
#> TCGA.5L.AAT1.01 2 0.000
#> TCGA.HN.A2OB.01 2 0.000
#> TCGA.GM.A5PV.01 2 0.000
#> TCGA.C8.A26V.01 2 0.000
#> TCGA.BH.A1EV.01 2 0.000
#> TCGA.E2.A1IJ.01 2 0.000
#> TCGA.LL.A440.01 1 0.000
#> TCGA.OK.A5Q2.01 2 1.000
#> TCGA.BH.A1FG.11 1 0.000
#> TCGA.OL.A66I.01 1 0.000
#> TCGA.A7.A6VW.01 1 0.000
#> TCGA.D8.A1JA.01 2 0.000
#> TCGA.AC.A2FF.11 1 0.000
#> TCGA.E9.A1R3.01 2 0.000
#> TCGA.E2.A1IN.01 2 0.000
#> TCGA.AR.A254.01 2 0.000
#> TCGA.AR.A0TW.01 2 0.000
#> TCGA.B6.A0I1.01 1 0.000
#> TCGA.BH.A8G0.01 1 0.000
#> TCGA.B6.A401.01 2 0.000
#> TCGA.BH.A0H9.01 2 0.000
#> TCGA.E2.A1LB.01 2 0.000
#> TCGA.B6.A0RG.01 2 0.000
#> TCGA.E9.A54X.01 2 0.000
#> TCGA.C8.A1HN.01 2 0.000
#> TCGA.LD.A9QF.01 1 0.000
#> TCGA.BH.A0HB.01 2 0.000
#> TCGA.LL.A73Y.01 1 0.000
#> TCGA.C8.A1HJ.01 1 0.000
#> TCGA.BH.A0W5.01 1 1.000
#> TCGA.A2.A25E.01 2 0.000
#> TCGA.AC.A3W7.01 2 0.000
#> TCGA.B6.A1KN.01 2 0.000
#> TCGA.A2.A1G1.01 1 0.000
#> TCGA.AC.A3W5.01 2 0.000
#> TCGA.A7.A13D.01 1 0.000
#> TCGA.A2.A3XY.01 1 0.000
#> TCGA.B6.A1KI.01 2 0.000
#> TCGA.AR.A24K.01 2 0.000
#> TCGA.E9.A1RI.01 2 0.000
#> TCGA.GM.A2DI.01 1 0.000
#> TCGA.A2.A0T6.01 2 0.000
#> TCGA.EW.A1OZ.01 2 0.000
#> TCGA.EW.A3E8.01 2 0.000
#> TCGA.OL.A5RU.01 2 0.000
#> TCGA.S3.AA12.01 2 0.000
#> TCGA.A2.A1FX.01 2 0.000
#> TCGA.BH.A0B8.11 1 0.000
#> TCGA.BH.A0AZ.11 1 0.000
#> TCGA.A7.A13G.01 2 0.000
#> TCGA.E2.A10F.01 2 0.000
#> TCGA.A7.A4SD.01 1 0.000
#> TCGA.BH.A0C3.01 2 0.498
#> TCGA.B6.A0RV.01 2 0.000
#> TCGA.LQ.A4E4.01 2 0.000
#> TCGA.AQ.A1H2.01 2 0.000
#> TCGA.D8.A27T.01 2 0.000
#> TCGA.E2.A1IH.01 2 0.000
#> TCGA.BH.A0DQ.11 1 0.000
#> TCGA.EW.A1IY.01 2 0.000
#> TCGA.B6.A0X4.01 2 0.000
#> TCGA.AR.A24O.01 2 0.751
#> TCGA.BH.A0HY.01 2 0.000
#> TCGA.E2.A15I.01 2 0.000
#> TCGA.D8.A1XQ.01 1 0.000
#> TCGA.C8.A278.01 2 0.249
#> TCGA.AC.A3HN.01 2 0.000
#> TCGA.BH.A1FB.11 1 0.000
#> TCGA.AC.A3BB.01 2 0.000
#> TCGA.A2.A0EU.01 2 0.000
#> TCGA.BH.A1FE.01 2 1.000
#> TCGA.BH.A0H7.01 2 0.000
#> TCGA.A2.A0EN.01 2 0.751
#> TCGA.BH.A1FE.06 1 0.000
#> TCGA.BH.A0BF.01 2 0.000
#> TCGA.A1.A0SG.01 2 0.000
#> TCGA.AC.A6IW.01 1 0.000
#> TCGA.EW.A1J5.01 2 0.000
#> TCGA.WT.AB41.01 2 0.000
#> TCGA.LL.A5YL.01 2 0.000
#> TCGA.D8.A1XR.01 2 0.000
#> TCGA.E9.A1RH.11 1 0.000
#> TCGA.AO.A0JB.01 2 0.000
#> TCGA.A7.A0CH.11 1 0.000
#> TCGA.C8.A27A.01 2 0.000
#> TCGA.AR.A1AK.01 2 0.000
#> TCGA.AC.A3EH.01 2 0.000
#> TCGA.C8.A1HK.01 2 0.000
#> TCGA.B6.A0WZ.01 2 0.000
#> TCGA.GM.A4E0.01 1 0.000
#> TCGA.A8.A0AD.01 2 0.000
#> TCGA.C8.A26X.01 2 1.000
#> TCGA.BH.A5IZ.01 1 0.000
#> TCGA.E9.A22A.01 1 0.000
#> TCGA.A7.A3J1.01 2 0.000
#> TCGA.D8.A1Y3.01 2 0.000
#> TCGA.AC.A3YJ.01 2 0.000
#> TCGA.LL.A8F5.01 1 0.000
#> TCGA.D8.A1XW.01 1 0.000
#> TCGA.D8.A1Y1.01 2 0.000
#> TCGA.BH.A0DK.01 2 0.000
#> TCGA.BH.A1F8.11 1 0.000
#> TCGA.D8.A1JE.01 2 0.000
#> TCGA.EW.A2FR.01 2 1.000
#> TCGA.E2.A105.01 2 0.000
#> TCGA.PL.A8LZ.01 1 0.000
#> TCGA.E9.A1NA.11 1 0.000
#> TCGA.BH.A0W4.01 2 0.000
#> TCGA.BH.A0E2.01 2 0.000
#> TCGA.BH.A0BJ.01 2 0.000
#> TCGA.BH.A203.01 2 0.000
#> TCGA.E2.A1B5.01 1 0.000
#> TCGA.E9.A1R7.01 2 0.000
#> TCGA.E2.A14U.01 2 1.000
#> TCGA.E2.A1LI.11 1 0.000
#> TCGA.E2.A10E.01 2 0.000
#> TCGA.E9.A249.01 2 0.000
#> TCGA.AC.A2BK.01 1 0.000
#> TCGA.BH.A1FD.11 1 0.000
#> TCGA.E2.A1BD.01 2 0.000
#> TCGA.GI.A2C9.01 1 0.000
#> TCGA.E2.A1LK.01 1 0.000
#> TCGA.BH.A1ET.01 2 0.000
#> TCGA.LD.A7W6.01 2 0.000
#> TCGA.C8.A1HE.01 2 0.000
#> TCGA.D8.A1XM.01 2 0.000
#> TCGA.AC.A7VB.01 2 0.000
#> TCGA.D8.A1JH.01 2 0.000
#> TCGA.BH.A1F6.11 1 0.000
#> TCGA.BH.A1ET.11 1 0.000
#> TCGA.E2.A1II.11 1 0.000
#> TCGA.BH.A0HA.11 1 0.000
#> TCGA.AO.A12C.01 2 0.000
#> TCGA.D8.A73W.01 2 0.000
#> TCGA.B6.A40B.01 2 0.000
#> TCGA.AO.A0JI.01 2 0.000
#> TCGA.BH.A1EU.01 2 1.000
#> TCGA.OL.A5D7.01 1 0.000
#> TCGA.A7.A4SE.01 1 0.000
#> TCGA.OL.A97C.01 1 0.000
#> TCGA.PE.A5DD.01 2 0.000
#> TCGA.A2.A04R.01 2 0.000
#> TCGA.BH.A1F5.01 2 0.000
#> TCGA.S3.AA0Z.01 1 0.000
#> TCGA.AC.A23E.01 2 0.000
#> TCGA.BH.A0B3.01 1 0.000
#> TCGA.D8.A1JS.01 2 0.000
#> TCGA.E2.A15K.11 1 0.000
#> TCGA.WT.AB44.01 2 0.000
#> TCGA.EW.A424.01 2 0.000
#> TCGA.BH.A1FR.01 2 0.000
#> TCGA.A7.A425.01 2 0.000
#> TCGA.B6.A0IK.01 2 0.000
#> TCGA.AR.A24U.01 1 0.000
#> TCGA.E9.A1RF.01 2 0.000
#> TCGA.B6.A408.01 2 0.000
#> TCGA.BH.A0HP.01 2 0.000
#> TCGA.E2.A1L7.01 2 0.000
#> TCGA.5T.A9QA.01 2 0.000
#> TCGA.A2.A0SY.01 2 0.000
#> TCGA.BH.A8FZ.01 1 0.751
#> TCGA.A2.A0YG.01 2 0.000
#> TCGA.AC.A2FG.01 2 0.000
#> TCGA.AR.A1AX.01 1 0.000
#> TCGA.AR.A1AL.01 2 0.000
#> TCGA.BH.A1EY.11 1 0.000
#> TCGA.AQ.A54N.01 1 0.000
#> TCGA.BH.A1EO.01 2 0.000
#> TCGA.BH.A0BZ.11 1 0.000
#> TCGA.D8.A27K.01 2 0.000
#> TCGA.BH.A28Q.01 2 0.000
#> TCGA.E9.A1NG.11 1 0.000
#> TCGA.EW.A1J1.01 2 0.000
#> TCGA.C8.A1HG.01 2 0.000
#> TCGA.D8.A1XK.01 1 0.000
#> TCGA.AQ.A0Y5.01 2 0.000
#> TCGA.3C.AAAU.01 2 0.000
#> TCGA.A2.A4S0.01 2 0.000
#> TCGA.BH.A0DV.11 1 0.000
#> TCGA.AR.A1AV.01 2 0.000
#> TCGA.AC.A8OQ.01 1 0.000
#> TCGA.BH.A0BS.11 1 0.000
#> TCGA.EW.A1PB.01 1 0.000
#> TCGA.A7.A3J0.01 2 0.000
#> TCGA.D8.A1JU.01 2 0.751
#> TCGA.A7.A6VX.01 2 0.000
#> TCGA.E2.A108.01 1 0.000
#> TCGA.BH.A0BT.01 2 0.000
#> TCGA.A2.A0YK.01 2 0.751
#> TCGA.E9.A1N8.01 1 0.000
#> TCGA.E2.A574.01 1 0.000
#> TCGA.A1.A0SO.01 1 0.000
#> TCGA.BH.A0DI.01 1 1.000
#> TCGA.E2.A1IG.01 2 0.000
#> TCGA.E2.A107.01 2 0.000
#> TCGA.5L.AAT0.01 2 0.000
#> TCGA.E9.A1NH.01 2 0.000
#> TCGA.D8.A27E.01 2 0.000
#> TCGA.AR.A24Q.01 1 0.000
#> TCGA.BH.A1F0.01 1 0.000
#> TCGA.E9.A1RB.11 1 0.000
#> TCGA.AR.A0U0.01 1 0.000
get_classes(res, k = 3)
#> class p
#> TCGA.OL.A66H.01 2 0.000
#> TCGA.3C.AALK.01 2 0.000
#> TCGA.AC.A5EH.01 2 0.000
#> TCGA.EW.A2FW.01 2 0.000
#> TCGA.E9.A1R0.01 2 0.000
#> TCGA.AR.A1AJ.01 3 0.000
#> TCGA.AC.A62Y.01 2 0.000
#> TCGA.E9.A1QZ.01 1 0.000
#> TCGA.E9.A1R2.01 2 0.000
#> TCGA.E9.A3X8.01 1 0.000
#> TCGA.AR.A255.01 2 0.000
#> TCGA.E2.A10B.01 2 0.000
#> TCGA.E9.A1N4.11 1 0.000
#> TCGA.AO.A0JD.01 2 0.000
#> TCGA.D8.A1JD.01 2 0.000
#> TCGA.D8.A1XA.01 2 0.000
#> TCGA.AO.A1KQ.01 2 0.000
#> TCGA.A8.A0A6.01 2 0.000
#> TCGA.BH.A1F2.11 1 0.000
#> TCGA.A7.A3RF.01 2 0.000
#> TCGA.A2.A0SW.01 2 0.000
#> TCGA.A7.A3IY.01 1 0.000
#> TCGA.GM.A2D9.01 2 0.000
#> TCGA.D8.A3Z5.01 2 0.000
#> TCGA.E9.A1ND.01 3 0.000
#> TCGA.EW.A1P5.01 2 0.000
#> TCGA.E9.A1RD.01 2 0.000
#> TCGA.AR.A1AQ.01 3 0.000
#> TCGA.LD.A66U.01 2 0.000
#> TCGA.BH.A1EN.01 2 0.000
#> TCGA.BH.A1FN.01 2 0.000
#> TCGA.EW.A1PD.01 2 0.000
#> TCGA.E9.A1N5.01 2 0.000
#> TCGA.D8.A1J8.01 2 0.000
#> TCGA.E9.A3QA.01 3 0.000
#> TCGA.S3.AA15.01 1 0.498
#> TCGA.BH.A0DP.11 1 0.000
#> TCGA.BH.A0H0.01 2 0.000
#> TCGA.A2.A3XX.01 3 0.000
#> TCGA.AC.A2FB.01 1 0.000
#> TCGA.AC.A3QP.01 2 0.000
#> TCGA.BH.A0BF.11 1 0.000
#> TCGA.A2.A0YC.01 2 0.000
#> TCGA.GM.A2DK.01 2 0.000
#> TCGA.GM.A2DC.01 2 0.000
#> TCGA.AR.A24N.01 2 0.000
#> TCGA.E2.A1B0.01 1 0.000
#> TCGA.BH.A1EY.01 2 0.000
#> TCGA.EW.A6S9.01 2 0.000
#> TCGA.AC.A8OS.01 2 0.000
#> TCGA.GM.A2DN.01 2 0.000
#> TCGA.AO.A03M.01 2 0.000
#> TCGA.A2.A3XT.01 3 0.000
#> TCGA.A2.A4RW.01 2 0.000
#> TCGA.AC.A6IV.01 1 0.000
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#> TCGA.A2.A0YH.01 2 0.000
#> TCGA.LL.A5YN.01 2 0.000
#> TCGA.AR.A1AO.01 1 0.000
#> TCGA.A2.A3XU.01 3 0.000
#> TCGA.AC.A23G.01 1 0.000
#> TCGA.GM.A3XN.01 2 0.000
#> TCGA.A7.A26J.01 2 0.000
#> TCGA.A2.A25B.01 2 0.000
#> TCGA.D8.A27W.01 2 0.000
#> TCGA.GM.A3XL.01 3 0.000
#> TCGA.E9.A2JS.01 2 0.000
#> TCGA.C8.A275.01 2 0.000
#> TCGA.E2.A1IK.01 2 0.000
#> TCGA.BH.A1FB.01 1 0.000
#> TCGA.C8.A3M8.01 2 0.000
#> TCGA.AN.A0XU.01 3 0.000
#> TCGA.A2.A3XW.01 1 0.000
#> TCGA.A7.A6VV.01 3 0.000
#> TCGA.BH.A1FE.11 1 0.747
#> TCGA.A7.A0DC.11 1 0.000
#> TCGA.D8.A1XU.01 2 0.000
#> TCGA.BH.A1ES.06 2 0.000
#> TCGA.D8.A1X6.01 2 0.000
#> TCGA.EW.A3U0.01 3 0.000
#> TCGA.AQ.A7U7.01 1 0.000
#> TCGA.A1.A0SI.01 2 0.000
#> TCGA.A2.A25A.01 1 0.751
#> TCGA.PL.A8LX.01 2 0.000
#> TCGA.E9.A1RH.01 1 0.249
#> TCGA.AO.A12E.01 2 0.000
#> TCGA.A7.A13H.01 2 0.000
#> TCGA.AO.A0JC.01 1 0.000
#> TCGA.EW.A6SA.01 2 0.000
#> TCGA.E9.A1R5.01 2 0.000
#> TCGA.E9.A54Y.01 2 0.000
#> TCGA.E9.A243.01 3 0.751
#> TCGA.AC.A3TN.01 2 0.000
#> TCGA.E2.A1IO.01 2 0.000
#> TCGA.OL.A5S0.01 3 0.000
#> TCGA.C8.A26Y.01 1 1.000
#> TCGA.A2.A25D.01 2 0.000
#> TCGA.EW.A1J3.01 2 0.000
#> TCGA.A2.A0EP.01 1 0.000
#> TCGA.BH.A1F8.01 2 0.000
#> TCGA.B6.A0X5.01 2 0.000
#> TCGA.AN.A0XW.01 2 0.000
#> TCGA.BH.A0AW.01 2 0.000
#> TCGA.BH.A0BJ.11 1 0.000
#> TCGA.D8.A27F.01 3 0.000
#> TCGA.BH.A0B6.01 2 0.000
#> TCGA.E9.A229.01 2 0.000
#> TCGA.D8.A1JK.01 2 0.000
#> TCGA.AQ.A04L.01 2 0.000
#> TCGA.B6.A0WV.01 2 0.000
#> TCGA.E2.A1LI.01 3 0.000
#> TCGA.A7.A26F.01 1 0.000
#> TCGA.GM.A5PX.01 2 0.000
#> TCGA.BH.A1FD.01 2 0.000
#> TCGA.A7.A13F.01 2 0.000
#> TCGA.AR.A5QN.01 2 0.000
#> TCGA.E2.A2P5.01 2 0.000
#> TCGA.AO.A1KS.01 2 0.000
#> TCGA.BH.A42U.01 1 0.000
#> TCGA.BH.A0DD.01 2 0.000
#> TCGA.B6.A0RE.01 3 0.000
#> TCGA.BH.A208.01 1 0.000
#> TCGA.EW.A1IX.01 2 0.000
#> TCGA.BH.A1F6.01 3 0.000
#> TCGA.BH.A0HX.01 2 0.000
#> TCGA.E2.A14N.01 3 0.000
#> TCGA.A2.A259.01 2 0.000
#> TCGA.GM.A2DD.01 1 0.000
#> TCGA.E2.A1B1.01 1 0.000
#> TCGA.D8.A73U.01 1 0.000
#> TCGA.D8.A27N.01 2 0.000
#> TCGA.D8.A1X9.01 2 0.000
#> TCGA.OL.A5RW.01 3 0.000
#> TCGA.AR.A0TR.01 2 0.000
#> TCGA.BH.A1F5.11 1 0.000
#> TCGA.BH.A1EO.11 1 0.000
#> TCGA.E9.A22E.01 2 0.000
#> TCGA.OL.A5RX.01 2 0.000
#> TCGA.A7.A0DC.01 2 0.000
#> TCGA.D8.A1XO.01 2 0.000
#> TCGA.AC.A23C.01 2 0.000
#> TCGA.E9.A1NE.01 1 0.000
#> TCGA.A7.A56D.01 2 0.000
#> TCGA.A1.A0SH.01 2 0.000
#> TCGA.C8.A9FZ.01 2 0.000
#> TCGA.C8.A8HR.01 1 0.000
#> TCGA.BH.A6R9.01 1 0.747
#> TCGA.AR.A5QP.01 2 0.000
#> TCGA.C8.A8HP.01 1 0.000
#> TCGA.AR.A24X.01 2 0.000
#> TCGA.A1.A0SB.01 3 0.000
#> TCGA.D8.A1Y0.01 2 0.000
#> TCGA.BH.A0GZ.01 2 0.000
#> TCGA.AC.A2FM.11 1 0.000
#> TCGA.B6.A0RM.01 2 0.000
#> TCGA.AR.A2LR.01 3 0.000
#> TCGA.BH.A2L8.01 2 0.000
#> TCGA.AR.A251.01 3 0.000
#> TCGA.AO.A12B.01 2 0.000
#> TCGA.BH.A202.01 2 0.000
#> TCGA.A7.A0D9.11 1 0.000
#> TCGA.BH.A0DH.01 2 0.000
#> TCGA.D8.A1JN.01 2 0.000
#> TCGA.EW.A1OV.01 2 0.000
#> TCGA.E2.A1IE.01 2 0.000
#> TCGA.AR.A1AR.01 3 0.000
#> TCGA.EW.A1P3.01 2 0.000
#> TCGA.BH.A8FY.01 2 0.000
#> TCGA.A1.A0SN.01 2 0.000
#> TCGA.E9.A295.01 2 0.000
#> TCGA.AO.A1KT.01 2 0.000
#> TCGA.AC.A2FB.11 1 0.000
#> TCGA.E2.A1IU.01 2 0.000
#> TCGA.AO.A0JL.01 3 0.000
#> TCGA.AC.A8OP.01 2 0.000
#> TCGA.E2.A1LS.11 1 0.000
#> TCGA.EW.A1P8.01 3 0.000
#> TCGA.GI.A2C8.01 2 0.000
#> TCGA.AR.A24P.01 2 0.000
#> TCGA.BH.A0BT.11 1 0.000
#> TCGA.BH.A0C0.11 1 0.000
#> TCGA.E9.A22H.01 2 0.000
#> TCGA.D8.A3Z6.01 2 0.000
#> TCGA.AR.A0U4.01 3 0.000
#> TCGA.AR.A2LK.01 2 0.000
#> TCGA.B6.A409.01 3 0.000
#> TCGA.E2.A1BC.11 1 0.000
#> TCGA.B6.A0X1.01 3 0.000
#> TCGA.A2.A0SX.01 3 0.000
#> TCGA.BH.A0C3.11 1 0.000
#> TCGA.BH.A0B2.01 2 0.000
#> TCGA.B6.A0RI.01 2 0.000
#> TCGA.E9.A248.01 1 0.000
#> TCGA.A2.A0SU.01 2 0.000
#> TCGA.BH.A204.11 1 0.000
#> TCGA.EW.A1P4.01 3 0.000
#> TCGA.AO.A128.01 3 0.000
#> TCGA.AR.A24T.01 2 0.000
#> TCGA.A8.A08O.01 2 0.000
#> TCGA.EW.A1P6.01 2 0.000
#> TCGA.AC.A2FE.01 2 0.000
#> TCGA.GM.A2DF.01 3 0.000
#> TCGA.D8.A1XF.01 2 0.000
#> TCGA.E9.A1N4.01 2 0.000
#> TCGA.A2.A0CT.01 2 0.000
#> TCGA.E9.A1RG.01 2 0.000
#> TCGA.XX.A899.01 2 0.000
#> TCGA.BH.A1F2.01 2 0.000
#> TCGA.GM.A3XG.01 1 0.000
#> TCGA.E9.A1N9.01 2 0.000
#> TCGA.A1.A0SP.01 3 0.000
#> TCGA.E9.A1NF.11 1 0.000
#> TCGA.AN.A0XT.01 2 0.000
#> TCGA.S3.AA17.01 2 0.000
#> TCGA.BH.A1EN.11 1 0.000
#> TCGA.BH.A0DZ.11 1 0.000
#> TCGA.AC.A2FF.01 1 0.000
#> TCGA.BH.A0HI.01 2 0.000
#> TCGA.E9.A1N5.11 1 0.498
#> TCGA.EW.A1PF.01 2 0.000
#> TCGA.B6.A0RL.01 2 0.000
#> TCGA.E2.A1L9.01 2 0.000
#> TCGA.A7.A26E.01 2 0.000
#> TCGA.BH.A0W3.01 2 0.000
#> TCGA.AO.A03L.01 2 0.000
#> TCGA.D8.A1J9.01 2 0.000
#> TCGA.LL.A7T0.01 2 0.000
#> TCGA.OL.A66O.01 2 0.000
#> TCGA.A7.A0CE.11 1 0.000
#> TCGA.AO.A03N.01 2 0.000
#> TCGA.BH.A0HF.01 2 0.000
#> TCGA.E2.A1LG.01 3 1.000
#> TCGA.A7.A6VY.01 3 0.000
#> TCGA.AC.A2QI.01 2 0.000
#> TCGA.A2.A4S2.01 2 0.000
#> TCGA.AR.A1AP.01 2 0.000
#> TCGA.EW.A1PC.01 2 0.000
#> TCGA.GM.A2DA.01 2 0.000
#> TCGA.3C.AALJ.01 2 0.000
#> TCGA.BH.A42T.01 2 0.000
#> TCGA.A7.A4SA.01 2 0.000
#> TCGA.A7.A26G.01 3 0.000
#> TCGA.A2.A0YJ.01 3 0.000
#> TCGA.A2.A3KC.01 2 0.000
#> TCGA.OL.A66L.01 2 0.000
#> TCGA.AR.A2LM.01 2 0.000
#> TCGA.E2.A10C.01 2 0.000
#> TCGA.AC.A7VC.01 3 1.000
#> TCGA.AR.A1AN.01 2 0.000
#> TCGA.5L.AAT1.01 2 0.000
#> TCGA.HN.A2OB.01 2 0.000
#> TCGA.GM.A5PV.01 2 0.000
#> TCGA.C8.A26V.01 2 0.000
#> TCGA.BH.A1EV.01 2 0.000
#> TCGA.E2.A1IJ.01 2 0.000
#> TCGA.LL.A440.01 1 0.000
#> TCGA.OK.A5Q2.01 1 0.000
#> TCGA.BH.A1FG.11 1 0.000
#> TCGA.OL.A66I.01 3 0.000
#> TCGA.A7.A6VW.01 3 0.000
#> TCGA.D8.A1JA.01 2 0.000
#> TCGA.AC.A2FF.11 1 0.000
#> TCGA.E9.A1R3.01 2 0.000
#> TCGA.E2.A1IN.01 2 0.000
#> TCGA.AR.A254.01 2 0.000
#> TCGA.AR.A0TW.01 2 0.000
#> TCGA.B6.A0I1.01 3 0.000
#> TCGA.BH.A8G0.01 1 0.000
#> TCGA.B6.A401.01 2 0.000
#> TCGA.BH.A0H9.01 2 0.000
#> TCGA.E2.A1LB.01 2 0.000
#> TCGA.B6.A0RG.01 2 0.000
#> TCGA.E9.A54X.01 2 0.000
#> TCGA.C8.A1HN.01 2 0.000
#> TCGA.LD.A9QF.01 1 0.000
#> TCGA.BH.A0HB.01 2 0.000
#> TCGA.LL.A73Y.01 3 0.000
#> TCGA.C8.A1HJ.01 3 0.000
#> TCGA.BH.A0W5.01 1 0.000
#> TCGA.A2.A25E.01 2 0.000
#> TCGA.AC.A3W7.01 2 0.000
#> TCGA.B6.A1KN.01 2 0.000
#> TCGA.A2.A1G1.01 3 0.000
#> TCGA.AC.A3W5.01 2 0.000
#> TCGA.A7.A13D.01 3 0.000
#> TCGA.A2.A3XY.01 3 0.000
#> TCGA.B6.A1KI.01 2 0.000
#> TCGA.AR.A24K.01 2 0.000
#> TCGA.E9.A1RI.01 2 0.000
#> TCGA.GM.A2DI.01 1 0.000
#> TCGA.A2.A0T6.01 2 0.000
#> TCGA.EW.A1OZ.01 2 0.000
#> TCGA.EW.A3E8.01 2 0.000
#> TCGA.OL.A5RU.01 2 0.000
#> TCGA.S3.AA12.01 2 0.000
#> TCGA.A2.A1FX.01 2 0.000
#> TCGA.BH.A0B8.11 1 0.000
#> TCGA.BH.A0AZ.11 1 0.000
#> TCGA.A7.A13G.01 2 0.000
#> TCGA.E2.A10F.01 2 0.000
#> TCGA.A7.A4SD.01 3 0.000
#> TCGA.BH.A0C3.01 2 0.000
#> TCGA.B6.A0RV.01 2 0.000
#> TCGA.LQ.A4E4.01 2 0.000
#> TCGA.AQ.A1H2.01 2 0.000
#> TCGA.D8.A27T.01 2 0.000
#> TCGA.E2.A1IH.01 2 0.000
#> TCGA.BH.A0DQ.11 1 0.000
#> TCGA.EW.A1IY.01 2 0.000
#> TCGA.B6.A0X4.01 2 0.000
#> TCGA.AR.A24O.01 2 0.000
#> TCGA.BH.A0HY.01 2 0.000
#> TCGA.E2.A15I.01 2 0.000
#> TCGA.D8.A1XQ.01 3 0.000
#> TCGA.C8.A278.01 2 0.000
#> TCGA.AC.A3HN.01 2 0.000
#> TCGA.BH.A1FB.11 1 0.000
#> TCGA.AC.A3BB.01 2 0.000
#> TCGA.A2.A0EU.01 2 0.000
#> TCGA.BH.A1FE.01 2 0.249
#> TCGA.BH.A0H7.01 2 0.000
#> TCGA.A2.A0EN.01 2 0.000
#> TCGA.BH.A1FE.06 1 0.000
#> TCGA.BH.A0BF.01 2 0.000
#> TCGA.A1.A0SG.01 2 0.000
#> TCGA.AC.A6IW.01 3 0.000
#> TCGA.EW.A1J5.01 2 0.000
#> TCGA.WT.AB41.01 2 0.000
#> TCGA.LL.A5YL.01 2 0.000
#> TCGA.D8.A1XR.01 2 0.000
#> TCGA.E9.A1RH.11 1 0.000
#> TCGA.AO.A0JB.01 2 0.000
#> TCGA.A7.A0CH.11 1 0.000
#> TCGA.C8.A27A.01 2 0.000
#> TCGA.AR.A1AK.01 2 0.000
#> TCGA.AC.A3EH.01 2 0.000
#> TCGA.C8.A1HK.01 2 0.000
#> TCGA.B6.A0WZ.01 2 0.000
#> TCGA.GM.A4E0.01 1 0.000
#> TCGA.A8.A0AD.01 2 0.000
#> TCGA.C8.A26X.01 1 0.502
#> TCGA.BH.A5IZ.01 3 0.000
#> TCGA.E9.A22A.01 1 0.000
#> TCGA.A7.A3J1.01 2 0.000
#> TCGA.D8.A1Y3.01 2 0.000
#> TCGA.AC.A3YJ.01 2 0.000
#> TCGA.LL.A8F5.01 3 0.000
#> TCGA.D8.A1XW.01 3 0.000
#> TCGA.D8.A1Y1.01 2 0.000
#> TCGA.BH.A0DK.01 2 0.000
#> TCGA.BH.A1F8.11 1 0.000
#> TCGA.D8.A1JE.01 2 0.000
#> TCGA.EW.A2FR.01 1 1.000
#> TCGA.E2.A105.01 2 0.000
#> TCGA.PL.A8LZ.01 3 0.000
#> TCGA.E9.A1NA.11 1 0.000
#> TCGA.BH.A0W4.01 2 0.000
#> TCGA.BH.A0E2.01 2 0.000
#> TCGA.BH.A0BJ.01 2 0.000
#> TCGA.BH.A203.01 2 0.000
#> TCGA.E2.A1B5.01 1 0.000
#> TCGA.E9.A1R7.01 2 0.000
#> TCGA.E2.A14U.01 2 0.751
#> TCGA.E2.A1LI.11 1 0.000
#> TCGA.E2.A10E.01 2 0.000
#> TCGA.E9.A249.01 2 0.000
#> TCGA.AC.A2BK.01 3 0.000
#> TCGA.BH.A1FD.11 1 0.000
#> TCGA.E2.A1BD.01 2 0.000
#> TCGA.GI.A2C9.01 3 0.000
#> TCGA.E2.A1LK.01 3 0.000
#> TCGA.BH.A1ET.01 2 0.000
#> TCGA.LD.A7W6.01 2 0.000
#> TCGA.C8.A1HE.01 2 0.000
#> TCGA.D8.A1XM.01 2 0.000
#> TCGA.AC.A7VB.01 2 0.000
#> TCGA.D8.A1JH.01 2 0.000
#> TCGA.BH.A1F6.11 1 0.000
#> TCGA.BH.A1ET.11 1 0.000
#> TCGA.E2.A1II.11 1 0.000
#> TCGA.BH.A0HA.11 1 1.000
#> TCGA.AO.A12C.01 2 0.000
#> TCGA.D8.A73W.01 2 0.000
#> TCGA.B6.A40B.01 2 0.000
#> TCGA.AO.A0JI.01 2 0.000
#> TCGA.BH.A1EU.01 2 0.249
#> TCGA.OL.A5D7.01 3 0.000
#> TCGA.A7.A4SE.01 3 0.000
#> TCGA.OL.A97C.01 1 0.000
#> TCGA.PE.A5DD.01 2 0.000
#> TCGA.A2.A04R.01 2 0.000
#> TCGA.BH.A1F5.01 2 0.000
#> TCGA.S3.AA0Z.01 3 0.000
#> TCGA.AC.A23E.01 2 0.000
#> TCGA.BH.A0B3.01 3 0.000
#> TCGA.D8.A1JS.01 2 0.000
#> TCGA.E2.A15K.11 1 0.000
#> TCGA.WT.AB44.01 2 0.000
#> TCGA.EW.A424.01 2 0.000
#> TCGA.BH.A1FR.01 2 0.000
#> TCGA.A7.A425.01 2 0.000
#> TCGA.B6.A0IK.01 2 0.000
#> TCGA.AR.A24U.01 1 0.000
#> TCGA.E9.A1RF.01 2 0.000
#> TCGA.B6.A408.01 2 0.000
#> TCGA.BH.A0HP.01 2 0.000
#> TCGA.E2.A1L7.01 2 0.000
#> TCGA.5T.A9QA.01 2 0.000
#> TCGA.A2.A0SY.01 2 0.000
#> TCGA.BH.A8FZ.01 1 0.000
#> TCGA.A2.A0YG.01 2 0.000
#> TCGA.AC.A2FG.01 2 0.000
#> TCGA.AR.A1AX.01 1 0.000
#> TCGA.AR.A1AL.01 2 0.000
#> TCGA.BH.A1EY.11 1 0.000
#> TCGA.AQ.A54N.01 3 0.000
#> TCGA.BH.A1EO.01 2 0.000
#> TCGA.BH.A0BZ.11 1 0.000
#> TCGA.D8.A27K.01 2 0.000
#> TCGA.BH.A28Q.01 2 0.000
#> TCGA.E9.A1NG.11 1 0.000
#> TCGA.EW.A1J1.01 2 0.000
#> TCGA.C8.A1HG.01 2 0.000
#> TCGA.D8.A1XK.01 3 0.000
#> TCGA.AQ.A0Y5.01 2 0.000
#> TCGA.3C.AAAU.01 2 0.000
#> TCGA.A2.A4S0.01 2 0.000
#> TCGA.BH.A0DV.11 1 0.000
#> TCGA.AR.A1AV.01 2 0.000
#> TCGA.AC.A8OQ.01 3 0.000
#> TCGA.BH.A0BS.11 1 0.000
#> TCGA.EW.A1PB.01 3 0.000
#> TCGA.A7.A3J0.01 2 0.000
#> TCGA.D8.A1JU.01 2 0.000
#> TCGA.A7.A6VX.01 2 0.000
#> TCGA.E2.A108.01 1 0.000
#> TCGA.BH.A0BT.01 2 0.000
#> TCGA.A2.A0YK.01 2 0.000
#> TCGA.E9.A1N8.01 3 0.000
#> TCGA.E2.A574.01 3 0.000
#> TCGA.A1.A0SO.01 3 1.000
#> TCGA.BH.A0DI.01 1 0.000
#> TCGA.E2.A1IG.01 2 0.000
#> TCGA.E2.A107.01 2 0.000
#> TCGA.5L.AAT0.01 2 0.000
#> TCGA.E9.A1NH.01 2 0.000
#> TCGA.D8.A27E.01 2 0.000
#> TCGA.AR.A24Q.01 3 0.000
#> TCGA.BH.A1F0.01 3 0.000
#> TCGA.E9.A1RB.11 1 0.000
#> TCGA.AR.A0U0.01 3 0.000
get_classes(res, k = 4)
#> class p
#> TCGA.OL.A66H.01 4 1.000
#> TCGA.3C.AALK.01 4 1.000
#> TCGA.AC.A5EH.01 4 0.249
#> TCGA.EW.A2FW.01 2 0.000
#> TCGA.E9.A1R0.01 4 0.000
#> TCGA.AR.A1AJ.01 3 0.000
#> TCGA.AC.A62Y.01 4 1.000
#> TCGA.E9.A1QZ.01 1 1.000
#> TCGA.E9.A1R2.01 4 1.000
#> TCGA.E9.A3X8.01 4 0.000
#> TCGA.AR.A255.01 4 0.000
#> TCGA.E2.A10B.01 4 1.000
#> TCGA.E9.A1N4.11 1 0.000
#> TCGA.AO.A0JD.01 4 1.000
#> TCGA.D8.A1JD.01 2 1.000
#> TCGA.D8.A1XA.01 2 0.000
#> TCGA.AO.A1KQ.01 2 0.000
#> TCGA.A8.A0A6.01 4 0.000
#> TCGA.BH.A1F2.11 1 0.000
#> TCGA.A7.A3RF.01 2 0.000
#> TCGA.A2.A0SW.01 2 1.000
#> TCGA.A7.A3IY.01 4 1.000
#> TCGA.GM.A2D9.01 2 0.000
#> TCGA.D8.A3Z5.01 4 0.000
#> TCGA.E9.A1ND.01 3 0.000
#> TCGA.EW.A1P5.01 2 0.000
#> TCGA.E9.A1RD.01 4 1.000
#> TCGA.AR.A1AQ.01 3 0.000
#> TCGA.LD.A66U.01 4 0.000
#> TCGA.BH.A1EN.01 2 1.000
#> TCGA.BH.A1FN.01 2 0.000
#> TCGA.EW.A1PD.01 2 1.000
#> TCGA.E9.A1N5.01 2 1.000
#> TCGA.D8.A1J8.01 2 0.249
#> TCGA.E9.A3QA.01 3 0.000
#> TCGA.S3.AA15.01 3 0.000
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#> TCGA.E2.A1L8.01 2 0.000
#> TCGA.BH.A0HK.11 1 0.000
#> TCGA.AC.A2QH.01 3 0.249
#> TCGA.A2.A0CO.01 4 1.000
#> TCGA.A2.A1FW.01 2 0.000
#> TCGA.BH.A0BM.11 1 0.000
#> TCGA.AC.A62V.01 2 0.000
#> TCGA.E2.A576.01 2 0.000
#> TCGA.GM.A3NW.01 2 0.000
#> TCGA.A7.A4SB.01 2 0.000
#> TCGA.E9.A245.01 2 0.000
#> TCGA.BH.A0AZ.01 4 0.000
#> TCGA.AO.A126.01 2 0.000
#> TCGA.AC.A8OR.01 2 0.000
#> TCGA.E2.A573.01 3 0.000
#> TCGA.E2.A1LE.01 4 0.000
#> TCGA.BH.A0E1.11 1 0.000
#> TCGA.OL.A6VO.01 3 0.000
#> TCGA.A7.A4SF.01 2 0.000
#> TCGA.A2.A0YH.01 4 1.000
#> TCGA.LL.A5YN.01 4 0.000
#> TCGA.AR.A1AO.01 1 0.000
#> TCGA.A2.A3XU.01 3 1.000
#> TCGA.AC.A23G.01 4 0.000
#> TCGA.GM.A3XN.01 4 0.000
#> TCGA.A7.A26J.01 2 0.000
#> TCGA.A2.A25B.01 2 0.000
#> TCGA.D8.A27W.01 2 1.000
#> TCGA.GM.A3XL.01 3 0.000
#> TCGA.E9.A2JS.01 2 0.000
#> TCGA.C8.A275.01 4 0.000
#> TCGA.E2.A1IK.01 4 0.000
#> TCGA.BH.A1FB.01 1 0.000
#> TCGA.C8.A3M8.01 2 0.000
#> TCGA.AN.A0XU.01 3 0.000
#> TCGA.A2.A3XW.01 1 0.000
#> TCGA.A7.A6VV.01 3 0.000
#> TCGA.BH.A1FE.11 1 0.000
#> TCGA.A7.A0DC.11 1 0.000
#> TCGA.D8.A1XU.01 2 1.000
#> TCGA.BH.A1ES.06 2 0.000
#> TCGA.D8.A1X6.01 2 0.000
#> TCGA.EW.A3U0.01 3 0.000
#> TCGA.AQ.A7U7.01 4 0.249
#> TCGA.A1.A0SI.01 4 0.000
#> TCGA.A2.A25A.01 4 0.000
#> TCGA.PL.A8LX.01 2 0.000
#> TCGA.E9.A1RH.01 4 0.000
#> TCGA.AO.A12E.01 4 0.000
#> TCGA.A7.A13H.01 4 0.000
#> TCGA.AO.A0JC.01 1 0.000
#> TCGA.EW.A6SA.01 2 0.000
#> TCGA.E9.A1R5.01 2 0.000
#> TCGA.E9.A54Y.01 2 0.000
#> TCGA.E9.A243.01 3 0.000
#> TCGA.AC.A3TN.01 2 0.000
#> TCGA.E2.A1IO.01 4 0.000
#> TCGA.OL.A5S0.01 3 0.000
#> TCGA.C8.A26Y.01 4 0.000
#> TCGA.A2.A25D.01 4 1.000
#> TCGA.EW.A1J3.01 2 0.000
#> TCGA.A2.A0EP.01 1 0.000
#> TCGA.BH.A1F8.01 2 0.000
#> TCGA.B6.A0X5.01 2 0.000
#> TCGA.AN.A0XW.01 4 0.000
#> TCGA.BH.A0AW.01 4 0.000
#> TCGA.BH.A0BJ.11 1 0.000
#> TCGA.D8.A27F.01 3 0.000
#> TCGA.BH.A0B6.01 4 0.000
#> TCGA.E9.A229.01 4 1.000
#> TCGA.D8.A1JK.01 4 0.000
#> TCGA.AQ.A04L.01 2 0.000
#> TCGA.B6.A0WV.01 2 0.000
#> TCGA.E2.A1LI.01 3 0.000
#> TCGA.A7.A26F.01 3 0.498
#> TCGA.GM.A5PX.01 4 0.000
#> TCGA.BH.A1FD.01 2 0.000
#> TCGA.A7.A13F.01 2 0.000
#> TCGA.AR.A5QN.01 4 1.000
#> TCGA.E2.A2P5.01 2 0.000
#> TCGA.AO.A1KS.01 2 0.000
#> TCGA.BH.A42U.01 1 0.000
#> TCGA.BH.A0DD.01 2 0.000
#> TCGA.B6.A0RE.01 3 0.000
#> TCGA.BH.A208.01 4 1.000
#> TCGA.EW.A1IX.01 4 0.000
#> TCGA.BH.A1F6.01 3 0.000
#> TCGA.BH.A0HX.01 2 0.000
#> TCGA.E2.A14N.01 3 0.000
#> TCGA.A2.A259.01 4 0.000
#> TCGA.GM.A2DD.01 4 0.249
#> TCGA.E2.A1B1.01 4 1.000
#> TCGA.D8.A73U.01 4 0.000
#> TCGA.D8.A27N.01 4 1.000
#> TCGA.D8.A1X9.01 2 0.000
#> TCGA.OL.A5RW.01 3 0.000
#> TCGA.AR.A0TR.01 2 0.000
#> TCGA.BH.A1F5.11 1 0.000
#> TCGA.BH.A1EO.11 1 0.000
#> TCGA.E9.A22E.01 4 0.000
#> TCGA.OL.A5RX.01 4 0.000
#> TCGA.A7.A0DC.01 2 0.000
#> TCGA.D8.A1XO.01 4 1.000
#> TCGA.AC.A23C.01 4 0.000
#> TCGA.E9.A1NE.01 1 0.498
#> TCGA.A7.A56D.01 4 1.000
#> TCGA.A1.A0SH.01 4 0.000
#> TCGA.C8.A9FZ.01 2 0.000
#> TCGA.C8.A8HR.01 1 0.000
#> TCGA.BH.A6R9.01 1 0.502
#> TCGA.AR.A5QP.01 4 0.000
#> TCGA.C8.A8HP.01 1 1.000
#> TCGA.AR.A24X.01 2 0.000
#> TCGA.A1.A0SB.01 3 0.000
#> TCGA.D8.A1Y0.01 4 1.000
#> TCGA.BH.A0GZ.01 2 0.000
#> TCGA.AC.A2FM.11 1 0.000
#> TCGA.B6.A0RM.01 2 0.000
#> TCGA.AR.A2LR.01 3 0.000
#> TCGA.BH.A2L8.01 4 0.000
#> TCGA.AR.A251.01 3 0.000
#> TCGA.AO.A12B.01 2 0.000
#> TCGA.BH.A202.01 4 0.000
#> TCGA.A7.A0D9.11 1 0.000
#> TCGA.BH.A0DH.01 2 0.000
#> TCGA.D8.A1JN.01 2 0.000
#> TCGA.EW.A1OV.01 4 0.000
#> TCGA.E2.A1IE.01 2 0.000
#> TCGA.AR.A1AR.01 3 0.000
#> TCGA.EW.A1P3.01 2 0.000
#> TCGA.BH.A8FY.01 2 0.000
#> TCGA.A1.A0SN.01 4 1.000
#> TCGA.E9.A295.01 4 1.000
#> TCGA.AO.A1KT.01 2 0.000
#> TCGA.AC.A2FB.11 1 0.000
#> TCGA.E2.A1IU.01 2 1.000
#> TCGA.AO.A0JL.01 3 0.000
#> TCGA.AC.A8OP.01 4 1.000
#> TCGA.E2.A1LS.11 1 0.000
#> TCGA.EW.A1P8.01 3 0.000
#> TCGA.GI.A2C8.01 4 0.000
#> TCGA.AR.A24P.01 4 1.000
#> TCGA.BH.A0BT.11 1 0.000
#> TCGA.BH.A0C0.11 1 0.000
#> TCGA.E9.A22H.01 2 0.000
#> TCGA.D8.A3Z6.01 2 1.000
#> TCGA.AR.A0U4.01 3 0.000
#> TCGA.AR.A2LK.01 2 0.000
#> TCGA.B6.A409.01 3 0.000
#> TCGA.E2.A1BC.11 1 0.000
#> TCGA.B6.A0X1.01 3 0.000
#> TCGA.A2.A0SX.01 3 0.000
#> TCGA.BH.A0C3.11 1 0.000
#> TCGA.BH.A0B2.01 4 0.000
#> TCGA.B6.A0RI.01 2 0.000
#> TCGA.E9.A248.01 1 1.000
#> TCGA.A2.A0SU.01 4 0.000
#> TCGA.BH.A204.11 1 0.000
#> TCGA.EW.A1P4.01 3 0.000
#> TCGA.AO.A128.01 3 0.000
#> TCGA.AR.A24T.01 4 0.000
#> TCGA.A8.A08O.01 2 0.000
#> TCGA.EW.A1P6.01 2 0.000
#> TCGA.AC.A2FE.01 4 0.000
#> TCGA.GM.A2DF.01 3 0.000
#> TCGA.D8.A1XF.01 2 0.000
#> TCGA.E9.A1N4.01 4 1.000
#> TCGA.A2.A0CT.01 2 0.000
#> TCGA.E9.A1RG.01 2 0.000
#> TCGA.XX.A899.01 4 0.000
#> TCGA.BH.A1F2.01 2 0.000
#> TCGA.GM.A3XG.01 1 0.000
#> TCGA.E9.A1N9.01 4 1.000
#> TCGA.A1.A0SP.01 3 0.000
#> TCGA.E9.A1NF.11 1 0.000
#> TCGA.AN.A0XT.01 2 0.000
#> TCGA.S3.AA17.01 4 0.000
#> TCGA.BH.A1EN.11 1 0.000
#> TCGA.BH.A0DZ.11 1 0.000
#> TCGA.AC.A2FF.01 1 0.000
#> TCGA.BH.A0HI.01 2 0.751
#> TCGA.E9.A1N5.11 1 0.000
#> TCGA.EW.A1PF.01 4 0.000
#> TCGA.B6.A0RL.01 2 0.000
#> TCGA.E2.A1L9.01 2 1.000
#> TCGA.A7.A26E.01 2 0.000
#> TCGA.BH.A0W3.01 2 0.000
#> TCGA.AO.A03L.01 4 1.000
#> TCGA.D8.A1J9.01 2 0.000
#> TCGA.LL.A7T0.01 2 0.000
#> TCGA.OL.A66O.01 2 0.000
#> TCGA.A7.A0CE.11 1 0.000
#> TCGA.AO.A03N.01 2 0.000
#> TCGA.BH.A0HF.01 4 0.000
#> TCGA.E2.A1LG.01 3 1.000
#> TCGA.A7.A6VY.01 3 0.000
#> TCGA.AC.A2QI.01 4 1.000
#> TCGA.A2.A4S2.01 4 0.000
#> TCGA.AR.A1AP.01 2 0.000
#> TCGA.EW.A1PC.01 2 0.000
#> TCGA.GM.A2DA.01 4 0.000
#> TCGA.3C.AALJ.01 2 0.000
#> TCGA.BH.A42T.01 2 0.000
#> TCGA.A7.A4SA.01 4 0.000
#> TCGA.A7.A26G.01 3 0.747
#> TCGA.A2.A0YJ.01 3 0.000
#> TCGA.A2.A3KC.01 4 0.000
#> TCGA.OL.A66L.01 4 1.000
#> TCGA.AR.A2LM.01 4 0.000
#> TCGA.E2.A10C.01 4 1.000
#> TCGA.AC.A7VC.01 3 0.498
#> TCGA.AR.A1AN.01 4 0.000
#> TCGA.5L.AAT1.01 4 0.000
#> TCGA.HN.A2OB.01 4 0.000
#> TCGA.GM.A5PV.01 4 1.000
#> TCGA.C8.A26V.01 2 0.000
#> TCGA.BH.A1EV.01 2 0.000
#> TCGA.E2.A1IJ.01 4 0.000
#> TCGA.LL.A440.01 1 0.000
#> TCGA.OK.A5Q2.01 4 0.000
#> TCGA.BH.A1FG.11 1 0.000
#> TCGA.OL.A66I.01 3 0.000
#> TCGA.A7.A6VW.01 3 0.000
#> TCGA.D8.A1JA.01 2 0.000
#> TCGA.AC.A2FF.11 1 0.000
#> TCGA.E9.A1R3.01 4 1.000
#> TCGA.E2.A1IN.01 2 0.000
#> TCGA.AR.A254.01 4 0.000
#> TCGA.AR.A0TW.01 4 1.000
#> TCGA.B6.A0I1.01 3 0.000
#> TCGA.BH.A8G0.01 4 1.000
#> TCGA.B6.A401.01 4 0.000
#> TCGA.BH.A0H9.01 2 0.000
#> TCGA.E2.A1LB.01 4 1.000
#> TCGA.B6.A0RG.01 2 0.000
#> TCGA.E9.A54X.01 2 0.000
#> TCGA.C8.A1HN.01 2 0.000
#> TCGA.LD.A9QF.01 1 0.000
#> TCGA.BH.A0HB.01 2 0.000
#> TCGA.LL.A73Y.01 3 0.000
#> TCGA.C8.A1HJ.01 3 0.000
#> TCGA.BH.A0W5.01 4 0.000
#> TCGA.A2.A25E.01 2 0.000
#> TCGA.AC.A3W7.01 4 1.000
#> TCGA.B6.A1KN.01 2 0.000
#> TCGA.A2.A1G1.01 3 0.000
#> TCGA.AC.A3W5.01 4 0.000
#> TCGA.A7.A13D.01 3 0.000
#> TCGA.A2.A3XY.01 3 0.000
#> TCGA.B6.A1KI.01 4 0.000
#> TCGA.AR.A24K.01 2 0.000
#> TCGA.E9.A1RI.01 4 0.000
#> TCGA.GM.A2DI.01 1 0.249
#> TCGA.A2.A0T6.01 4 0.000
#> TCGA.EW.A1OZ.01 2 0.000
#> TCGA.EW.A3E8.01 4 0.000
#> TCGA.OL.A5RU.01 4 0.000
#> TCGA.S3.AA12.01 2 0.000
#> TCGA.A2.A1FX.01 2 0.000
#> TCGA.BH.A0B8.11 1 0.000
#> TCGA.BH.A0AZ.11 1 0.000
#> TCGA.A7.A13G.01 2 0.000
#> TCGA.E2.A10F.01 4 0.000
#> TCGA.A7.A4SD.01 3 0.000
#> TCGA.BH.A0C3.01 4 0.000
#> TCGA.B6.A0RV.01 4 0.000
#> TCGA.LQ.A4E4.01 2 0.000
#> TCGA.AQ.A1H2.01 2 0.000
#> TCGA.D8.A27T.01 2 1.000
#> TCGA.E2.A1IH.01 4 1.000
#> TCGA.BH.A0DQ.11 1 0.000
#> TCGA.EW.A1IY.01 4 0.000
#> TCGA.B6.A0X4.01 2 0.000
#> TCGA.AR.A24O.01 4 0.000
#> TCGA.BH.A0HY.01 2 0.000
#> TCGA.E2.A15I.01 2 1.000
#> TCGA.D8.A1XQ.01 3 0.000
#> TCGA.C8.A278.01 4 0.000
#> TCGA.AC.A3HN.01 4 0.000
#> TCGA.BH.A1FB.11 1 0.000
#> TCGA.AC.A3BB.01 4 0.000
#> TCGA.A2.A0EU.01 2 0.000
#> TCGA.BH.A1FE.01 4 0.000
#> TCGA.BH.A0H7.01 2 0.000
#> TCGA.A2.A0EN.01 4 0.000
#> TCGA.BH.A1FE.06 1 0.000
#> TCGA.BH.A0BF.01 4 0.000
#> TCGA.A1.A0SG.01 2 0.000
#> TCGA.AC.A6IW.01 3 0.000
#> TCGA.EW.A1J5.01 2 0.000
#> TCGA.WT.AB41.01 4 0.000
#> TCGA.LL.A5YL.01 4 0.249
#> TCGA.D8.A1XR.01 2 0.000
#> TCGA.E9.A1RH.11 1 0.000
#> TCGA.AO.A0JB.01 2 0.000
#> TCGA.A7.A0CH.11 1 0.000
#> TCGA.C8.A27A.01 2 0.000
#> TCGA.AR.A1AK.01 4 0.000
#> TCGA.AC.A3EH.01 2 0.000
#> TCGA.C8.A1HK.01 2 0.000
#> TCGA.B6.A0WZ.01 2 0.000
#> TCGA.GM.A4E0.01 1 0.249
#> TCGA.A8.A0AD.01 2 0.000
#> TCGA.C8.A26X.01 4 0.000
#> TCGA.BH.A5IZ.01 3 0.000
#> TCGA.E9.A22A.01 1 0.000
#> TCGA.A7.A3J1.01 4 0.000
#> TCGA.D8.A1Y3.01 4 1.000
#> TCGA.AC.A3YJ.01 2 0.000
#> TCGA.LL.A8F5.01 3 0.000
#> TCGA.D8.A1XW.01 3 0.000
#> TCGA.D8.A1Y1.01 2 0.000
#> TCGA.BH.A0DK.01 4 0.000
#> TCGA.BH.A1F8.11 1 0.000
#> TCGA.D8.A1JE.01 4 1.000
#> TCGA.EW.A2FR.01 4 0.000
#> TCGA.E2.A105.01 2 0.000
#> TCGA.PL.A8LZ.01 3 0.000
#> TCGA.E9.A1NA.11 1 0.000
#> TCGA.BH.A0W4.01 4 0.249
#> TCGA.BH.A0E2.01 2 0.000
#> TCGA.BH.A0BJ.01 4 0.000
#> TCGA.BH.A203.01 4 0.000
#> TCGA.E2.A1B5.01 1 0.000
#> TCGA.E9.A1R7.01 2 0.000
#> TCGA.E2.A14U.01 4 0.000
#> TCGA.E2.A1LI.11 1 0.000
#> TCGA.E2.A10E.01 2 0.000
#> TCGA.E9.A249.01 2 0.000
#> TCGA.AC.A2BK.01 3 0.000
#> TCGA.BH.A1FD.11 1 0.000
#> TCGA.E2.A1BD.01 2 0.000
#> TCGA.GI.A2C9.01 3 0.000
#> TCGA.E2.A1LK.01 3 0.000
#> TCGA.BH.A1ET.01 2 0.000
#> TCGA.LD.A7W6.01 2 0.000
#> TCGA.C8.A1HE.01 2 0.000
#> TCGA.D8.A1XM.01 4 0.000
#> TCGA.AC.A7VB.01 2 0.000
#> TCGA.D8.A1JH.01 4 0.000
#> TCGA.BH.A1F6.11 1 0.000
#> TCGA.BH.A1ET.11 1 0.000
#> TCGA.E2.A1II.11 1 0.000
#> TCGA.BH.A0HA.11 1 0.000
#> TCGA.AO.A12C.01 2 0.000
#> TCGA.D8.A73W.01 2 0.502
#> TCGA.B6.A40B.01 2 1.000
#> TCGA.AO.A0JI.01 2 0.000
#> TCGA.BH.A1EU.01 4 0.000
#> TCGA.OL.A5D7.01 3 0.000
#> TCGA.A7.A4SE.01 3 0.000
#> TCGA.OL.A97C.01 1 1.000
#> TCGA.PE.A5DD.01 2 0.000
#> TCGA.A2.A04R.01 2 0.000
#> TCGA.BH.A1F5.01 2 0.000
#> TCGA.S3.AA0Z.01 3 0.000
#> TCGA.AC.A23E.01 2 0.000
#> TCGA.BH.A0B3.01 3 0.000
#> TCGA.D8.A1JS.01 2 0.000
#> TCGA.E2.A15K.11 1 0.000
#> TCGA.WT.AB44.01 2 0.000
#> TCGA.EW.A424.01 2 0.000
#> TCGA.BH.A1FR.01 4 0.751
#> TCGA.A7.A425.01 4 0.000
#> TCGA.B6.A0IK.01 4 0.000
#> TCGA.AR.A24U.01 1 1.000
#> TCGA.E9.A1RF.01 4 0.000
#> TCGA.B6.A408.01 2 0.000
#> TCGA.BH.A0HP.01 4 0.000
#> TCGA.E2.A1L7.01 2 1.000
#> TCGA.5T.A9QA.01 2 0.000
#> TCGA.A2.A0SY.01 2 0.000
#> TCGA.BH.A8FZ.01 4 0.249
#> TCGA.A2.A0YG.01 2 0.000
#> TCGA.AC.A2FG.01 4 0.000
#> TCGA.AR.A1AX.01 1 0.000
#> TCGA.AR.A1AL.01 4 0.000
#> TCGA.BH.A1EY.11 1 0.000
#> TCGA.AQ.A54N.01 3 0.000
#> TCGA.BH.A1EO.01 4 1.000
#> TCGA.BH.A0BZ.11 1 0.000
#> TCGA.D8.A27K.01 4 0.000
#> TCGA.BH.A28Q.01 2 0.000
#> TCGA.E9.A1NG.11 1 0.000
#> TCGA.EW.A1J1.01 2 0.000
#> TCGA.C8.A1HG.01 4 1.000
#> TCGA.D8.A1XK.01 3 0.000
#> TCGA.AQ.A0Y5.01 2 1.000
#> TCGA.3C.AAAU.01 2 0.000
#> TCGA.A2.A4S0.01 2 0.000
#> TCGA.BH.A0DV.11 1 0.000
#> TCGA.AR.A1AV.01 2 0.000
#> TCGA.AC.A8OQ.01 3 0.000
#> TCGA.BH.A0BS.11 1 0.000
#> TCGA.EW.A1PB.01 3 0.000
#> TCGA.A7.A3J0.01 2 0.000
#> TCGA.D8.A1JU.01 4 0.000
#> TCGA.A7.A6VX.01 2 0.000
#> TCGA.E2.A108.01 1 0.000
#> TCGA.BH.A0BT.01 2 0.000
#> TCGA.A2.A0YK.01 4 0.000
#> TCGA.E9.A1N8.01 3 0.000
#> TCGA.E2.A574.01 3 0.000
#> TCGA.A1.A0SO.01 3 1.000
#> TCGA.BH.A0DI.01 4 0.000
#> TCGA.E2.A1IG.01 2 0.000
#> TCGA.E2.A107.01 4 1.000
#> TCGA.5L.AAT0.01 4 0.000
#> TCGA.E9.A1NH.01 2 0.000
#> TCGA.D8.A27E.01 4 0.249
#> TCGA.AR.A24Q.01 3 0.000
#> TCGA.BH.A1F0.01 3 0.000
#> TCGA.E9.A1RB.11 1 0.000
#> TCGA.AR.A0U0.01 3 0.000
get_classes(res, k = 5)
#> class p
#> TCGA.OL.A66H.01 5 1.000
#> TCGA.3C.AALK.01 5 1.000
#> TCGA.AC.A5EH.01 4 1.000
#> TCGA.EW.A2FW.01 2 1.000
#> TCGA.E9.A1R0.01 4 0.000
#> TCGA.AR.A1AJ.01 3 0.000
#> TCGA.AC.A62Y.01 5 0.000
#> TCGA.E9.A1QZ.01 4 1.000
#> TCGA.E9.A1R2.01 5 1.000
#> TCGA.E9.A3X8.01 4 0.000
#> TCGA.AR.A255.01 4 1.000
#> TCGA.E2.A10B.01 4 1.000
#> TCGA.E9.A1N4.11 1 0.498
#> TCGA.AO.A0JD.01 4 1.000
#> TCGA.D8.A1JD.01 5 1.000
#> TCGA.D8.A1XA.01 2 0.000
#> TCGA.AO.A1KQ.01 5 0.000
#> TCGA.A8.A0A6.01 4 0.000
#> TCGA.BH.A1F2.11 1 0.000
#> TCGA.A7.A3RF.01 5 1.000
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#> TCGA.AR.A5QQ.01 3 1.000
#> TCGA.D8.A1XG.01 5 0.000
#> TCGA.AR.A0TZ.01 2 0.000
#> TCGA.AR.A0U3.01 2 0.000
#> TCGA.A2.A0YE.01 3 1.000
#> TCGA.BH.A0HN.01 2 1.000
#> TCGA.E2.A1LB.11 1 0.747
#> TCGA.AO.A0JF.01 4 0.000
#> TCGA.A2.A0T0.01 3 1.000
#> TCGA.EW.A1OX.01 2 0.000
#> TCGA.AR.A24V.01 5 1.000
#> TCGA.AN.A0XS.01 5 0.498
#> TCGA.C8.A8HQ.01 5 1.000
#> TCGA.AC.A2B8.01 4 0.000
#> TCGA.A2.A4S3.01 4 0.000
#> TCGA.A2.A0CR.01 4 1.000
#> TCGA.BH.A1FH.11 1 0.000
#> TCGA.BH.A1FJ.11 1 0.000
#> TCGA.LL.A6FP.01 2 0.249
#> TCGA.E2.A1L8.01 5 0.249
#> TCGA.BH.A0HK.11 1 0.000
#> TCGA.AC.A2QH.01 3 1.000
#> TCGA.A2.A0CO.01 5 1.000
#> TCGA.A2.A1FW.01 2 0.000
#> TCGA.BH.A0BM.11 1 0.000
#> TCGA.AC.A62V.01 2 0.502
#> TCGA.E2.A576.01 2 0.000
#> TCGA.GM.A3NW.01 2 0.249
#> TCGA.A7.A4SB.01 5 1.000
#> TCGA.E9.A245.01 5 0.000
#> TCGA.BH.A0AZ.01 4 0.000
#> TCGA.AO.A126.01 2 0.498
#> TCGA.AC.A8OR.01 5 0.249
#> TCGA.E2.A573.01 3 0.000
#> TCGA.E2.A1LE.01 4 0.000
#> TCGA.BH.A0E1.11 1 0.000
#> TCGA.OL.A6VO.01 3 0.000
#> TCGA.A7.A4SF.01 2 1.000
#> TCGA.A2.A0YH.01 5 1.000
#> TCGA.LL.A5YN.01 4 0.000
#> TCGA.AR.A1AO.01 1 0.747
#> TCGA.A2.A3XU.01 3 1.000
#> TCGA.AC.A23G.01 4 0.000
#> TCGA.GM.A3XN.01 4 0.000
#> TCGA.A7.A26J.01 2 1.000
#> TCGA.A2.A25B.01 2 0.249
#> TCGA.D8.A27W.01 5 1.000
#> TCGA.GM.A3XL.01 3 0.000
#> TCGA.E9.A2JS.01 2 0.000
#> TCGA.C8.A275.01 4 0.000
#> TCGA.E2.A1IK.01 4 0.000
#> TCGA.BH.A1FB.01 1 1.000
#> TCGA.C8.A3M8.01 2 0.751
#> TCGA.AN.A0XU.01 3 0.000
#> TCGA.A2.A3XW.01 1 1.000
#> TCGA.A7.A6VV.01 3 0.747
#> TCGA.BH.A1FE.11 1 0.000
#> TCGA.A7.A0DC.11 1 1.000
#> TCGA.D8.A1XU.01 5 0.249
#> TCGA.BH.A1ES.06 2 0.249
#> TCGA.D8.A1X6.01 2 1.000
#> TCGA.EW.A3U0.01 3 0.747
#> TCGA.AQ.A7U7.01 4 0.000
#> TCGA.A1.A0SI.01 4 1.000
#> TCGA.A2.A25A.01 4 0.000
#> TCGA.PL.A8LX.01 5 0.253
#> TCGA.E9.A1RH.01 4 0.000
#> TCGA.AO.A12E.01 4 1.000
#> TCGA.A7.A13H.01 4 0.000
#> TCGA.AO.A0JC.01 1 0.249
#> TCGA.EW.A6SA.01 2 0.000
#> TCGA.E9.A1R5.01 2 1.000
#> TCGA.E9.A54Y.01 2 0.000
#> TCGA.E9.A243.01 3 1.000
#> TCGA.AC.A3TN.01 2 0.000
#> TCGA.E2.A1IO.01 4 0.000
#> TCGA.OL.A5S0.01 3 0.000
#> TCGA.C8.A26Y.01 4 0.000
#> TCGA.A2.A25D.01 5 1.000
#> TCGA.EW.A1J3.01 2 1.000
#> TCGA.A2.A0EP.01 1 0.249
#> TCGA.BH.A1F8.01 2 1.000
#> TCGA.B6.A0X5.01 5 1.000
#> TCGA.AN.A0XW.01 4 0.000
#> TCGA.BH.A0AW.01 4 0.253
#> TCGA.BH.A0BJ.11 1 0.000
#> TCGA.D8.A27F.01 3 0.000
#> TCGA.BH.A0B6.01 4 0.000
#> TCGA.E9.A229.01 5 0.249
#> TCGA.D8.A1JK.01 4 0.000
#> TCGA.AQ.A04L.01 2 0.000
#> TCGA.B6.A0WV.01 2 0.000
#> TCGA.E2.A1LI.01 3 0.000
#> TCGA.A7.A26F.01 3 1.000
#> TCGA.GM.A5PX.01 4 0.000
#> TCGA.BH.A1FD.01 2 0.498
#> TCGA.A7.A13F.01 2 0.000
#> TCGA.AR.A5QN.01 5 1.000
#> TCGA.E2.A2P5.01 2 0.502
#> TCGA.AO.A1KS.01 2 0.000
#> TCGA.BH.A42U.01 1 1.000
#> TCGA.BH.A0DD.01 2 0.000
#> TCGA.B6.A0RE.01 3 0.000
#> TCGA.BH.A208.01 4 0.253
#> TCGA.EW.A1IX.01 4 0.747
#> TCGA.BH.A1F6.01 3 0.000
#> TCGA.BH.A0HX.01 2 1.000
#> TCGA.E2.A14N.01 3 0.249
#> TCGA.A2.A259.01 4 0.000
#> TCGA.GM.A2DD.01 4 1.000
#> TCGA.E2.A1B1.01 4 1.000
#> TCGA.D8.A73U.01 4 0.000
#> TCGA.D8.A27N.01 4 1.000
#> TCGA.D8.A1X9.01 2 0.249
#> TCGA.OL.A5RW.01 3 0.000
#> TCGA.AR.A0TR.01 2 1.000
#> TCGA.BH.A1F5.11 1 1.000
#> TCGA.BH.A1EO.11 1 0.000
#> TCGA.E9.A22E.01 4 0.000
#> TCGA.OL.A5RX.01 4 0.000
#> TCGA.A7.A0DC.01 5 1.000
#> TCGA.D8.A1XO.01 5 0.751
#> TCGA.AC.A23C.01 4 0.000
#> TCGA.E9.A1NE.01 4 1.000
#> TCGA.A7.A56D.01 5 1.000
#> TCGA.A1.A0SH.01 4 0.000
#> TCGA.C8.A9FZ.01 2 0.000
#> TCGA.C8.A8HR.01 1 1.000
#> TCGA.BH.A6R9.01 3 1.000
#> TCGA.AR.A5QP.01 4 0.000
#> TCGA.C8.A8HP.01 1 1.000
#> TCGA.AR.A24X.01 2 1.000
#> TCGA.A1.A0SB.01 3 1.000
#> TCGA.D8.A1Y0.01 5 1.000
#> TCGA.BH.A0GZ.01 2 1.000
#> TCGA.AC.A2FM.11 1 0.747
#> TCGA.B6.A0RM.01 2 1.000
#> TCGA.AR.A2LR.01 3 0.747
#> TCGA.BH.A2L8.01 4 0.000
#> TCGA.AR.A251.01 3 0.000
#> TCGA.AO.A12B.01 5 1.000
#> TCGA.BH.A202.01 4 0.000
#> TCGA.A7.A0D9.11 1 0.000
#> TCGA.BH.A0DH.01 2 0.000
#> TCGA.D8.A1JN.01 2 0.000
#> TCGA.EW.A1OV.01 4 0.000
#> TCGA.E2.A1IE.01 2 0.502
#> TCGA.AR.A1AR.01 3 0.747
#> TCGA.EW.A1P3.01 5 0.253
#> TCGA.BH.A8FY.01 2 0.000
#> TCGA.A1.A0SN.01 5 1.000
#> TCGA.E9.A295.01 5 1.000
#> TCGA.AO.A1KT.01 2 1.000
#> TCGA.AC.A2FB.11 1 0.000
#> TCGA.E2.A1IU.01 5 0.000
#> TCGA.AO.A0JL.01 3 0.000
#> TCGA.AC.A8OP.01 5 1.000
#> TCGA.E2.A1LS.11 1 0.000
#> TCGA.EW.A1P8.01 3 0.498
#> TCGA.GI.A2C8.01 4 1.000
#> TCGA.AR.A24P.01 5 1.000
#> TCGA.BH.A0BT.11 1 0.747
#> TCGA.BH.A0C0.11 1 0.000
#> TCGA.E9.A22H.01 5 0.000
#> TCGA.D8.A3Z6.01 5 1.000
#> TCGA.AR.A0U4.01 3 0.249
#> TCGA.AR.A2LK.01 2 0.000
#> TCGA.B6.A409.01 3 0.249
#> TCGA.E2.A1BC.11 1 0.000
#> TCGA.B6.A0X1.01 3 0.000
#> TCGA.A2.A0SX.01 3 0.249
#> TCGA.BH.A0C3.11 1 0.249
#> TCGA.BH.A0B2.01 4 0.000
#> TCGA.B6.A0RI.01 5 1.000
#> TCGA.E9.A248.01 4 1.000
#> TCGA.A2.A0SU.01 4 1.000
#> TCGA.BH.A204.11 1 0.000
#> TCGA.EW.A1P4.01 3 0.747
#> TCGA.AO.A128.01 3 0.249
#> TCGA.AR.A24T.01 4 0.000
#> TCGA.A8.A08O.01 5 0.000
#> TCGA.EW.A1P6.01 5 1.000
#> TCGA.AC.A2FE.01 4 0.000
#> TCGA.GM.A2DF.01 3 0.000
#> TCGA.D8.A1XF.01 2 0.000
#> TCGA.E9.A1N4.01 5 0.000
#> TCGA.A2.A0CT.01 2 0.000
#> TCGA.E9.A1RG.01 5 0.751
#> TCGA.XX.A899.01 4 0.000
#> TCGA.BH.A1F2.01 5 0.000
#> TCGA.GM.A3XG.01 1 1.000
#> TCGA.E9.A1N9.01 4 1.000
#> TCGA.A1.A0SP.01 3 1.000
#> TCGA.E9.A1NF.11 1 0.000
#> TCGA.AN.A0XT.01 5 0.000
#> TCGA.S3.AA17.01 4 0.249
#> TCGA.BH.A1EN.11 1 0.000
#> TCGA.BH.A0DZ.11 1 0.000
#> TCGA.AC.A2FF.01 1 1.000
#> TCGA.BH.A0HI.01 5 1.000
#> TCGA.E9.A1N5.11 1 0.747
#> TCGA.EW.A1PF.01 4 0.000
#> TCGA.B6.A0RL.01 2 0.000
#> TCGA.E2.A1L9.01 5 0.000
#> TCGA.A7.A26E.01 5 0.747
#> TCGA.BH.A0W3.01 2 0.502
#> TCGA.AO.A03L.01 5 1.000
#> TCGA.D8.A1J9.01 2 0.502
#> TCGA.LL.A7T0.01 2 0.000
#> TCGA.OL.A66O.01 2 0.000
#> TCGA.A7.A0CE.11 1 0.000
#> TCGA.AO.A03N.01 5 1.000
#> TCGA.BH.A0HF.01 4 1.000
#> TCGA.E2.A1LG.01 3 1.000
#> TCGA.A7.A6VY.01 3 0.747
#> TCGA.AC.A2QI.01 5 0.751
#> TCGA.A2.A4S2.01 4 1.000
#> TCGA.AR.A1AP.01 2 0.498
#> TCGA.EW.A1PC.01 2 0.000
#> TCGA.GM.A2DA.01 4 0.000
#> TCGA.3C.AALJ.01 2 1.000
#> TCGA.BH.A42T.01 2 0.000
#> TCGA.A7.A4SA.01 4 0.000
#> TCGA.A7.A26G.01 3 1.000
#> TCGA.A2.A0YJ.01 3 0.000
#> TCGA.A2.A3KC.01 4 0.000
#> TCGA.OL.A66L.01 5 1.000
#> TCGA.AR.A2LM.01 4 1.000
#> TCGA.E2.A10C.01 2 1.000
#> TCGA.AC.A7VC.01 3 1.000
#> TCGA.AR.A1AN.01 4 0.000
#> TCGA.5L.AAT1.01 4 0.000
#> TCGA.HN.A2OB.01 4 0.000
#> TCGA.GM.A5PV.01 5 0.000
#> TCGA.C8.A26V.01 2 0.000
#> TCGA.BH.A1EV.01 2 0.000
#> TCGA.E2.A1IJ.01 4 0.000
#> TCGA.LL.A440.01 1 1.000
#> TCGA.OK.A5Q2.01 4 0.000
#> TCGA.BH.A1FG.11 1 0.000
#> TCGA.OL.A66I.01 3 0.000
#> TCGA.A7.A6VW.01 3 0.249
#> TCGA.D8.A1JA.01 2 1.000
#> TCGA.AC.A2FF.11 1 0.000
#> TCGA.E9.A1R3.01 5 0.000
#> TCGA.E2.A1IN.01 2 1.000
#> TCGA.AR.A254.01 4 0.253
#> TCGA.AR.A0TW.01 5 1.000
#> TCGA.B6.A0I1.01 3 0.249
#> TCGA.BH.A8G0.01 4 1.000
#> TCGA.B6.A401.01 4 0.000
#> TCGA.BH.A0H9.01 5 0.000
#> TCGA.E2.A1LB.01 5 1.000
#> TCGA.B6.A0RG.01 2 1.000
#> TCGA.E9.A54X.01 5 0.000
#> TCGA.C8.A1HN.01 2 0.751
#> TCGA.LD.A9QF.01 1 1.000
#> TCGA.BH.A0HB.01 5 1.000
#> TCGA.LL.A73Y.01 3 0.498
#> TCGA.C8.A1HJ.01 3 0.000
#> TCGA.BH.A0W5.01 4 0.000
#> TCGA.A2.A25E.01 5 0.751
#> TCGA.AC.A3W7.01 5 1.000
#> TCGA.B6.A1KN.01 2 0.000
#> TCGA.A2.A1G1.01 3 0.000
#> TCGA.AC.A3W5.01 4 0.502
#> TCGA.A7.A13D.01 3 0.000
#> TCGA.A2.A3XY.01 3 0.249
#> TCGA.B6.A1KI.01 4 1.000
#> TCGA.AR.A24K.01 2 1.000
#> TCGA.E9.A1RI.01 4 0.249
#> TCGA.GM.A2DI.01 1 1.000
#> TCGA.A2.A0T6.01 4 0.751
#> TCGA.EW.A1OZ.01 2 0.000
#> TCGA.EW.A3E8.01 4 0.000
#> TCGA.OL.A5RU.01 4 0.000
#> TCGA.S3.AA12.01 2 0.249
#> TCGA.A2.A1FX.01 5 1.000
#> TCGA.BH.A0B8.11 1 0.000
#> TCGA.BH.A0AZ.11 1 1.000
#> TCGA.A7.A13G.01 5 0.000
#> TCGA.E2.A10F.01 4 1.000
#> TCGA.A7.A4SD.01 3 1.000
#> TCGA.BH.A0C3.01 4 0.000
#> TCGA.B6.A0RV.01 4 0.000
#> TCGA.LQ.A4E4.01 2 0.000
#> TCGA.AQ.A1H2.01 2 0.000
#> TCGA.D8.A27T.01 5 1.000
#> TCGA.E2.A1IH.01 5 1.000
#> TCGA.BH.A0DQ.11 1 1.000
#> TCGA.EW.A1IY.01 4 0.000
#> TCGA.B6.A0X4.01 5 1.000
#> TCGA.AR.A24O.01 4 0.000
#> TCGA.BH.A0HY.01 2 0.000
#> TCGA.E2.A15I.01 5 0.000
#> TCGA.D8.A1XQ.01 3 0.498
#> TCGA.C8.A278.01 4 0.000
#> TCGA.AC.A3HN.01 4 0.000
#> TCGA.BH.A1FB.11 1 0.000
#> TCGA.AC.A3BB.01 4 0.000
#> TCGA.A2.A0EU.01 2 1.000
#> TCGA.BH.A1FE.01 4 0.000
#> TCGA.BH.A0H7.01 2 0.502
#> TCGA.A2.A0EN.01 4 0.000
#> TCGA.BH.A1FE.06 1 0.747
#> TCGA.BH.A0BF.01 4 0.000
#> TCGA.A1.A0SG.01 5 0.000
#> TCGA.AC.A6IW.01 3 0.000
#> TCGA.EW.A1J5.01 5 1.000
#> TCGA.WT.AB41.01 4 0.000
#> TCGA.LL.A5YL.01 4 1.000
#> TCGA.D8.A1XR.01 5 0.502
#> TCGA.E9.A1RH.11 1 0.000
#> TCGA.AO.A0JB.01 5 0.249
#> TCGA.A7.A0CH.11 1 0.000
#> TCGA.C8.A27A.01 2 1.000
#> TCGA.AR.A1AK.01 4 0.000
#> TCGA.AC.A3EH.01 2 0.000
#> TCGA.C8.A1HK.01 2 1.000
#> TCGA.B6.A0WZ.01 5 1.000
#> TCGA.GM.A4E0.01 4 1.000
#> TCGA.A8.A0AD.01 5 0.751
#> TCGA.C8.A26X.01 4 0.000
#> TCGA.BH.A5IZ.01 3 0.747
#> TCGA.E9.A22A.01 4 1.000
#> TCGA.A7.A3J1.01 4 0.000
#> TCGA.D8.A1Y3.01 2 1.000
#> TCGA.AC.A3YJ.01 5 0.751
#> TCGA.LL.A8F5.01 3 0.498
#> TCGA.D8.A1XW.01 3 1.000
#> TCGA.D8.A1Y1.01 5 1.000
#> TCGA.BH.A0DK.01 4 0.000
#> TCGA.BH.A1F8.11 1 0.000
#> TCGA.D8.A1JE.01 5 0.249
#> TCGA.EW.A2FR.01 4 0.000
#> TCGA.E2.A105.01 2 0.000
#> TCGA.PL.A8LZ.01 3 0.249
#> TCGA.E9.A1NA.11 1 0.000
#> TCGA.BH.A0W4.01 4 1.000
#> TCGA.BH.A0E2.01 2 0.000
#> TCGA.BH.A0BJ.01 4 0.000
#> TCGA.BH.A203.01 4 0.000
#> TCGA.E2.A1B5.01 1 1.000
#> TCGA.E9.A1R7.01 2 0.751
#> TCGA.E2.A14U.01 4 0.000
#> TCGA.E2.A1LI.11 1 0.249
#> TCGA.E2.A10E.01 2 0.000
#> TCGA.E9.A249.01 2 1.000
#> TCGA.AC.A2BK.01 3 0.249
#> TCGA.BH.A1FD.11 1 0.000
#> TCGA.E2.A1BD.01 2 0.000
#> TCGA.GI.A2C9.01 3 0.000
#> TCGA.E2.A1LK.01 3 0.000
#> TCGA.BH.A1ET.01 5 0.747
#> TCGA.LD.A7W6.01 5 0.498
#> TCGA.C8.A1HE.01 2 0.249
#> TCGA.D8.A1XM.01 4 0.000
#> TCGA.AC.A7VB.01 2 0.000
#> TCGA.D8.A1JH.01 4 0.000
#> TCGA.BH.A1F6.11 1 0.000
#> TCGA.BH.A1ET.11 1 0.000
#> TCGA.E2.A1II.11 1 0.000
#> TCGA.BH.A0HA.11 1 0.000
#> TCGA.AO.A12C.01 5 1.000
#> TCGA.D8.A73W.01 5 0.498
#> TCGA.B6.A40B.01 5 1.000
#> TCGA.AO.A0JI.01 2 0.000
#> TCGA.BH.A1EU.01 4 0.000
#> TCGA.OL.A5D7.01 3 0.000
#> TCGA.A7.A4SE.01 3 0.000
#> TCGA.OL.A97C.01 1 1.000
#> TCGA.PE.A5DD.01 2 0.000
#> TCGA.A2.A04R.01 2 0.000
#> TCGA.BH.A1F5.01 2 1.000
#> TCGA.S3.AA0Z.01 3 0.000
#> TCGA.AC.A23E.01 5 0.000
#> TCGA.BH.A0B3.01 3 0.000
#> TCGA.D8.A1JS.01 2 1.000
#> TCGA.E2.A15K.11 1 0.000
#> TCGA.WT.AB44.01 2 0.249
#> TCGA.EW.A424.01 2 0.000
#> TCGA.BH.A1FR.01 4 1.000
#> TCGA.A7.A425.01 4 1.000
#> TCGA.B6.A0IK.01 4 0.000
#> TCGA.AR.A24U.01 4 1.000
#> TCGA.E9.A1RF.01 4 0.000
#> TCGA.B6.A408.01 2 1.000
#> TCGA.BH.A0HP.01 4 0.000
#> TCGA.E2.A1L7.01 2 1.000
#> TCGA.5T.A9QA.01 2 0.000
#> TCGA.A2.A0SY.01 2 1.000
#> TCGA.BH.A8FZ.01 4 0.000
#> TCGA.A2.A0YG.01 2 0.000
#> TCGA.AC.A2FG.01 4 1.000
#> TCGA.AR.A1AX.01 1 1.000
#> TCGA.AR.A1AL.01 4 0.000
#> TCGA.BH.A1EY.11 1 0.747
#> TCGA.AQ.A54N.01 3 0.000
#> TCGA.BH.A1EO.01 2 1.000
#> TCGA.BH.A0BZ.11 1 0.000
#> TCGA.D8.A27K.01 4 1.000
#> TCGA.BH.A28Q.01 2 0.502
#> TCGA.E9.A1NG.11 1 0.000
#> TCGA.EW.A1J1.01 5 1.000
#> TCGA.C8.A1HG.01 5 0.498
#> TCGA.D8.A1XK.01 3 0.000
#> TCGA.AQ.A0Y5.01 5 0.249
#> TCGA.3C.AAAU.01 2 1.000
#> TCGA.A2.A4S0.01 5 0.249
#> TCGA.BH.A0DV.11 1 0.498
#> TCGA.AR.A1AV.01 2 0.000
#> TCGA.AC.A8OQ.01 3 1.000
#> TCGA.BH.A0BS.11 1 0.000
#> TCGA.EW.A1PB.01 3 0.000
#> TCGA.A7.A3J0.01 5 0.502
#> TCGA.D8.A1JU.01 4 0.000
#> TCGA.A7.A6VX.01 2 0.502
#> TCGA.E2.A108.01 1 1.000
#> TCGA.BH.A0BT.01 2 1.000
#> TCGA.A2.A0YK.01 4 0.000
#> TCGA.E9.A1N8.01 3 0.747
#> TCGA.E2.A574.01 3 0.000
#> TCGA.A1.A0SO.01 3 1.000
#> TCGA.BH.A0DI.01 4 0.000
#> TCGA.E2.A1IG.01 2 1.000
#> TCGA.E2.A107.01 2 1.000
#> TCGA.5L.AAT0.01 4 0.000
#> TCGA.E9.A1NH.01 5 0.249
#> TCGA.D8.A27E.01 5 0.000
#> TCGA.AR.A24Q.01 3 0.000
#> TCGA.BH.A1F0.01 3 0.249
#> TCGA.E9.A1RB.11 1 0.000
#> TCGA.AR.A0U0.01 3 0.000
get_classes(res, k = 6)
#> class p
#> TCGA.OL.A66H.01 2 1.000
#> TCGA.3C.AALK.01 2 0.000
#> TCGA.AC.A5EH.01 2 0.249
#> TCGA.EW.A2FW.01 6 0.000
#> TCGA.E9.A1R0.01 2 1.000
#> TCGA.AR.A1AJ.01 3 1.000
#> TCGA.AC.A62Y.01 5 0.000
#> TCGA.E9.A1QZ.01 4 0.000
#> TCGA.E9.A1R2.01 2 0.249
#> TCGA.E9.A3X8.01 4 0.000
#> TCGA.AR.A255.01 2 0.000
#> TCGA.E2.A10B.01 2 0.000
#> TCGA.E9.A1N4.11 1 1.000
#> TCGA.AO.A0JD.01 2 0.249
#> TCGA.D8.A1JD.01 2 0.000
#> TCGA.D8.A1XA.01 6 0.000
#> TCGA.AO.A1KQ.01 5 0.000
#> TCGA.A8.A0A6.01 2 0.000
#> TCGA.BH.A1F2.11 1 0.000
#> TCGA.A7.A3RF.01 6 1.000
#> TCGA.A2.A0SW.01 2 0.000
#> TCGA.A7.A3IY.01 4 0.000
#> TCGA.GM.A2D9.01 6 0.000
#> TCGA.D8.A3Z5.01 2 0.249
#> TCGA.E9.A1ND.01 3 1.000
#> TCGA.EW.A1P5.01 6 0.249
#> TCGA.E9.A1RD.01 2 0.751
#> TCGA.AR.A1AQ.01 3 1.000
#> TCGA.LD.A66U.01 2 0.000
#> TCGA.BH.A1EN.01 2 0.747
#> TCGA.BH.A1FN.01 5 0.000
#> TCGA.EW.A1PD.01 2 0.000
#> TCGA.E9.A1N5.01 2 0.000
#> TCGA.D8.A1J8.01 2 0.000
#> TCGA.E9.A3QA.01 3 1.000
#> TCGA.S3.AA15.01 1 1.000
#> TCGA.BH.A0DP.11 4 0.000
#> TCGA.BH.A0H0.01 6 0.000
#> TCGA.A2.A3XX.01 3 0.249
#> TCGA.AC.A2FB.01 4 0.000
#> TCGA.AC.A3QP.01 4 0.000
#> TCGA.BH.A0BF.11 1 0.000
#> TCGA.A2.A0YC.01 6 0.000
#> TCGA.GM.A2DK.01 2 1.000
#> TCGA.GM.A2DC.01 6 0.000
#> TCGA.AR.A24N.01 6 0.249
#> TCGA.E2.A1B0.01 4 0.000
#> TCGA.BH.A1EY.01 2 1.000
#> TCGA.EW.A6S9.01 6 0.000
#> TCGA.AC.A8OS.01 2 1.000
#> TCGA.GM.A2DN.01 4 0.000
#> TCGA.AO.A03M.01 4 0.000
#> TCGA.A2.A3XT.01 3 0.747
#> TCGA.A2.A4RW.01 4 0.249
#> TCGA.AC.A6IV.01 4 0.000
#> TCGA.LL.A7SZ.01 4 1.000
#> TCGA.A1.A0SJ.01 2 0.000
#> TCGA.AR.A2LJ.01 4 0.000
#> TCGA.AQ.A1H3.01 2 0.000
#> TCGA.D8.A1JB.01 4 0.000
#> TCGA.BH.A0BC.01 2 0.751
#> TCGA.BH.A1EW.01 2 0.000
#> TCGA.BH.A1FG.01 6 0.000
#> TCGA.EW.A1P7.01 1 1.000
#> TCGA.GM.A2DH.01 4 1.000
#> TCGA.D8.A27P.01 5 0.000
#> TCGA.EW.A2FS.01 2 1.000
#> TCGA.E2.A1IL.01 5 0.000
#> TCGA.A7.A3IZ.01 6 0.000
#> TCGA.E2.A570.01 2 0.000
#> TCGA.OL.A66J.01 2 0.000
#> TCGA.AR.A2LO.01 4 0.000
#> TCGA.BH.A1FC.11 1 0.000
#> TCGA.E9.A5FL.01 3 1.000
#> TCGA.BH.A201.01 5 1.000
#> TCGA.LL.A5YM.01 6 0.000
#> TCGA.BH.A0H9.11 1 0.000
#> TCGA.AC.A4ZE.01 6 0.000
#> TCGA.A2.A0T2.01 3 0.000
#> TCGA.AR.A0TP.01 3 1.000
#> TCGA.S3.AA14.01 2 0.502
#> TCGA.B6.A0RS.01 2 1.000
#> TCGA.EW.A1P0.01 6 0.000
#> TCGA.AR.A1AT.01 2 0.000
#> TCGA.A2.A1G0.01 2 0.751
#> TCGA.BH.A208.11 1 0.747
#> TCGA.AR.A24H.01 6 0.000
#> TCGA.D8.A1XV.01 6 0.000
#> TCGA.AR.A2LQ.01 4 1.000
#> TCGA.AC.A3OD.01 4 0.000
#> TCGA.BH.A0DI.11 1 1.000
#> TCGA.AR.A0TU.01 3 0.000
#> TCGA.AN.A0XV.01 2 0.000
#> TCGA.A2.A0YT.01 6 0.000
#> TCGA.BH.A0B5.01 6 0.000
#> TCGA.D8.A1JI.01 6 0.000
#> TCGA.UU.A93S.01 2 0.747
#> TCGA.E9.A1N6.11 1 0.000
#> TCGA.E9.A1R6.01 6 0.000
#> TCGA.D8.A1XZ.01 6 0.000
#> TCGA.BH.A0B8.01 6 0.000
#> TCGA.LL.A6FQ.01 6 0.000
#> TCGA.XX.A89A.01 4 0.000
#> TCGA.EW.A1OY.01 6 0.000
#> TCGA.A7.A13G.11 1 0.000
#> TCGA.B6.A0RP.01 5 0.000
#> TCGA.LL.A9Q3.01 2 0.249
#> TCGA.A1.A0SQ.01 6 0.000
#> TCGA.AR.A5QM.01 4 1.000
#> TCGA.A7.A26I.01 3 0.747
#> TCGA.E2.A1B6.01 1 1.000
#> TCGA.PE.A5DE.01 2 1.000
#> TCGA.E9.A1RB.01 5 0.000
#> TCGA.A2.A0ST.01 1 1.000
#> TCGA.B6.A0RO.01 2 0.249
#> TCGA.AC.A23H.01 2 0.249
#> TCGA.AC.A2BM.01 2 0.747
#> TCGA.BH.A0WA.01 3 0.000
#> TCGA.EW.A1J6.01 6 0.000
#> TCGA.D8.A27V.01 2 0.249
#> TCGA.B6.A40C.01 6 0.000
#> TCGA.A2.A1FZ.01 4 0.249
#> TCGA.A7.A26H.01 2 0.000
#> TCGA.BH.A0H7.11 1 1.000
#> TCGA.BH.A0BA.01 2 0.000
#> TCGA.BH.AB28.01 2 0.000
#> TCGA.E2.A2P6.01 6 0.000
#> TCGA.B6.A0RT.01 1 1.000
#> TCGA.AR.A1AY.01 3 0.000
#> TCGA.A2.A25C.01 5 0.249
#> TCGA.S3.AA10.01 3 0.000
#> TCGA.OL.A5DA.01 6 0.751
#> TCGA.D8.A27R.01 2 0.000
#> TCGA.EW.A6SB.01 3 1.000
#> TCGA.A7.A5ZV.01 3 0.498
#> TCGA.LL.A50Y.01 6 0.000
#> TCGA.B6.A0WX.01 3 1.000
#> TCGA.LL.A442.01 5 0.000
#> TCGA.C8.A26Z.01 6 0.000
#> TCGA.BH.A1FU.01 4 0.000
#> TCGA.AO.A1KO.01 1 1.000
#> TCGA.BH.A0E0.01 3 1.000
#> TCGA.A7.A0DB.11 1 0.000
#> TCGA.E9.A2JT.01 1 1.000
#> TCGA.OL.A5D6.01 4 0.498
#> TCGA.BH.A0AU.11 1 0.000
#> TCGA.BH.A1FJ.01 6 0.000
#> TCGA.E9.A1RC.11 1 0.000
#> TCGA.E9.A1NE.11 1 0.000
#> TCGA.E2.A3DX.01 4 0.000
#> TCGA.A1.A0SE.01 2 1.000
#> TCGA.BH.A1FM.11 1 0.000
#> TCGA.E9.A3HO.01 6 0.000
#> TCGA.D8.A1XT.01 4 0.000
#> TCGA.C8.A1HI.01 2 0.249
#> TCGA.E9.A1NA.01 2 1.000
#> TCGA.A2.A0T4.01 2 1.000
#> TCGA.BH.A0BS.01 5 0.000
#> TCGA.BH.A203.11 1 0.000
#> TCGA.MS.A51U.01 4 0.000
#> TCGA.E2.A1B5.11 1 0.000
#> TCGA.B6.A0WT.01 6 0.000
#> TCGA.B6.A0RN.01 6 0.000
#> TCGA.D8.A1Y2.01 4 0.249
#> TCGA.PL.A8LY.01 1 0.000
#> TCGA.B6.A0RU.01 3 1.000
#> TCGA.EW.A1PH.01 3 0.000
#> TCGA.D8.A1XJ.01 2 0.000
#> TCGA.BH.A0DG.01 4 1.000
#> TCGA.C8.A3M7.01 4 0.000
#> TCGA.BH.A1EW.11 4 1.000
#> TCGA.E2.A1L6.01 2 0.751
#> TCGA.D8.A1XY.01 5 0.000
#> TCGA.D8.A27G.01 2 0.249
#> TCGA.E2.A109.01 6 0.000
#> TCGA.AR.A1AM.01 4 0.000
#> TCGA.4H.AAAK.01 2 0.249
#> TCGA.AC.A5XS.01 2 1.000
#> TCGA.AC.A5EI.01 4 0.000
#> TCGA.BH.A1EU.11 1 0.000
#> TCGA.A2.A3XS.01 3 0.000
#> TCGA.3C.AALI.01 2 0.751
#> TCGA.OL.A5RY.01 1 1.000
#> TCGA.E2.A1IF.01 4 0.000
#> TCGA.AC.A2FO.01 4 0.000
#> TCGA.BH.A209.01 4 0.000
#> TCGA.AR.A24S.01 2 0.249
#> TCGA.A2.A3KD.01 2 1.000
#> TCGA.B6.A1KF.01 3 0.000
#> TCGA.BH.A1FL.01 6 0.000
#> TCGA.BH.A0B3.11 1 1.000
#> TCGA.E2.A15K.01 5 0.000
#> TCGA.E2.A15K.06 6 0.000
#> TCGA.E9.A1NI.01 6 0.000
#> TCGA.AC.A2FK.01 1 0.000
#> TCGA.E9.A226.01 4 1.000
#> TCGA.E2.A1AZ.01 3 1.000
#> TCGA.D8.A1X8.01 2 0.000
#> TCGA.A2.A0T5.01 2 0.000
#> TCGA.AO.A12G.01 2 0.249
#> TCGA.C8.A1HO.01 6 0.000
#> TCGA.LD.A74U.01 4 0.000
#> TCGA.AR.A0TQ.01 2 0.249
#> TCGA.AO.A0JE.01 4 1.000
#> TCGA.AC.A62X.01 3 0.000
#> TCGA.AN.A0XR.01 6 0.000
#> TCGA.E9.A1RF.11 1 0.000
#> TCGA.E9.A228.01 2 0.502
#> TCGA.E9.A1RA.01 4 1.000
#> TCGA.BH.A0HA.01 6 0.000
#> TCGA.E2.A1L7.11 1 1.000
#> TCGA.D8.A1XS.01 5 0.000
#> TCGA.OL.A6VR.01 5 0.000
#> TCGA.E9.A22G.01 3 0.000
#> TCGA.LL.A740.01 4 1.000
#> TCGA.AC.A2FG.11 1 0.249
#> TCGA.E9.A1RI.11 1 0.000
#> TCGA.AR.A1AS.01 6 0.000
#> TCGA.D8.A27M.01 3 1.000
#> TCGA.E9.A1N8.11 1 0.000
#> TCGA.BH.A0BZ.01 2 0.000
#> TCGA.BH.A0RX.01 3 1.000
#> TCGA.S3.A6ZG.01 6 0.000
#> TCGA.AR.A1AW.01 4 0.000
#> TCGA.AN.A0XP.01 5 0.000
#> TCGA.EW.A2FV.01 2 0.249
#> TCGA.D8.A1XD.01 6 0.751
#> TCGA.A2.A4S1.01 3 1.000
#> TCGA.AR.A24M.01 5 0.000
#> TCGA.BH.A1FH.01 4 1.000
#> TCGA.D8.A1JM.01 3 0.498
#> TCGA.AC.A6NO.01 6 1.000
#> TCGA.BH.A0DV.01 4 0.000
#> TCGA.BH.A0AY.11 1 0.000
#> TCGA.E2.A572.01 6 0.000
#> TCGA.BH.A1ES.01 6 0.000
#> TCGA.A2.A0YI.01 4 0.502
#> TCGA.AC.A2QJ.01 3 1.000
#> TCGA.EW.A1PE.01 5 0.000
#> TCGA.BH.A0H6.01 6 0.000
#> TCGA.BH.A0BM.01 5 0.249
#> TCGA.A7.A2KD.01 5 0.000
#> TCGA.E2.A1II.01 3 1.000
#> TCGA.D8.A27I.01 4 0.000
#> TCGA.A2.A0YD.01 2 0.249
#> TCGA.BH.A0C0.01 4 0.000
#> TCGA.B6.A3ZX.01 3 1.000
#> TCGA.E9.A1NG.01 4 0.000
#> TCGA.S3.A6ZH.01 6 0.000
#> TCGA.HN.A2NL.01 3 0.747
#> TCGA.EW.A1IW.01 2 0.000
#> TCGA.JL.A3YW.01 4 0.000
#> TCGA.BH.A1F0.11 1 0.000
#> TCGA.AN.A0XN.01 2 0.000
#> TCGA.A1.A0SK.01 3 1.000
#> TCGA.E9.A6HE.01 2 0.000
#> TCGA.BH.A1FR.11 1 0.000
#> TCGA.BH.A1EX.01 5 0.000
#> TCGA.LL.A441.01 3 1.000
#> TCGA.AO.A125.01 6 0.000
#> TCGA.C8.A26W.01 5 0.747
#> TCGA.A2.A0YM.01 3 0.000
#> TCGA.BH.A0DP.01 2 0.000
#> TCGA.UL.AAZ6.01 6 0.000
#> TCGA.A2.A0CK.01 6 1.000
#> TCGA.AR.A2LN.01 4 0.000
#> TCGA.D8.A1JF.01 2 0.249
#> TCGA.OL.A6VQ.01 2 0.502
#> TCGA.LL.A5YP.01 3 0.249
#> TCGA.AR.A252.01 4 0.000
#> TCGA.A2.A25F.01 1 1.000
#> TCGA.PE.A5DC.01 6 0.000
#> TCGA.EW.A6SC.01 6 1.000
#> TCGA.GM.A2DO.01 4 0.000
#> TCGA.E9.A1ND.11 1 0.000
#> TCGA.E2.A1LL.01 4 0.000
#> TCGA.C8.A273.01 6 0.000
#> TCGA.E9.A1RD.11 1 0.000
#> TCGA.AR.A0U2.01 6 0.000
#> TCGA.C8.A1HL.01 6 0.000
#> TCGA.BH.A1FN.11 1 0.000
#> TCGA.BH.A0AU.01 2 0.249
#> TCGA.A2.A0T1.01 4 0.000
#> TCGA.BH.A28O.01 1 1.000
#> TCGA.AR.A24W.01 4 0.000
#> TCGA.EW.A1P1.01 1 0.747
#> TCGA.E2.A9RU.01 6 0.000
#> TCGA.AR.A0TT.01 4 0.000
#> TCGA.E2.A1IO.11 1 0.000
#> TCGA.AC.A3W6.01 4 0.000
#> TCGA.D8.A1JJ.01 2 0.000
#> TCGA.OL.A66P.01 4 0.000
#> TCGA.E2.A1B4.01 6 0.000
#> TCGA.B6.A1KC.01 6 0.000
#> TCGA.E9.A5UP.01 6 0.000
#> TCGA.A2.A1G4.01 6 0.000
#> TCGA.AR.A24L.01 2 1.000
#> TCGA.BH.A0H3.01 2 0.000
#> TCGA.LL.A73Z.01 4 0.000
#> TCGA.EW.A1IZ.01 4 0.000
#> TCGA.AO.A0JA.01 2 0.000
#> TCGA.AR.A0TX.01 4 0.000
#> TCGA.AO.A0JG.01 2 0.000
#> TCGA.OL.A66N.01 2 0.000
#> TCGA.A2.A1FV.01 6 0.000
#> TCGA.D8.A1XC.01 6 0.249
#> TCGA.A7.A4SC.01 4 1.000
#> TCGA.AR.A2LH.01 4 1.000
#> TCGA.LL.A6FR.01 3 0.000
#> TCGA.A7.A13F.11 1 0.000
#> TCGA.GM.A2DB.01 4 0.000
#> TCGA.LL.A5YO.01 4 1.000
#> TCGA.E9.A1N3.01 5 0.000
#> TCGA.PL.A8LV.01 3 1.000
#> TCGA.AO.A1KR.01 3 1.000
#> TCGA.AN.A0XL.01 2 0.502
#> TCGA.E2.A15J.01 6 0.000
#> TCGA.E9.A244.01 3 0.249
#> TCGA.E9.A24A.01 5 0.000
#> TCGA.BH.A1EV.11 1 0.000
#> TCGA.GM.A2DL.01 2 0.000
#> TCGA.S3.AA11.01 6 0.000
#> TCGA.AC.A3QQ.01 6 0.000
#> TCGA.Z7.A8R5.01 4 0.000
#> TCGA.B6.A400.01 3 0.000
#> TCGA.AQ.A54O.01 5 0.000
#> TCGA.BH.A1FC.01 3 0.000
#> TCGA.E9.A22B.01 2 1.000
#> TCGA.A2.A3XV.01 2 0.000
#> TCGA.AC.A6IX.06 4 0.000
#> TCGA.BH.A0B9.01 3 0.249
#> TCGA.BH.A18V.06 3 1.000
#> TCGA.AC.A6IX.01 2 0.249
#> TCGA.D8.A1JT.01 6 0.000
#> TCGA.AR.A2LL.01 2 0.751
#> TCGA.D8.A1X7.01 5 0.000
#> TCGA.E9.A247.01 6 0.000
#> TCGA.D8.A1X5.01 6 0.000
#> TCGA.AO.A03U.01 1 1.000
#> TCGA.A8.A075.01 5 0.000
#> TCGA.D8.A73X.01 6 0.000
#> TCGA.B6.A0WY.01 4 0.000
#> TCGA.E9.A1R4.01 2 0.751
#> TCGA.E9.A3Q9.01 5 0.000
#> TCGA.BH.A0E1.01 5 0.000
#> TCGA.EW.A423.01 6 0.000
#> TCGA.BH.A1ES.11 1 0.000
#> TCGA.EW.A1J2.01 2 0.000
#> TCGA.BH.A0GY.01 2 0.249
#> TCGA.W8.A86G.01 4 1.000
#> TCGA.A7.A5ZW.01 4 0.000
#> TCGA.E2.A106.01 6 0.000
#> TCGA.AR.A0TV.01 6 0.249
#> TCGA.E2.A56Z.01 6 0.000
#> TCGA.AC.A2FM.01 6 0.000
#> TCGA.C8.A1HF.01 2 0.000
#> TCGA.C8.A27B.01 3 0.000
#> TCGA.E2.A15I.11 1 0.000
#> TCGA.A7.A13E.01 3 0.000
#> TCGA.A2.A1G6.01 4 1.000
#> TCGA.B6.A402.01 3 0.000
#> TCGA.A2.A0T7.01 4 0.000
#> TCGA.A7.A0D9.01 6 0.000
#> TCGA.AC.A5XU.01 6 0.000
#> TCGA.BH.A0DH.11 1 0.000
#> TCGA.BH.A204.01 6 0.000
#> TCGA.B6.A0WW.01 6 0.000
#> TCGA.A2.A3XZ.01 4 0.000
#> TCGA.AR.A1AI.01 3 0.000
#> TCGA.BH.A0BC.11 1 0.000
#> TCGA.D8.A1XL.01 2 1.000
#> TCGA.E9.A5UO.01 6 0.000
#> TCGA.A7.A13E.11 1 0.000
#> TCGA.A2.A0SV.01 2 0.000
#> TCGA.OL.A5RZ.01 6 0.000
#> TCGA.E2.A1LS.01 3 0.751
#> TCGA.AO.A0JJ.01 2 0.751
#> TCGA.BH.A0BA.11 1 0.000
#> TCGA.AR.A24R.01 6 0.000
#> TCGA.AO.A1KP.01 6 0.000
#> TCGA.D8.A1JL.01 3 0.502
#> TCGA.E2.A1LH.01 3 1.000
#> TCGA.B6.A0X7.01 2 0.000
#> TCGA.BH.A0DK.11 4 1.000
#> TCGA.D8.A4Z1.01 4 0.000
#> TCGA.E9.A1RE.01 6 0.000
#> TCGA.OL.A5RV.01 2 0.249
#> TCGA.E2.A1BC.01 2 0.249
#> TCGA.GM.A2DM.01 5 0.000
#> TCGA.A2.A0YF.01 6 0.000
#> TCGA.A2.A3Y0.01 3 0.253
#> TCGA.AC.A3YI.01 4 1.000
#> TCGA.E9.A22D.01 4 0.000
#> TCGA.BH.A0E0.11 1 0.000
#> TCGA.C8.A274.01 6 0.000
#> TCGA.BH.A0B2.11 1 0.000
#> TCGA.A1.A0SF.01 2 0.000
#> TCGA.EW.A6SD.01 2 0.751
#> TCGA.C8.A1HM.01 2 0.000
#> TCGA.A7.A426.01 4 1.000
#> TCGA.E9.A1RC.01 6 0.498
#> TCGA.AR.A1AU.01 2 0.000
#> TCGA.AO.A129.01 3 1.000
#> TCGA.A2.A4RX.01 3 1.000
#> TCGA.BH.A6R8.01 6 0.000
#> TCGA.BH.A1FM.01 6 0.000
#> TCGA.D8.A1JP.01 2 0.249
#> TCGA.E2.A1IP.01 3 1.000
#> TCGA.AO.A0JM.01 6 0.000
#> TCGA.E9.A1N6.01 2 0.000
#> TCGA.BH.A0DS.01 2 0.249
#> TCGA.V7.A7HQ.01 6 0.000
#> TCGA.D8.A27L.01 4 1.000
#> TCGA.A2.A4RY.01 4 0.502
#> TCGA.E9.A1NF.01 2 0.249
#> TCGA.EW.A1PA.01 2 0.249
#> TCGA.BH.A0BV.11 1 0.000
#> TCGA.AC.A3TM.01 2 0.000
#> TCGA.BH.A0DG.11 1 0.000
#> TCGA.D8.A27H.01 3 0.249
#> TCGA.AC.A23H.11 1 0.000
#> TCGA.AR.A2LE.01 6 0.000
#> TCGA.EW.A1PG.01 4 0.000
#> TCGA.GM.A3NY.01 6 0.000
#> TCGA.BH.A5J0.01 2 0.000
#> TCGA.E9.A1NC.01 3 1.000
#> TCGA.BH.A0HK.01 6 0.000
#> TCGA.AR.A24Z.01 6 0.000
#> TCGA.A1.A0SM.01 2 0.000
#> TCGA.AO.A124.01 3 0.000
#> TCGA.S3.A6ZF.01 6 0.000
#> TCGA.Z7.A8R6.01 6 0.000
#> TCGA.OL.A66K.01 6 0.000
#> TCGA.E2.A1IF.11 1 0.000
#> TCGA.D8.A1JC.01 6 0.249
#> TCGA.LD.A7W5.01 4 0.000
#> TCGA.BH.A209.11 1 0.249
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#> TCGA.D8.A1JU.01 4 0.000
#> TCGA.A7.A6VX.01 6 0.000
#> TCGA.E2.A108.01 4 1.000
#> TCGA.BH.A0BT.01 6 0.000
#> TCGA.A2.A0YK.01 4 0.000
#> TCGA.E9.A1N8.01 3 0.502
#> TCGA.E2.A574.01 3 0.000
#> TCGA.A1.A0SO.01 3 1.000
#> TCGA.BH.A0DI.01 4 0.000
#> TCGA.E2.A1IG.01 6 0.000
#> TCGA.E2.A107.01 2 0.000
#> TCGA.5L.AAT0.01 2 0.000
#> TCGA.E9.A1NH.01 5 0.000
#> TCGA.D8.A27E.01 5 0.000
#> TCGA.AR.A24Q.01 3 0.000
#> TCGA.BH.A1F0.01 1 1.000
#> TCGA.E9.A1RB.11 1 0.000
#> TCGA.AR.A0U0.01 3 1.000
get_classes(res, k = 7)
#> class p
#> TCGA.OL.A66H.01 7 1.000
#> TCGA.3C.AALK.01 2 1.000
#> TCGA.AC.A5EH.01 2 1.000
#> TCGA.EW.A2FW.01 6 0.000
#> TCGA.E9.A1R0.01 2 0.000
#> TCGA.AR.A1AJ.01 3 0.000
#> TCGA.AC.A62Y.01 5 0.000
#> TCGA.E9.A1QZ.01 4 0.000
#> TCGA.E9.A1R2.01 7 0.747
#> TCGA.E9.A3X8.01 4 0.000
#> TCGA.AR.A255.01 2 0.000
#> TCGA.E2.A10B.01 2 0.747
#> TCGA.E9.A1N4.11 1 0.000
#> TCGA.AO.A0JD.01 2 1.000
#> TCGA.D8.A1JD.01 7 0.000
#> TCGA.D8.A1XA.01 6 0.000
#> TCGA.AO.A1KQ.01 7 1.000
#> TCGA.A8.A0A6.01 2 0.000
#> TCGA.BH.A1F2.11 1 0.000
#> TCGA.A7.A3RF.01 5 1.000
#> TCGA.A2.A0SW.01 7 0.000
#> TCGA.A7.A3IY.01 4 0.000
#> TCGA.GM.A2D9.01 6 0.000
#> TCGA.D8.A3Z5.01 2 0.000
#> TCGA.E9.A1ND.01 3 0.000
#> TCGA.EW.A1P5.01 6 0.000
#> TCGA.E9.A1RD.01 7 1.000
#> TCGA.AR.A1AQ.01 3 0.000
#> TCGA.LD.A66U.01 2 0.000
#> TCGA.BH.A1EN.01 7 0.747
#> TCGA.BH.A1FN.01 5 0.000
#> TCGA.EW.A1PD.01 5 1.000
#> TCGA.E9.A1N5.01 7 0.751
#> TCGA.D8.A1J8.01 7 1.000
#> TCGA.E9.A3QA.01 3 0.000
#> TCGA.S3.AA15.01 3 0.249
#> TCGA.BH.A0DP.11 4 0.000
#> TCGA.BH.A0H0.01 6 0.000
#> TCGA.A2.A3XX.01 3 0.000
#> TCGA.AC.A2FB.01 4 0.000
#> TCGA.AC.A3QP.01 2 0.751
#> TCGA.BH.A0BF.11 1 0.000
#> TCGA.A2.A0YC.01 6 0.000
#> TCGA.GM.A2DK.01 2 0.000
#> TCGA.GM.A2DC.01 6 0.000
#> TCGA.AR.A24N.01 6 0.000
#> TCGA.E2.A1B0.01 4 0.747
#> TCGA.BH.A1EY.01 2 0.000
#> TCGA.EW.A6S9.01 6 0.000
#> TCGA.AC.A8OS.01 2 0.000
#> TCGA.GM.A2DN.01 4 0.000
#> TCGA.AO.A03M.01 2 0.000
#> TCGA.A2.A3XT.01 3 0.000
#> TCGA.A2.A4RW.01 2 0.000
#> TCGA.AC.A6IV.01 4 0.000
#> TCGA.LL.A7SZ.01 2 0.000
#> TCGA.A1.A0SJ.01 6 1.000
#> TCGA.AR.A2LJ.01 4 1.000
#> TCGA.AQ.A1H3.01 7 1.000
#> TCGA.D8.A1JB.01 4 0.000
#> TCGA.BH.A0BC.01 2 0.000
#> TCGA.BH.A1EW.01 2 0.000
#> TCGA.BH.A1FG.01 6 0.000
#> TCGA.EW.A1P7.01 3 1.000
#> TCGA.GM.A2DH.01 2 0.000
#> TCGA.D8.A27P.01 5 0.000
#> TCGA.EW.A2FS.01 2 0.000
#> TCGA.E2.A1IL.01 5 0.000
#> TCGA.A7.A3IZ.01 6 0.000
#> TCGA.E2.A570.01 7 0.498
#> TCGA.OL.A66J.01 7 1.000
#> TCGA.AR.A2LO.01 4 0.000
#> TCGA.BH.A1FC.11 1 0.000
#> TCGA.E9.A5FL.01 4 0.000
#> TCGA.BH.A201.01 2 0.000
#> TCGA.LL.A5YM.01 6 0.000
#> TCGA.BH.A0H9.11 1 0.000
#> TCGA.AC.A4ZE.01 6 0.000
#> TCGA.A2.A0T2.01 3 0.000
#> TCGA.AR.A0TP.01 3 0.000
#> TCGA.S3.AA14.01 7 1.000
#> TCGA.B6.A0RS.01 2 0.000
#> TCGA.EW.A1P0.01 6 0.000
#> TCGA.AR.A1AT.01 2 0.000
#> TCGA.A2.A1G0.01 2 1.000
#> TCGA.BH.A208.11 1 0.000
#> TCGA.AR.A24H.01 6 0.000
#> TCGA.D8.A1XV.01 6 0.000
#> TCGA.AR.A2LQ.01 4 0.000
#> TCGA.AC.A3OD.01 2 0.000
#> TCGA.BH.A0DI.11 1 0.000
#> TCGA.AR.A0TU.01 3 0.000
#> TCGA.AN.A0XV.01 7 0.249
#> TCGA.A2.A0YT.01 6 0.000
#> TCGA.BH.A0B5.01 6 0.000
#> TCGA.D8.A1JI.01 6 0.000
#> TCGA.UU.A93S.01 2 0.498
#> TCGA.E9.A1N6.11 1 0.000
#> TCGA.E9.A1R6.01 6 0.000
#> TCGA.D8.A1XZ.01 6 0.000
#> TCGA.BH.A0B8.01 6 0.000
#> TCGA.LL.A6FQ.01 6 0.000
#> TCGA.XX.A89A.01 2 0.000
#> TCGA.EW.A1OY.01 6 0.000
#> TCGA.A7.A13G.11 1 0.000
#> TCGA.B6.A0RP.01 5 1.000
#> TCGA.LL.A9Q3.01 7 1.000
#> TCGA.A1.A0SQ.01 6 0.000
#> TCGA.AR.A5QM.01 2 0.000
#> TCGA.A7.A26I.01 3 0.000
#> TCGA.E2.A1B6.01 3 1.000
#> TCGA.PE.A5DE.01 2 0.000
#> TCGA.E9.A1RB.01 5 1.000
#> TCGA.A2.A0ST.01 3 0.751
#> TCGA.B6.A0RO.01 7 1.000
#> TCGA.AC.A23H.01 2 0.498
#> TCGA.AC.A2BM.01 7 1.000
#> TCGA.BH.A0WA.01 3 0.000
#> TCGA.EW.A1J6.01 6 0.000
#> TCGA.D8.A27V.01 7 0.747
#> TCGA.B6.A40C.01 6 0.000
#> TCGA.A2.A1FZ.01 2 0.000
#> TCGA.A7.A26H.01 7 1.000
#> TCGA.BH.A0H7.11 1 0.000
#> TCGA.BH.A0BA.01 7 1.000
#> TCGA.BH.AB28.01 2 0.249
#> TCGA.E2.A2P6.01 6 0.000
#> TCGA.B6.A0RT.01 3 1.000
#> TCGA.AR.A1AY.01 3 0.000
#> TCGA.A2.A25C.01 5 1.000
#> TCGA.S3.AA10.01 3 0.000
#> TCGA.OL.A5DA.01 6 0.498
#> TCGA.D8.A27R.01 2 0.000
#> TCGA.EW.A6SB.01 3 0.000
#> TCGA.A7.A5ZV.01 3 0.000
#> TCGA.LL.A50Y.01 6 0.000
#> TCGA.B6.A0WX.01 3 0.000
#> TCGA.LL.A442.01 5 0.000
#> TCGA.C8.A26Z.01 6 0.000
#> TCGA.BH.A1FU.01 4 0.000
#> TCGA.AO.A1KO.01 1 0.000
#> TCGA.BH.A0E0.01 3 0.000
#> TCGA.A7.A0DB.11 1 0.000
#> TCGA.E9.A2JT.01 4 1.000
#> TCGA.OL.A5D6.01 2 0.000
#> TCGA.BH.A0AU.11 1 0.000
#> TCGA.BH.A1FJ.01 6 0.000
#> TCGA.E9.A1RC.11 1 0.000
#> TCGA.E9.A1NE.11 1 0.000
#> TCGA.E2.A3DX.01 4 0.000
#> TCGA.A1.A0SE.01 2 0.000
#> TCGA.BH.A1FM.11 1 0.000
#> TCGA.E9.A3HO.01 6 0.000
#> TCGA.D8.A1XT.01 2 0.498
#> TCGA.C8.A1HI.01 2 0.000
#> TCGA.E9.A1NA.01 6 1.000
#> TCGA.A2.A0T4.01 2 0.000
#> TCGA.BH.A0BS.01 5 0.000
#> TCGA.BH.A203.11 1 0.000
#> TCGA.MS.A51U.01 4 0.000
#> TCGA.E2.A1B5.11 1 0.000
#> TCGA.B6.A0WT.01 6 1.000
#> TCGA.B6.A0RN.01 6 0.000
#> TCGA.D8.A1Y2.01 2 0.000
#> TCGA.PL.A8LY.01 1 0.000
#> TCGA.B6.A0RU.01 3 0.000
#> TCGA.EW.A1PH.01 3 0.000
#> TCGA.D8.A1XJ.01 7 1.000
#> TCGA.BH.A0DG.01 2 0.000
#> TCGA.C8.A3M7.01 2 0.000
#> TCGA.BH.A1EW.11 4 0.000
#> TCGA.E2.A1L6.01 2 1.000
#> TCGA.D8.A1XY.01 7 0.000
#> TCGA.D8.A27G.01 2 0.000
#> TCGA.E2.A109.01 6 0.000
#> TCGA.AR.A1AM.01 2 0.000
#> TCGA.4H.AAAK.01 7 1.000
#> TCGA.AC.A5XS.01 2 0.000
#> TCGA.AC.A5EI.01 4 0.000
#> TCGA.BH.A1EU.11 1 0.000
#> TCGA.A2.A3XS.01 3 0.000
#> TCGA.3C.AALI.01 7 0.751
#> TCGA.OL.A5RY.01 4 0.000
#> TCGA.E2.A1IF.01 4 0.249
#> TCGA.AC.A2FO.01 2 0.000
#> TCGA.BH.A209.01 4 0.000
#> TCGA.AR.A24S.01 7 1.000
#> TCGA.A2.A3KD.01 2 0.000
#> TCGA.B6.A1KF.01 3 0.000
#> TCGA.BH.A1FL.01 6 0.000
#> TCGA.BH.A0B3.11 1 0.751
#> TCGA.E2.A15K.01 5 0.751
#> TCGA.E2.A15K.06 6 0.000
#> TCGA.E9.A1NI.01 6 0.000
#> TCGA.AC.A2FK.01 1 0.000
#> TCGA.E9.A226.01 2 0.000
#> TCGA.E2.A1AZ.01 3 0.000
#> TCGA.D8.A1X8.01 7 1.000
#> TCGA.A2.A0T5.01 7 1.000
#> TCGA.AO.A12G.01 7 1.000
#> TCGA.C8.A1HO.01 6 0.000
#> TCGA.LD.A74U.01 2 0.000
#> TCGA.AR.A0TQ.01 2 0.000
#> TCGA.AO.A0JE.01 2 0.000
#> TCGA.AC.A62X.01 3 0.000
#> TCGA.AN.A0XR.01 6 0.000
#> TCGA.E9.A1RF.11 1 0.000
#> TCGA.E9.A228.01 2 0.249
#> TCGA.E9.A1RA.01 2 0.000
#> TCGA.BH.A0HA.01 6 0.000
#> TCGA.E2.A1L7.11 4 0.249
#> TCGA.D8.A1XS.01 5 0.000
#> TCGA.OL.A6VR.01 5 0.000
#> TCGA.E9.A22G.01 3 0.000
#> TCGA.LL.A740.01 2 0.000
#> TCGA.AC.A2FG.11 1 0.000
#> TCGA.E9.A1RI.11 1 0.000
#> TCGA.AR.A1AS.01 6 0.000
#> TCGA.D8.A27M.01 3 0.000
#> TCGA.E9.A1N8.11 1 0.000
#> TCGA.BH.A0BZ.01 2 0.000
#> TCGA.BH.A0RX.01 3 0.000
#> TCGA.S3.A6ZG.01 6 0.000
#> TCGA.AR.A1AW.01 4 0.000
#> TCGA.AN.A0XP.01 5 0.498
#> TCGA.EW.A2FV.01 2 0.000
#> TCGA.D8.A1XD.01 6 1.000
#> TCGA.A2.A4S1.01 3 0.000
#> TCGA.AR.A24M.01 5 0.253
#> TCGA.BH.A1FH.01 4 0.000
#> TCGA.D8.A1JM.01 3 0.000
#> TCGA.AC.A6NO.01 6 0.000
#> TCGA.BH.A0DV.01 4 0.000
#> TCGA.BH.A0AY.11 1 0.000
#> TCGA.E2.A572.01 6 0.751
#> TCGA.BH.A1ES.01 6 0.000
#> TCGA.A2.A0YI.01 2 0.000
#> TCGA.AC.A2QJ.01 3 0.000
#> TCGA.EW.A1PE.01 5 0.000
#> TCGA.BH.A0H6.01 6 0.000
#> TCGA.BH.A0BM.01 5 1.000
#> TCGA.A7.A2KD.01 7 1.000
#> TCGA.E2.A1II.01 3 0.000
#> TCGA.D8.A27I.01 4 0.000
#> TCGA.A2.A0YD.01 2 0.000
#> TCGA.BH.A0C0.01 4 0.000
#> TCGA.B6.A3ZX.01 3 0.498
#> TCGA.E9.A1NG.01 4 0.000
#> TCGA.S3.A6ZH.01 6 0.000
#> TCGA.HN.A2NL.01 3 0.000
#> TCGA.EW.A1IW.01 2 0.000
#> TCGA.JL.A3YW.01 4 0.000
#> TCGA.BH.A1F0.11 1 0.000
#> TCGA.AN.A0XN.01 2 0.000
#> TCGA.A1.A0SK.01 3 0.253
#> TCGA.E9.A6HE.01 7 1.000
#> TCGA.BH.A1FR.11 1 0.000
#> TCGA.BH.A1EX.01 7 0.751
#> TCGA.LL.A441.01 3 0.000
#> TCGA.AO.A125.01 6 0.000
#> TCGA.C8.A26W.01 7 1.000
#> TCGA.A2.A0YM.01 3 0.000
#> TCGA.BH.A0DP.01 2 0.000
#> TCGA.UL.AAZ6.01 6 0.000
#> TCGA.A2.A0CK.01 6 1.000
#> TCGA.AR.A2LN.01 2 0.000
#> TCGA.D8.A1JF.01 2 0.000
#> TCGA.OL.A6VQ.01 2 0.000
#> TCGA.LL.A5YP.01 3 0.000
#> TCGA.AR.A252.01 4 0.000
#> TCGA.A2.A25F.01 3 1.000
#> TCGA.PE.A5DC.01 6 0.000
#> TCGA.EW.A6SC.01 7 1.000
#> TCGA.GM.A2DO.01 4 0.000
#> TCGA.E9.A1ND.11 1 0.000
#> TCGA.E2.A1LL.01 4 0.000
#> TCGA.C8.A273.01 6 0.751
#> TCGA.E9.A1RD.11 1 0.000
#> TCGA.AR.A0U2.01 6 0.000
#> TCGA.C8.A1HL.01 6 0.000
#> TCGA.BH.A1FN.11 1 0.000
#> TCGA.BH.A0AU.01 7 0.000
#> TCGA.A2.A0T1.01 4 0.000
#> TCGA.BH.A28O.01 4 0.498
#> TCGA.AR.A24W.01 4 0.000
#> TCGA.EW.A1P1.01 1 0.000
#> TCGA.E2.A9RU.01 6 0.000
#> TCGA.AR.A0TT.01 2 0.000
#> TCGA.E2.A1IO.11 1 0.000
#> TCGA.AC.A3W6.01 2 0.000
#> TCGA.D8.A1JJ.01 7 1.000
#> TCGA.OL.A66P.01 4 0.000
#> TCGA.E2.A1B4.01 6 0.000
#> TCGA.B6.A1KC.01 6 0.000
#> TCGA.E9.A5UP.01 6 0.000
#> TCGA.A2.A1G4.01 6 0.000
#> TCGA.AR.A24L.01 2 1.000
#> TCGA.BH.A0H3.01 2 0.000
#> TCGA.LL.A73Z.01 4 0.000
#> TCGA.EW.A1IZ.01 4 0.000
#> TCGA.AO.A0JA.01 7 1.000
#> TCGA.AR.A0TX.01 2 1.000
#> TCGA.AO.A0JG.01 2 1.000
#> TCGA.OL.A66N.01 7 1.000
#> TCGA.A2.A1FV.01 6 0.000
#> TCGA.D8.A1XC.01 6 0.249
#> TCGA.A7.A4SC.01 2 0.000
#> TCGA.AR.A2LH.01 4 0.000
#> TCGA.LL.A6FR.01 3 0.000
#> TCGA.A7.A13F.11 1 0.000
#> TCGA.GM.A2DB.01 4 0.000
#> TCGA.LL.A5YO.01 4 0.000
#> TCGA.E9.A1N3.01 5 0.000
#> TCGA.PL.A8LV.01 3 0.000
#> TCGA.AO.A1KR.01 3 0.000
#> TCGA.AN.A0XL.01 7 1.000
#> TCGA.E2.A15J.01 6 0.000
#> TCGA.E9.A244.01 3 0.000
#> TCGA.E9.A24A.01 2 1.000
#> TCGA.BH.A1EV.11 1 0.000
#> TCGA.GM.A2DL.01 2 0.000
#> TCGA.S3.AA11.01 6 1.000
#> TCGA.AC.A3QQ.01 6 0.000
#> TCGA.Z7.A8R5.01 4 0.000
#> TCGA.B6.A400.01 3 0.000
#> TCGA.AQ.A54O.01 5 0.000
#> TCGA.BH.A1FC.01 3 0.000
#> TCGA.E9.A22B.01 2 0.000
#> TCGA.A2.A3XV.01 2 0.498
#> TCGA.AC.A6IX.06 4 0.000
#> TCGA.BH.A0B9.01 3 0.000
#> TCGA.BH.A18V.06 3 0.000
#> TCGA.AC.A6IX.01 2 0.000
#> TCGA.D8.A1JT.01 6 0.000
#> TCGA.AR.A2LL.01 6 0.000
#> TCGA.D8.A1X7.01 5 0.000
#> TCGA.E9.A247.01 6 0.000
#> TCGA.D8.A1X5.01 6 1.000
#> TCGA.AO.A03U.01 1 0.000
#> TCGA.A8.A075.01 5 0.502
#> TCGA.D8.A73X.01 6 0.000
#> TCGA.B6.A0WY.01 2 0.000
#> TCGA.E9.A1R4.01 2 0.000
#> TCGA.E9.A3Q9.01 5 0.000
#> TCGA.BH.A0E1.01 5 0.000
#> TCGA.EW.A423.01 6 0.000
#> TCGA.BH.A1ES.11 1 0.000
#> TCGA.EW.A1J2.01 2 0.000
#> TCGA.BH.A0GY.01 7 1.000
#> TCGA.W8.A86G.01 2 0.000
#> TCGA.A7.A5ZW.01 4 0.000
#> TCGA.E2.A106.01 6 0.000
#> TCGA.AR.A0TV.01 6 0.000
#> TCGA.E2.A56Z.01 6 0.000
#> TCGA.AC.A2FM.01 6 0.000
#> TCGA.C8.A1HF.01 2 1.000
#> TCGA.C8.A27B.01 3 0.000
#> TCGA.E2.A15I.11 1 0.000
#> TCGA.A7.A13E.01 3 0.000
#> TCGA.A2.A1G6.01 4 0.249
#> TCGA.B6.A402.01 3 0.000
#> TCGA.A2.A0T7.01 2 0.000
#> TCGA.A7.A0D9.01 6 0.000
#> TCGA.AC.A5XU.01 6 0.000
#> TCGA.BH.A0DH.11 1 0.000
#> TCGA.BH.A204.01 6 0.000
#> TCGA.B6.A0WW.01 6 0.000
#> TCGA.A2.A3XZ.01 4 0.000
#> TCGA.AR.A1AI.01 3 0.000
#> TCGA.BH.A0BC.11 1 0.000
#> TCGA.D8.A1XL.01 5 1.000
#> TCGA.E9.A5UO.01 6 0.000
#> TCGA.A7.A13E.11 1 0.000
#> TCGA.A2.A0SV.01 7 1.000
#> TCGA.OL.A5RZ.01 6 0.000
#> TCGA.E2.A1LS.01 3 0.000
#> TCGA.AO.A0JJ.01 2 0.000
#> TCGA.BH.A0BA.11 1 0.000
#> TCGA.AR.A24R.01 6 0.000
#> TCGA.AO.A1KP.01 6 0.000
#> TCGA.D8.A1JL.01 3 0.000
#> TCGA.E2.A1LH.01 3 0.000
#> TCGA.B6.A0X7.01 7 1.000
#> TCGA.BH.A0DK.11 4 0.000
#> TCGA.D8.A4Z1.01 4 0.000
#> TCGA.E9.A1RE.01 6 0.000
#> TCGA.OL.A5RV.01 2 0.000
#> TCGA.E2.A1BC.01 2 0.747
#> TCGA.GM.A2DM.01 5 0.000
#> TCGA.A2.A0YF.01 6 0.000
#> TCGA.A2.A3Y0.01 3 0.000
#> TCGA.AC.A3YI.01 4 0.000
#> TCGA.E9.A22D.01 4 0.751
#> TCGA.BH.A0E0.11 1 0.000
#> TCGA.C8.A274.01 6 0.000
#> TCGA.BH.A0B2.11 1 0.000
#> TCGA.A1.A0SF.01 2 1.000
#> TCGA.EW.A6SD.01 2 1.000
#> TCGA.C8.A1HM.01 7 0.000
#> TCGA.A7.A426.01 2 0.000
#> TCGA.E9.A1RC.01 6 0.000
#> TCGA.AR.A1AU.01 2 0.000
#> TCGA.AO.A129.01 3 0.000
#> TCGA.A2.A4RX.01 3 0.000
#> TCGA.BH.A6R8.01 6 0.000
#> TCGA.BH.A1FM.01 6 0.000
#> TCGA.D8.A1JP.01 5 1.000
#> TCGA.E2.A1IP.01 3 0.000
#> TCGA.AO.A0JM.01 6 0.000
#> TCGA.E9.A1N6.01 7 0.000
#> TCGA.BH.A0DS.01 6 0.747
#> TCGA.V7.A7HQ.01 5 0.751
#> TCGA.D8.A27L.01 2 0.000
#> TCGA.A2.A4RY.01 4 0.000
#> TCGA.E9.A1NF.01 2 1.000
#> TCGA.EW.A1PA.01 7 0.751
#> TCGA.BH.A0BV.11 1 0.000
#> TCGA.AC.A3TM.01 7 1.000
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#> TCGA.BH.A1EO.01 2 1.000
#> TCGA.BH.A0BZ.11 1 0.000
#> TCGA.D8.A27K.01 2 1.000
#> TCGA.BH.A28Q.01 6 0.000
#> TCGA.E9.A1NG.11 1 0.000
#> TCGA.EW.A1J1.01 5 0.000
#> TCGA.C8.A1HG.01 7 1.000
#> TCGA.D8.A1XK.01 3 0.000
#> TCGA.AQ.A0Y5.01 7 0.000
#> TCGA.3C.AAAU.01 6 0.000
#> TCGA.A2.A4S0.01 5 0.000
#> TCGA.BH.A0DV.11 1 0.000
#> TCGA.AR.A1AV.01 6 0.000
#> TCGA.AC.A8OQ.01 3 0.000
#> TCGA.BH.A0BS.11 1 0.000
#> TCGA.EW.A1PB.01 3 0.000
#> TCGA.A7.A3J0.01 5 0.000
#> TCGA.D8.A1JU.01 2 0.249
#> TCGA.A7.A6VX.01 6 0.000
#> TCGA.E2.A108.01 4 0.000
#> TCGA.BH.A0BT.01 6 0.000
#> TCGA.A2.A0YK.01 4 0.249
#> TCGA.E9.A1N8.01 3 0.000
#> TCGA.E2.A574.01 3 0.000
#> TCGA.A1.A0SO.01 3 0.000
#> TCGA.BH.A0DI.01 4 0.000
#> TCGA.E2.A1IG.01 6 0.000
#> TCGA.E2.A107.01 7 0.747
#> TCGA.5L.AAT0.01 2 0.000
#> TCGA.E9.A1NH.01 5 1.000
#> TCGA.D8.A27E.01 5 0.000
#> TCGA.AR.A24Q.01 3 0.000
#> TCGA.BH.A1F0.01 3 1.000
#> TCGA.E9.A1RB.11 1 0.000
#> TCGA.AR.A0U0.01 3 0.000
get_classes(res, k = 8)
#> class p
#> TCGA.OL.A66H.01 5 0.000
#> TCGA.3C.AALK.01 5 0.498
#> TCGA.AC.A5EH.01 5 0.751
#> TCGA.EW.A2FW.01 7 0.000
#> TCGA.E9.A1R0.01 2 0.000
#> TCGA.AR.A1AJ.01 8 0.000
#> TCGA.AC.A62Y.01 5 0.000
#> TCGA.E9.A1QZ.01 4 0.000
#> TCGA.E9.A1R2.01 5 1.000
#> TCGA.E9.A3X8.01 4 0.000
#> TCGA.AR.A255.01 2 0.498
#> TCGA.E2.A10B.01 5 0.498
#> TCGA.E9.A1N4.11 1 0.000
#> TCGA.AO.A0JD.01 5 0.000
#> TCGA.D8.A1JD.01 5 0.000
#> TCGA.D8.A1XA.01 7 0.000
#> TCGA.AO.A1KQ.01 5 1.000
#> TCGA.A8.A0A6.01 2 0.000
#> TCGA.BH.A1F2.11 1 0.000
#> TCGA.A7.A3RF.01 7 0.000
#> TCGA.A2.A0SW.01 5 1.000
#> TCGA.A7.A3IY.01 4 0.000
#> TCGA.GM.A2D9.01 6 0.000
#> TCGA.D8.A3Z5.01 2 0.000
#> TCGA.E9.A1ND.01 8 0.751
#> TCGA.EW.A1P5.01 6 1.000
#> TCGA.E9.A1RD.01 5 0.000
#> TCGA.AR.A1AQ.01 8 1.000
#> TCGA.LD.A66U.01 2 0.000
#> TCGA.BH.A1EN.01 6 0.498
#> TCGA.BH.A1FN.01 5 1.000
#> TCGA.EW.A1PD.01 5 0.498
#> TCGA.E9.A1N5.01 5 0.000
#> TCGA.D8.A1J8.01 6 0.502
#> TCGA.E9.A3QA.01 8 0.000
#> TCGA.S3.AA15.01 8 0.000
#> TCGA.BH.A0DP.11 4 0.000
#> TCGA.BH.A0H0.01 7 0.751
#> TCGA.A2.A3XX.01 3 0.000
#> TCGA.AC.A2FB.01 4 0.000
#> TCGA.AC.A3QP.01 4 0.000
#> TCGA.BH.A0BF.11 1 0.000
#> TCGA.A2.A0YC.01 6 0.000
#> TCGA.GM.A2DK.01 2 0.000
#> TCGA.GM.A2DC.01 6 0.000
#> TCGA.AR.A24N.01 6 0.000
#> TCGA.E2.A1B0.01 2 0.000
#> TCGA.BH.A1EY.01 2 0.000
#> TCGA.EW.A6S9.01 5 1.000
#> TCGA.AC.A8OS.01 2 0.000
#> TCGA.GM.A2DN.01 4 0.249
#> TCGA.AO.A03M.01 2 0.000
#> TCGA.A2.A3XT.01 3 1.000
#> TCGA.A2.A4RW.01 4 0.000
#> TCGA.AC.A6IV.01 4 0.000
#> TCGA.LL.A7SZ.01 2 0.000
#> TCGA.A1.A0SJ.01 6 0.000
#> TCGA.AR.A2LJ.01 4 0.000
#> TCGA.AQ.A1H3.01 5 1.000
#> TCGA.D8.A1JB.01 4 0.000
#> TCGA.BH.A0BC.01 2 0.000
#> TCGA.BH.A1EW.01 2 0.000
#> TCGA.BH.A1FG.01 7 1.000
#> TCGA.EW.A1P7.01 8 0.000
#> TCGA.GM.A2DH.01 2 0.000
#> TCGA.D8.A27P.01 5 0.000
#> TCGA.EW.A2FS.01 2 0.000
#> TCGA.E2.A1IL.01 5 0.253
#> TCGA.A7.A3IZ.01 7 0.000
#> TCGA.E2.A570.01 5 0.000
#> TCGA.OL.A66J.01 5 1.000
#> TCGA.AR.A2LO.01 4 0.000
#> TCGA.BH.A1FC.11 1 0.000
#> TCGA.E9.A5FL.01 8 1.000
#> TCGA.BH.A201.01 5 0.000
#> TCGA.LL.A5YM.01 7 1.000
#> TCGA.BH.A0H9.11 1 0.000
#> TCGA.AC.A4ZE.01 7 0.000
#> TCGA.A2.A0T2.01 3 0.000
#> TCGA.AR.A0TP.01 3 0.000
#> TCGA.S3.AA14.01 5 0.000
#> TCGA.B6.A0RS.01 2 0.000
#> TCGA.EW.A1P0.01 7 0.000
#> TCGA.AR.A1AT.01 2 0.000
#> TCGA.A2.A1G0.01 5 0.000
#> TCGA.BH.A208.11 1 0.000
#> TCGA.AR.A24H.01 7 0.000
#> TCGA.D8.A1XV.01 7 0.000
#> TCGA.AR.A2LQ.01 4 1.000
#> TCGA.AC.A3OD.01 4 0.000
#> TCGA.BH.A0DI.11 1 0.249
#> TCGA.AR.A0TU.01 3 1.000
#> TCGA.AN.A0XV.01 5 1.000
#> TCGA.A2.A0YT.01 7 0.000
#> TCGA.BH.A0B5.01 6 0.000
#> TCGA.D8.A1JI.01 7 0.000
#> TCGA.UU.A93S.01 2 0.000
#> TCGA.E9.A1N6.11 1 0.000
#> TCGA.E9.A1R6.01 7 0.000
#> TCGA.D8.A1XZ.01 7 1.000
#> TCGA.BH.A0B8.01 7 0.000
#> TCGA.LL.A6FQ.01 7 0.000
#> TCGA.XX.A89A.01 2 0.000
#> TCGA.EW.A1OY.01 7 0.000
#> TCGA.A7.A13G.11 1 0.000
#> TCGA.B6.A0RP.01 5 0.498
#> TCGA.LL.A9Q3.01 6 0.498
#> TCGA.A1.A0SQ.01 7 0.000
#> TCGA.AR.A5QM.01 2 0.000
#> TCGA.A7.A26I.01 3 0.000
#> TCGA.E2.A1B6.01 8 0.000
#> TCGA.PE.A5DE.01 2 0.000
#> TCGA.E9.A1RB.01 5 0.000
#> TCGA.A2.A0ST.01 8 0.000
#> TCGA.B6.A0RO.01 5 0.000
#> TCGA.AC.A23H.01 5 1.000
#> TCGA.AC.A2BM.01 5 0.751
#> TCGA.BH.A0WA.01 3 0.000
#> TCGA.EW.A1J6.01 5 1.000
#> TCGA.D8.A27V.01 5 0.000
#> TCGA.B6.A40C.01 6 0.000
#> TCGA.A2.A1FZ.01 4 1.000
#> TCGA.A7.A26H.01 5 0.751
#> TCGA.BH.A0H7.11 1 0.000
#> TCGA.BH.A0BA.01 6 0.751
#> TCGA.BH.AB28.01 2 0.751
#> TCGA.E2.A2P6.01 7 0.000
#> TCGA.B6.A0RT.01 8 0.000
#> TCGA.AR.A1AY.01 3 0.000
#> TCGA.A2.A25C.01 5 0.000
#> TCGA.S3.AA10.01 3 1.000
#> TCGA.OL.A5DA.01 6 0.000
#> TCGA.D8.A27R.01 2 0.000
#> TCGA.EW.A6SB.01 8 0.000
#> TCGA.A7.A5ZV.01 3 0.000
#> TCGA.LL.A50Y.01 6 1.000
#> TCGA.B6.A0WX.01 3 1.000
#> TCGA.LL.A442.01 7 1.000
#> TCGA.C8.A26Z.01 7 0.000
#> TCGA.BH.A1FU.01 4 0.000
#> TCGA.AO.A1KO.01 1 0.000
#> TCGA.BH.A0E0.01 3 1.000
#> TCGA.A7.A0DB.11 1 0.000
#> TCGA.E9.A2JT.01 8 0.000
#> TCGA.OL.A5D6.01 2 0.000
#> TCGA.BH.A0AU.11 1 0.000
#> TCGA.BH.A1FJ.01 7 0.000
#> TCGA.E9.A1RC.11 1 0.000
#> TCGA.E9.A1NE.11 1 0.000
#> TCGA.E2.A3DX.01 4 0.000
#> TCGA.A1.A0SE.01 2 0.000
#> TCGA.BH.A1FM.11 1 0.000
#> TCGA.E9.A3HO.01 7 0.000
#> TCGA.D8.A1XT.01 2 0.000
#> TCGA.C8.A1HI.01 2 0.000
#> TCGA.E9.A1NA.01 6 0.000
#> TCGA.A2.A0T4.01 2 0.000
#> TCGA.BH.A0BS.01 7 1.000
#> TCGA.BH.A203.11 1 0.000
#> TCGA.MS.A51U.01 4 0.000
#> TCGA.E2.A1B5.11 1 0.000
#> TCGA.B6.A0WT.01 5 1.000
#> TCGA.B6.A0RN.01 7 0.000
#> TCGA.D8.A1Y2.01 2 0.000
#> TCGA.PL.A8LY.01 1 0.000
#> TCGA.B6.A0RU.01 3 0.000
#> TCGA.EW.A1PH.01 3 0.000
#> TCGA.D8.A1XJ.01 6 0.751
#> TCGA.BH.A0DG.01 2 0.502
#> TCGA.C8.A3M7.01 2 0.000
#> TCGA.BH.A1EW.11 4 0.000
#> TCGA.E2.A1L6.01 5 0.249
#> TCGA.D8.A1XY.01 5 0.000
#> TCGA.D8.A27G.01 2 0.000
#> TCGA.E2.A109.01 7 0.000
#> TCGA.AR.A1AM.01 2 0.000
#> TCGA.4H.AAAK.01 5 0.498
#> TCGA.AC.A5XS.01 2 0.000
#> TCGA.AC.A5EI.01 4 0.000
#> TCGA.BH.A1EU.11 1 0.000
#> TCGA.A2.A3XS.01 3 0.000
#> TCGA.3C.AALI.01 5 0.253
#> TCGA.OL.A5RY.01 8 0.000
#> TCGA.E2.A1IF.01 4 0.000
#> TCGA.AC.A2FO.01 4 1.000
#> TCGA.BH.A209.01 4 0.000
#> TCGA.AR.A24S.01 5 0.000
#> TCGA.A2.A3KD.01 2 0.000
#> TCGA.B6.A1KF.01 3 0.000
#> TCGA.BH.A1FL.01 7 0.000
#> TCGA.BH.A0B3.11 1 0.000
#> TCGA.E2.A15K.01 5 0.253
#> TCGA.E2.A15K.06 7 0.000
#> TCGA.E9.A1NI.01 7 0.000
#> TCGA.AC.A2FK.01 1 0.000
#> TCGA.E9.A226.01 2 1.000
#> TCGA.E2.A1AZ.01 3 1.000
#> TCGA.D8.A1X8.01 5 0.000
#> TCGA.A2.A0T5.01 5 0.000
#> TCGA.AO.A12G.01 6 0.249
#> TCGA.C8.A1HO.01 7 0.000
#> TCGA.LD.A74U.01 2 0.000
#> TCGA.AR.A0TQ.01 2 0.000
#> TCGA.AO.A0JE.01 2 0.000
#> TCGA.AC.A62X.01 3 0.000
#> TCGA.AN.A0XR.01 7 0.000
#> TCGA.E9.A1RF.11 1 0.000
#> TCGA.E9.A228.01 5 0.747
#> TCGA.E9.A1RA.01 2 0.000
#> TCGA.BH.A0HA.01 7 1.000
#> TCGA.E2.A1L7.11 1 0.000
#> TCGA.D8.A1XS.01 7 1.000
#> TCGA.OL.A6VR.01 5 1.000
#> TCGA.E9.A22G.01 3 0.000
#> TCGA.LL.A740.01 2 0.000
#> TCGA.AC.A2FG.11 1 0.000
#> TCGA.E9.A1RI.11 1 0.000
#> TCGA.AR.A1AS.01 7 0.000
#> TCGA.D8.A27M.01 8 0.000
#> TCGA.E9.A1N8.11 1 0.000
#> TCGA.BH.A0BZ.01 2 0.000
#> TCGA.BH.A0RX.01 8 0.000
#> TCGA.S3.A6ZG.01 6 1.000
#> TCGA.AR.A1AW.01 4 0.000
#> TCGA.AN.A0XP.01 5 1.000
#> TCGA.EW.A2FV.01 2 0.000
#> TCGA.D8.A1XD.01 6 0.000
#> TCGA.A2.A4S1.01 8 1.000
#> TCGA.AR.A24M.01 5 1.000
#> TCGA.BH.A1FH.01 4 0.000
#> TCGA.D8.A1JM.01 3 1.000
#> TCGA.AC.A6NO.01 7 1.000
#> TCGA.BH.A0DV.01 4 0.000
#> TCGA.BH.A0AY.11 1 0.000
#> TCGA.E2.A572.01 7 0.253
#> TCGA.BH.A1ES.01 7 1.000
#> TCGA.A2.A0YI.01 2 0.000
#> TCGA.AC.A2QJ.01 8 1.000
#> TCGA.EW.A1PE.01 5 0.000
#> TCGA.BH.A0H6.01 5 1.000
#> TCGA.BH.A0BM.01 5 0.000
#> TCGA.A7.A2KD.01 5 0.000
#> TCGA.E2.A1II.01 8 0.000
#> TCGA.D8.A27I.01 4 0.000
#> TCGA.A2.A0YD.01 2 0.000
#> TCGA.BH.A0C0.01 4 0.249
#> TCGA.B6.A3ZX.01 8 0.000
#> TCGA.E9.A1NG.01 4 0.000
#> TCGA.S3.A6ZH.01 7 0.000
#> TCGA.HN.A2NL.01 3 0.000
#> TCGA.EW.A1IW.01 2 0.751
#> TCGA.JL.A3YW.01 2 1.000
#> TCGA.BH.A1F0.11 1 0.000
#> TCGA.AN.A0XN.01 6 0.751
#> TCGA.A1.A0SK.01 3 0.502
#> TCGA.E9.A6HE.01 5 1.000
#> TCGA.BH.A1FR.11 1 0.000
#> TCGA.BH.A1EX.01 5 0.498
#> TCGA.LL.A441.01 8 0.000
#> TCGA.AO.A125.01 7 0.000
#> TCGA.C8.A26W.01 5 0.000
#> TCGA.A2.A0YM.01 3 0.000
#> TCGA.BH.A0DP.01 5 0.751
#> TCGA.UL.AAZ6.01 7 0.000
#> TCGA.A2.A0CK.01 6 0.498
#> TCGA.AR.A2LN.01 2 0.000
#> TCGA.D8.A1JF.01 2 0.000
#> TCGA.OL.A6VQ.01 2 0.249
#> TCGA.LL.A5YP.01 3 0.000
#> TCGA.AR.A252.01 4 0.000
#> TCGA.A2.A25F.01 8 0.000
#> TCGA.PE.A5DC.01 6 1.000
#> TCGA.EW.A6SC.01 5 0.000
#> TCGA.GM.A2DO.01 4 0.000
#> TCGA.E9.A1ND.11 1 0.000
#> TCGA.E2.A1LL.01 2 1.000
#> TCGA.C8.A273.01 6 0.498
#> TCGA.E9.A1RD.11 1 0.000
#> TCGA.AR.A0U2.01 7 0.000
#> TCGA.C8.A1HL.01 7 0.000
#> TCGA.BH.A1FN.11 1 0.000
#> TCGA.BH.A0AU.01 5 0.000
#> TCGA.A2.A0T1.01 4 0.000
#> TCGA.BH.A28O.01 1 0.747
#> TCGA.AR.A24W.01 4 0.000
#> TCGA.EW.A1P1.01 1 0.000
#> TCGA.E2.A9RU.01 6 0.000
#> TCGA.AR.A0TT.01 2 0.000
#> TCGA.E2.A1IO.11 1 0.000
#> TCGA.AC.A3W6.01 4 0.000
#> TCGA.D8.A1JJ.01 5 0.000
#> TCGA.OL.A66P.01 4 1.000
#> TCGA.E2.A1B4.01 7 0.253
#> TCGA.B6.A1KC.01 7 0.000
#> TCGA.E9.A5UP.01 7 0.000
#> TCGA.A2.A1G4.01 7 1.000
#> TCGA.AR.A24L.01 2 1.000
#> TCGA.BH.A0H3.01 2 0.000
#> TCGA.LL.A73Z.01 4 0.000
#> TCGA.EW.A1IZ.01 4 0.000
#> TCGA.AO.A0JA.01 6 1.000
#> TCGA.AR.A0TX.01 2 0.498
#> TCGA.AO.A0JG.01 5 0.249
#> TCGA.OL.A66N.01 5 1.000
#> TCGA.A2.A1FV.01 7 0.000
#> TCGA.D8.A1XC.01 7 0.000
#> TCGA.A7.A4SC.01 2 0.000
#> TCGA.AR.A2LH.01 4 1.000
#> TCGA.LL.A6FR.01 3 0.000
#> TCGA.A7.A13F.11 1 0.000
#> TCGA.GM.A2DB.01 2 0.000
#> TCGA.LL.A5YO.01 8 0.000
#> TCGA.E9.A1N3.01 5 0.000
#> TCGA.PL.A8LV.01 3 1.000
#> TCGA.AO.A1KR.01 3 1.000
#> TCGA.AN.A0XL.01 5 0.000
#> TCGA.E2.A15J.01 7 0.000
#> TCGA.E9.A244.01 3 0.000
#> TCGA.E9.A24A.01 5 0.000
#> TCGA.BH.A1EV.11 1 0.000
#> TCGA.GM.A2DL.01 2 0.000
#> TCGA.S3.AA11.01 6 1.000
#> TCGA.AC.A3QQ.01 6 1.000
#> TCGA.Z7.A8R5.01 4 0.000
#> TCGA.B6.A400.01 3 0.000
#> TCGA.AQ.A54O.01 5 1.000
#> TCGA.BH.A1FC.01 3 1.000
#> TCGA.E9.A22B.01 2 0.249
#> TCGA.A2.A3XV.01 2 0.000
#> TCGA.AC.A6IX.06 4 0.000
#> TCGA.BH.A0B9.01 3 1.000
#> TCGA.BH.A18V.06 8 0.000
#> TCGA.AC.A6IX.01 2 0.000
#> TCGA.D8.A1JT.01 7 0.000
#> TCGA.AR.A2LL.01 6 0.000
#> TCGA.D8.A1X7.01 5 1.000
#> TCGA.E9.A247.01 7 0.253
#> TCGA.D8.A1X5.01 6 0.498
#> TCGA.AO.A03U.01 1 1.000
#> TCGA.A8.A075.01 5 0.000
#> TCGA.D8.A73X.01 6 1.000
#> TCGA.B6.A0WY.01 4 0.751
#> TCGA.E9.A1R4.01 2 0.000
#> TCGA.E9.A3Q9.01 5 0.000
#> TCGA.BH.A0E1.01 5 1.000
#> TCGA.EW.A423.01 7 0.000
#> TCGA.BH.A1ES.11 1 0.000
#> TCGA.EW.A1J2.01 2 0.000
#> TCGA.BH.A0GY.01 5 0.000
#> TCGA.W8.A86G.01 2 0.000
#> TCGA.A7.A5ZW.01 4 0.000
#> TCGA.E2.A106.01 7 0.000
#> TCGA.AR.A0TV.01 6 0.000
#> TCGA.E2.A56Z.01 7 0.000
#> TCGA.AC.A2FM.01 7 0.000
#> TCGA.C8.A1HF.01 5 1.000
#> TCGA.C8.A27B.01 3 0.498
#> TCGA.E2.A15I.11 1 0.000
#> TCGA.A7.A13E.01 3 0.000
#> TCGA.A2.A1G6.01 4 0.747
#> TCGA.B6.A402.01 3 0.000
#> TCGA.A2.A0T7.01 2 0.498
#> TCGA.A7.A0D9.01 7 0.253
#> TCGA.AC.A5XU.01 7 0.000
#> TCGA.BH.A0DH.11 1 0.000
#> TCGA.BH.A204.01 7 0.000
#> TCGA.B6.A0WW.01 6 0.498
#> TCGA.A2.A3XZ.01 4 0.000
#> TCGA.AR.A1AI.01 8 1.000
#> TCGA.BH.A0BC.11 1 0.000
#> TCGA.D8.A1XL.01 5 1.000
#> TCGA.E9.A5UO.01 7 0.000
#> TCGA.A7.A13E.11 1 0.000
#> TCGA.A2.A0SV.01 6 0.502
#> TCGA.OL.A5RZ.01 7 0.000
#> TCGA.E2.A1LS.01 3 0.000
#> TCGA.AO.A0JJ.01 2 0.000
#> TCGA.BH.A0BA.11 1 0.000
#> TCGA.AR.A24R.01 6 0.000
#> TCGA.AO.A1KP.01 7 0.000
#> TCGA.D8.A1JL.01 8 1.000
#> TCGA.E2.A1LH.01 8 0.253
#> TCGA.B6.A0X7.01 6 0.751
#> TCGA.BH.A0DK.11 4 0.000
#> TCGA.D8.A4Z1.01 4 0.000
#> TCGA.E9.A1RE.01 7 0.000
#> TCGA.OL.A5RV.01 2 0.000
#> TCGA.E2.A1BC.01 5 0.000
#> TCGA.GM.A2DM.01 5 0.000
#> TCGA.A2.A0YF.01 7 0.000
#> TCGA.A2.A3Y0.01 8 1.000
#> TCGA.AC.A3YI.01 4 0.747
#> TCGA.E9.A22D.01 4 0.249
#> TCGA.BH.A0E0.11 1 0.000
#> TCGA.C8.A274.01 7 0.000
#> TCGA.BH.A0B2.11 1 0.000
#> TCGA.A1.A0SF.01 5 0.000
#> TCGA.EW.A6SD.01 2 1.000
#> TCGA.C8.A1HM.01 5 1.000
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#> TCGA.D8.A1JS.01 7 0.000
#> TCGA.E2.A15K.11 1 0.000
#> TCGA.WT.AB44.01 6 0.000
#> TCGA.EW.A424.01 6 0.000
#> TCGA.BH.A1FR.01 5 0.000
#> TCGA.A7.A425.01 5 0.000
#> TCGA.B6.A0IK.01 2 0.000
#> TCGA.AR.A24U.01 4 0.000
#> TCGA.E9.A1RF.01 2 0.000
#> TCGA.B6.A408.01 6 1.000
#> TCGA.BH.A0HP.01 2 0.000
#> TCGA.E2.A1L7.01 6 0.000
#> TCGA.5T.A9QA.01 6 0.000
#> TCGA.A2.A0SY.01 6 0.000
#> TCGA.BH.A8FZ.01 4 0.000
#> TCGA.A2.A0YG.01 6 0.498
#> TCGA.AC.A2FG.01 5 0.000
#> TCGA.AR.A1AX.01 4 0.000
#> TCGA.AR.A1AL.01 2 0.000
#> TCGA.BH.A1EY.11 1 0.000
#> TCGA.AQ.A54N.01 3 0.000
#> TCGA.BH.A1EO.01 5 1.000
#> TCGA.BH.A0BZ.11 1 0.000
#> TCGA.D8.A27K.01 5 0.000
#> TCGA.BH.A28Q.01 6 0.000
#> TCGA.E9.A1NG.11 1 0.000
#> TCGA.EW.A1J1.01 7 0.253
#> TCGA.C8.A1HG.01 5 0.000
#> TCGA.D8.A1XK.01 3 1.000
#> TCGA.AQ.A0Y5.01 5 0.000
#> TCGA.3C.AAAU.01 7 0.000
#> TCGA.A2.A4S0.01 5 0.253
#> TCGA.BH.A0DV.11 1 0.000
#> TCGA.AR.A1AV.01 7 0.000
#> TCGA.AC.A8OQ.01 8 1.000
#> TCGA.BH.A0BS.11 1 0.000
#> TCGA.EW.A1PB.01 8 0.502
#> TCGA.A7.A3J0.01 5 1.000
#> TCGA.D8.A1JU.01 4 0.000
#> TCGA.A7.A6VX.01 7 0.000
#> TCGA.E2.A108.01 8 1.000
#> TCGA.BH.A0BT.01 7 0.000
#> TCGA.A2.A0YK.01 4 0.000
#> TCGA.E9.A1N8.01 3 0.000
#> TCGA.E2.A574.01 3 0.000
#> TCGA.A1.A0SO.01 3 1.000
#> TCGA.BH.A0DI.01 4 0.000
#> TCGA.E2.A1IG.01 7 0.000
#> TCGA.E2.A107.01 6 1.000
#> TCGA.5L.AAT0.01 2 0.000
#> TCGA.E9.A1NH.01 5 0.000
#> TCGA.D8.A27E.01 5 0.000
#> TCGA.AR.A24Q.01 3 0.000
#> TCGA.BH.A1F0.01 8 0.000
#> TCGA.E9.A1RB.11 1 0.000
#> TCGA.AR.A0U0.01 8 1.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node014-leaf , Node015 , Node021 , Node022 , Node023 , Node024 , Node031 , Node032 , Node033 , Node034 , Node041 , Node042 , Node043 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["01"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 155 columns.
#> Top rows (1000) are extracted by 'SD' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.974 0.990 0.4922 0.508 0.508
#> 3 3 1.000 0.996 0.999 0.2000 0.892 0.788
#> 4 4 1.000 0.984 0.994 0.2425 0.808 0.557
#> 5 5 1.000 0.975 0.990 0.0686 0.911 0.687
#> 6 6 0.942 0.909 0.938 0.0175 0.990 0.955
#> 7 7 0.855 0.804 0.882 0.0298 0.975 0.881
#> 8 8 0.834 0.664 0.839 0.0231 0.988 0.935
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2 3 4
There is also optional best \(k\) = 2 3 4 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.E9.A1QZ.01 2 0.000 0.987 0.00 1.00
#> TCGA.E9.A1N4.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A1F2.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A0DP.11 1 0.000 0.992 1.00 0.00
#> TCGA.AC.A2FB.01 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A0BF.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A1FC.11 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A0H9.11 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A208.11 1 0.000 0.992 1.00 0.00
#> TCGA.AR.A2LQ.01 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A0DI.11 1 0.000 0.992 1.00 0.00
#> TCGA.E9.A1N6.11 1 0.000 0.992 1.00 0.00
#> TCGA.A7.A13G.11 2 0.000 0.987 0.00 1.00
#> TCGA.E2.A1B6.01 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A0H7.11 1 0.000 0.992 1.00 0.00
#> TCGA.B6.A0RT.01 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A1FU.01 2 0.000 0.987 0.00 1.00
#> TCGA.AO.A1KO.01 1 0.000 0.992 1.00 0.00
#> TCGA.A7.A0DB.11 2 0.000 0.987 0.00 1.00
#> TCGA.E9.A2JT.01 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A0AU.11 1 0.000 0.992 1.00 0.00
#> TCGA.E9.A1RC.11 2 0.000 0.987 0.00 1.00
#> TCGA.E9.A1NE.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A1FM.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A203.11 1 0.000 0.992 1.00 0.00
#> TCGA.E2.A1B5.11 1 0.000 0.992 1.00 0.00
#> TCGA.PL.A8LY.01 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A1EW.11 1 0.000 0.992 1.00 0.00
#> TCGA.AC.A5EI.01 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A1EU.11 1 0.000 0.992 1.00 0.00
#> TCGA.OL.A5RY.01 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A209.01 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A0B3.11 1 0.000 0.992 1.00 0.00
#> TCGA.AC.A2FK.01 1 0.000 0.992 1.00 0.00
#> TCGA.E9.A1RF.11 2 0.000 0.987 0.00 1.00
#> TCGA.E2.A1L7.11 1 0.000 0.992 1.00 0.00
#> TCGA.AC.A2FG.11 1 0.000 0.992 1.00 0.00
#> TCGA.E9.A1RI.11 2 0.000 0.987 0.00 1.00
#> TCGA.E9.A1N8.11 2 0.990 0.213 0.44 0.56
#> TCGA.AR.A1AW.01 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A1FH.01 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A0AY.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A1F0.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A1FR.11 1 0.000 0.992 1.00 0.00
#> TCGA.AR.A252.01 2 0.000 0.987 0.00 1.00
#> TCGA.A2.A25F.01 2 0.000 0.987 0.00 1.00
#> TCGA.GM.A2DO.01 2 0.000 0.987 0.00 1.00
#> TCGA.E9.A1ND.11 2 0.000 0.987 0.00 1.00
#> TCGA.E9.A1RD.11 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A1FN.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A28O.01 1 0.000 0.992 1.00 0.00
#> TCGA.EW.A1P1.01 2 0.000 0.987 0.00 1.00
#> TCGA.E2.A1IO.11 2 0.000 0.987 0.00 1.00
#> TCGA.LL.A73Z.01 1 0.000 0.992 1.00 0.00
#> TCGA.AR.A2LH.01 2 0.000 0.987 0.00 1.00
#> TCGA.A7.A13F.11 1 0.000 0.992 1.00 0.00
#> TCGA.LL.A5YO.01 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A1EV.11 1 0.000 0.992 1.00 0.00
#> TCGA.Z7.A8R5.01 1 0.000 0.992 1.00 0.00
#> TCGA.AO.A03U.01 1 0.995 0.135 0.54 0.46
#> TCGA.BH.A1ES.11 1 0.000 0.992 1.00 0.00
#> TCGA.E2.A15I.11 2 0.000 0.987 0.00 1.00
#> TCGA.A2.A1G6.01 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A0DH.11 1 0.000 0.992 1.00 0.00
#> TCGA.A2.A3XZ.01 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A0BC.11 1 0.000 0.992 1.00 0.00
#> TCGA.A7.A13E.11 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A0BA.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A0DK.11 1 0.000 0.992 1.00 0.00
#> TCGA.D8.A4Z1.01 1 0.000 0.992 1.00 0.00
#> TCGA.AC.A3YI.01 1 0.242 0.952 0.96 0.04
#> TCGA.BH.A0E0.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A0B2.11 1 0.000 0.992 1.00 0.00
#> TCGA.A2.A4RY.01 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A0BV.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A0DG.11 1 0.000 0.992 1.00 0.00
#> TCGA.AC.A23H.11 1 0.000 0.992 1.00 0.00
#> TCGA.EW.A1PG.01 1 0.000 0.992 1.00 0.00
#> TCGA.E2.A1IF.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A209.11 2 0.000 0.987 0.00 1.00
#> TCGA.E9.A1R7.11 2 0.000 0.987 0.00 1.00
#> TCGA.AR.A5QQ.01 2 0.000 0.987 0.00 1.00
#> TCGA.E2.A1LB.11 1 0.000 0.992 1.00 0.00
#> TCGA.A2.A0CR.01 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A1FH.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A1FJ.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A0HK.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A0BM.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A0E1.11 1 0.000 0.992 1.00 0.00
#> TCGA.AR.A1AO.01 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A1FB.01 2 0.000 0.987 0.00 1.00
#> TCGA.A2.A3XW.01 1 0.680 0.776 0.82 0.18
#> TCGA.BH.A1FE.11 1 0.000 0.992 1.00 0.00
#> TCGA.A7.A0DC.11 1 0.000 0.992 1.00 0.00
#> TCGA.AO.A0JC.01 2 0.000 0.987 0.00 1.00
#> TCGA.A2.A0EP.01 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A0BJ.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A42U.01 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A1F5.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A1EO.11 2 0.000 0.987 0.00 1.00
#> TCGA.E9.A1NE.01 2 0.000 0.987 0.00 1.00
#> TCGA.C8.A8HR.01 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A6R9.01 2 0.000 0.987 0.00 1.00
#> TCGA.C8.A8HP.01 2 0.000 0.987 0.00 1.00
#> TCGA.AC.A2FM.11 1 0.000 0.992 1.00 0.00
#> TCGA.A7.A0D9.11 2 0.000 0.987 0.00 1.00
#> TCGA.AC.A2FB.11 1 0.000 0.992 1.00 0.00
#> TCGA.E2.A1LS.11 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A0BT.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A0C0.11 1 0.000 0.992 1.00 0.00
#> TCGA.E2.A1BC.11 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A0C3.11 1 0.000 0.992 1.00 0.00
#> TCGA.E9.A248.01 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A204.11 2 0.000 0.987 0.00 1.00
#> TCGA.GM.A3XG.01 1 0.000 0.992 1.00 0.00
#> TCGA.E9.A1NF.11 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A1EN.11 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A0DZ.11 1 0.000 0.992 1.00 0.00
#> TCGA.AC.A2FF.01 2 0.000 0.987 0.00 1.00
#> TCGA.E9.A1N5.11 1 0.000 0.992 1.00 0.00
#> TCGA.A7.A0CE.11 1 0.000 0.992 1.00 0.00
#> TCGA.LL.A440.01 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A1FG.11 1 0.000 0.992 1.00 0.00
#> TCGA.AC.A2FF.11 1 0.000 0.992 1.00 0.00
#> TCGA.LD.A9QF.01 2 0.000 0.987 0.00 1.00
#> TCGA.GM.A2DI.01 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A0B8.11 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A0AZ.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A0DQ.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A1FB.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A1FE.06 2 0.000 0.987 0.00 1.00
#> TCGA.E9.A1RH.11 2 0.000 0.987 0.00 1.00
#> TCGA.A7.A0CH.11 1 0.000 0.992 1.00 0.00
#> TCGA.GM.A4E0.01 2 0.000 0.987 0.00 1.00
#> TCGA.E9.A22A.01 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A1F8.11 1 0.000 0.992 1.00 0.00
#> TCGA.E9.A1NA.11 1 0.000 0.992 1.00 0.00
#> TCGA.E2.A1B5.01 2 0.000 0.987 0.00 1.00
#> TCGA.E2.A1LI.11 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A1FD.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A1F6.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A1ET.11 1 0.000 0.992 1.00 0.00
#> TCGA.E2.A1II.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A0HA.11 1 0.000 0.992 1.00 0.00
#> TCGA.OL.A97C.01 1 0.000 0.992 1.00 0.00
#> TCGA.E2.A15K.11 1 0.000 0.992 1.00 0.00
#> TCGA.AR.A24U.01 2 0.000 0.987 0.00 1.00
#> TCGA.AR.A1AX.01 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A1EY.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A0BZ.11 2 0.958 0.385 0.38 0.62
#> TCGA.E9.A1NG.11 2 0.000 0.987 0.00 1.00
#> TCGA.BH.A0DV.11 1 0.000 0.992 1.00 0.00
#> TCGA.BH.A0BS.11 1 0.000 0.992 1.00 0.00
#> TCGA.E2.A108.01 2 0.000 0.987 0.00 1.00
#> TCGA.E9.A1RB.11 2 0.000 0.987 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.E9.A1QZ.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.E9.A1N4.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A1F2.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A0DP.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.AC.A2FB.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BH.A0BF.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A1FC.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.BH.A0H9.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.BH.A208.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.AR.A2LQ.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A0DI.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.E9.A1N6.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.A7.A13G.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.E2.A1B6.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BH.A0H7.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.B6.A0RT.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BH.A1FU.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.AO.A1KO.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.A7.A0DB.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.E9.A2JT.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BH.A0AU.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.E9.A1RC.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.E9.A1NE.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A1FM.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A203.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.E2.A1B5.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.PL.A8LY.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A1EW.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.AC.A5EI.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A1EU.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.OL.A5RY.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BH.A209.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BH.A0B3.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.AC.A2FK.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.E9.A1RF.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.E2.A1L7.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.AC.A2FG.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.E9.A1RI.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.E9.A1N8.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.AR.A1AW.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BH.A1FH.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A0AY.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A1F0.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A1FR.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.AR.A252.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.A2.A25F.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.GM.A2DO.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.E9.A1ND.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.E9.A1RD.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.BH.A1FN.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A28O.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.EW.A1P1.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.E2.A1IO.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.LL.A73Z.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.AR.A2LH.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.A7.A13F.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.LL.A5YO.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BH.A1EV.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.Z7.A8R5.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.AO.A03U.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A1ES.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.E2.A15I.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.A2.A1G6.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A0DH.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.A2.A3XZ.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BH.A0BC.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.A7.A13E.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.BH.A0BA.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A0DK.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.D8.A4Z1.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.AC.A3YI.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A0E0.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A0B2.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.A2.A4RY.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A0BV.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A0DG.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.AC.A23H.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.EW.A1PG.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.E2.A1IF.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A209.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.E9.A1R7.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.AR.A5QQ.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.E2.A1LB.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.A2.A0CR.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BH.A1FH.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A1FJ.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A0HK.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A0BM.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A0E1.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.AR.A1AO.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BH.A1FB.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.A2.A3XW.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A1FE.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.A7.A0DC.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.AO.A0JC.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.A2.A0EP.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BH.A0BJ.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A42U.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A1F5.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A1EO.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.E9.A1NE.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.C8.A8HR.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BH.A6R9.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.C8.A8HP.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.AC.A2FM.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.A7.A0D9.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.AC.A2FB.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.E2.A1LS.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.BH.A0BT.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A0C0.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.E2.A1BC.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.BH.A0C3.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.E9.A248.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BH.A204.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.GM.A3XG.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.E9.A1NF.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.BH.A1EN.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.BH.A0DZ.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.AC.A2FF.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.E9.A1N5.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.A7.A0CE.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.LL.A440.01 2 0.429 0.737 0.18 0.82 0.00
#> TCGA.BH.A1FG.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.AC.A2FF.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.LD.A9QF.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.GM.A2DI.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BH.A0B8.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.BH.A0AZ.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A0DQ.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A1FB.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A1FE.06 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.E9.A1RH.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.A7.A0CH.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.GM.A4E0.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.E9.A22A.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BH.A1F8.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.E9.A1NA.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.E2.A1B5.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.E2.A1LI.11 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BH.A1FD.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A1F6.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.BH.A1ET.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.E2.A1II.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A0HA.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.OL.A97C.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.E2.A15K.11 3 0.153 0.946 0.04 0.00 0.96
#> TCGA.AR.A24U.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.AR.A1AX.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BH.A1EY.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A0BZ.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.E9.A1NG.11 3 0.000 0.998 0.00 0.00 1.00
#> TCGA.BH.A0DV.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BH.A0BS.11 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.E2.A108.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.E9.A1RB.11 3 0.000 0.998 0.00 0.00 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.E9.A1QZ.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.E9.A1N4.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.BH.A1F2.11 4 0.0707 0.976 0.02 0.00 0.00 0.98
#> TCGA.BH.A0DP.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.AC.A2FB.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.BH.A0BF.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.BH.A1FC.11 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.BH.A0H9.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.BH.A208.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.AR.A2LQ.01 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.BH.A0DI.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.E9.A1N6.11 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.A7.A13G.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.E2.A1B6.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.BH.A0H7.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.B6.A0RT.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.BH.A1FU.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.AO.A1KO.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.A7.A0DB.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.E9.A2JT.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.BH.A0AU.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.E9.A1RC.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.E9.A1NE.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.BH.A1FM.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.BH.A203.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.E2.A1B5.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.PL.A8LY.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.BH.A1EW.11 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.AC.A5EI.01 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.BH.A1EU.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.OL.A5RY.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.BH.A209.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.BH.A0B3.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.AC.A2FK.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.E9.A1RF.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.E2.A1L7.11 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.AC.A2FG.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.E9.A1RI.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.E9.A1N8.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.AR.A1AW.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.BH.A1FH.01 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.BH.A0AY.11 1 0.0707 0.971 0.98 0.00 0.00 0.02
#> TCGA.BH.A1F0.11 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.BH.A1FR.11 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.AR.A252.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.A2.A25F.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.GM.A2DO.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.E9.A1ND.11 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.E9.A1RD.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.BH.A1FN.11 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.BH.A28O.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.EW.A1P1.01 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.E2.A1IO.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.LL.A73Z.01 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.AR.A2LH.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.A7.A13F.11 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.LL.A5YO.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.BH.A1EV.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.Z7.A8R5.01 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.AO.A03U.01 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.BH.A1ES.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.E2.A15I.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.A2.A1G6.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.BH.A0DH.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.A2.A3XZ.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.BH.A0BC.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.A7.A13E.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.BH.A0BA.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.BH.A0DK.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.D8.A4Z1.01 1 0.3610 0.752 0.80 0.00 0.00 0.20
#> TCGA.AC.A3YI.01 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.BH.A0E0.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.BH.A0B2.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.A2.A4RY.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.BH.A0BV.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.BH.A0DG.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.AC.A23H.11 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.EW.A1PG.01 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.E2.A1IF.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.BH.A209.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.E9.A1R7.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.AR.A5QQ.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.E2.A1LB.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.A2.A0CR.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.BH.A1FH.11 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.BH.A1FJ.11 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.BH.A0HK.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.BH.A0BM.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.BH.A0E1.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.AR.A1AO.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.BH.A1FB.01 2 0.4948 0.215 0.00 0.56 0.00 0.44
#> TCGA.A2.A3XW.01 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.BH.A1FE.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.A7.A0DC.11 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.AO.A0JC.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.A2.A0EP.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.BH.A0BJ.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.BH.A42U.01 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.BH.A1F5.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.BH.A1EO.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.E9.A1NE.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.C8.A8HR.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.BH.A6R9.01 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.C8.A8HP.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.AC.A2FM.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.A7.A0D9.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.AC.A2FB.11 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.E2.A1LS.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.BH.A0BT.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.BH.A0C0.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.E2.A1BC.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.BH.A0C3.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.E9.A248.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.BH.A204.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.GM.A3XG.01 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.E9.A1NF.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.BH.A1EN.11 3 0.1211 0.957 0.00 0.00 0.96 0.04
#> TCGA.BH.A0DZ.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.AC.A2FF.01 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.E9.A1N5.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.A7.A0CE.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.LL.A440.01 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.BH.A1FG.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.AC.A2FF.11 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.LD.A9QF.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.GM.A2DI.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.BH.A0B8.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.BH.A0AZ.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.BH.A0DQ.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.BH.A1FB.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.BH.A1FE.06 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.E9.A1RH.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.A7.A0CH.11 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.GM.A4E0.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.E9.A22A.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.BH.A1F8.11 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.E9.A1NA.11 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.E2.A1B5.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.E2.A1LI.11 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.BH.A1FD.11 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.BH.A1F6.11 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.BH.A1ET.11 4 0.0707 0.976 0.02 0.00 0.00 0.98
#> TCGA.E2.A1II.11 1 0.3801 0.721 0.78 0.00 0.00 0.22
#> TCGA.BH.A0HA.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.OL.A97C.01 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.E2.A15K.11 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.AR.A24U.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.AR.A1AX.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.BH.A1EY.11 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.BH.A0BZ.11 4 0.0000 0.999 0.00 0.00 0.00 1.00
#> TCGA.E9.A1NG.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
#> TCGA.BH.A0DV.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.BH.A0BS.11 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.E2.A108.01 2 0.0000 0.985 0.00 1.00 0.00 0.00
#> TCGA.E9.A1RB.11 3 0.0000 0.998 0.00 0.00 1.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.E9.A1QZ.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.E9.A1N4.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.BH.A1F2.11 4 0.0000 0.967 0.00 0.0 0.00 1.00 0.00
#> TCGA.BH.A0DP.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.AC.A2FB.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.BH.A0BF.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.BH.A1FC.11 5 0.0000 0.975 0.00 0.0 0.00 0.00 1.00
#> TCGA.BH.A0H9.11 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
#> TCGA.BH.A208.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.AR.A2LQ.01 5 0.0000 0.975 0.00 0.0 0.00 0.00 1.00
#> TCGA.BH.A0DI.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.E9.A1N6.11 4 0.0000 0.967 0.00 0.0 0.00 1.00 0.00
#> TCGA.A7.A13G.11 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
#> TCGA.E2.A1B6.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.BH.A0H7.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.B6.A0RT.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.BH.A1FU.01 5 0.0000 0.975 0.00 0.0 0.00 0.00 1.00
#> TCGA.AO.A1KO.01 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.A7.A0DB.11 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
#> TCGA.E9.A2JT.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.BH.A0AU.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.E9.A1RC.11 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
#> TCGA.E9.A1NE.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.BH.A1FM.11 1 0.3274 0.704 0.78 0.0 0.00 0.22 0.00
#> TCGA.BH.A203.11 4 0.0000 0.967 0.00 0.0 0.00 1.00 0.00
#> TCGA.E2.A1B5.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.PL.A8LY.01 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.BH.A1EW.11 5 0.0000 0.975 0.00 0.0 0.00 0.00 1.00
#> TCGA.AC.A5EI.01 5 0.0000 0.975 0.00 0.0 0.00 0.00 1.00
#> TCGA.BH.A1EU.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.OL.A5RY.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.BH.A209.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.BH.A0B3.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.AC.A2FK.01 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.E9.A1RF.11 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
#> TCGA.E2.A1L7.11 5 0.0609 0.959 0.00 0.0 0.00 0.02 0.98
#> TCGA.AC.A2FG.11 4 0.1410 0.906 0.06 0.0 0.00 0.94 0.00
#> TCGA.E9.A1RI.11 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
#> TCGA.E9.A1N8.11 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
#> TCGA.AR.A1AW.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.BH.A1FH.01 4 0.3895 0.544 0.32 0.0 0.00 0.68 0.00
#> TCGA.BH.A0AY.11 4 0.1043 0.928 0.04 0.0 0.00 0.96 0.00
#> TCGA.BH.A1F0.11 4 0.0000 0.967 0.00 0.0 0.00 1.00 0.00
#> TCGA.BH.A1FR.11 4 0.0000 0.967 0.00 0.0 0.00 1.00 0.00
#> TCGA.AR.A252.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.A2.A25F.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.GM.A2DO.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.E9.A1ND.11 4 0.0000 0.967 0.00 0.0 0.00 1.00 0.00
#> TCGA.E9.A1RD.11 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
#> TCGA.BH.A1FN.11 4 0.0000 0.967 0.00 0.0 0.00 1.00 0.00
#> TCGA.BH.A28O.01 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.EW.A1P1.01 5 0.0000 0.975 0.00 0.0 0.00 0.00 1.00
#> TCGA.E2.A1IO.11 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
#> TCGA.LL.A73Z.01 5 0.0000 0.975 0.00 0.0 0.00 0.00 1.00
#> TCGA.AR.A2LH.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.A7.A13F.11 4 0.0000 0.967 0.00 0.0 0.00 1.00 0.00
#> TCGA.LL.A5YO.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.BH.A1EV.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.Z7.A8R5.01 5 0.0000 0.975 0.00 0.0 0.00 0.00 1.00
#> TCGA.AO.A03U.01 5 0.0000 0.975 0.00 0.0 0.00 0.00 1.00
#> TCGA.BH.A1ES.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.E2.A15I.11 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
#> TCGA.A2.A1G6.01 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.BH.A0DH.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.A2.A3XZ.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.BH.A0BC.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.A7.A13E.11 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
#> TCGA.BH.A0BA.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.BH.A0DK.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.D8.A4Z1.01 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.AC.A3YI.01 5 0.0000 0.975 0.00 0.0 0.00 0.00 1.00
#> TCGA.BH.A0E0.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.BH.A0B2.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.A2.A4RY.01 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.BH.A0BV.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.BH.A0DG.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.AC.A23H.11 4 0.0000 0.967 0.00 0.0 0.00 1.00 0.00
#> TCGA.EW.A1PG.01 5 0.0000 0.975 0.00 0.0 0.00 0.00 1.00
#> TCGA.E2.A1IF.11 4 0.3561 0.660 0.26 0.0 0.00 0.74 0.00
#> TCGA.BH.A209.11 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
#> TCGA.E9.A1R7.11 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
#> TCGA.AR.A5QQ.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.E2.A1LB.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.A2.A0CR.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.BH.A1FH.11 4 0.0000 0.967 0.00 0.0 0.00 1.00 0.00
#> TCGA.BH.A1FJ.11 4 0.0000 0.967 0.00 0.0 0.00 1.00 0.00
#> TCGA.BH.A0HK.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.BH.A0BM.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.BH.A0E1.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.AR.A1AO.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.BH.A1FB.01 5 0.0000 0.975 0.00 0.0 0.00 0.00 1.00
#> TCGA.A2.A3XW.01 5 0.0000 0.975 0.00 0.0 0.00 0.00 1.00
#> TCGA.BH.A1FE.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.A7.A0DC.11 5 0.1732 0.899 0.00 0.0 0.00 0.08 0.92
#> TCGA.AO.A0JC.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.A2.A0EP.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.BH.A0BJ.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.BH.A42U.01 5 0.0000 0.975 0.00 0.0 0.00 0.00 1.00
#> TCGA.BH.A1F5.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.BH.A1EO.11 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
#> TCGA.E9.A1NE.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.C8.A8HR.01 5 0.0000 0.975 0.00 0.0 0.00 0.00 1.00
#> TCGA.BH.A6R9.01 5 0.0000 0.975 0.00 0.0 0.00 0.00 1.00
#> TCGA.C8.A8HP.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.AC.A2FM.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.A7.A0D9.11 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
#> TCGA.AC.A2FB.11 4 0.0000 0.967 0.00 0.0 0.00 1.00 0.00
#> TCGA.E2.A1LS.11 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
#> TCGA.BH.A0BT.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.BH.A0C0.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.E2.A1BC.11 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
#> TCGA.BH.A0C3.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.E9.A248.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.BH.A204.11 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
#> TCGA.GM.A3XG.01 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.E9.A1NF.11 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
#> TCGA.BH.A1EN.11 3 0.3274 0.720 0.00 0.0 0.78 0.22 0.00
#> TCGA.BH.A0DZ.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.AC.A2FF.01 5 0.0000 0.975 0.00 0.0 0.00 0.00 1.00
#> TCGA.E9.A1N5.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.A7.A0CE.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.LL.A440.01 5 0.0000 0.975 0.00 0.0 0.00 0.00 1.00
#> TCGA.BH.A1FG.11 4 0.0000 0.967 0.00 0.0 0.00 1.00 0.00
#> TCGA.AC.A2FF.11 4 0.0000 0.967 0.00 0.0 0.00 1.00 0.00
#> TCGA.LD.A9QF.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.GM.A2DI.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.BH.A0B8.11 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
#> TCGA.BH.A0AZ.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.BH.A0DQ.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.BH.A1FB.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.BH.A1FE.06 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
#> TCGA.E9.A1RH.11 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
#> TCGA.A7.A0CH.11 5 0.0000 0.975 0.00 0.0 0.00 0.00 1.00
#> TCGA.GM.A4E0.01 5 0.3109 0.747 0.00 0.2 0.00 0.00 0.80
#> TCGA.E9.A22A.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.BH.A1F8.11 4 0.0000 0.967 0.00 0.0 0.00 1.00 0.00
#> TCGA.E9.A1NA.11 4 0.0000 0.967 0.00 0.0 0.00 1.00 0.00
#> TCGA.E2.A1B5.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.E2.A1LI.11 5 0.0000 0.975 0.00 0.0 0.00 0.00 1.00
#> TCGA.BH.A1FD.11 4 0.0000 0.967 0.00 0.0 0.00 1.00 0.00
#> TCGA.BH.A1F6.11 4 0.0000 0.967 0.00 0.0 0.00 1.00 0.00
#> TCGA.BH.A1ET.11 4 0.0000 0.967 0.00 0.0 0.00 1.00 0.00
#> TCGA.E2.A1II.11 4 0.0000 0.967 0.00 0.0 0.00 1.00 0.00
#> TCGA.BH.A0HA.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.OL.A97C.01 5 0.3109 0.733 0.20 0.0 0.00 0.00 0.80
#> TCGA.E2.A15K.11 4 0.0000 0.967 0.00 0.0 0.00 1.00 0.00
#> TCGA.AR.A24U.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.AR.A1AX.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.BH.A1EY.11 4 0.0000 0.967 0.00 0.0 0.00 1.00 0.00
#> TCGA.BH.A0BZ.11 4 0.0000 0.967 0.00 0.0 0.00 1.00 0.00
#> TCGA.E9.A1NG.11 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
#> TCGA.BH.A0DV.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.BH.A0BS.11 1 0.0000 0.995 1.00 0.0 0.00 0.00 0.00
#> TCGA.E2.A108.01 2 0.0000 1.000 0.00 1.0 0.00 0.00 0.00
#> TCGA.E9.A1RB.11 3 0.0000 0.991 0.00 0.0 1.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.E9.A1QZ.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.E9.A1N4.11 1 0.0937 0.956 0.96 0.0 0.00 0.00 0.00 0.04
#> TCGA.BH.A1F2.11 4 0.0000 0.917 0.00 0.0 0.00 1.00 0.00 0.00
#> TCGA.BH.A0DP.11 1 0.0937 0.944 0.96 0.0 0.00 0.00 0.00 0.04
#> TCGA.AC.A2FB.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BF.11 1 0.0547 0.961 0.98 0.0 0.00 0.00 0.00 0.02
#> TCGA.BH.A1FC.11 5 0.3679 0.770 0.00 0.0 0.00 0.04 0.76 0.20
#> TCGA.BH.A0H9.11 3 0.0000 0.957 0.00 0.0 1.00 0.00 0.00 0.00
#> TCGA.BH.A208.11 1 0.0937 0.956 0.96 0.0 0.00 0.00 0.00 0.04
#> TCGA.AR.A2LQ.01 5 0.1556 0.855 0.00 0.0 0.00 0.00 0.92 0.08
#> TCGA.BH.A0DI.11 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.E9.A1N6.11 4 0.0000 0.917 0.00 0.0 0.00 1.00 0.00 0.00
#> TCGA.A7.A13G.11 3 0.0000 0.957 0.00 0.0 1.00 0.00 0.00 0.00
#> TCGA.E2.A1B6.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A0H7.11 1 0.0937 0.944 0.96 0.0 0.00 0.00 0.00 0.04
#> TCGA.B6.A0RT.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FU.01 5 0.1814 0.868 0.00 0.0 0.00 0.00 0.90 0.10
#> TCGA.AO.A1KO.01 1 0.0937 0.956 0.96 0.0 0.00 0.00 0.00 0.04
#> TCGA.A7.A0DB.11 3 0.0000 0.957 0.00 0.0 1.00 0.00 0.00 0.00
#> TCGA.E9.A2JT.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A0AU.11 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RC.11 6 0.3864 0.840 0.00 0.0 0.48 0.00 0.00 0.52
#> TCGA.E9.A1NE.11 1 0.2190 0.910 0.90 0.0 0.00 0.06 0.00 0.04
#> TCGA.BH.A1FM.11 1 0.3523 0.761 0.78 0.0 0.00 0.18 0.00 0.04
#> TCGA.BH.A203.11 4 0.1480 0.879 0.02 0.0 0.00 0.94 0.00 0.04
#> TCGA.E2.A1B5.11 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.PL.A8LY.01 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A1EW.11 5 0.1814 0.846 0.00 0.0 0.00 0.00 0.90 0.10
#> TCGA.AC.A5EI.01 5 0.2941 0.772 0.00 0.0 0.00 0.00 0.78 0.22
#> TCGA.BH.A1EU.11 1 0.1480 0.945 0.94 0.0 0.00 0.02 0.00 0.04
#> TCGA.OL.A5RY.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A209.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A0B3.11 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.AC.A2FK.01 1 0.0937 0.956 0.96 0.0 0.00 0.00 0.00 0.04
#> TCGA.E9.A1RF.11 6 0.3864 0.840 0.00 0.0 0.48 0.00 0.00 0.52
#> TCGA.E2.A1L7.11 5 0.2094 0.847 0.00 0.0 0.00 0.02 0.90 0.08
#> TCGA.AC.A2FG.11 4 0.2474 0.809 0.08 0.0 0.00 0.88 0.00 0.04
#> TCGA.E9.A1RI.11 3 0.0000 0.957 0.00 0.0 1.00 0.00 0.00 0.00
#> TCGA.E9.A1N8.11 3 0.1556 0.838 0.00 0.0 0.92 0.00 0.00 0.08
#> TCGA.AR.A1AW.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FH.01 4 0.6734 0.248 0.32 0.0 0.00 0.46 0.10 0.12
#> TCGA.BH.A0AY.11 4 0.0937 0.891 0.04 0.0 0.00 0.96 0.00 0.00
#> TCGA.BH.A1F0.11 4 0.0000 0.917 0.00 0.0 0.00 1.00 0.00 0.00
#> TCGA.BH.A1FR.11 4 0.0000 0.917 0.00 0.0 0.00 1.00 0.00 0.00
#> TCGA.AR.A252.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.A2.A25F.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.GM.A2DO.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.E9.A1ND.11 4 0.3567 0.748 0.00 0.0 0.10 0.80 0.00 0.10
#> TCGA.E9.A1RD.11 3 0.1556 0.838 0.00 0.0 0.92 0.00 0.00 0.08
#> TCGA.BH.A1FN.11 4 0.0000 0.917 0.00 0.0 0.00 1.00 0.00 0.00
#> TCGA.BH.A28O.01 1 0.0547 0.961 0.98 0.0 0.00 0.00 0.00 0.02
#> TCGA.EW.A1P1.01 5 0.1814 0.868 0.00 0.0 0.00 0.00 0.90 0.10
#> TCGA.E2.A1IO.11 3 0.0000 0.957 0.00 0.0 1.00 0.00 0.00 0.00
#> TCGA.LL.A73Z.01 5 0.1814 0.846 0.00 0.0 0.00 0.00 0.90 0.10
#> TCGA.AR.A2LH.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.A7.A13F.11 4 0.0000 0.917 0.00 0.0 0.00 1.00 0.00 0.00
#> TCGA.LL.A5YO.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A1EV.11 1 0.2474 0.889 0.88 0.0 0.00 0.08 0.00 0.04
#> TCGA.Z7.A8R5.01 5 0.1556 0.855 0.00 0.0 0.00 0.00 0.92 0.08
#> TCGA.AO.A03U.01 5 0.1814 0.868 0.00 0.0 0.00 0.00 0.90 0.10
#> TCGA.BH.A1ES.11 1 0.0937 0.956 0.96 0.0 0.00 0.00 0.00 0.04
#> TCGA.E2.A15I.11 3 0.0000 0.957 0.00 0.0 1.00 0.00 0.00 0.00
#> TCGA.A2.A1G6.01 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DH.11 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.A2.A3XZ.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BC.11 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.A7.A13E.11 3 0.0547 0.931 0.00 0.0 0.98 0.00 0.00 0.02
#> TCGA.BH.A0BA.11 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DK.11 1 0.0937 0.944 0.96 0.0 0.00 0.00 0.00 0.04
#> TCGA.D8.A4Z1.01 1 0.3985 0.715 0.76 0.0 0.00 0.00 0.14 0.10
#> TCGA.AC.A3YI.01 5 0.0547 0.867 0.00 0.0 0.00 0.00 0.98 0.02
#> TCGA.BH.A0E0.11 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A0B2.11 1 0.1480 0.938 0.94 0.0 0.00 0.04 0.00 0.02
#> TCGA.A2.A4RY.01 1 0.3787 0.744 0.78 0.0 0.00 0.00 0.12 0.10
#> TCGA.BH.A0BV.11 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DG.11 1 0.0937 0.956 0.96 0.0 0.00 0.00 0.00 0.04
#> TCGA.AC.A23H.11 4 0.1556 0.878 0.00 0.0 0.00 0.92 0.00 0.08
#> TCGA.EW.A1PG.01 5 0.1267 0.860 0.00 0.0 0.00 0.00 0.94 0.06
#> TCGA.E2.A1IF.11 4 0.4420 0.415 0.34 0.0 0.00 0.62 0.00 0.04
#> TCGA.BH.A209.11 6 0.3982 0.618 0.00 0.0 0.20 0.00 0.06 0.74
#> TCGA.E9.A1R7.11 3 0.0000 0.957 0.00 0.0 1.00 0.00 0.00 0.00
#> TCGA.AR.A5QQ.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.E2.A1LB.11 1 0.0937 0.956 0.96 0.0 0.00 0.00 0.00 0.04
#> TCGA.A2.A0CR.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FH.11 4 0.0000 0.917 0.00 0.0 0.00 1.00 0.00 0.00
#> TCGA.BH.A1FJ.11 4 0.0000 0.917 0.00 0.0 0.00 1.00 0.00 0.00
#> TCGA.BH.A0HK.11 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BM.11 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A0E1.11 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AO.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FB.01 5 0.1814 0.868 0.00 0.0 0.00 0.00 0.90 0.10
#> TCGA.A2.A3XW.01 5 0.0937 0.871 0.00 0.0 0.00 0.00 0.96 0.04
#> TCGA.BH.A1FE.11 1 0.0937 0.956 0.96 0.0 0.00 0.00 0.00 0.04
#> TCGA.A7.A0DC.11 5 0.3315 0.690 0.00 0.0 0.00 0.20 0.78 0.02
#> TCGA.AO.A0JC.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.A2.A0EP.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BJ.11 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A42U.01 5 0.1556 0.855 0.00 0.0 0.00 0.00 0.92 0.08
#> TCGA.BH.A1F5.11 1 0.0547 0.956 0.98 0.0 0.00 0.00 0.00 0.02
#> TCGA.BH.A1EO.11 3 0.0000 0.957 0.00 0.0 1.00 0.00 0.00 0.00
#> TCGA.E9.A1NE.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.C8.A8HR.01 5 0.1814 0.868 0.00 0.0 0.00 0.00 0.90 0.10
#> TCGA.BH.A6R9.01 5 0.1814 0.868 0.00 0.0 0.00 0.00 0.90 0.10
#> TCGA.C8.A8HP.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.AC.A2FM.11 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.A7.A0D9.11 3 0.0000 0.957 0.00 0.0 1.00 0.00 0.00 0.00
#> TCGA.AC.A2FB.11 4 0.0000 0.917 0.00 0.0 0.00 1.00 0.00 0.00
#> TCGA.E2.A1LS.11 6 0.3864 0.840 0.00 0.0 0.48 0.00 0.00 0.52
#> TCGA.BH.A0BT.11 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A0C0.11 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.E2.A1BC.11 3 0.0000 0.957 0.00 0.0 1.00 0.00 0.00 0.00
#> TCGA.BH.A0C3.11 1 0.0937 0.956 0.96 0.0 0.00 0.00 0.00 0.04
#> TCGA.E9.A248.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A204.11 6 0.3864 0.840 0.00 0.0 0.48 0.00 0.00 0.52
#> TCGA.GM.A3XG.01 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.E9.A1NF.11 3 0.0000 0.957 0.00 0.0 1.00 0.00 0.00 0.00
#> TCGA.BH.A1EN.11 3 0.3787 0.525 0.00 0.0 0.78 0.12 0.00 0.10
#> TCGA.BH.A0DZ.11 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.AC.A2FF.01 5 0.1814 0.868 0.00 0.0 0.00 0.00 0.90 0.10
#> TCGA.E9.A1N5.11 1 0.1865 0.929 0.92 0.0 0.00 0.04 0.00 0.04
#> TCGA.A7.A0CE.11 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.LL.A440.01 5 0.1814 0.868 0.00 0.0 0.00 0.00 0.90 0.10
#> TCGA.BH.A1FG.11 4 0.0937 0.895 0.00 0.0 0.00 0.96 0.00 0.04
#> TCGA.AC.A2FF.11 4 0.0547 0.908 0.00 0.0 0.00 0.98 0.00 0.02
#> TCGA.LD.A9QF.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.GM.A2DI.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A0B8.11 3 0.0000 0.957 0.00 0.0 1.00 0.00 0.00 0.00
#> TCGA.BH.A0AZ.11 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DQ.11 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FB.11 1 0.0937 0.956 0.96 0.0 0.00 0.00 0.00 0.04
#> TCGA.BH.A1FE.06 3 0.0000 0.957 0.00 0.0 1.00 0.00 0.00 0.00
#> TCGA.E9.A1RH.11 3 0.0000 0.957 0.00 0.0 1.00 0.00 0.00 0.00
#> TCGA.A7.A0CH.11 5 0.0000 0.869 0.00 0.0 0.00 0.00 1.00 0.00
#> TCGA.GM.A4E0.01 5 0.4475 0.645 0.00 0.2 0.00 0.00 0.70 0.10
#> TCGA.E9.A22A.01 2 0.1814 0.886 0.00 0.9 0.00 0.00 0.00 0.10
#> TCGA.BH.A1F8.11 4 0.0000 0.917 0.00 0.0 0.00 1.00 0.00 0.00
#> TCGA.E9.A1NA.11 4 0.0000 0.917 0.00 0.0 0.00 1.00 0.00 0.00
#> TCGA.E2.A1B5.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.E2.A1LI.11 5 0.1814 0.868 0.00 0.0 0.00 0.00 0.90 0.10
#> TCGA.BH.A1FD.11 4 0.0000 0.917 0.00 0.0 0.00 1.00 0.00 0.00
#> TCGA.BH.A1F6.11 4 0.1814 0.856 0.00 0.0 0.00 0.90 0.00 0.10
#> TCGA.BH.A1ET.11 4 0.0000 0.917 0.00 0.0 0.00 1.00 0.00 0.00
#> TCGA.E2.A1II.11 4 0.0000 0.917 0.00 0.0 0.00 1.00 0.00 0.00
#> TCGA.BH.A0HA.11 1 0.0000 0.965 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.OL.A97C.01 5 0.5628 0.405 0.24 0.0 0.00 0.00 0.54 0.22
#> TCGA.E2.A15K.11 4 0.1814 0.856 0.00 0.0 0.00 0.90 0.00 0.10
#> TCGA.AR.A24U.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AX.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.BH.A1EY.11 4 0.0000 0.917 0.00 0.0 0.00 1.00 0.00 0.00
#> TCGA.BH.A0BZ.11 4 0.2350 0.842 0.00 0.0 0.00 0.88 0.02 0.10
#> TCGA.E9.A1NG.11 3 0.0000 0.957 0.00 0.0 1.00 0.00 0.00 0.00
#> TCGA.BH.A0DV.11 1 0.0937 0.956 0.96 0.0 0.00 0.00 0.00 0.04
#> TCGA.BH.A0BS.11 1 0.0937 0.956 0.96 0.0 0.00 0.00 0.00 0.04
#> TCGA.E2.A108.01 2 0.0000 0.996 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RB.11 6 0.3647 0.762 0.00 0.0 0.36 0.00 0.00 0.64
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.E9.A1QZ.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1N4.11 1 0.2016 0.881 0.90 0.0 0.00 0.00 0.00 0.06 0.04
#> TCGA.BH.A1F2.11 4 0.0000 0.847 0.00 0.0 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0DP.11 1 0.2081 0.814 0.86 0.0 0.00 0.00 0.00 0.00 0.14
#> TCGA.AC.A2FB.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BF.11 1 0.1363 0.895 0.94 0.0 0.00 0.00 0.00 0.02 0.04
#> TCGA.BH.A1FC.11 5 0.4737 0.538 0.00 0.0 0.00 0.06 0.68 0.20 0.06
#> TCGA.BH.A0H9.11 3 0.0000 0.895 0.00 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A208.11 1 0.3449 0.811 0.78 0.0 0.00 0.00 0.00 0.14 0.08
#> TCGA.AR.A2LQ.01 7 0.3139 0.639 0.00 0.0 0.00 0.00 0.30 0.00 0.70
#> TCGA.BH.A0DI.11 1 0.0000 0.904 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1N6.11 4 0.0504 0.846 0.00 0.0 0.00 0.98 0.00 0.00 0.02
#> TCGA.A7.A13G.11 3 0.0000 0.895 0.00 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1B6.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0H7.11 1 0.2259 0.801 0.84 0.0 0.00 0.00 0.00 0.00 0.16
#> TCGA.B6.A0RT.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FU.01 5 0.0000 0.796 0.00 0.0 0.00 0.00 1.00 0.00 0.00
#> TCGA.AO.A1KO.01 1 0.1664 0.889 0.92 0.0 0.00 0.00 0.00 0.06 0.02
#> TCGA.A7.A0DB.11 3 0.0000 0.895 0.00 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A2JT.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0AU.11 1 0.0000 0.904 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RC.11 6 0.3546 0.769 0.00 0.0 0.46 0.00 0.00 0.54 0.00
#> TCGA.E9.A1NE.11 1 0.4937 0.714 0.68 0.0 0.00 0.06 0.00 0.14 0.12
#> TCGA.BH.A1FM.11 1 0.6332 0.327 0.48 0.0 0.00 0.26 0.00 0.14 0.12
#> TCGA.BH.A203.11 4 0.4475 0.690 0.04 0.0 0.00 0.72 0.00 0.14 0.10
#> TCGA.E2.A1B5.11 1 0.0504 0.903 0.98 0.0 0.00 0.00 0.00 0.00 0.02
#> TCGA.PL.A8LY.01 1 0.0504 0.901 0.98 0.0 0.00 0.00 0.00 0.00 0.02
#> TCGA.BH.A1EW.11 7 0.2945 0.669 0.00 0.0 0.00 0.00 0.26 0.00 0.74
#> TCGA.AC.A5EI.01 7 0.3388 0.647 0.00 0.0 0.00 0.00 0.20 0.04 0.76
#> TCGA.BH.A1EU.11 1 0.3965 0.792 0.76 0.0 0.00 0.02 0.00 0.12 0.10
#> TCGA.OL.A5RY.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A209.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0B3.11 1 0.0000 0.904 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A2FK.01 1 0.3670 0.799 0.76 0.0 0.00 0.00 0.00 0.14 0.10
#> TCGA.E9.A1RF.11 6 0.3546 0.769 0.00 0.0 0.46 0.00 0.00 0.54 0.00
#> TCGA.E2.A1L7.11 7 0.2945 0.669 0.00 0.0 0.00 0.00 0.26 0.00 0.74
#> TCGA.AC.A2FG.11 4 0.6181 0.427 0.22 0.0 0.00 0.52 0.00 0.14 0.12
#> TCGA.E9.A1RI.11 3 0.0000 0.895 0.00 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1N8.11 3 0.3208 0.698 0.00 0.0 0.82 0.02 0.00 0.12 0.04
#> TCGA.AR.A1AW.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FH.01 7 0.4500 0.393 0.08 0.0 0.00 0.22 0.00 0.02 0.68
#> TCGA.BH.A0AY.11 4 0.4569 0.626 0.18 0.0 0.00 0.70 0.00 0.04 0.08
#> TCGA.BH.A1F0.11 4 0.0504 0.841 0.00 0.0 0.00 0.98 0.00 0.02 0.00
#> TCGA.BH.A1FR.11 4 0.0504 0.841 0.00 0.0 0.00 0.98 0.00 0.02 0.00
#> TCGA.AR.A252.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A25F.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A2DO.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1ND.11 4 0.4331 0.628 0.00 0.0 0.06 0.72 0.00 0.18 0.04
#> TCGA.E9.A1RD.11 3 0.2722 0.727 0.00 0.0 0.84 0.00 0.00 0.12 0.04
#> TCGA.BH.A1FN.11 4 0.1718 0.832 0.00 0.0 0.00 0.92 0.00 0.04 0.04
#> TCGA.BH.A28O.01 1 0.2572 0.869 0.86 0.0 0.00 0.00 0.00 0.06 0.08
#> TCGA.EW.A1P1.01 5 0.0000 0.796 0.00 0.0 0.00 0.00 1.00 0.00 0.00
#> TCGA.E2.A1IO.11 3 0.1006 0.870 0.00 0.0 0.96 0.00 0.00 0.02 0.02
#> TCGA.LL.A73Z.01 7 0.2945 0.669 0.00 0.0 0.00 0.00 0.26 0.00 0.74
#> TCGA.AR.A2LH.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A13F.11 4 0.0504 0.847 0.00 0.0 0.00 0.98 0.00 0.00 0.02
#> TCGA.LL.A5YO.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1EV.11 1 0.4298 0.786 0.74 0.0 0.00 0.04 0.00 0.12 0.10
#> TCGA.Z7.A8R5.01 7 0.3358 0.563 0.00 0.0 0.00 0.00 0.36 0.00 0.64
#> TCGA.AO.A03U.01 5 0.3388 0.634 0.00 0.0 0.00 0.00 0.76 0.04 0.20
#> TCGA.BH.A1ES.11 1 0.3284 0.824 0.80 0.0 0.00 0.00 0.00 0.10 0.10
#> TCGA.E2.A15I.11 3 0.0504 0.884 0.00 0.0 0.98 0.00 0.00 0.00 0.02
#> TCGA.A2.A1G6.01 1 0.0000 0.904 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DH.11 1 0.0863 0.889 0.96 0.0 0.00 0.00 0.00 0.00 0.04
#> TCGA.A2.A3XZ.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BC.11 1 0.0000 0.904 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A13E.11 3 0.2512 0.757 0.00 0.0 0.86 0.00 0.00 0.10 0.04
#> TCGA.BH.A0BA.11 1 0.1166 0.879 0.94 0.0 0.00 0.00 0.00 0.00 0.06
#> TCGA.BH.A0DK.11 1 0.2081 0.814 0.86 0.0 0.00 0.00 0.00 0.00 0.14
#> TCGA.D8.A4Z1.01 7 0.2945 0.486 0.26 0.0 0.00 0.00 0.00 0.00 0.74
#> TCGA.AC.A3YI.01 5 0.3413 0.181 0.00 0.0 0.00 0.00 0.62 0.00 0.38
#> TCGA.BH.A0E0.11 1 0.0000 0.904 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0B2.11 1 0.4422 0.760 0.72 0.0 0.00 0.08 0.00 0.04 0.16
#> TCGA.A2.A4RY.01 7 0.2945 0.486 0.26 0.0 0.00 0.00 0.00 0.00 0.74
#> TCGA.BH.A0BV.11 1 0.0000 0.904 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DG.11 1 0.2803 0.854 0.84 0.0 0.00 0.00 0.00 0.06 0.10
#> TCGA.AC.A23H.11 4 0.2259 0.765 0.00 0.0 0.00 0.84 0.00 0.16 0.00
#> TCGA.EW.A1PG.01 7 0.3558 0.269 0.00 0.0 0.00 0.00 0.48 0.00 0.52
#> TCGA.E2.A1IF.11 4 0.6468 0.202 0.32 0.0 0.00 0.42 0.00 0.14 0.12
#> TCGA.BH.A209.11 6 0.3370 0.492 0.00 0.0 0.06 0.00 0.16 0.78 0.00
#> TCGA.E9.A1R7.11 3 0.0000 0.895 0.00 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A5QQ.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1LB.11 1 0.3487 0.815 0.78 0.0 0.00 0.00 0.00 0.12 0.10
#> TCGA.A2.A0CR.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FH.11 4 0.0000 0.847 0.00 0.0 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A1FJ.11 4 0.1363 0.839 0.00 0.0 0.00 0.94 0.00 0.02 0.04
#> TCGA.BH.A0HK.11 1 0.0863 0.896 0.96 0.0 0.00 0.00 0.00 0.00 0.04
#> TCGA.BH.A0BM.11 1 0.0000 0.904 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0E1.11 1 0.0000 0.904 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AO.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FB.01 5 0.0000 0.796 0.00 0.0 0.00 0.00 1.00 0.00 0.00
#> TCGA.A2.A3XW.01 5 0.3745 0.489 0.00 0.0 0.00 0.00 0.70 0.04 0.26
#> TCGA.BH.A1FE.11 1 0.3670 0.795 0.76 0.0 0.00 0.00 0.00 0.14 0.10
#> TCGA.A7.A0DC.11 7 0.6008 0.295 0.00 0.0 0.00 0.20 0.30 0.04 0.46
#> TCGA.AO.A0JC.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0EP.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BJ.11 1 0.0863 0.900 0.96 0.0 0.00 0.00 0.00 0.00 0.04
#> TCGA.BH.A42U.01 7 0.3358 0.565 0.00 0.0 0.00 0.00 0.36 0.00 0.64
#> TCGA.BH.A1F5.11 1 0.2569 0.818 0.84 0.0 0.00 0.00 0.00 0.02 0.14
#> TCGA.BH.A1EO.11 3 0.0000 0.895 0.00 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1NE.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A8HR.01 5 0.0000 0.796 0.00 0.0 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A6R9.01 5 0.1363 0.777 0.00 0.0 0.00 0.00 0.94 0.02 0.04
#> TCGA.C8.A8HP.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A2FM.11 1 0.0504 0.903 0.98 0.0 0.00 0.00 0.00 0.02 0.00
#> TCGA.A7.A0D9.11 3 0.0863 0.847 0.00 0.0 0.96 0.00 0.00 0.04 0.00
#> TCGA.AC.A2FB.11 4 0.0000 0.847 0.00 0.0 0.00 1.00 0.00 0.00 0.00
#> TCGA.E2.A1LS.11 6 0.3546 0.769 0.00 0.0 0.46 0.00 0.00 0.54 0.00
#> TCGA.BH.A0BT.11 1 0.0000 0.904 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0C0.11 1 0.0000 0.904 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1BC.11 3 0.0000 0.895 0.00 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0C3.11 1 0.2016 0.880 0.90 0.0 0.00 0.00 0.00 0.04 0.06
#> TCGA.E9.A248.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A204.11 6 0.3525 0.771 0.00 0.0 0.44 0.00 0.00 0.56 0.00
#> TCGA.GM.A3XG.01 1 0.0000 0.904 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1NF.11 3 0.0000 0.895 0.00 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1EN.11 3 0.5795 0.132 0.00 0.0 0.52 0.26 0.00 0.18 0.04
#> TCGA.BH.A0DZ.11 1 0.0000 0.904 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A2FF.01 5 0.0504 0.785 0.00 0.0 0.00 0.00 0.98 0.00 0.02
#> TCGA.E9.A1N5.11 1 0.4748 0.735 0.70 0.0 0.00 0.06 0.00 0.14 0.10
#> TCGA.A7.A0CE.11 1 0.1433 0.871 0.92 0.0 0.00 0.00 0.00 0.00 0.08
#> TCGA.LL.A440.01 5 0.1433 0.758 0.00 0.0 0.00 0.00 0.92 0.00 0.08
#> TCGA.BH.A1FG.11 4 0.4145 0.710 0.02 0.0 0.00 0.74 0.00 0.14 0.10
#> TCGA.AC.A2FF.11 4 0.2016 0.828 0.00 0.0 0.00 0.90 0.00 0.04 0.06
#> TCGA.LD.A9QF.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A2DI.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0B8.11 3 0.0000 0.895 0.00 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0AZ.11 1 0.0000 0.904 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DQ.11 1 0.0000 0.904 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FB.11 1 0.0863 0.900 0.96 0.0 0.00 0.00 0.00 0.04 0.00
#> TCGA.BH.A1FE.06 3 0.0000 0.895 0.00 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RH.11 3 0.0000 0.895 0.00 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A0CH.11 5 0.4882 0.106 0.00 0.0 0.00 0.04 0.56 0.04 0.36
#> TCGA.GM.A4E0.01 5 0.1671 0.674 0.00 0.1 0.00 0.00 0.90 0.00 0.00
#> TCGA.E9.A22A.01 2 0.3139 0.594 0.00 0.7 0.00 0.00 0.30 0.00 0.00
#> TCGA.BH.A1F8.11 4 0.0000 0.847 0.00 0.0 0.00 1.00 0.00 0.00 0.00
#> TCGA.E9.A1NA.11 4 0.0504 0.846 0.00 0.0 0.00 0.98 0.00 0.00 0.02
#> TCGA.E2.A1B5.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1LI.11 5 0.0000 0.796 0.00 0.0 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A1FD.11 4 0.0000 0.847 0.00 0.0 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A1F6.11 4 0.2912 0.736 0.00 0.0 0.00 0.82 0.00 0.14 0.04
#> TCGA.BH.A1ET.11 4 0.1363 0.840 0.00 0.0 0.00 0.94 0.00 0.02 0.04
#> TCGA.E2.A1II.11 4 0.2829 0.788 0.00 0.0 0.00 0.84 0.00 0.08 0.08
#> TCGA.BH.A0HA.11 1 0.0000 0.904 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A97C.01 7 0.3396 0.627 0.02 0.0 0.00 0.00 0.14 0.04 0.80
#> TCGA.E2.A15K.11 4 0.2163 0.786 0.00 0.0 0.00 0.88 0.00 0.10 0.02
#> TCGA.AR.A24U.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AX.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1EY.11 4 0.1006 0.845 0.00 0.0 0.00 0.96 0.00 0.02 0.02
#> TCGA.BH.A0BZ.11 4 0.4055 0.663 0.00 0.0 0.00 0.74 0.04 0.18 0.04
#> TCGA.E9.A1NG.11 3 0.1363 0.850 0.00 0.0 0.94 0.00 0.00 0.04 0.02
#> TCGA.BH.A0DV.11 1 0.0000 0.904 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BS.11 1 0.1006 0.900 0.96 0.0 0.00 0.00 0.00 0.02 0.02
#> TCGA.E2.A108.01 2 0.0000 0.989 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RB.11 6 0.2832 0.680 0.00 0.0 0.24 0.00 0.00 0.76 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.E9.A1QZ.01 2 0.0471 0.9723 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.E9.A1N4.11 1 0.2267 0.6577 0.82 0.00 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.BH.A1F2.11 4 0.0000 0.7670 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DP.11 1 0.2407 0.6994 0.86 0.00 0.00 0.00 0.00 0.00 0.06 0.08
#> TCGA.AC.A2FB.01 2 0.0471 0.9723 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.BH.A0BF.11 1 0.4147 0.4523 0.68 0.00 0.00 0.04 0.00 0.00 0.04 0.24
#> TCGA.BH.A1FC.11 5 0.5954 0.3315 0.00 0.00 0.00 0.08 0.52 0.14 0.02 0.24
#> TCGA.BH.A0H9.11 3 0.0000 0.8683 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A208.11 1 0.4777 -0.2725 0.50 0.00 0.00 0.08 0.00 0.00 0.02 0.40
#> TCGA.AR.A2LQ.01 7 0.3015 0.4840 0.00 0.00 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.BH.A0DI.11 1 0.0471 0.7367 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.E9.A1N6.11 4 0.2025 0.7063 0.00 0.00 0.00 0.88 0.00 0.00 0.02 0.10
#> TCGA.A7.A13G.11 3 0.0471 0.8636 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.E2.A1B6.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0H7.11 1 0.2648 0.6897 0.84 0.00 0.00 0.00 0.00 0.00 0.08 0.08
#> TCGA.B6.A0RT.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FU.01 5 0.0000 0.7494 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AO.A1KO.01 1 0.2406 0.6222 0.80 0.00 0.00 0.00 0.00 0.00 0.00 0.20
#> TCGA.A7.A0DB.11 3 0.0808 0.8530 0.00 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.E9.A2JT.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0AU.11 1 0.0000 0.7390 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RC.11 6 0.2650 0.9017 0.00 0.00 0.24 0.00 0.00 0.76 0.00 0.00
#> TCGA.E9.A1NE.11 1 0.4813 -0.4999 0.44 0.00 0.00 0.14 0.00 0.00 0.00 0.42
#> TCGA.BH.A1FM.11 8 0.5203 0.7810 0.28 0.00 0.00 0.30 0.00 0.00 0.00 0.42
#> TCGA.BH.A203.11 4 0.3237 0.1401 0.00 0.00 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.E2.A1B5.11 1 0.2725 0.6873 0.82 0.00 0.00 0.00 0.00 0.00 0.04 0.14
#> TCGA.PL.A8LY.01 1 0.2114 0.6867 0.84 0.00 0.00 0.00 0.00 0.00 0.00 0.16
#> TCGA.BH.A1EW.11 7 0.3293 0.5804 0.00 0.00 0.00 0.00 0.22 0.00 0.74 0.04
#> TCGA.AC.A5EI.01 7 0.3586 0.5184 0.00 0.00 0.00 0.00 0.04 0.06 0.78 0.12
#> TCGA.BH.A1EU.11 1 0.4340 -0.0766 0.54 0.00 0.00 0.08 0.00 0.00 0.00 0.38
#> TCGA.OL.A5RY.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A209.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0B3.11 1 0.2350 0.7078 0.86 0.00 0.00 0.00 0.00 0.00 0.04 0.10
#> TCGA.AC.A2FK.01 1 0.3942 0.2940 0.62 0.00 0.00 0.02 0.00 0.00 0.02 0.34
#> TCGA.E9.A1RF.11 6 0.2650 0.9017 0.00 0.00 0.24 0.00 0.00 0.76 0.00 0.00
#> TCGA.E2.A1L7.11 7 0.3843 0.5656 0.00 0.00 0.00 0.04 0.24 0.00 0.70 0.02
#> TCGA.AC.A2FG.11 4 0.4693 -0.5177 0.12 0.00 0.00 0.46 0.00 0.00 0.00 0.42
#> TCGA.E9.A1RI.11 3 0.0471 0.8636 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.E9.A1N8.11 3 0.4224 0.6411 0.00 0.00 0.70 0.02 0.00 0.14 0.00 0.14
#> TCGA.AR.A1AW.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FH.01 7 0.4644 0.4564 0.02 0.00 0.00 0.18 0.00 0.00 0.64 0.16
#> TCGA.BH.A0AY.11 4 0.5469 -0.1021 0.16 0.00 0.00 0.54 0.00 0.00 0.06 0.24
#> TCGA.BH.A1F0.11 4 0.0941 0.7607 0.00 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.BH.A1FR.11 4 0.1275 0.7553 0.00 0.00 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.AR.A252.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A25F.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A2DO.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1ND.11 4 0.5440 0.4618 0.00 0.00 0.04 0.58 0.02 0.14 0.00 0.22
#> TCGA.E9.A1RD.11 3 0.3785 0.6640 0.00 0.00 0.72 0.00 0.00 0.14 0.00 0.14
#> TCGA.BH.A1FN.11 4 0.1341 0.7355 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.BH.A28O.01 1 0.3036 0.6683 0.78 0.00 0.00 0.00 0.00 0.00 0.04 0.18
#> TCGA.EW.A1P1.01 5 0.0000 0.7494 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E2.A1IO.11 3 0.1607 0.8375 0.00 0.00 0.92 0.00 0.00 0.04 0.00 0.04
#> TCGA.LL.A73Z.01 7 0.2938 0.5133 0.00 0.00 0.00 0.00 0.30 0.00 0.70 0.00
#> TCGA.AR.A2LH.01 2 0.0471 0.9723 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.A7.A13F.11 4 0.0941 0.7584 0.00 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.LL.A5YO.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1EV.11 8 0.5787 0.5908 0.32 0.00 0.00 0.18 0.00 0.00 0.06 0.44
#> TCGA.Z7.A8R5.01 7 0.3083 0.4561 0.00 0.00 0.00 0.00 0.34 0.00 0.66 0.00
#> TCGA.AO.A03U.01 5 0.3675 0.6194 0.00 0.00 0.00 0.00 0.76 0.02 0.14 0.08
#> TCGA.BH.A1ES.11 1 0.3658 0.1468 0.58 0.00 0.00 0.02 0.00 0.00 0.00 0.40
#> TCGA.E2.A15I.11 3 0.1275 0.8464 0.00 0.00 0.94 0.00 0.00 0.04 0.00 0.02
#> TCGA.A2.A1G6.01 1 0.0808 0.7326 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.BH.A0DH.11 1 0.2407 0.6973 0.86 0.00 0.00 0.00 0.00 0.00 0.06 0.08
#> TCGA.A2.A3XZ.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BC.11 1 0.0000 0.7390 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A13E.11 3 0.2862 0.7692 0.00 0.00 0.82 0.00 0.00 0.08 0.00 0.10
#> TCGA.BH.A0BA.11 1 0.2407 0.6973 0.86 0.00 0.00 0.00 0.00 0.00 0.06 0.08
#> TCGA.BH.A0DK.11 1 0.2407 0.6994 0.86 0.00 0.00 0.00 0.00 0.00 0.06 0.08
#> TCGA.D8.A4Z1.01 7 0.3735 0.5118 0.22 0.00 0.00 0.00 0.02 0.00 0.72 0.04
#> TCGA.AC.A3YI.01 5 0.3737 -0.0348 0.00 0.00 0.00 0.00 0.50 0.00 0.48 0.02
#> TCGA.BH.A0E0.11 1 0.0471 0.7370 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.BH.A0B2.11 1 0.6036 -0.4686 0.40 0.00 0.00 0.20 0.00 0.00 0.08 0.32
#> TCGA.A2.A4RY.01 7 0.3843 0.4936 0.24 0.00 0.00 0.00 0.02 0.00 0.70 0.04
#> TCGA.BH.A0BV.11 1 0.0808 0.7370 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.BH.A0DG.11 1 0.4657 0.0841 0.50 0.00 0.00 0.04 0.00 0.00 0.04 0.42
#> TCGA.AC.A23H.11 4 0.2132 0.7277 0.00 0.00 0.00 0.88 0.00 0.08 0.00 0.04
#> TCGA.EW.A1PG.01 5 0.3729 -0.0205 0.00 0.00 0.00 0.00 0.52 0.00 0.46 0.02
#> TCGA.E2.A1IF.11 8 0.5068 0.6780 0.20 0.00 0.00 0.38 0.00 0.00 0.00 0.42
#> TCGA.BH.A209.11 6 0.1341 0.7125 0.00 0.00 0.00 0.00 0.08 0.92 0.00 0.00
#> TCGA.E9.A1R7.11 3 0.0000 0.8683 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A5QQ.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1LB.11 1 0.4105 0.1071 0.54 0.00 0.00 0.02 0.00 0.00 0.02 0.42
#> TCGA.A2.A0CR.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FH.11 4 0.0941 0.7604 0.00 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.BH.A1FJ.11 4 0.0471 0.7641 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BH.A0HK.11 1 0.3601 0.6364 0.76 0.00 0.00 0.02 0.00 0.00 0.06 0.16
#> TCGA.BH.A0BM.11 1 0.0000 0.7390 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0E1.11 1 0.0471 0.7367 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.AR.A1AO.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FB.01 5 0.0471 0.7474 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.A2.A3XW.01 5 0.4833 0.4154 0.00 0.00 0.00 0.00 0.58 0.02 0.28 0.12
#> TCGA.BH.A1FE.11 1 0.3971 -0.0320 0.54 0.00 0.00 0.04 0.00 0.00 0.00 0.42
#> TCGA.A7.A0DC.11 7 0.6211 0.3082 0.00 0.00 0.00 0.22 0.20 0.00 0.44 0.14
#> TCGA.AO.A0JC.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0EP.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BJ.11 1 0.1765 0.7180 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.BH.A42U.01 7 0.3514 0.4337 0.00 0.00 0.00 0.00 0.34 0.00 0.64 0.02
#> TCGA.BH.A1F5.11 1 0.2623 0.7000 0.84 0.00 0.00 0.00 0.00 0.00 0.10 0.06
#> TCGA.BH.A1EO.11 3 0.0471 0.8636 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.E9.A1NE.01 2 0.0471 0.9723 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.C8.A8HR.01 5 0.0000 0.7494 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A6R9.01 5 0.1091 0.7318 0.00 0.00 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.C8.A8HP.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A2FM.11 1 0.1091 0.7273 0.94 0.00 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.A7.A0D9.11 3 0.1765 0.7633 0.00 0.00 0.88 0.00 0.00 0.12 0.00 0.00
#> TCGA.AC.A2FB.11 4 0.0000 0.7670 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1LS.11 6 0.2650 0.9017 0.00 0.00 0.24 0.00 0.00 0.76 0.00 0.00
#> TCGA.BH.A0BT.11 1 0.0000 0.7390 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0C0.11 1 0.0471 0.7370 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.E2.A1BC.11 3 0.0471 0.8636 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.BH.A0C3.11 1 0.2756 0.5489 0.74 0.00 0.00 0.00 0.00 0.00 0.00 0.26
#> TCGA.E9.A248.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A204.11 6 0.2650 0.9017 0.00 0.00 0.24 0.00 0.00 0.76 0.00 0.00
#> TCGA.GM.A3XG.01 1 0.0808 0.7326 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.E9.A1NF.11 3 0.0471 0.8636 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.BH.A1EN.11 3 0.6192 0.2382 0.00 0.00 0.44 0.24 0.00 0.14 0.00 0.18
#> TCGA.BH.A0DZ.11 1 0.2350 0.7078 0.86 0.00 0.00 0.00 0.00 0.00 0.04 0.10
#> TCGA.AC.A2FF.01 5 0.0471 0.7396 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.E9.A1N5.11 1 0.4562 -0.3726 0.46 0.00 0.00 0.10 0.00 0.00 0.00 0.44
#> TCGA.A7.A0CE.11 1 0.2623 0.7009 0.84 0.00 0.00 0.00 0.00 0.00 0.06 0.10
#> TCGA.LL.A440.01 5 0.1557 0.7274 0.00 0.00 0.00 0.00 0.92 0.00 0.06 0.02
#> TCGA.BH.A1FG.11 4 0.3083 0.3252 0.00 0.00 0.00 0.66 0.00 0.00 0.00 0.34
#> TCGA.AC.A2FF.11 4 0.3154 0.6688 0.00 0.00 0.00 0.78 0.00 0.00 0.06 0.16
#> TCGA.LD.A9QF.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A2DI.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0B8.11 3 0.0000 0.8683 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0AZ.11 1 0.0000 0.7390 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DQ.11 1 0.1563 0.7306 0.90 0.00 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.BH.A1FB.11 1 0.1947 0.6756 0.86 0.00 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.BH.A1FE.06 3 0.0000 0.8683 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RH.11 3 0.0000 0.8683 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A0CH.11 5 0.4370 0.1540 0.00 0.00 0.00 0.00 0.52 0.00 0.40 0.08
#> TCGA.GM.A4E0.01 5 0.0471 0.7330 0.00 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.E9.A22A.01 2 0.2852 0.6410 0.00 0.72 0.00 0.00 0.28 0.00 0.00 0.00
#> TCGA.BH.A1F8.11 4 0.0000 0.7670 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1NA.11 4 0.0000 0.7670 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1B5.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1LI.11 5 0.0000 0.7494 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A1FD.11 4 0.0808 0.7619 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.BH.A1F6.11 4 0.4503 0.5549 0.00 0.00 0.02 0.66 0.00 0.14 0.00 0.18
#> TCGA.BH.A1ET.11 4 0.2404 0.6636 0.00 0.00 0.00 0.84 0.00 0.00 0.02 0.14
#> TCGA.E2.A1II.11 4 0.2534 0.5816 0.00 0.00 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.BH.A0HA.11 1 0.0000 0.7390 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A97C.01 7 0.3444 0.5041 0.00 0.00 0.00 0.00 0.02 0.06 0.78 0.14
#> TCGA.E2.A15K.11 4 0.3434 0.6445 0.00 0.00 0.00 0.76 0.00 0.10 0.00 0.14
#> TCGA.AR.A24U.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AX.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1EY.11 4 0.0941 0.7641 0.00 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.BH.A0BZ.11 4 0.5152 0.4879 0.00 0.00 0.02 0.60 0.02 0.14 0.00 0.22
#> TCGA.E9.A1NG.11 3 0.2648 0.7840 0.00 0.00 0.84 0.00 0.00 0.08 0.00 0.08
#> TCGA.BH.A0DV.11 1 0.1563 0.7059 0.90 0.00 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.BH.A0BS.11 1 0.2267 0.6728 0.82 0.00 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.E2.A108.01 2 0.0000 0.9867 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RB.11 6 0.1765 0.8376 0.00 0.00 0.12 0.00 0.00 0.88 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node01. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0115-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0151-leaf , Node0152-leaf , Node0153-leaf , Node0154-leaf , Node0211-leaf , Node0212 , Node0213 , Node0221 , Node0222 , Node0231-leaf , Node0232 , Node0233-leaf , Node0241-leaf , Node0242 , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0331-leaf , Node0332-leaf , Node0341-leaf , Node0342-leaf , Node0343-leaf , Node0411 , Node0412-leaf , Node0413 , Node0421-leaf , Node0422 , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["011"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 50 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 8.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.998 0.999 0.47115 0.530 0.530
#> 3 3 1.000 0.997 0.999 0.41361 0.804 0.630
#> 4 4 0.816 0.875 0.890 0.09354 0.882 0.673
#> 5 5 1.000 0.981 0.989 0.08799 0.935 0.760
#> 6 6 0.895 0.878 0.910 0.02545 1.000 1.000
#> 7 7 0.904 0.820 0.871 0.02004 0.963 0.823
#> 8 8 0.918 0.807 0.871 0.00958 0.969 0.827
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 8
#> attr(,"optional")
#> [1] 2 3 5 7
There is also optional best \(k\) = 2 3 5 7 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.E9.A1N4.11 2 0.000 0.999 0.00 1.00
#> TCGA.BH.A0DP.11 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A0BF.11 2 0.000 0.999 0.00 1.00
#> TCGA.BH.A208.11 2 0.000 0.999 0.00 1.00
#> TCGA.BH.A0DI.11 2 0.242 0.958 0.04 0.96
#> TCGA.BH.A0H7.11 1 0.000 1.000 1.00 0.00
#> TCGA.AO.A1KO.01 2 0.000 0.999 0.00 1.00
#> TCGA.BH.A0AU.11 2 0.000 0.999 0.00 1.00
#> TCGA.E9.A1NE.11 2 0.000 0.999 0.00 1.00
#> TCGA.BH.A1FM.11 2 0.000 0.999 0.00 1.00
#> TCGA.E2.A1B5.11 2 0.000 0.999 0.00 1.00
#> TCGA.PL.A8LY.01 2 0.000 0.999 0.00 1.00
#> TCGA.BH.A1EU.11 2 0.000 0.999 0.00 1.00
#> TCGA.BH.A0B3.11 1 0.000 1.000 1.00 0.00
#> TCGA.AC.A2FK.01 2 0.000 0.999 0.00 1.00
#> TCGA.BH.A28O.01 2 0.000 0.999 0.00 1.00
#> TCGA.BH.A1EV.11 2 0.000 0.999 0.00 1.00
#> TCGA.BH.A1ES.11 2 0.000 0.999 0.00 1.00
#> TCGA.A2.A1G6.01 2 0.000 0.999 0.00 1.00
#> TCGA.BH.A0DH.11 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A0BC.11 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A0BA.11 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A0DK.11 1 0.000 1.000 1.00 0.00
#> TCGA.D8.A4Z1.01 2 0.000 0.999 0.00 1.00
#> TCGA.BH.A0E0.11 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A0B2.11 1 0.000 1.000 1.00 0.00
#> TCGA.A2.A4RY.01 2 0.000 0.999 0.00 1.00
#> TCGA.BH.A0BV.11 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A0DG.11 2 0.000 0.999 0.00 1.00
#> TCGA.E2.A1LB.11 2 0.000 0.999 0.00 1.00
#> TCGA.BH.A0HK.11 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A0BM.11 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A0E1.11 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A1FE.11 2 0.000 0.999 0.00 1.00
#> TCGA.BH.A0BJ.11 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A1F5.11 2 0.000 0.999 0.00 1.00
#> TCGA.AC.A2FM.11 2 0.000 0.999 0.00 1.00
#> TCGA.BH.A0BT.11 2 0.000 0.999 0.00 1.00
#> TCGA.BH.A0C0.11 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A0C3.11 2 0.000 0.999 0.00 1.00
#> TCGA.GM.A3XG.01 2 0.000 0.999 0.00 1.00
#> TCGA.BH.A0DZ.11 1 0.000 1.000 1.00 0.00
#> TCGA.E9.A1N5.11 2 0.000 0.999 0.00 1.00
#> TCGA.A7.A0CE.11 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A0AZ.11 2 0.000 0.999 0.00 1.00
#> TCGA.BH.A0DQ.11 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A1FB.11 2 0.000 0.999 0.00 1.00
#> TCGA.BH.A0HA.11 2 0.000 0.999 0.00 1.00
#> TCGA.BH.A0DV.11 2 0.000 0.999 0.00 1.00
#> TCGA.BH.A0BS.11 2 0.000 0.999 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.E9.A1N4.11 2 0.000 1.000 0 1.00 0.00
#> TCGA.BH.A0DP.11 1 0.000 1.000 1 0.00 0.00
#> TCGA.BH.A0BF.11 3 0.000 0.994 0 0.00 1.00
#> TCGA.BH.A208.11 3 0.000 0.994 0 0.00 1.00
#> TCGA.BH.A0DI.11 3 0.000 0.994 0 0.00 1.00
#> TCGA.BH.A0H7.11 1 0.000 1.000 1 0.00 0.00
#> TCGA.AO.A1KO.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.BH.A0AU.11 2 0.000 1.000 0 1.00 0.00
#> TCGA.E9.A1NE.11 2 0.000 1.000 0 1.00 0.00
#> TCGA.BH.A1FM.11 2 0.000 1.000 0 1.00 0.00
#> TCGA.E2.A1B5.11 3 0.000 0.994 0 0.00 1.00
#> TCGA.PL.A8LY.01 3 0.000 0.994 0 0.00 1.00
#> TCGA.BH.A1EU.11 3 0.000 0.994 0 0.00 1.00
#> TCGA.BH.A0B3.11 1 0.000 1.000 1 0.00 0.00
#> TCGA.AC.A2FK.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.BH.A28O.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.BH.A1EV.11 2 0.000 1.000 0 1.00 0.00
#> TCGA.BH.A1ES.11 3 0.000 0.994 0 0.00 1.00
#> TCGA.A2.A1G6.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.BH.A0DH.11 1 0.000 1.000 1 0.00 0.00
#> TCGA.BH.A0BC.11 1 0.000 1.000 1 0.00 0.00
#> TCGA.BH.A0BA.11 1 0.000 1.000 1 0.00 0.00
#> TCGA.BH.A0DK.11 1 0.000 1.000 1 0.00 0.00
#> TCGA.D8.A4Z1.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.BH.A0E0.11 1 0.000 1.000 1 0.00 0.00
#> TCGA.BH.A0B2.11 1 0.000 1.000 1 0.00 0.00
#> TCGA.A2.A4RY.01 3 0.207 0.936 0 0.06 0.94
#> TCGA.BH.A0BV.11 1 0.000 1.000 1 0.00 0.00
#> TCGA.BH.A0DG.11 2 0.000 1.000 0 1.00 0.00
#> TCGA.E2.A1LB.11 2 0.000 1.000 0 1.00 0.00
#> TCGA.BH.A0HK.11 1 0.000 1.000 1 0.00 0.00
#> TCGA.BH.A0BM.11 1 0.000 1.000 1 0.00 0.00
#> TCGA.BH.A0E1.11 1 0.000 1.000 1 0.00 0.00
#> TCGA.BH.A1FE.11 2 0.000 1.000 0 1.00 0.00
#> TCGA.BH.A0BJ.11 1 0.000 1.000 1 0.00 0.00
#> TCGA.BH.A1F5.11 2 0.000 1.000 0 1.00 0.00
#> TCGA.AC.A2FM.11 2 0.000 1.000 0 1.00 0.00
#> TCGA.BH.A0BT.11 3 0.000 0.994 0 0.00 1.00
#> TCGA.BH.A0C0.11 1 0.000 1.000 1 0.00 0.00
#> TCGA.BH.A0C3.11 2 0.000 1.000 0 1.00 0.00
#> TCGA.GM.A3XG.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.BH.A0DZ.11 1 0.000 1.000 1 0.00 0.00
#> TCGA.E9.A1N5.11 2 0.000 1.000 0 1.00 0.00
#> TCGA.A7.A0CE.11 1 0.000 1.000 1 0.00 0.00
#> TCGA.BH.A0AZ.11 3 0.000 0.994 0 0.00 1.00
#> TCGA.BH.A0DQ.11 1 0.000 1.000 1 0.00 0.00
#> TCGA.BH.A1FB.11 2 0.000 1.000 0 1.00 0.00
#> TCGA.BH.A0HA.11 3 0.000 0.994 0 0.00 1.00
#> TCGA.BH.A0DV.11 3 0.000 0.994 0 0.00 1.00
#> TCGA.BH.A0BS.11 2 0.000 1.000 0 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.E9.A1N4.11 2 0.000 0.997 0.0 1.00 0.00 0.00
#> TCGA.BH.A0DP.11 1 0.441 0.826 0.7 0.00 0.30 0.00
#> TCGA.BH.A0BF.11 3 0.441 0.722 0.0 0.00 0.70 0.30
#> TCGA.BH.A208.11 3 0.441 0.722 0.0 0.00 0.70 0.30
#> TCGA.BH.A0DI.11 4 0.000 1.000 0.0 0.00 0.00 1.00
#> TCGA.BH.A0H7.11 1 0.441 0.826 0.7 0.00 0.30 0.00
#> TCGA.AO.A1KO.01 2 0.000 0.997 0.0 1.00 0.00 0.00
#> TCGA.BH.A0AU.11 3 0.441 0.711 0.0 0.30 0.70 0.00
#> TCGA.E9.A1NE.11 2 0.000 0.997 0.0 1.00 0.00 0.00
#> TCGA.BH.A1FM.11 2 0.000 0.997 0.0 1.00 0.00 0.00
#> TCGA.E2.A1B5.11 4 0.000 1.000 0.0 0.00 0.00 1.00
#> TCGA.PL.A8LY.01 3 0.441 0.722 0.0 0.00 0.70 0.30
#> TCGA.BH.A1EU.11 3 0.441 0.722 0.0 0.00 0.70 0.30
#> TCGA.BH.A0B3.11 1 0.441 0.826 0.7 0.00 0.30 0.00
#> TCGA.AC.A2FK.01 2 0.000 0.997 0.0 1.00 0.00 0.00
#> TCGA.BH.A28O.01 2 0.000 0.997 0.0 1.00 0.00 0.00
#> TCGA.BH.A1EV.11 2 0.121 0.949 0.0 0.96 0.04 0.00
#> TCGA.BH.A1ES.11 3 0.441 0.722 0.0 0.00 0.70 0.30
#> TCGA.A2.A1G6.01 2 0.000 0.997 0.0 1.00 0.00 0.00
#> TCGA.BH.A0DH.11 1 0.441 0.826 0.7 0.00 0.30 0.00
#> TCGA.BH.A0BC.11 1 0.000 0.864 1.0 0.00 0.00 0.00
#> TCGA.BH.A0BA.11 1 0.441 0.826 0.7 0.00 0.30 0.00
#> TCGA.BH.A0DK.11 1 0.441 0.826 0.7 0.00 0.30 0.00
#> TCGA.D8.A4Z1.01 3 0.441 0.711 0.0 0.30 0.70 0.00
#> TCGA.BH.A0E0.11 1 0.441 0.826 0.7 0.00 0.30 0.00
#> TCGA.BH.A0B2.11 1 0.000 0.864 1.0 0.00 0.00 0.00
#> TCGA.A2.A4RY.01 3 0.566 0.731 0.0 0.08 0.70 0.22
#> TCGA.BH.A0BV.11 1 0.000 0.864 1.0 0.00 0.00 0.00
#> TCGA.BH.A0DG.11 3 0.441 0.711 0.0 0.30 0.70 0.00
#> TCGA.E2.A1LB.11 2 0.000 0.997 0.0 1.00 0.00 0.00
#> TCGA.BH.A0HK.11 1 0.000 0.864 1.0 0.00 0.00 0.00
#> TCGA.BH.A0BM.11 1 0.000 0.864 1.0 0.00 0.00 0.00
#> TCGA.BH.A0E1.11 1 0.000 0.864 1.0 0.00 0.00 0.00
#> TCGA.BH.A1FE.11 2 0.000 0.997 0.0 1.00 0.00 0.00
#> TCGA.BH.A0BJ.11 1 0.000 0.864 1.0 0.00 0.00 0.00
#> TCGA.BH.A1F5.11 2 0.000 0.997 0.0 1.00 0.00 0.00
#> TCGA.AC.A2FM.11 2 0.000 0.997 0.0 1.00 0.00 0.00
#> TCGA.BH.A0BT.11 4 0.000 1.000 0.0 0.00 0.00 1.00
#> TCGA.BH.A0C0.11 1 0.000 0.864 1.0 0.00 0.00 0.00
#> TCGA.BH.A0C3.11 3 0.441 0.711 0.0 0.30 0.70 0.00
#> TCGA.GM.A3XG.01 2 0.000 0.997 0.0 1.00 0.00 0.00
#> TCGA.BH.A0DZ.11 1 0.441 0.826 0.7 0.00 0.30 0.00
#> TCGA.E9.A1N5.11 2 0.000 0.997 0.0 1.00 0.00 0.00
#> TCGA.A7.A0CE.11 1 0.000 0.864 1.0 0.00 0.00 0.00
#> TCGA.BH.A0AZ.11 4 0.000 1.000 0.0 0.00 0.00 1.00
#> TCGA.BH.A0DQ.11 1 0.000 0.864 1.0 0.00 0.00 0.00
#> TCGA.BH.A1FB.11 2 0.000 0.997 0.0 1.00 0.00 0.00
#> TCGA.BH.A0HA.11 4 0.000 1.000 0.0 0.00 0.00 1.00
#> TCGA.BH.A0DV.11 3 0.441 0.722 0.0 0.00 0.70 0.30
#> TCGA.BH.A0BS.11 3 0.441 0.711 0.0 0.30 0.70 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.E9.A1N4.11 2 0.0000 0.997 0.00 1.00 0.00 0 0.00
#> TCGA.BH.A0DP.11 5 0.0000 1.000 0.00 0.00 0.00 0 1.00
#> TCGA.BH.A0BF.11 3 0.0000 1.000 0.00 0.00 1.00 0 0.00
#> TCGA.BH.A208.11 3 0.0000 1.000 0.00 0.00 1.00 0 0.00
#> TCGA.BH.A0DI.11 4 0.0000 1.000 0.00 0.00 0.00 1 0.00
#> TCGA.BH.A0H7.11 5 0.0000 1.000 0.00 0.00 0.00 0 1.00
#> TCGA.AO.A1KO.01 2 0.0000 0.997 0.00 1.00 0.00 0 0.00
#> TCGA.BH.A0AU.11 3 0.0000 1.000 0.00 0.00 1.00 0 0.00
#> TCGA.E9.A1NE.11 2 0.0000 0.997 0.00 1.00 0.00 0 0.00
#> TCGA.BH.A1FM.11 2 0.0000 0.997 0.00 1.00 0.00 0 0.00
#> TCGA.E2.A1B5.11 4 0.0000 1.000 0.00 0.00 0.00 1 0.00
#> TCGA.PL.A8LY.01 3 0.0000 1.000 0.00 0.00 1.00 0 0.00
#> TCGA.BH.A1EU.11 3 0.0000 1.000 0.00 0.00 1.00 0 0.00
#> TCGA.BH.A0B3.11 5 0.0000 1.000 0.00 0.00 0.00 0 1.00
#> TCGA.AC.A2FK.01 2 0.0000 0.997 0.00 1.00 0.00 0 0.00
#> TCGA.BH.A28O.01 2 0.0000 0.997 0.00 1.00 0.00 0 0.00
#> TCGA.BH.A1EV.11 2 0.1043 0.952 0.00 0.96 0.04 0 0.00
#> TCGA.BH.A1ES.11 3 0.0000 1.000 0.00 0.00 1.00 0 0.00
#> TCGA.A2.A1G6.01 2 0.0000 0.997 0.00 1.00 0.00 0 0.00
#> TCGA.BH.A0DH.11 5 0.0000 1.000 0.00 0.00 0.00 0 1.00
#> TCGA.BH.A0BC.11 1 0.0000 0.938 1.00 0.00 0.00 0 0.00
#> TCGA.BH.A0BA.11 5 0.0000 1.000 0.00 0.00 0.00 0 1.00
#> TCGA.BH.A0DK.11 5 0.0000 1.000 0.00 0.00 0.00 0 1.00
#> TCGA.D8.A4Z1.01 3 0.0000 1.000 0.00 0.00 1.00 0 0.00
#> TCGA.BH.A0E0.11 5 0.0000 1.000 0.00 0.00 0.00 0 1.00
#> TCGA.BH.A0B2.11 1 0.2020 0.901 0.90 0.00 0.00 0 0.10
#> TCGA.A2.A4RY.01 3 0.0000 1.000 0.00 0.00 1.00 0 0.00
#> TCGA.BH.A0BV.11 1 0.0609 0.936 0.98 0.00 0.00 0 0.02
#> TCGA.BH.A0DG.11 3 0.0000 1.000 0.00 0.00 1.00 0 0.00
#> TCGA.E2.A1LB.11 2 0.0000 0.997 0.00 1.00 0.00 0 0.00
#> TCGA.BH.A0HK.11 1 0.0000 0.938 1.00 0.00 0.00 0 0.00
#> TCGA.BH.A0BM.11 1 0.0000 0.938 1.00 0.00 0.00 0 0.00
#> TCGA.BH.A0E1.11 1 0.2929 0.835 0.82 0.00 0.00 0 0.18
#> TCGA.BH.A1FE.11 2 0.0000 0.997 0.00 1.00 0.00 0 0.00
#> TCGA.BH.A0BJ.11 1 0.2929 0.835 0.82 0.00 0.00 0 0.18
#> TCGA.BH.A1F5.11 2 0.0000 0.997 0.00 1.00 0.00 0 0.00
#> TCGA.AC.A2FM.11 2 0.0000 0.997 0.00 1.00 0.00 0 0.00
#> TCGA.BH.A0BT.11 4 0.0000 1.000 0.00 0.00 0.00 1 0.00
#> TCGA.BH.A0C0.11 1 0.0000 0.938 1.00 0.00 0.00 0 0.00
#> TCGA.BH.A0C3.11 3 0.0000 1.000 0.00 0.00 1.00 0 0.00
#> TCGA.GM.A3XG.01 2 0.0000 0.997 0.00 1.00 0.00 0 0.00
#> TCGA.BH.A0DZ.11 5 0.0000 1.000 0.00 0.00 0.00 0 1.00
#> TCGA.E9.A1N5.11 2 0.0000 0.997 0.00 1.00 0.00 0 0.00
#> TCGA.A7.A0CE.11 1 0.0000 0.938 1.00 0.00 0.00 0 0.00
#> TCGA.BH.A0AZ.11 4 0.0000 1.000 0.00 0.00 0.00 1 0.00
#> TCGA.BH.A0DQ.11 1 0.1043 0.931 0.96 0.00 0.00 0 0.04
#> TCGA.BH.A1FB.11 2 0.0000 0.997 0.00 1.00 0.00 0 0.00
#> TCGA.BH.A0HA.11 4 0.0000 1.000 0.00 0.00 0.00 1 0.00
#> TCGA.BH.A0DV.11 3 0.0000 1.000 0.00 0.00 1.00 0 0.00
#> TCGA.BH.A0BS.11 3 0.0000 1.000 0.00 0.00 1.00 0 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.E9.A1N4.11 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DP.11 5 0.0000 0.962 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BH.A0BF.11 3 0.2790 0.824 0.00 0.00 0.84 0.02 0.00 0.14
#> TCGA.BH.A208.11 3 0.4566 0.768 0.00 0.00 0.70 0.16 0.00 0.14
#> TCGA.BH.A0DI.11 4 0.3409 0.859 0.00 0.00 0.00 0.70 0.00 0.30
#> TCGA.BH.A0H7.11 5 0.0000 0.962 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AO.A1KO.01 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0AU.11 3 0.0000 0.831 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E9.A1NE.11 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FM.11 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1B5.11 4 0.0000 0.881 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.PL.A8LY.01 3 0.2956 0.813 0.00 0.00 0.84 0.12 0.00 0.04
#> TCGA.BH.A1EU.11 3 0.4566 0.768 0.00 0.00 0.70 0.16 0.00 0.14
#> TCGA.BH.A0B3.11 5 0.2454 0.844 0.16 0.00 0.00 0.00 0.84 0.00
#> TCGA.AC.A2FK.01 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A28O.01 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1EV.11 2 0.3198 0.672 0.00 0.74 0.26 0.00 0.00 0.00
#> TCGA.BH.A1ES.11 3 0.4566 0.768 0.00 0.00 0.70 0.16 0.00 0.14
#> TCGA.A2.A1G6.01 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DH.11 5 0.0000 0.962 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BH.A0BC.11 1 0.3198 0.837 0.74 0.00 0.00 0.00 0.00 0.26
#> TCGA.BH.A0BA.11 5 0.0000 0.962 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BH.A0DK.11 5 0.0000 0.962 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D8.A4Z1.01 3 0.3409 0.629 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.BH.A0E0.11 5 0.0000 0.962 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BH.A0B2.11 1 0.1267 0.822 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.A2.A4RY.01 3 0.3499 0.632 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.BH.A0BV.11 1 0.0547 0.832 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.BH.A0DG.11 3 0.0000 0.831 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E2.A1LB.11 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0HK.11 1 0.3076 0.840 0.76 0.00 0.00 0.00 0.00 0.24
#> TCGA.BH.A0BM.11 1 0.2941 0.844 0.78 0.00 0.00 0.00 0.00 0.22
#> TCGA.BH.A0E1.11 1 0.2260 0.760 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.BH.A1FE.11 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BJ.11 1 0.1814 0.798 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.BH.A1F5.11 2 0.0547 0.961 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.AC.A2FM.11 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BT.11 4 0.2454 0.907 0.00 0.00 0.00 0.84 0.00 0.16
#> TCGA.BH.A0C0.11 1 0.3076 0.840 0.76 0.00 0.00 0.00 0.00 0.24
#> TCGA.BH.A0C3.11 3 0.0000 0.831 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.GM.A3XG.01 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DZ.11 5 0.1814 0.898 0.10 0.00 0.00 0.00 0.90 0.00
#> TCGA.E9.A1N5.11 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A0CE.11 1 0.3198 0.837 0.74 0.00 0.00 0.00 0.00 0.26
#> TCGA.BH.A0AZ.11 4 0.2454 0.907 0.00 0.00 0.00 0.84 0.00 0.16
#> TCGA.BH.A0DQ.11 1 0.1092 0.837 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.BH.A1FB.11 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0HA.11 4 0.0000 0.881 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A0DV.11 3 0.2260 0.827 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.BH.A0BS.11 3 0.0000 0.831 0.00 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.E9.A1N4.11 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DP.11 5 0.0000 0.936 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A0BF.11 3 0.2422 0.527 0.00 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.BH.A208.11 3 0.2376 0.389 0.00 0.00 0.86 0.00 0.00 0.12 0.02
#> TCGA.BH.A0DI.11 4 0.4629 0.631 0.00 0.00 0.00 0.64 0.00 0.20 0.16
#> TCGA.BH.A0H7.11 5 0.0000 0.936 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AO.A1KO.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0AU.11 3 0.3546 0.468 0.00 0.00 0.54 0.00 0.00 0.00 0.46
#> TCGA.E9.A1NE.11 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FM.11 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1B5.11 4 0.2572 0.796 0.00 0.00 0.20 0.80 0.00 0.00 0.00
#> TCGA.PL.A8LY.01 3 0.3139 0.483 0.00 0.00 0.70 0.00 0.00 0.00 0.30
#> TCGA.BH.A1EU.11 3 0.0000 0.492 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0B3.11 5 0.2945 0.694 0.00 0.00 0.00 0.00 0.74 0.26 0.00
#> TCGA.AC.A2FK.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A28O.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1EV.11 2 0.3413 0.370 0.00 0.62 0.00 0.00 0.00 0.00 0.38
#> TCGA.BH.A1ES.11 3 0.0000 0.492 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A1G6.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DH.11 5 0.0000 0.936 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A0BC.11 1 0.0863 0.948 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.BH.A0BA.11 5 0.0000 0.936 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A0DK.11 5 0.0000 0.936 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D8.A4Z1.01 7 0.3519 0.863 0.00 0.00 0.22 0.00 0.00 0.04 0.74
#> TCGA.BH.A0E0.11 5 0.0000 0.936 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A0B2.11 6 0.3755 0.969 0.34 0.00 0.00 0.00 0.02 0.64 0.00
#> TCGA.A2.A4RY.01 7 0.3841 0.860 0.00 0.00 0.28 0.00 0.00 0.04 0.68
#> TCGA.BH.A0BV.11 6 0.3358 0.960 0.36 0.00 0.00 0.00 0.00 0.64 0.00
#> TCGA.BH.A0DG.11 3 0.3546 0.468 0.00 0.00 0.54 0.00 0.00 0.00 0.46
#> TCGA.E2.A1LB.11 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0HK.11 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BM.11 1 0.0863 0.948 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.BH.A0E1.11 6 0.4070 0.946 0.34 0.00 0.00 0.00 0.04 0.62 0.00
#> TCGA.BH.A1FE.11 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BJ.11 6 0.3755 0.969 0.34 0.00 0.00 0.00 0.02 0.64 0.00
#> TCGA.BH.A1F5.11 2 0.0504 0.951 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.AC.A2FM.11 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BT.11 4 0.0000 0.825 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0C0.11 1 0.0504 0.956 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.BH.A0C3.11 3 0.3546 0.468 0.00 0.00 0.54 0.00 0.00 0.00 0.46
#> TCGA.GM.A3XG.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DZ.11 5 0.2259 0.820 0.00 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.E9.A1N5.11 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A0CE.11 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0AZ.11 4 0.0000 0.825 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0DQ.11 6 0.3358 0.960 0.36 0.00 0.00 0.00 0.00 0.64 0.00
#> TCGA.BH.A1FB.11 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0HA.11 4 0.2572 0.796 0.00 0.00 0.20 0.80 0.00 0.00 0.00
#> TCGA.BH.A0DV.11 3 0.2422 0.527 0.00 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.BH.A0BS.11 3 0.3546 0.468 0.00 0.00 0.54 0.00 0.00 0.00 0.46
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.E9.A1N4.11 2 0.0000 0.998242 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DP.11 5 0.0000 0.956465 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0BF.11 3 0.4367 0.500303 0.00 0.00 0.70 0.00 0.00 0.12 0.14 0.04
#> TCGA.BH.A208.11 7 0.6871 -0.074707 0.00 0.00 0.24 0.02 0.00 0.26 0.32 0.16
#> TCGA.BH.A0DI.11 8 0.2267 0.000000 0.00 0.00 0.00 0.18 0.00 0.00 0.00 0.82
#> TCGA.BH.A0H7.11 5 0.0000 0.956465 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AO.A1KO.01 2 0.0000 0.998242 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0AU.11 3 0.0471 0.607544 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.E9.A1NE.11 2 0.0000 0.998242 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FM.11 2 0.0000 0.998242 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1B5.11 4 0.0471 0.940010 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.PL.A8LY.01 3 0.1275 0.594206 0.00 0.00 0.94 0.04 0.00 0.00 0.02 0.00
#> TCGA.BH.A1EU.11 3 0.5817 0.357882 0.00 0.00 0.56 0.02 0.00 0.12 0.20 0.10
#> TCGA.BH.A0B3.11 5 0.2114 0.808338 0.00 0.00 0.00 0.00 0.84 0.16 0.00 0.00
#> TCGA.AC.A2FK.01 2 0.0000 0.998242 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A28O.01 2 0.0000 0.998242 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1EV.11 3 0.3714 -0.000674 0.00 0.44 0.54 0.00 0.00 0.00 0.02 0.00
#> TCGA.BH.A1ES.11 3 0.5817 0.357882 0.00 0.00 0.56 0.02 0.00 0.12 0.20 0.10
#> TCGA.A2.A1G6.01 2 0.0000 0.998242 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DH.11 5 0.0000 0.956465 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0BC.11 1 0.1275 0.905439 0.94 0.00 0.00 0.00 0.00 0.04 0.00 0.02
#> TCGA.BH.A0BA.11 5 0.0000 0.956465 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0DK.11 5 0.0000 0.956465 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A4Z1.01 7 0.3015 0.524065 0.00 0.00 0.32 0.00 0.00 0.00 0.68 0.00
#> TCGA.BH.A0E0.11 5 0.0000 0.956465 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0B2.11 6 0.3374 0.960959 0.30 0.00 0.00 0.00 0.02 0.68 0.00 0.00
#> TCGA.A2.A4RY.01 7 0.3015 0.524065 0.00 0.00 0.32 0.00 0.00 0.00 0.68 0.00
#> TCGA.BH.A0BV.11 6 0.3083 0.933537 0.34 0.00 0.00 0.00 0.00 0.66 0.00 0.00
#> TCGA.BH.A0DG.11 3 0.0471 0.607544 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.E2.A1LB.11 2 0.0000 0.998242 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0HK.11 1 0.0808 0.942216 0.96 0.00 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.BH.A0BM.11 1 0.0471 0.959678 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.BH.A0E1.11 6 0.3675 0.931434 0.30 0.00 0.00 0.00 0.04 0.66 0.00 0.00
#> TCGA.BH.A1FE.11 2 0.0000 0.998242 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BJ.11 6 0.3374 0.960959 0.30 0.00 0.00 0.00 0.02 0.68 0.00 0.00
#> TCGA.BH.A1F5.11 2 0.0471 0.976798 0.00 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A2FM.11 2 0.0000 0.998242 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BT.11 4 0.0808 0.939187 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.BH.A0C0.11 1 0.0471 0.959678 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.BH.A0C3.11 3 0.0471 0.615375 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.GM.A3XG.01 2 0.0000 0.998242 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DZ.11 5 0.1563 0.880663 0.00 0.00 0.00 0.00 0.90 0.10 0.00 0.00
#> TCGA.E9.A1N5.11 2 0.0000 0.998242 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A0CE.11 1 0.0000 0.953157 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0AZ.11 4 0.0808 0.939187 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.BH.A0DQ.11 6 0.3015 0.951581 0.32 0.00 0.00 0.00 0.00 0.68 0.00 0.00
#> TCGA.BH.A1FB.11 2 0.0000 0.998242 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0HA.11 4 0.0471 0.940010 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.BH.A0DV.11 3 0.3837 0.534887 0.00 0.00 0.76 0.00 0.00 0.10 0.10 0.04
#> TCGA.BH.A0BS.11 3 0.0471 0.607544 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node01. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0115-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0151-leaf , Node0152-leaf , Node0153-leaf , Node0154-leaf , Node0211-leaf , Node0212 , Node0213 , Node0221 , Node0222 , Node0231-leaf , Node0232 , Node0233-leaf , Node0241-leaf , Node0242 , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0331-leaf , Node0332-leaf , Node0341-leaf , Node0342-leaf , Node0343-leaf , Node0411 , Node0412-leaf , Node0413 , Node0421-leaf , Node0422 , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["012"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 29 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.1339 0.867 0.867
#> 3 3 0.869 0.963 0.982 3.1545 0.581 0.517
#> 4 4 0.801 0.866 0.927 0.2784 0.739 0.475
#> 5 5 0.687 0.747 0.848 0.0960 0.837 0.500
#> 6 6 0.738 0.609 0.772 0.0473 0.966 0.841
#> 7 7 0.738 0.487 0.709 0.0348 0.914 0.611
#> 8 8 0.789 0.619 0.816 0.0291 0.933 0.625
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.E9.A1QZ.01 2 0 1 0 1
#> TCGA.AC.A2FB.01 2 0 1 0 1
#> TCGA.E2.A1B6.01 2 0 1 0 1
#> TCGA.B6.A0RT.01 2 0 1 0 1
#> TCGA.E9.A2JT.01 2 0 1 0 1
#> TCGA.OL.A5RY.01 2 0 1 0 1
#> TCGA.BH.A209.01 1 0 1 1 0
#> TCGA.AR.A1AW.01 2 0 1 0 1
#> TCGA.AR.A252.01 2 0 1 0 1
#> TCGA.A2.A25F.01 2 0 1 0 1
#> TCGA.GM.A2DO.01 2 0 1 0 1
#> TCGA.AR.A2LH.01 2 0 1 0 1
#> TCGA.LL.A5YO.01 2 0 1 0 1
#> TCGA.A2.A3XZ.01 2 0 1 0 1
#> TCGA.AR.A5QQ.01 2 0 1 0 1
#> TCGA.A2.A0CR.01 2 0 1 0 1
#> TCGA.AR.A1AO.01 2 0 1 0 1
#> TCGA.AO.A0JC.01 2 0 1 0 1
#> TCGA.A2.A0EP.01 2 0 1 0 1
#> TCGA.E9.A1NE.01 2 0 1 0 1
#> TCGA.C8.A8HP.01 2 0 1 0 1
#> TCGA.E9.A248.01 2 0 1 0 1
#> TCGA.LD.A9QF.01 2 0 1 0 1
#> TCGA.GM.A2DI.01 2 0 1 0 1
#> TCGA.E9.A22A.01 1 0 1 1 0
#> TCGA.E2.A1B5.01 2 0 1 0 1
#> TCGA.AR.A24U.01 2 0 1 0 1
#> TCGA.AR.A1AX.01 2 0 1 0 1
#> TCGA.E2.A108.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.E9.A1QZ.01 2 0.369 0.850 0 0.86 0.14
#> TCGA.AC.A2FB.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.E2.A1B6.01 2 0.000 0.961 0 1.00 0.00
#> TCGA.B6.A0RT.01 2 0.000 0.961 0 1.00 0.00
#> TCGA.E9.A2JT.01 2 0.000 0.961 0 1.00 0.00
#> TCGA.OL.A5RY.01 2 0.334 0.871 0 0.88 0.12
#> TCGA.BH.A209.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.AR.A1AW.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.AR.A252.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.A2.A25F.01 2 0.000 0.961 0 1.00 0.00
#> TCGA.GM.A2DO.01 2 0.000 0.961 0 1.00 0.00
#> TCGA.AR.A2LH.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.LL.A5YO.01 2 0.000 0.961 0 1.00 0.00
#> TCGA.A2.A3XZ.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.AR.A5QQ.01 2 0.000 0.961 0 1.00 0.00
#> TCGA.A2.A0CR.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.AR.A1AO.01 2 0.000 0.961 0 1.00 0.00
#> TCGA.AO.A0JC.01 2 0.000 0.961 0 1.00 0.00
#> TCGA.A2.A0EP.01 2 0.000 0.961 0 1.00 0.00
#> TCGA.E9.A1NE.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.C8.A8HP.01 2 0.000 0.961 0 1.00 0.00
#> TCGA.E9.A248.01 2 0.000 0.961 0 1.00 0.00
#> TCGA.LD.A9QF.01 2 0.369 0.850 0 0.86 0.14
#> TCGA.GM.A2DI.01 2 0.000 0.961 0 1.00 0.00
#> TCGA.E9.A22A.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.E2.A1B5.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.AR.A24U.01 2 0.334 0.871 0 0.88 0.12
#> TCGA.AR.A1AX.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.E2.A108.01 3 0.000 1.000 0 0.00 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.E9.A1QZ.01 2 0.1211 0.824 0 0.96 0.04 0.00
#> TCGA.AC.A2FB.01 3 0.0707 0.931 0 0.02 0.98 0.00
#> TCGA.E2.A1B6.01 4 0.1211 0.991 0 0.04 0.00 0.96
#> TCGA.B6.A0RT.01 4 0.1211 0.991 0 0.04 0.00 0.96
#> TCGA.E9.A2JT.01 2 0.4624 0.526 0 0.66 0.00 0.34
#> TCGA.OL.A5RY.01 2 0.0000 0.851 0 1.00 0.00 0.00
#> TCGA.BH.A209.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.AR.A1AW.01 3 0.1211 0.882 0 0.00 0.96 0.04
#> TCGA.AR.A252.01 3 0.0707 0.931 0 0.02 0.98 0.00
#> TCGA.A2.A25F.01 4 0.1211 0.991 0 0.04 0.00 0.96
#> TCGA.GM.A2DO.01 2 0.3400 0.749 0 0.82 0.00 0.18
#> TCGA.AR.A2LH.01 3 0.3400 0.809 0 0.18 0.82 0.00
#> TCGA.LL.A5YO.01 2 0.4406 0.599 0 0.70 0.00 0.30
#> TCGA.A2.A3XZ.01 3 0.0707 0.931 0 0.02 0.98 0.00
#> TCGA.AR.A5QQ.01 2 0.0000 0.851 0 1.00 0.00 0.00
#> TCGA.A2.A0CR.01 3 0.0707 0.931 0 0.02 0.98 0.00
#> TCGA.AR.A1AO.01 4 0.1211 0.991 0 0.04 0.00 0.96
#> TCGA.AO.A0JC.01 4 0.1211 0.991 0 0.04 0.00 0.96
#> TCGA.A2.A0EP.01 4 0.2011 0.943 0 0.08 0.00 0.92
#> TCGA.E9.A1NE.01 2 0.4277 0.512 0 0.72 0.28 0.00
#> TCGA.C8.A8HP.01 2 0.2647 0.795 0 0.88 0.00 0.12
#> TCGA.E9.A248.01 4 0.1211 0.991 0 0.04 0.00 0.96
#> TCGA.LD.A9QF.01 2 0.0000 0.851 0 1.00 0.00 0.00
#> TCGA.GM.A2DI.01 2 0.0000 0.851 0 1.00 0.00 0.00
#> TCGA.E9.A22A.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.E2.A1B5.01 3 0.0707 0.931 0 0.02 0.98 0.00
#> TCGA.AR.A24U.01 2 0.0000 0.851 0 1.00 0.00 0.00
#> TCGA.AR.A1AX.01 2 0.1211 0.824 0 0.96 0.04 0.00
#> TCGA.E2.A108.01 3 0.3400 0.809 0 0.18 0.82 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.E9.A1QZ.01 5 0.2516 0.6410 0.00 0.14 0.00 0.00 0.86
#> TCGA.AC.A2FB.01 3 0.2516 0.9122 0.00 0.00 0.86 0.00 0.14
#> TCGA.E2.A1B6.01 4 0.0000 0.8924 0.00 0.00 0.00 1.00 0.00
#> TCGA.B6.A0RT.01 4 0.3424 0.7876 0.00 0.24 0.00 0.76 0.00
#> TCGA.E9.A2JT.01 2 0.3421 0.7375 0.00 0.84 0.00 0.08 0.08
#> TCGA.OL.A5RY.01 2 0.3895 0.6163 0.00 0.68 0.00 0.00 0.32
#> TCGA.BH.A209.01 1 0.1043 0.9788 0.96 0.04 0.00 0.00 0.00
#> TCGA.AR.A1AW.01 3 0.0000 0.7866 0.00 0.00 1.00 0.00 0.00
#> TCGA.AR.A252.01 3 0.3684 0.8092 0.00 0.00 0.72 0.00 0.28
#> TCGA.A2.A25F.01 4 0.2732 0.8251 0.00 0.16 0.00 0.84 0.00
#> TCGA.GM.A2DO.01 2 0.3697 0.7354 0.00 0.82 0.00 0.08 0.10
#> TCGA.AR.A2LH.01 5 0.2280 0.7351 0.00 0.00 0.12 0.00 0.88
#> TCGA.LL.A5YO.01 2 0.2516 0.6412 0.00 0.86 0.00 0.14 0.00
#> TCGA.A2.A3XZ.01 3 0.3106 0.9108 0.00 0.02 0.84 0.00 0.14
#> TCGA.AR.A5QQ.01 2 0.3690 0.7108 0.00 0.78 0.00 0.02 0.20
#> TCGA.A2.A0CR.01 3 0.2929 0.9131 0.00 0.00 0.82 0.00 0.18
#> TCGA.AR.A1AO.01 4 0.1732 0.8692 0.00 0.08 0.00 0.92 0.00
#> TCGA.AO.A0JC.01 4 0.0000 0.8924 0.00 0.00 0.00 1.00 0.00
#> TCGA.A2.A0EP.01 2 0.4262 -0.0892 0.00 0.56 0.00 0.44 0.00
#> TCGA.E9.A1NE.01 5 0.1732 0.7650 0.00 0.00 0.08 0.00 0.92
#> TCGA.C8.A8HP.01 2 0.2012 0.7177 0.00 0.92 0.00 0.06 0.02
#> TCGA.E9.A248.01 4 0.0000 0.8924 0.00 0.00 0.00 1.00 0.00
#> TCGA.LD.A9QF.01 2 0.3895 0.6163 0.00 0.68 0.00 0.00 0.32
#> TCGA.GM.A2DI.01 5 0.3796 0.3481 0.00 0.30 0.00 0.00 0.70
#> TCGA.E9.A22A.01 1 0.0000 0.9788 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1B5.01 3 0.2929 0.9131 0.00 0.00 0.82 0.00 0.18
#> TCGA.AR.A24U.01 2 0.3983 0.6075 0.00 0.66 0.00 0.00 0.34
#> TCGA.AR.A1AX.01 5 0.0609 0.7741 0.00 0.02 0.00 0.00 0.98
#> TCGA.E2.A108.01 5 0.2280 0.7351 0.00 0.00 0.12 0.00 0.88
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.E9.A1QZ.01 5 0.3821 0.3056 0.00 0.04 0.00 0.00 0.74 0.22
#> TCGA.AC.A2FB.01 3 0.0547 0.7992 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.E2.A1B6.01 4 0.3578 0.7387 0.00 0.34 0.00 0.66 0.00 0.00
#> TCGA.B6.A0RT.01 4 0.0547 0.6449 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.E9.A2JT.01 6 0.5227 0.5792 0.00 0.10 0.00 0.24 0.02 0.64
#> TCGA.OL.A5RY.01 6 0.0547 0.7064 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.BH.A209.01 1 0.0000 0.9776 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AW.01 3 0.5095 0.3092 0.00 0.42 0.50 0.00 0.08 0.00
#> TCGA.AR.A252.01 3 0.2048 0.6534 0.00 0.00 0.88 0.00 0.12 0.00
#> TCGA.A2.A25F.01 4 0.2790 0.6908 0.00 0.14 0.00 0.84 0.00 0.02
#> TCGA.GM.A2DO.01 6 0.7278 0.4775 0.00 0.14 0.00 0.20 0.24 0.42
#> TCGA.AR.A2LH.01 5 0.4246 0.6242 0.00 0.00 0.40 0.00 0.58 0.02
#> TCGA.LL.A5YO.01 6 0.5754 0.3557 0.00 0.10 0.00 0.44 0.02 0.44
#> TCGA.A2.A3XZ.01 3 0.2512 0.7571 0.00 0.06 0.88 0.00 0.06 0.00
#> TCGA.AR.A5QQ.01 6 0.0547 0.7034 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.A2.A0CR.01 3 0.0000 0.7997 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A1AO.01 4 0.2793 0.7120 0.00 0.20 0.00 0.80 0.00 0.00
#> TCGA.AO.A0JC.01 4 0.3578 0.7387 0.00 0.34 0.00 0.66 0.00 0.00
#> TCGA.A2.A0EP.01 4 0.5291 -0.1425 0.00 0.08 0.00 0.60 0.02 0.30
#> TCGA.E9.A1NE.01 5 0.4246 0.6242 0.00 0.00 0.40 0.00 0.58 0.02
#> TCGA.C8.A8HP.01 6 0.3688 0.6604 0.00 0.04 0.00 0.14 0.02 0.80
#> TCGA.E9.A248.01 4 0.3578 0.7387 0.00 0.34 0.00 0.66 0.00 0.00
#> TCGA.LD.A9QF.01 6 0.0547 0.7064 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.GM.A2DI.01 5 0.5544 -0.0834 0.00 0.08 0.00 0.02 0.50 0.40
#> TCGA.E9.A22A.01 1 0.0937 0.9776 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.E2.A1B5.01 3 0.0000 0.7997 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A24U.01 6 0.3829 0.5563 0.00 0.06 0.00 0.00 0.18 0.76
#> TCGA.AR.A1AX.01 5 0.5346 0.6236 0.00 0.04 0.38 0.00 0.54 0.04
#> TCGA.E2.A108.01 5 0.5058 0.6138 0.00 0.04 0.40 0.00 0.54 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.E9.A1QZ.01 5 0.2509 0.27845 0.0 0.02 0.00 0.00 0.88 0.04 0.06
#> TCGA.AC.A2FB.01 3 0.0504 0.80196 0.0 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.E2.A1B6.01 2 0.3525 1.00000 0.0 0.56 0.00 0.44 0.00 0.00 0.00
#> TCGA.B6.A0RT.01 4 0.0000 0.24301 0.0 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E9.A2JT.01 6 0.5157 0.29434 0.0 0.04 0.00 0.30 0.02 0.60 0.04
#> TCGA.OL.A5RY.01 6 0.0000 0.72894 0.0 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BH.A209.01 1 0.0000 0.93795 1.0 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AW.01 3 0.5612 0.12733 0.0 0.36 0.36 0.00 0.00 0.00 0.28
#> TCGA.AR.A252.01 3 0.0504 0.78757 0.0 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.A2.A25F.01 4 0.2945 -0.30790 0.0 0.26 0.00 0.74 0.00 0.00 0.00
#> TCGA.GM.A2DO.01 5 0.7046 -0.26024 0.0 0.06 0.00 0.10 0.44 0.28 0.12
#> TCGA.AR.A2LH.01 5 0.5016 0.42545 0.0 0.00 0.42 0.00 0.46 0.00 0.12
#> TCGA.LL.A5YO.01 4 0.5748 0.12564 0.0 0.04 0.00 0.52 0.00 0.28 0.16
#> TCGA.A2.A3XZ.01 3 0.2376 0.73471 0.0 0.02 0.86 0.00 0.00 0.00 0.12
#> TCGA.AR.A5QQ.01 6 0.1671 0.70943 0.0 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.A2.A0CR.01 3 0.0000 0.80391 0.0 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AO.01 4 0.3139 -0.44671 0.0 0.30 0.00 0.70 0.00 0.00 0.00
#> TCGA.AO.A0JC.01 2 0.3525 1.00000 0.0 0.56 0.00 0.44 0.00 0.00 0.00
#> TCGA.A2.A0EP.01 4 0.4841 0.29187 0.0 0.02 0.00 0.66 0.02 0.24 0.06
#> TCGA.E9.A1NE.01 5 0.4978 0.47032 0.0 0.00 0.38 0.00 0.50 0.00 0.12
#> TCGA.C8.A8HP.01 6 0.5398 0.36880 0.0 0.04 0.00 0.16 0.00 0.60 0.20
#> TCGA.E9.A248.01 2 0.3525 1.00000 0.0 0.56 0.00 0.44 0.00 0.00 0.00
#> TCGA.LD.A9QF.01 6 0.0000 0.72894 0.0 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.GM.A2DI.01 5 0.4778 -0.00758 0.0 0.02 0.00 0.00 0.58 0.34 0.06
#> TCGA.E9.A22A.01 1 0.2016 0.93795 0.9 0.00 0.00 0.00 0.04 0.00 0.06
#> TCGA.E2.A1B5.01 3 0.0000 0.80391 0.0 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A24U.01 6 0.3867 0.59001 0.0 0.00 0.00 0.00 0.14 0.74 0.12
#> TCGA.AR.A1AX.01 5 0.5381 0.47696 0.0 0.00 0.36 0.00 0.50 0.02 0.12
#> TCGA.E2.A108.01 5 0.4978 0.47032 0.0 0.00 0.38 0.00 0.50 0.00 0.12
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.E9.A1QZ.01 5 0.3658 -0.360 0.0 0.00 0.00 0.00 0.58 0.02 0.40 0.00
#> TCGA.AC.A2FB.01 3 0.0000 0.913 0.0 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1B6.01 2 0.0000 0.935 0.0 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0RT.01 4 0.3404 0.601 0.0 0.24 0.00 0.72 0.00 0.00 0.04 0.00
#> TCGA.E9.A2JT.01 4 0.3637 0.531 0.0 0.04 0.00 0.80 0.00 0.08 0.06 0.02
#> TCGA.OL.A5RY.01 6 0.1557 0.803 0.0 0.00 0.00 0.06 0.00 0.92 0.02 0.00
#> TCGA.BH.A209.01 1 0.0000 0.917 1.0 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AW.01 8 0.1947 0.000 0.0 0.00 0.14 0.00 0.00 0.00 0.00 0.86
#> TCGA.AR.A252.01 3 0.0808 0.880 0.0 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.A2.A25F.01 4 0.3658 0.486 0.0 0.40 0.00 0.58 0.00 0.00 0.02 0.00
#> TCGA.GM.A2DO.01 7 0.6864 0.000 0.0 0.02 0.00 0.24 0.24 0.04 0.40 0.06
#> TCGA.AR.A2LH.01 5 0.3083 0.581 0.0 0.00 0.34 0.00 0.66 0.00 0.00 0.00
#> TCGA.LL.A5YO.01 4 0.2940 0.568 0.0 0.02 0.00 0.84 0.00 0.02 0.10 0.02
#> TCGA.A2.A3XZ.01 3 0.3303 0.660 0.0 0.00 0.76 0.02 0.00 0.00 0.20 0.02
#> TCGA.AR.A5QQ.01 6 0.0471 0.789 0.0 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.A2.A0CR.01 3 0.0000 0.913 0.0 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AO.01 2 0.2547 0.785 0.0 0.84 0.00 0.12 0.00 0.00 0.04 0.00
#> TCGA.AO.A0JC.01 2 0.0000 0.935 0.0 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0EP.01 4 0.1091 0.648 0.0 0.06 0.00 0.94 0.00 0.00 0.00 0.00
#> TCGA.E9.A1NE.01 5 0.2756 0.655 0.0 0.00 0.26 0.00 0.74 0.00 0.00 0.00
#> TCGA.C8.A8HP.01 6 0.5575 0.377 0.0 0.00 0.00 0.28 0.00 0.48 0.20 0.04
#> TCGA.E9.A248.01 2 0.0000 0.935 0.0 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LD.A9QF.01 6 0.1557 0.803 0.0 0.00 0.00 0.06 0.00 0.92 0.02 0.00
#> TCGA.GM.A2DI.01 5 0.4849 -0.233 0.0 0.00 0.00 0.22 0.54 0.00 0.24 0.00
#> TCGA.E9.A22A.01 1 0.2020 0.917 0.9 0.00 0.00 0.02 0.00 0.00 0.06 0.02
#> TCGA.E2.A1B5.01 3 0.0000 0.913 0.0 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A24U.01 6 0.2624 0.687 0.0 0.00 0.00 0.00 0.06 0.86 0.06 0.02
#> TCGA.AR.A1AX.01 5 0.3198 0.655 0.0 0.00 0.26 0.00 0.72 0.00 0.02 0.00
#> TCGA.E2.A108.01 5 0.3198 0.655 0.0 0.00 0.26 0.00 0.72 0.00 0.02 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node01. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0115-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0151-leaf , Node0152-leaf , Node0153-leaf , Node0154-leaf , Node0211-leaf , Node0212 , Node0213 , Node0221 , Node0222 , Node0231-leaf , Node0232 , Node0233-leaf , Node0241-leaf , Node0242 , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0331-leaf , Node0332-leaf , Node0341-leaf , Node0342-leaf , Node0343-leaf , Node0411 , Node0412-leaf , Node0413 , Node0421-leaf , Node0422 , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["013"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 25 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.3806 0.620 0.620
#> 3 3 1.000 0.990 0.986 0.6763 0.740 0.581
#> 4 4 1.000 0.959 0.984 0.1791 0.880 0.667
#> 5 5 0.953 0.865 0.964 0.0130 0.983 0.931
#> 6 6 0.897 0.789 0.912 0.0460 1.000 1.000
#> 7 7 0.866 0.632 0.884 0.0216 0.930 0.720
#> 8 8 0.841 0.619 0.822 0.0350 0.973 0.871
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.BH.A0H9.11 1 0 1 1 0
#> TCGA.A7.A13G.11 1 0 1 1 0
#> TCGA.A7.A0DB.11 1 0 1 1 0
#> TCGA.E9.A1RC.11 2 0 1 0 1
#> TCGA.E9.A1RF.11 2 0 1 0 1
#> TCGA.E9.A1RI.11 1 0 1 1 0
#> TCGA.E9.A1N8.11 1 0 1 1 0
#> TCGA.E9.A1RD.11 1 0 1 1 0
#> TCGA.E2.A1IO.11 1 0 1 1 0
#> TCGA.E2.A15I.11 1 0 1 1 0
#> TCGA.A7.A13E.11 1 0 1 1 0
#> TCGA.BH.A209.11 2 0 1 0 1
#> TCGA.E9.A1R7.11 1 0 1 1 0
#> TCGA.BH.A1EO.11 1 0 1 1 0
#> TCGA.A7.A0D9.11 1 0 1 1 0
#> TCGA.E2.A1LS.11 2 0 1 0 1
#> TCGA.E2.A1BC.11 1 0 1 1 0
#> TCGA.BH.A204.11 2 0 1 0 1
#> TCGA.E9.A1NF.11 1 0 1 1 0
#> TCGA.BH.A1EN.11 1 0 1 1 0
#> TCGA.BH.A0B8.11 1 0 1 1 0
#> TCGA.BH.A1FE.06 1 0 1 1 0
#> TCGA.E9.A1RH.11 1 0 1 1 0
#> TCGA.E9.A1NG.11 1 0 1 1 0
#> TCGA.E9.A1RB.11 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.BH.A0H9.11 3 0.000 1.000 0.00 0 1.00
#> TCGA.A7.A13G.11 3 0.000 1.000 0.00 0 1.00
#> TCGA.A7.A0DB.11 1 0.000 0.969 1.00 0 0.00
#> TCGA.E9.A1RC.11 2 0.000 1.000 0.00 1 0.00
#> TCGA.E9.A1RF.11 2 0.000 1.000 0.00 1 0.00
#> TCGA.E9.A1RI.11 1 0.153 0.986 0.96 0 0.04
#> TCGA.E9.A1N8.11 1 0.153 0.986 0.96 0 0.04
#> TCGA.E9.A1RD.11 1 0.153 0.986 0.96 0 0.04
#> TCGA.E2.A1IO.11 1 0.153 0.986 0.96 0 0.04
#> TCGA.E2.A15I.11 3 0.000 1.000 0.00 0 1.00
#> TCGA.A7.A13E.11 1 0.000 0.969 1.00 0 0.00
#> TCGA.BH.A209.11 2 0.000 1.000 0.00 1 0.00
#> TCGA.E9.A1R7.11 1 0.153 0.986 0.96 0 0.04
#> TCGA.BH.A1EO.11 1 0.000 0.969 1.00 0 0.00
#> TCGA.A7.A0D9.11 1 0.000 0.969 1.00 0 0.00
#> TCGA.E2.A1LS.11 2 0.000 1.000 0.00 1 0.00
#> TCGA.E2.A1BC.11 3 0.000 1.000 0.00 0 1.00
#> TCGA.BH.A204.11 2 0.000 1.000 0.00 1 0.00
#> TCGA.E9.A1NF.11 1 0.153 0.986 0.96 0 0.04
#> TCGA.BH.A1EN.11 1 0.153 0.986 0.96 0 0.04
#> TCGA.BH.A0B8.11 3 0.000 1.000 0.00 0 1.00
#> TCGA.BH.A1FE.06 3 0.000 1.000 0.00 0 1.00
#> TCGA.E9.A1RH.11 1 0.153 0.986 0.96 0 0.04
#> TCGA.E9.A1NG.11 1 0.153 0.986 0.96 0 0.04
#> TCGA.E9.A1RB.11 2 0.000 1.000 0.00 1 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.BH.A0H9.11 3 0.000 1.000 0.00 0 1 0.00
#> TCGA.A7.A13G.11 3 0.000 1.000 0.00 0 1 0.00
#> TCGA.A7.A0DB.11 4 0.000 0.843 0.00 0 0 1.00
#> TCGA.E9.A1RC.11 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.E9.A1RF.11 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.E9.A1RI.11 1 0.000 1.000 1.00 0 0 0.00
#> TCGA.E9.A1N8.11 1 0.000 1.000 1.00 0 0 0.00
#> TCGA.E9.A1RD.11 1 0.000 1.000 1.00 0 0 0.00
#> TCGA.E2.A1IO.11 1 0.000 1.000 1.00 0 0 0.00
#> TCGA.E2.A15I.11 3 0.000 1.000 0.00 0 1 0.00
#> TCGA.A7.A13E.11 4 0.121 0.836 0.04 0 0 0.96
#> TCGA.BH.A209.11 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.E9.A1R7.11 1 0.000 1.000 1.00 0 0 0.00
#> TCGA.BH.A1EO.11 4 0.471 0.446 0.36 0 0 0.64
#> TCGA.A7.A0D9.11 4 0.000 0.843 0.00 0 0 1.00
#> TCGA.E2.A1LS.11 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.E2.A1BC.11 3 0.000 1.000 0.00 0 1 0.00
#> TCGA.BH.A204.11 2 0.000 1.000 0.00 1 0 0.00
#> TCGA.E9.A1NF.11 1 0.000 1.000 1.00 0 0 0.00
#> TCGA.BH.A1EN.11 1 0.000 1.000 1.00 0 0 0.00
#> TCGA.BH.A0B8.11 3 0.000 1.000 0.00 0 1 0.00
#> TCGA.BH.A1FE.06 3 0.000 1.000 0.00 0 1 0.00
#> TCGA.E9.A1RH.11 1 0.000 1.000 1.00 0 0 0.00
#> TCGA.E9.A1NG.11 1 0.000 1.000 1.00 0 0 0.00
#> TCGA.E9.A1RB.11 2 0.000 1.000 0.00 1 0 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.BH.A0H9.11 3 0.0000 1.000 0.00 0 1.00 0.00 0.00
#> TCGA.A7.A13G.11 3 0.0000 1.000 0.00 0 1.00 0.00 0.00
#> TCGA.A7.A0DB.11 4 0.0000 0.559 0.00 0 0.00 1.00 0.00
#> TCGA.E9.A1RC.11 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.E9.A1RF.11 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.E9.A1RI.11 1 0.0609 0.969 0.98 0 0.00 0.00 0.02
#> TCGA.E9.A1N8.11 1 0.0000 0.984 1.00 0 0.00 0.00 0.00
#> TCGA.E9.A1RD.11 1 0.0000 0.984 1.00 0 0.00 0.00 0.00
#> TCGA.E2.A1IO.11 1 0.0000 0.984 1.00 0 0.00 0.00 0.00
#> TCGA.E2.A15I.11 3 0.0000 1.000 0.00 0 1.00 0.00 0.00
#> TCGA.A7.A13E.11 4 0.4132 0.551 0.26 0 0.00 0.72 0.02
#> TCGA.BH.A209.11 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.E9.A1R7.11 1 0.0000 0.984 1.00 0 0.00 0.00 0.00
#> TCGA.BH.A1EO.11 4 0.4302 0.203 0.48 0 0.00 0.52 0.00
#> TCGA.A7.A0D9.11 4 0.0000 0.559 0.00 0 0.00 1.00 0.00
#> TCGA.E2.A1LS.11 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.E2.A1BC.11 3 0.0000 1.000 0.00 0 1.00 0.00 0.00
#> TCGA.BH.A204.11 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.E9.A1NF.11 1 0.1732 0.889 0.92 0 0.00 0.08 0.00
#> TCGA.BH.A1EN.11 1 0.0000 0.984 1.00 0 0.00 0.00 0.00
#> TCGA.BH.A0B8.11 3 0.0000 1.000 0.00 0 1.00 0.00 0.00
#> TCGA.BH.A1FE.06 5 0.1043 0.000 0.00 0 0.04 0.00 0.96
#> TCGA.E9.A1RH.11 1 0.0000 0.984 1.00 0 0.00 0.00 0.00
#> TCGA.E9.A1NG.11 1 0.0000 0.984 1.00 0 0.00 0.00 0.00
#> TCGA.E9.A1RB.11 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.BH.A0H9.11 6 0.1267 0.940 0.00 0.00 0.06 0.00 0.00 0.94
#> TCGA.A7.A13G.11 6 0.0000 0.986 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.A7.A0DB.11 4 0.0000 0.576 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E9.A1RC.11 2 0.0000 0.982 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RF.11 2 0.0000 0.982 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RI.11 1 0.4576 0.356 0.56 0.00 0.40 0.04 0.00 0.00
#> TCGA.E9.A1N8.11 1 0.0937 0.876 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.E9.A1RD.11 1 0.0547 0.868 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.E2.A1IO.11 1 0.0000 0.876 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A15I.11 6 0.0000 0.986 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.A7.A13E.11 4 0.5071 0.444 0.08 0.00 0.40 0.52 0.00 0.00
#> TCGA.BH.A209.11 2 0.1480 0.954 0.00 0.94 0.04 0.00 0.02 0.00
#> TCGA.E9.A1R7.11 1 0.0937 0.876 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.BH.A1EO.11 4 0.5202 0.385 0.26 0.00 0.14 0.60 0.00 0.00
#> TCGA.A7.A0D9.11 4 0.3156 0.519 0.00 0.00 0.18 0.80 0.02 0.00
#> TCGA.E2.A1LS.11 2 0.0000 0.982 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1BC.11 6 0.0000 0.986 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BH.A204.11 2 0.0000 0.982 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1NF.11 1 0.4536 0.601 0.70 0.00 0.12 0.18 0.00 0.00
#> TCGA.BH.A1EN.11 1 0.0000 0.876 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0B8.11 6 0.0000 0.986 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BH.A1FE.06 5 0.0937 0.000 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.E9.A1RH.11 1 0.0937 0.865 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.E9.A1NG.11 1 0.0937 0.876 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.E9.A1RB.11 2 0.0937 0.966 0.00 0.96 0.04 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.BH.A0H9.11 6 0.3000 0.8423 0.00 0.00 0.04 0.00 0.02 0.84 0.10
#> TCGA.A7.A13G.11 6 0.0504 0.9488 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.A7.A0DB.11 4 0.3370 0.7045 0.00 0.00 0.06 0.78 0.00 0.00 0.16
#> TCGA.E9.A1RC.11 2 0.0000 0.9821 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RF.11 2 0.0000 0.9821 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RI.11 7 0.4283 0.0000 0.48 0.00 0.04 0.00 0.00 0.00 0.48
#> TCGA.E9.A1N8.11 1 0.0504 0.6298 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.E9.A1RD.11 1 0.2016 0.5591 0.90 0.00 0.04 0.00 0.00 0.00 0.06
#> TCGA.E2.A1IO.11 1 0.0504 0.6175 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.E2.A15I.11 6 0.0000 0.9494 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A7.A13E.11 3 0.2912 0.0000 0.04 0.00 0.82 0.14 0.00 0.00 0.00
#> TCGA.BH.A209.11 2 0.1363 0.9536 0.00 0.94 0.02 0.00 0.00 0.00 0.04
#> TCGA.E9.A1R7.11 1 0.0863 0.6275 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.BH.A1EO.11 1 0.7070 -0.2659 0.30 0.00 0.20 0.24 0.00 0.00 0.26
#> TCGA.A7.A0D9.11 4 0.0000 0.7114 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E2.A1LS.11 2 0.0000 0.9821 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1BC.11 6 0.0504 0.9448 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.BH.A204.11 2 0.0000 0.9821 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1NF.11 1 0.4773 0.0711 0.66 0.00 0.12 0.02 0.00 0.00 0.20
#> TCGA.BH.A1EN.11 1 0.2572 0.5048 0.86 0.00 0.06 0.00 0.00 0.00 0.08
#> TCGA.BH.A0B8.11 6 0.0504 0.9488 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.BH.A1FE.06 5 0.0000 0.0000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E9.A1RH.11 1 0.1671 0.5369 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.E9.A1NG.11 1 0.1006 0.6194 0.96 0.00 0.02 0.00 0.00 0.00 0.02
#> TCGA.E9.A1RB.11 2 0.0863 0.9658 0.00 0.96 0.00 0.00 0.00 0.00 0.04
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.BH.A0H9.11 6 0.4367 0.679 0.00 0.00 0.12 0.00 0.04 0.70 0.00 0.14
#> TCGA.A7.A13G.11 6 0.0000 0.900 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A7.A0DB.11 4 0.3178 0.775 0.00 0.00 0.04 0.80 0.00 0.00 0.02 0.14
#> TCGA.E9.A1RC.11 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RF.11 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RI.11 7 0.2406 0.000 0.20 0.00 0.00 0.00 0.00 0.00 0.80 0.00
#> TCGA.E9.A1N8.11 1 0.0471 0.674 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.E9.A1RD.11 1 0.3660 0.578 0.70 0.00 0.00 0.00 0.00 0.00 0.06 0.24
#> TCGA.E2.A1IO.11 1 0.2348 0.658 0.88 0.00 0.02 0.00 0.00 0.00 0.06 0.04
#> TCGA.E2.A15I.11 6 0.0808 0.895 0.00 0.00 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.A7.A13E.11 3 0.3847 0.000 0.04 0.00 0.78 0.10 0.00 0.00 0.06 0.02
#> TCGA.BH.A209.11 2 0.1607 0.935 0.00 0.92 0.00 0.00 0.00 0.00 0.04 0.04
#> TCGA.E9.A1R7.11 1 0.1275 0.659 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.BH.A1EO.11 8 0.6163 0.000 0.28 0.00 0.04 0.14 0.00 0.00 0.06 0.48
#> TCGA.A7.A0D9.11 4 0.0000 0.781 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1LS.11 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1BC.11 6 0.0471 0.900 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.BH.A204.11 2 0.0000 0.979 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1NF.11 1 0.5617 -0.434 0.46 0.00 0.00 0.06 0.00 0.00 0.14 0.34
#> TCGA.BH.A1EN.11 1 0.4650 0.515 0.66 0.00 0.06 0.00 0.00 0.00 0.08 0.20
#> TCGA.BH.A0B8.11 6 0.1275 0.877 0.00 0.00 0.04 0.00 0.00 0.94 0.02 0.00
#> TCGA.BH.A1FE.06 5 0.0471 0.000 0.00 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.E9.A1RH.11 1 0.4512 0.533 0.66 0.00 0.04 0.00 0.00 0.00 0.08 0.22
#> TCGA.E9.A1NG.11 1 0.0808 0.665 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.E9.A1RB.11 2 0.0808 0.962 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node01. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0115-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0151-leaf , Node0152-leaf , Node0153-leaf , Node0154-leaf , Node0211-leaf , Node0212 , Node0213 , Node0221 , Node0222 , Node0231-leaf , Node0232 , Node0233-leaf , Node0241-leaf , Node0242 , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0331-leaf , Node0332-leaf , Node0341-leaf , Node0342-leaf , Node0343-leaf , Node0411 , Node0412-leaf , Node0413 , Node0421-leaf , Node0422 , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["015"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 24 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.1603 0.841 0.841
#> 3 3 1.000 0.972 0.987 1.3881 0.793 0.754
#> 4 4 1.000 0.991 0.995 0.7875 0.681 0.497
#> 5 5 0.913 0.894 0.971 0.0300 0.993 0.977
#> 6 6 0.870 0.831 0.955 0.0492 0.924 0.759
#> 7 7 0.771 0.700 0.902 0.0266 0.993 0.971
#> 8 8 0.739 0.607 0.857 0.0261 0.989 0.955
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.BH.A1FC.11 2 0 1 0 1
#> TCGA.AR.A2LQ.01 2 0 1 0 1
#> TCGA.BH.A1FU.01 2 0 1 0 1
#> TCGA.BH.A1EW.11 2 0 1 0 1
#> TCGA.AC.A5EI.01 1 0 1 1 0
#> TCGA.E2.A1L7.11 2 0 1 0 1
#> TCGA.EW.A1P1.01 2 0 1 0 1
#> TCGA.LL.A73Z.01 2 0 1 0 1
#> TCGA.Z7.A8R5.01 2 0 1 0 1
#> TCGA.AO.A03U.01 2 0 1 0 1
#> TCGA.AC.A3YI.01 2 0 1 0 1
#> TCGA.EW.A1PG.01 2 0 1 0 1
#> TCGA.BH.A1FB.01 2 0 1 0 1
#> TCGA.A2.A3XW.01 2 0 1 0 1
#> TCGA.A7.A0DC.11 2 0 1 0 1
#> TCGA.BH.A42U.01 2 0 1 0 1
#> TCGA.C8.A8HR.01 2 0 1 0 1
#> TCGA.BH.A6R9.01 2 0 1 0 1
#> TCGA.AC.A2FF.01 2 0 1 0 1
#> TCGA.LL.A440.01 2 0 1 0 1
#> TCGA.A7.A0CH.11 2 0 1 0 1
#> TCGA.GM.A4E0.01 2 0 1 0 1
#> TCGA.E2.A1LI.11 2 0 1 0 1
#> TCGA.OL.A97C.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.BH.A1FC.11 2 0.0 0.982 0 1.00 0.00
#> TCGA.AR.A2LQ.01 2 0.0 0.982 0 1.00 0.00
#> TCGA.BH.A1FU.01 2 0.4 0.820 0 0.84 0.16
#> TCGA.BH.A1EW.11 2 0.0 0.982 0 1.00 0.00
#> TCGA.AC.A5EI.01 1 0.0 1.000 1 0.00 0.00
#> TCGA.E2.A1L7.11 2 0.0 0.982 0 1.00 0.00
#> TCGA.EW.A1P1.01 2 0.0 0.982 0 1.00 0.00
#> TCGA.LL.A73Z.01 3 0.0 1.000 0 0.00 1.00
#> TCGA.Z7.A8R5.01 3 0.0 1.000 0 0.00 1.00
#> TCGA.AO.A03U.01 2 0.0 0.982 0 1.00 0.00
#> TCGA.AC.A3YI.01 2 0.0 0.982 0 1.00 0.00
#> TCGA.EW.A1PG.01 2 0.0 0.982 0 1.00 0.00
#> TCGA.BH.A1FB.01 2 0.0 0.982 0 1.00 0.00
#> TCGA.A2.A3XW.01 2 0.0 0.982 0 1.00 0.00
#> TCGA.A7.A0DC.11 2 0.0 0.982 0 1.00 0.00
#> TCGA.BH.A42U.01 2 0.0 0.982 0 1.00 0.00
#> TCGA.C8.A8HR.01 2 0.0 0.982 0 1.00 0.00
#> TCGA.BH.A6R9.01 3 0.0 1.000 0 0.00 1.00
#> TCGA.AC.A2FF.01 2 0.0 0.982 0 1.00 0.00
#> TCGA.LL.A440.01 2 0.0 0.982 0 1.00 0.00
#> TCGA.A7.A0CH.11 2 0.0 0.982 0 1.00 0.00
#> TCGA.GM.A4E0.01 2 0.4 0.820 0 0.84 0.16
#> TCGA.E2.A1LI.11 2 0.0 0.982 0 1.00 0.00
#> TCGA.OL.A97C.01 1 0.0 1.000 1 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.BH.A1FC.11 4 0.0000 1.000 0 0.00 0.00 1.00
#> TCGA.AR.A2LQ.01 2 0.0000 0.988 0 1.00 0.00 0.00
#> TCGA.BH.A1FU.01 2 0.0000 0.988 0 1.00 0.00 0.00
#> TCGA.BH.A1EW.11 2 0.0000 0.988 0 1.00 0.00 0.00
#> TCGA.AC.A5EI.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.E2.A1L7.11 4 0.0000 1.000 0 0.00 0.00 1.00
#> TCGA.EW.A1P1.01 4 0.0000 1.000 0 0.00 0.00 1.00
#> TCGA.LL.A73Z.01 3 0.0000 0.987 0 0.00 1.00 0.00
#> TCGA.Z7.A8R5.01 3 0.0707 0.973 0 0.02 0.98 0.00
#> TCGA.AO.A03U.01 4 0.0000 1.000 0 0.00 0.00 1.00
#> TCGA.AC.A3YI.01 2 0.0707 0.985 0 0.98 0.00 0.02
#> TCGA.EW.A1PG.01 2 0.0000 0.988 0 1.00 0.00 0.00
#> TCGA.BH.A1FB.01 2 0.0707 0.985 0 0.98 0.00 0.02
#> TCGA.A2.A3XW.01 4 0.0000 1.000 0 0.00 0.00 1.00
#> TCGA.A7.A0DC.11 4 0.0000 1.000 0 0.00 0.00 1.00
#> TCGA.BH.A42U.01 2 0.0000 0.988 0 1.00 0.00 0.00
#> TCGA.C8.A8HR.01 2 0.0707 0.985 0 0.98 0.00 0.02
#> TCGA.BH.A6R9.01 3 0.0000 0.987 0 0.00 1.00 0.00
#> TCGA.AC.A2FF.01 2 0.0707 0.985 0 0.98 0.00 0.02
#> TCGA.LL.A440.01 2 0.0707 0.985 0 0.98 0.00 0.02
#> TCGA.A7.A0CH.11 4 0.0000 1.000 0 0.00 0.00 1.00
#> TCGA.GM.A4E0.01 2 0.0000 0.988 0 1.00 0.00 0.00
#> TCGA.E2.A1LI.11 4 0.0000 1.000 0 0.00 0.00 1.00
#> TCGA.OL.A97C.01 1 0.0000 1.000 1 0.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.BH.A1FC.11 4 0.0000 1.000 0 0.00 0.00 1.00 0.00
#> TCGA.AR.A2LQ.01 2 0.0000 0.944 0 1.00 0.00 0.00 0.00
#> TCGA.BH.A1FU.01 2 0.3109 0.779 0 0.80 0.20 0.00 0.00
#> TCGA.BH.A1EW.11 2 0.0000 0.944 0 1.00 0.00 0.00 0.00
#> TCGA.AC.A5EI.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
#> TCGA.E2.A1L7.11 4 0.0000 1.000 0 0.00 0.00 1.00 0.00
#> TCGA.EW.A1P1.01 4 0.0000 1.000 0 0.00 0.00 1.00 0.00
#> TCGA.LL.A73Z.01 3 0.2929 0.717 0 0.00 0.82 0.00 0.18
#> TCGA.Z7.A8R5.01 3 0.0000 0.746 0 0.00 1.00 0.00 0.00
#> TCGA.AO.A03U.01 4 0.0000 1.000 0 0.00 0.00 1.00 0.00
#> TCGA.AC.A3YI.01 2 0.0000 0.944 0 1.00 0.00 0.00 0.00
#> TCGA.EW.A1PG.01 2 0.0000 0.944 0 1.00 0.00 0.00 0.00
#> TCGA.BH.A1FB.01 2 0.0609 0.941 0 0.98 0.00 0.02 0.00
#> TCGA.A2.A3XW.01 4 0.0000 1.000 0 0.00 0.00 1.00 0.00
#> TCGA.A7.A0DC.11 4 0.0000 1.000 0 0.00 0.00 1.00 0.00
#> TCGA.BH.A42U.01 2 0.0000 0.944 0 1.00 0.00 0.00 0.00
#> TCGA.C8.A8HR.01 2 0.0609 0.941 0 0.98 0.00 0.02 0.00
#> TCGA.BH.A6R9.01 5 0.0000 0.000 0 0.00 0.00 0.00 1.00
#> TCGA.AC.A2FF.01 2 0.0609 0.941 0 0.98 0.00 0.02 0.00
#> TCGA.LL.A440.01 2 0.0609 0.941 0 0.98 0.00 0.02 0.00
#> TCGA.A7.A0CH.11 4 0.0000 1.000 0 0.00 0.00 1.00 0.00
#> TCGA.GM.A4E0.01 2 0.3424 0.730 0 0.76 0.24 0.00 0.00
#> TCGA.E2.A1LI.11 4 0.0000 1.000 0 0.00 0.00 1.00 0.00
#> TCGA.OL.A97C.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.BH.A1FC.11 4 0.0937 0.969 0 0.04 0.00 0.96 0.00 0.00
#> TCGA.AR.A2LQ.01 2 0.1814 0.849 0 0.90 0.00 0.00 0.00 0.10
#> TCGA.BH.A1FU.01 6 0.4078 0.524 0 0.34 0.00 0.00 0.02 0.64
#> TCGA.BH.A1EW.11 2 0.0000 0.983 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A5EI.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1L7.11 4 0.0547 0.974 0 0.02 0.00 0.98 0.00 0.00
#> TCGA.EW.A1P1.01 4 0.0937 0.969 0 0.04 0.00 0.96 0.00 0.00
#> TCGA.LL.A73Z.01 3 0.0000 0.000 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.Z7.A8R5.01 6 0.2260 0.370 0 0.00 0.14 0.00 0.00 0.86
#> TCGA.AO.A03U.01 4 0.1092 0.940 0 0.00 0.00 0.96 0.02 0.02
#> TCGA.AC.A3YI.01 2 0.0000 0.983 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1PG.01 2 0.0000 0.983 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FB.01 2 0.0000 0.983 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A3XW.01 4 0.0547 0.952 0 0.00 0.00 0.98 0.00 0.02
#> TCGA.A7.A0DC.11 4 0.0937 0.969 0 0.04 0.00 0.96 0.00 0.00
#> TCGA.BH.A42U.01 2 0.0000 0.983 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A8HR.01 2 0.0000 0.983 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A6R9.01 5 0.0937 0.000 0 0.00 0.04 0.00 0.96 0.00
#> TCGA.AC.A2FF.01 2 0.0000 0.983 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.LL.A440.01 2 0.0000 0.983 0 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A0CH.11 4 0.0547 0.974 0 0.02 0.00 0.98 0.00 0.00
#> TCGA.GM.A4E0.01 6 0.2793 0.619 0 0.20 0.00 0.00 0.00 0.80
#> TCGA.E2.A1LI.11 4 0.0547 0.974 0 0.02 0.00 0.98 0.00 0.00
#> TCGA.OL.A97C.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.BH.A1FC.11 4 0.0863 0.924 0.00 0.04 0.00 0.96 0 0.00 0.00
#> TCGA.AR.A2LQ.01 2 0.1886 0.818 0.00 0.88 0.00 0.00 0 0.00 0.12
#> TCGA.BH.A1FU.01 7 0.4850 0.000 0.00 0.12 0.00 0.00 0 0.32 0.56
#> TCGA.BH.A1EW.11 2 0.1006 0.920 0.00 0.96 0.00 0.02 0 0.00 0.02
#> TCGA.AC.A5EI.01 1 0.2422 0.844 0.82 0.00 0.00 0.00 0 0.00 0.18
#> TCGA.E2.A1L7.11 4 0.0863 0.924 0.00 0.04 0.00 0.96 0 0.00 0.00
#> TCGA.EW.A1P1.01 4 0.0863 0.924 0.00 0.04 0.00 0.96 0 0.00 0.00
#> TCGA.LL.A73Z.01 3 0.0000 0.000 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.Z7.A8R5.01 6 0.0863 0.179 0.00 0.00 0.04 0.00 0 0.96 0.00
#> TCGA.AO.A03U.01 4 0.2708 0.757 0.00 0.00 0.00 0.78 0 0.00 0.22
#> TCGA.AC.A3YI.01 2 0.0863 0.927 0.00 0.96 0.00 0.04 0 0.00 0.00
#> TCGA.EW.A1PG.01 2 0.0863 0.902 0.00 0.96 0.00 0.00 0 0.00 0.04
#> TCGA.BH.A1FB.01 2 0.1166 0.924 0.00 0.94 0.00 0.06 0 0.00 0.00
#> TCGA.A2.A3XW.01 4 0.2422 0.791 0.00 0.00 0.00 0.82 0 0.00 0.18
#> TCGA.A7.A0DC.11 4 0.1363 0.924 0.00 0.04 0.00 0.94 0 0.00 0.02
#> TCGA.BH.A42U.01 2 0.0863 0.902 0.00 0.96 0.00 0.00 0 0.00 0.04
#> TCGA.C8.A8HR.01 2 0.2016 0.906 0.00 0.90 0.00 0.06 0 0.00 0.04
#> TCGA.BH.A6R9.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.AC.A2FF.01 2 0.1664 0.915 0.00 0.92 0.00 0.06 0 0.00 0.02
#> TCGA.LL.A440.01 2 0.1166 0.924 0.00 0.94 0.00 0.06 0 0.00 0.00
#> TCGA.A7.A0CH.11 4 0.1363 0.924 0.00 0.04 0.00 0.94 0 0.00 0.02
#> TCGA.GM.A4E0.01 6 0.5007 -0.287 0.00 0.16 0.00 0.00 0 0.56 0.28
#> TCGA.E2.A1LI.11 4 0.1363 0.921 0.00 0.04 0.00 0.94 0 0.00 0.02
#> TCGA.OL.A97C.01 1 0.0000 0.844 1.00 0.00 0.00 0.00 0 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.BH.A1FC.11 4 0.0000 0.888 0.00 0.00 0 1.00 0 0.00 0.00 0.00
#> TCGA.AR.A2LQ.01 2 0.2719 0.630 0.02 0.80 0 0.00 0 0.00 0.18 0.00
#> TCGA.BH.A1FU.01 7 0.2818 0.505 0.00 0.12 0 0.00 0 0.06 0.82 0.00
#> TCGA.BH.A1EW.11 2 0.0941 0.852 0.00 0.96 0 0.02 0 0.00 0.02 0.00
#> TCGA.AC.A5EI.01 1 0.3318 0.000 0.54 0.00 0 0.00 0 0.00 0.00 0.46
#> TCGA.E2.A1L7.11 4 0.0000 0.888 0.00 0.00 0 1.00 0 0.00 0.00 0.00
#> TCGA.EW.A1P1.01 4 0.0471 0.871 0.00 0.02 0 0.98 0 0.00 0.00 0.00
#> TCGA.LL.A73Z.01 3 0.0000 0.000 0.00 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.Z7.A8R5.01 6 0.0000 0.000 0.00 0.00 0 0.00 0 1.00 0.00 0.00
#> TCGA.AO.A03U.01 4 0.4873 0.329 0.36 0.00 0 0.48 0 0.00 0.16 0.00
#> TCGA.AC.A3YI.01 2 0.0808 0.859 0.00 0.96 0 0.04 0 0.00 0.00 0.00
#> TCGA.EW.A1PG.01 2 0.0471 0.834 0.00 0.98 0 0.00 0 0.00 0.02 0.00
#> TCGA.BH.A1FB.01 2 0.2267 0.817 0.00 0.82 0 0.18 0 0.00 0.00 0.00
#> TCGA.A2.A3XW.01 4 0.3385 0.704 0.16 0.00 0 0.76 0 0.00 0.08 0.00
#> TCGA.A7.A0DC.11 4 0.0000 0.888 0.00 0.00 0 1.00 0 0.00 0.00 0.00
#> TCGA.BH.A42U.01 2 0.0808 0.822 0.00 0.96 0 0.00 0 0.00 0.04 0.00
#> TCGA.C8.A8HR.01 2 0.2224 0.852 0.00 0.86 0 0.12 0 0.00 0.02 0.00
#> TCGA.BH.A6R9.01 5 0.0000 0.000 0.00 0.00 0 0.00 1 0.00 0.00 0.00
#> TCGA.AC.A2FF.01 2 0.2404 0.844 0.00 0.84 0 0.14 0 0.00 0.02 0.00
#> TCGA.LL.A440.01 2 0.2114 0.834 0.00 0.84 0 0.16 0 0.00 0.00 0.00
#> TCGA.A7.A0CH.11 4 0.0000 0.888 0.00 0.00 0 1.00 0 0.00 0.00 0.00
#> TCGA.GM.A4E0.01 7 0.5852 0.375 0.10 0.12 0 0.00 0 0.36 0.42 0.00
#> TCGA.E2.A1LI.11 4 0.0000 0.888 0.00 0.00 0 1.00 0 0.00 0.00 0.00
#> TCGA.OL.A97C.01 8 0.0000 0.000 0.00 0.00 0 0.00 0 0.00 0.00 1.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node014-leaf , Node015 , Node021 , Node022 , Node023 , Node024 , Node031 , Node032 , Node033 , Node034 , Node041 , Node042 , Node043 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["02"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 311 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.993 0.997 0.4980 0.502 0.502
#> 3 3 0.882 0.887 0.951 0.3278 0.703 0.476
#> 4 4 1.000 0.973 0.985 0.1249 0.764 0.429
#> 5 5 0.835 0.761 0.876 0.0647 0.914 0.688
#> 6 6 0.801 0.693 0.827 0.0420 0.915 0.628
#> 7 7 0.821 0.630 0.782 0.0279 0.929 0.631
#> 8 8 0.832 0.763 0.838 0.0204 0.942 0.653
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.EW.A2FW.01 1 0.000 0.999 1.00 0.00
#> TCGA.D8.A1JD.01 1 0.000 0.999 1.00 0.00
#> TCGA.D8.A1XA.01 1 0.000 0.999 1.00 0.00
#> TCGA.AO.A1KQ.01 1 0.000 0.999 1.00 0.00
#> TCGA.A7.A3RF.01 1 0.000 0.999 1.00 0.00
#> TCGA.A2.A0SW.01 1 0.000 0.999 1.00 0.00
#> TCGA.GM.A2D9.01 2 0.000 0.995 0.00 1.00
#> TCGA.EW.A1P5.01 1 0.000 0.999 1.00 0.00
#> TCGA.BH.A1EN.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A1FN.01 1 0.000 0.999 1.00 0.00
#> TCGA.EW.A1PD.01 2 0.000 0.995 0.00 1.00
#> TCGA.E9.A1N5.01 1 0.000 0.999 1.00 0.00
#> TCGA.D8.A1J8.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A0H0.01 1 0.000 0.999 1.00 0.00
#> TCGA.A2.A0YC.01 1 0.000 0.999 1.00 0.00
#> TCGA.GM.A2DC.01 2 0.000 0.995 0.00 1.00
#> TCGA.AR.A24N.01 2 0.000 0.995 0.00 1.00
#> TCGA.EW.A6S9.01 1 0.000 0.999 1.00 0.00
#> TCGA.A1.A0SJ.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A1FG.01 1 0.000 0.999 1.00 0.00
#> TCGA.E2.A1IL.01 1 0.000 0.999 1.00 0.00
#> TCGA.A7.A3IZ.01 2 0.000 0.995 0.00 1.00
#> TCGA.E2.A570.01 1 0.000 0.999 1.00 0.00
#> TCGA.LL.A5YM.01 2 0.000 0.995 0.00 1.00
#> TCGA.AC.A4ZE.01 2 0.000 0.995 0.00 1.00
#> TCGA.EW.A1P0.01 1 0.000 0.999 1.00 0.00
#> TCGA.AR.A24H.01 2 0.000 0.995 0.00 1.00
#> TCGA.D8.A1XV.01 2 0.000 0.995 0.00 1.00
#> TCGA.AN.A0XV.01 2 0.000 0.995 0.00 1.00
#> TCGA.A2.A0YT.01 1 0.000 0.999 1.00 0.00
#> TCGA.BH.A0B5.01 1 0.000 0.999 1.00 0.00
#> TCGA.D8.A1JI.01 1 0.000 0.999 1.00 0.00
#> TCGA.E9.A1R6.01 2 0.000 0.995 0.00 1.00
#> TCGA.D8.A1XZ.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A0B8.01 1 0.000 0.999 1.00 0.00
#> TCGA.LL.A6FQ.01 1 0.000 0.999 1.00 0.00
#> TCGA.EW.A1OY.01 1 0.000 0.999 1.00 0.00
#> TCGA.B6.A0RP.01 1 0.000 0.999 1.00 0.00
#> TCGA.LL.A9Q3.01 2 0.000 0.995 0.00 1.00
#> TCGA.A1.A0SQ.01 1 0.000 0.999 1.00 0.00
#> TCGA.E9.A1RB.01 1 0.000 0.999 1.00 0.00
#> TCGA.B6.A0RO.01 1 0.000 0.999 1.00 0.00
#> TCGA.AC.A2BM.01 1 0.000 0.999 1.00 0.00
#> TCGA.EW.A1J6.01 1 0.000 0.999 1.00 0.00
#> TCGA.B6.A40C.01 2 0.000 0.995 0.00 1.00
#> TCGA.A7.A26H.01 2 0.000 0.995 0.00 1.00
#> TCGA.E2.A2P6.01 2 0.000 0.995 0.00 1.00
#> TCGA.A2.A25C.01 1 0.000 0.999 1.00 0.00
#> TCGA.OL.A5DA.01 2 0.000 0.995 0.00 1.00
#> TCGA.LL.A50Y.01 2 0.000 0.995 0.00 1.00
#> TCGA.LL.A442.01 1 0.000 0.999 1.00 0.00
#> TCGA.C8.A26Z.01 1 0.000 0.999 1.00 0.00
#> TCGA.BH.A1FJ.01 2 0.141 0.976 0.02 0.98
#> TCGA.E9.A3HO.01 2 0.000 0.995 0.00 1.00
#> TCGA.E9.A1NA.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A0BS.01 1 0.000 0.999 1.00 0.00
#> TCGA.B6.A0WT.01 1 0.000 0.999 1.00 0.00
#> TCGA.B6.A0RN.01 2 0.000 0.995 0.00 1.00
#> TCGA.D8.A1XJ.01 2 0.000 0.995 0.00 1.00
#> TCGA.E2.A109.01 2 0.000 0.995 0.00 1.00
#> TCGA.3C.AALI.01 1 0.000 0.999 1.00 0.00
#> TCGA.BH.A1FL.01 2 0.000 0.995 0.00 1.00
#> TCGA.E2.A15K.01 1 0.000 0.999 1.00 0.00
#> TCGA.E2.A15K.06 1 0.000 0.999 1.00 0.00
#> TCGA.E9.A1NI.01 1 0.000 0.999 1.00 0.00
#> TCGA.AO.A12G.01 2 0.000 0.995 0.00 1.00
#> TCGA.C8.A1HO.01 2 0.000 0.995 0.00 1.00
#> TCGA.AN.A0XR.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A0HA.01 1 0.000 0.999 1.00 0.00
#> TCGA.D8.A1XS.01 1 0.000 0.999 1.00 0.00
#> TCGA.OL.A6VR.01 1 0.000 0.999 1.00 0.00
#> TCGA.AR.A1AS.01 1 0.000 0.999 1.00 0.00
#> TCGA.S3.A6ZG.01 2 0.000 0.995 0.00 1.00
#> TCGA.AN.A0XP.01 1 0.000 0.999 1.00 0.00
#> TCGA.D8.A1XD.01 1 0.680 0.779 0.82 0.18
#> TCGA.AR.A24M.01 1 0.000 0.999 1.00 0.00
#> TCGA.AC.A6NO.01 1 0.000 0.999 1.00 0.00
#> TCGA.E2.A572.01 1 0.000 0.999 1.00 0.00
#> TCGA.BH.A1ES.01 2 0.990 0.217 0.44 0.56
#> TCGA.EW.A1PE.01 1 0.000 0.999 1.00 0.00
#> TCGA.BH.A0H6.01 1 0.000 0.999 1.00 0.00
#> TCGA.A7.A2KD.01 1 0.000 0.999 1.00 0.00
#> TCGA.S3.A6ZH.01 1 0.000 0.999 1.00 0.00
#> TCGA.BH.A1EX.01 1 0.000 0.999 1.00 0.00
#> TCGA.AO.A125.01 2 0.000 0.995 0.00 1.00
#> TCGA.UL.AAZ6.01 2 0.000 0.995 0.00 1.00
#> TCGA.A2.A0CK.01 1 0.000 0.999 1.00 0.00
#> TCGA.PE.A5DC.01 2 0.000 0.995 0.00 1.00
#> TCGA.EW.A6SC.01 1 0.000 0.999 1.00 0.00
#> TCGA.C8.A273.01 1 0.000 0.999 1.00 0.00
#> TCGA.AR.A0U2.01 1 0.000 0.999 1.00 0.00
#> TCGA.C8.A1HL.01 1 0.000 0.999 1.00 0.00
#> TCGA.E2.A9RU.01 2 0.000 0.995 0.00 1.00
#> TCGA.D8.A1JJ.01 2 0.000 0.995 0.00 1.00
#> TCGA.E2.A1B4.01 1 0.000 0.999 1.00 0.00
#> TCGA.B6.A1KC.01 2 0.000 0.995 0.00 1.00
#> TCGA.E9.A5UP.01 2 0.000 0.995 0.00 1.00
#> TCGA.A2.A1G4.01 2 0.000 0.995 0.00 1.00
#> TCGA.A2.A1FV.01 1 0.000 0.999 1.00 0.00
#> TCGA.D8.A1XC.01 1 0.000 0.999 1.00 0.00
#> TCGA.E2.A15J.01 2 0.000 0.995 0.00 1.00
#> TCGA.S3.AA11.01 1 0.000 0.999 1.00 0.00
#> TCGA.AC.A3QQ.01 1 0.000 0.999 1.00 0.00
#> TCGA.AQ.A54O.01 1 0.000 0.999 1.00 0.00
#> TCGA.D8.A1JT.01 1 0.000 0.999 1.00 0.00
#> TCGA.AR.A2LL.01 2 0.000 0.995 0.00 1.00
#> TCGA.D8.A1X7.01 1 0.000 0.999 1.00 0.00
#> TCGA.E9.A247.01 2 0.000 0.995 0.00 1.00
#> TCGA.D8.A1X5.01 1 0.000 0.999 1.00 0.00
#> TCGA.A8.A075.01 1 0.000 0.999 1.00 0.00
#> TCGA.D8.A73X.01 2 0.000 0.995 0.00 1.00
#> TCGA.E9.A3Q9.01 1 0.000 0.999 1.00 0.00
#> TCGA.BH.A0E1.01 1 0.000 0.999 1.00 0.00
#> TCGA.EW.A423.01 2 0.000 0.995 0.00 1.00
#> TCGA.E2.A106.01 1 0.000 0.999 1.00 0.00
#> TCGA.AR.A0TV.01 2 0.000 0.995 0.00 1.00
#> TCGA.E2.A56Z.01 1 0.000 0.999 1.00 0.00
#> TCGA.AC.A2FM.01 2 0.000 0.995 0.00 1.00
#> TCGA.A7.A0D9.01 1 0.000 0.999 1.00 0.00
#> TCGA.AC.A5XU.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A204.01 1 0.000 0.999 1.00 0.00
#> TCGA.B6.A0WW.01 2 0.000 0.995 0.00 1.00
#> TCGA.D8.A1XL.01 1 0.000 0.999 1.00 0.00
#> TCGA.E9.A5UO.01 2 0.000 0.995 0.00 1.00
#> TCGA.A2.A0SV.01 2 0.000 0.995 0.00 1.00
#> TCGA.OL.A5RZ.01 1 0.000 0.999 1.00 0.00
#> TCGA.AR.A24R.01 2 0.000 0.995 0.00 1.00
#> TCGA.AO.A1KP.01 2 0.000 0.995 0.00 1.00
#> TCGA.E9.A1RE.01 2 0.000 0.995 0.00 1.00
#> TCGA.GM.A2DM.01 1 0.000 0.999 1.00 0.00
#> TCGA.A2.A0YF.01 1 0.000 0.999 1.00 0.00
#> TCGA.C8.A274.01 2 0.000 0.995 0.00 1.00
#> TCGA.C8.A1HM.01 1 0.000 0.999 1.00 0.00
#> TCGA.E9.A1RC.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A6R8.01 1 0.000 0.999 1.00 0.00
#> TCGA.BH.A1FM.01 1 0.000 0.999 1.00 0.00
#> TCGA.D8.A1JP.01 2 0.000 0.995 0.00 1.00
#> TCGA.AO.A0JM.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A0DS.01 2 0.000 0.995 0.00 1.00
#> TCGA.V7.A7HQ.01 1 0.000 0.999 1.00 0.00
#> TCGA.EW.A1PA.01 2 0.000 0.995 0.00 1.00
#> TCGA.AC.A3TM.01 2 0.000 0.995 0.00 1.00
#> TCGA.AR.A2LE.01 1 0.000 0.999 1.00 0.00
#> TCGA.GM.A3NY.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A5J0.01 1 0.000 0.999 1.00 0.00
#> TCGA.BH.A0HK.01 2 0.000 0.995 0.00 1.00
#> TCGA.AR.A24Z.01 1 0.000 0.999 1.00 0.00
#> TCGA.S3.A6ZF.01 2 0.000 0.995 0.00 1.00
#> TCGA.Z7.A8R6.01 1 0.000 0.999 1.00 0.00
#> TCGA.OL.A66K.01 2 0.000 0.995 0.00 1.00
#> TCGA.D8.A1JC.01 1 0.000 0.999 1.00 0.00
#> TCGA.JL.A3YX.01 1 0.000 0.999 1.00 0.00
#> TCGA.AN.A0XO.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A0DQ.01 1 0.000 0.999 1.00 0.00
#> TCGA.B6.A2IU.01 1 0.000 0.999 1.00 0.00
#> TCGA.AR.A250.01 2 0.000 0.995 0.00 1.00
#> TCGA.OL.A5D8.01 2 0.000 0.995 0.00 1.00
#> TCGA.AQ.A04H.01 2 0.000 0.995 0.00 1.00
#> TCGA.D8.A1XG.01 1 0.000 0.999 1.00 0.00
#> TCGA.AR.A0TZ.01 2 0.000 0.995 0.00 1.00
#> TCGA.AR.A0U3.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A0HN.01 1 0.000 0.999 1.00 0.00
#> TCGA.EW.A1OX.01 2 0.000 0.995 0.00 1.00
#> TCGA.AR.A24V.01 1 0.000 0.999 1.00 0.00
#> TCGA.AN.A0XS.01 1 0.000 0.999 1.00 0.00
#> TCGA.LL.A6FP.01 1 0.000 0.999 1.00 0.00
#> TCGA.E2.A1L8.01 1 0.000 0.999 1.00 0.00
#> TCGA.A2.A1FW.01 2 0.000 0.995 0.00 1.00
#> TCGA.AC.A62V.01 1 0.000 0.999 1.00 0.00
#> TCGA.E2.A576.01 2 0.000 0.995 0.00 1.00
#> TCGA.GM.A3NW.01 2 0.000 0.995 0.00 1.00
#> TCGA.A7.A4SB.01 1 0.000 0.999 1.00 0.00
#> TCGA.E9.A245.01 1 0.000 0.999 1.00 0.00
#> TCGA.AO.A126.01 2 0.584 0.837 0.14 0.86
#> TCGA.AC.A8OR.01 1 0.000 0.999 1.00 0.00
#> TCGA.A7.A4SF.01 1 0.000 0.999 1.00 0.00
#> TCGA.A7.A26J.01 1 0.000 0.999 1.00 0.00
#> TCGA.A2.A25B.01 1 0.000 0.999 1.00 0.00
#> TCGA.D8.A27W.01 2 0.000 0.995 0.00 1.00
#> TCGA.E9.A2JS.01 2 0.000 0.995 0.00 1.00
#> TCGA.C8.A3M8.01 2 0.000 0.995 0.00 1.00
#> TCGA.D8.A1XU.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A1ES.06 2 0.000 0.995 0.00 1.00
#> TCGA.D8.A1X6.01 1 0.000 0.999 1.00 0.00
#> TCGA.PL.A8LX.01 1 0.000 0.999 1.00 0.00
#> TCGA.EW.A6SA.01 2 0.000 0.995 0.00 1.00
#> TCGA.E9.A1R5.01 2 0.000 0.995 0.00 1.00
#> TCGA.E9.A54Y.01 2 0.402 0.911 0.08 0.92
#> TCGA.AC.A3TN.01 2 0.000 0.995 0.00 1.00
#> TCGA.EW.A1J3.01 1 0.000 0.999 1.00 0.00
#> TCGA.BH.A1F8.01 2 0.000 0.995 0.00 1.00
#> TCGA.B6.A0X5.01 1 0.000 0.999 1.00 0.00
#> TCGA.AQ.A04L.01 2 0.000 0.995 0.00 1.00
#> TCGA.B6.A0WV.01 1 0.000 0.999 1.00 0.00
#> TCGA.BH.A1FD.01 2 0.000 0.995 0.00 1.00
#> TCGA.A7.A13F.01 2 0.000 0.995 0.00 1.00
#> TCGA.E2.A2P5.01 2 0.000 0.995 0.00 1.00
#> TCGA.AO.A1KS.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A0DD.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A0HX.01 1 0.000 0.999 1.00 0.00
#> TCGA.D8.A1X9.01 2 0.000 0.995 0.00 1.00
#> TCGA.AR.A0TR.01 1 0.000 0.999 1.00 0.00
#> TCGA.A7.A0DC.01 1 0.000 0.999 1.00 0.00
#> TCGA.C8.A9FZ.01 2 0.000 0.995 0.00 1.00
#> TCGA.AR.A24X.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A0GZ.01 2 0.000 0.995 0.00 1.00
#> TCGA.B6.A0RM.01 1 0.000 0.999 1.00 0.00
#> TCGA.AO.A12B.01 1 0.000 0.999 1.00 0.00
#> TCGA.BH.A0DH.01 2 0.000 0.995 0.00 1.00
#> TCGA.D8.A1JN.01 2 0.000 0.995 0.00 1.00
#> TCGA.E2.A1IE.01 1 0.000 0.999 1.00 0.00
#> TCGA.EW.A1P3.01 1 0.000 0.999 1.00 0.00
#> TCGA.BH.A8FY.01 2 0.000 0.995 0.00 1.00
#> TCGA.AO.A1KT.01 2 0.141 0.976 0.02 0.98
#> TCGA.E2.A1IU.01 1 0.000 0.999 1.00 0.00
#> TCGA.E9.A22H.01 1 0.000 0.999 1.00 0.00
#> TCGA.D8.A3Z6.01 1 0.000 0.999 1.00 0.00
#> TCGA.AR.A2LK.01 2 0.000 0.995 0.00 1.00
#> TCGA.B6.A0RI.01 1 0.000 0.999 1.00 0.00
#> TCGA.A8.A08O.01 1 0.000 0.999 1.00 0.00
#> TCGA.EW.A1P6.01 1 0.000 0.999 1.00 0.00
#> TCGA.D8.A1XF.01 2 0.000 0.995 0.00 1.00
#> TCGA.A2.A0CT.01 2 0.000 0.995 0.00 1.00
#> TCGA.E9.A1RG.01 1 0.000 0.999 1.00 0.00
#> TCGA.BH.A1F2.01 1 0.000 0.999 1.00 0.00
#> TCGA.AN.A0XT.01 1 0.000 0.999 1.00 0.00
#> TCGA.BH.A0HI.01 1 0.000 0.999 1.00 0.00
#> TCGA.B6.A0RL.01 2 0.000 0.995 0.00 1.00
#> TCGA.E2.A1L9.01 1 0.000 0.999 1.00 0.00
#> TCGA.A7.A26E.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A0W3.01 1 0.000 0.999 1.00 0.00
#> TCGA.D8.A1J9.01 2 0.000 0.995 0.00 1.00
#> TCGA.LL.A7T0.01 2 0.000 0.995 0.00 1.00
#> TCGA.OL.A66O.01 2 0.000 0.995 0.00 1.00
#> TCGA.AO.A03N.01 1 0.000 0.999 1.00 0.00
#> TCGA.AR.A1AP.01 2 0.000 0.995 0.00 1.00
#> TCGA.EW.A1PC.01 2 0.000 0.995 0.00 1.00
#> TCGA.3C.AALJ.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A42T.01 2 0.000 0.995 0.00 1.00
#> TCGA.C8.A26V.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A1EV.01 2 0.000 0.995 0.00 1.00
#> TCGA.D8.A1JA.01 2 0.000 0.995 0.00 1.00
#> TCGA.E2.A1IN.01 1 0.000 0.999 1.00 0.00
#> TCGA.BH.A0H9.01 1 0.000 0.999 1.00 0.00
#> TCGA.B6.A0RG.01 1 0.000 0.999 1.00 0.00
#> TCGA.E9.A54X.01 1 0.000 0.999 1.00 0.00
#> TCGA.C8.A1HN.01 1 0.000 0.999 1.00 0.00
#> TCGA.BH.A0HB.01 1 0.000 0.999 1.00 0.00
#> TCGA.A2.A25E.01 1 0.000 0.999 1.00 0.00
#> TCGA.B6.A1KN.01 2 0.000 0.995 0.00 1.00
#> TCGA.AR.A24K.01 2 0.000 0.995 0.00 1.00
#> TCGA.EW.A1OZ.01 2 0.000 0.995 0.00 1.00
#> TCGA.S3.AA12.01 1 0.000 0.999 1.00 0.00
#> TCGA.A2.A1FX.01 1 0.000 0.999 1.00 0.00
#> TCGA.A7.A13G.01 1 0.000 0.999 1.00 0.00
#> TCGA.LQ.A4E4.01 2 0.000 0.995 0.00 1.00
#> TCGA.AQ.A1H2.01 1 0.000 0.999 1.00 0.00
#> TCGA.D8.A27T.01 1 0.000 0.999 1.00 0.00
#> TCGA.B6.A0X4.01 1 0.000 0.999 1.00 0.00
#> TCGA.BH.A0HY.01 2 0.000 0.995 0.00 1.00
#> TCGA.E2.A15I.01 1 0.000 0.999 1.00 0.00
#> TCGA.A2.A0EU.01 1 0.000 0.999 1.00 0.00
#> TCGA.BH.A0H7.01 1 0.000 0.999 1.00 0.00
#> TCGA.A1.A0SG.01 1 0.000 0.999 1.00 0.00
#> TCGA.EW.A1J5.01 1 0.000 0.999 1.00 0.00
#> TCGA.D8.A1XR.01 1 0.000 0.999 1.00 0.00
#> TCGA.AO.A0JB.01 1 0.000 0.999 1.00 0.00
#> TCGA.C8.A27A.01 1 0.000 0.999 1.00 0.00
#> TCGA.AC.A3EH.01 2 0.000 0.995 0.00 1.00
#> TCGA.C8.A1HK.01 1 0.000 0.999 1.00 0.00
#> TCGA.B6.A0WZ.01 1 0.000 0.999 1.00 0.00
#> TCGA.A8.A0AD.01 1 0.000 0.999 1.00 0.00
#> TCGA.AC.A3YJ.01 1 0.000 0.999 1.00 0.00
#> TCGA.D8.A1Y1.01 1 0.000 0.999 1.00 0.00
#> TCGA.E2.A105.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A0E2.01 2 0.000 0.995 0.00 1.00
#> TCGA.E9.A1R7.01 2 0.000 0.995 0.00 1.00
#> TCGA.E2.A10E.01 2 0.000 0.995 0.00 1.00
#> TCGA.E9.A249.01 1 0.000 0.999 1.00 0.00
#> TCGA.E2.A1BD.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A1ET.01 1 0.000 0.999 1.00 0.00
#> TCGA.LD.A7W6.01 1 0.000 0.999 1.00 0.00
#> TCGA.C8.A1HE.01 2 0.000 0.995 0.00 1.00
#> TCGA.AC.A7VB.01 2 0.000 0.995 0.00 1.00
#> TCGA.AO.A12C.01 2 0.000 0.995 0.00 1.00
#> TCGA.D8.A73W.01 1 0.000 0.999 1.00 0.00
#> TCGA.B6.A40B.01 2 0.000 0.995 0.00 1.00
#> TCGA.AO.A0JI.01 2 0.000 0.995 0.00 1.00
#> TCGA.PE.A5DD.01 2 0.000 0.995 0.00 1.00
#> TCGA.A2.A04R.01 1 0.000 0.999 1.00 0.00
#> TCGA.BH.A1F5.01 1 0.000 0.999 1.00 0.00
#> TCGA.AC.A23E.01 1 0.000 0.999 1.00 0.00
#> TCGA.D8.A1JS.01 1 0.000 0.999 1.00 0.00
#> TCGA.WT.AB44.01 2 0.000 0.995 0.00 1.00
#> TCGA.EW.A424.01 2 0.000 0.995 0.00 1.00
#> TCGA.B6.A408.01 1 0.000 0.999 1.00 0.00
#> TCGA.E2.A1L7.01 2 0.000 0.995 0.00 1.00
#> TCGA.5T.A9QA.01 2 0.000 0.995 0.00 1.00
#> TCGA.A2.A0SY.01 2 0.000 0.995 0.00 1.00
#> TCGA.A2.A0YG.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A28Q.01 2 0.000 0.995 0.00 1.00
#> TCGA.EW.A1J1.01 1 0.000 0.999 1.00 0.00
#> TCGA.AQ.A0Y5.01 2 0.000 0.995 0.00 1.00
#> TCGA.3C.AAAU.01 1 0.000 0.999 1.00 0.00
#> TCGA.A2.A4S0.01 1 0.000 0.999 1.00 0.00
#> TCGA.AR.A1AV.01 2 0.000 0.995 0.00 1.00
#> TCGA.A7.A3J0.01 1 0.000 0.999 1.00 0.00
#> TCGA.A7.A6VX.01 1 0.000 0.999 1.00 0.00
#> TCGA.BH.A0BT.01 1 0.000 0.999 1.00 0.00
#> TCGA.E2.A1IG.01 1 0.000 0.999 1.00 0.00
#> TCGA.E9.A1NH.01 1 0.000 0.999 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.EW.A2FW.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.D8.A1JD.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.D8.A1XA.01 1 0.6126 0.207 0.60 0.00 0.40
#> TCGA.AO.A1KQ.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.A7.A3RF.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.A2.A0SW.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.GM.A2D9.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.EW.A1P5.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.BH.A1EN.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.BH.A1FN.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.EW.A1PD.01 3 0.6045 0.247 0.00 0.38 0.62
#> TCGA.E9.A1N5.01 3 0.6244 0.343 0.44 0.00 0.56
#> TCGA.D8.A1J8.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.BH.A0H0.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.A2.A0YC.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.GM.A2DC.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.AR.A24N.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.EW.A6S9.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.A1.A0SJ.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.BH.A1FG.01 3 0.5948 0.526 0.36 0.00 0.64
#> TCGA.E2.A1IL.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.A7.A3IZ.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.E2.A570.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.LL.A5YM.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.AC.A4ZE.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.EW.A1P0.01 3 0.5948 0.526 0.36 0.00 0.64
#> TCGA.AR.A24H.01 2 0.5835 0.567 0.00 0.66 0.34
#> TCGA.D8.A1XV.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.AN.A0XV.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.A2.A0YT.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.BH.A0B5.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.D8.A1JI.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.E9.A1R6.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.D8.A1XZ.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.BH.A0B8.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.LL.A6FQ.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.EW.A1OY.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.B6.A0RP.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.LL.A9Q3.01 2 0.6045 0.491 0.00 0.62 0.38
#> TCGA.A1.A0SQ.01 3 0.5835 0.557 0.34 0.00 0.66
#> TCGA.E9.A1RB.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.B6.A0RO.01 3 0.6192 0.395 0.42 0.00 0.58
#> TCGA.AC.A2BM.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.EW.A1J6.01 3 0.6045 0.486 0.38 0.00 0.62
#> TCGA.B6.A40C.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.A7.A26H.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.E2.A2P6.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.A2.A25C.01 3 0.5948 0.526 0.36 0.00 0.64
#> TCGA.OL.A5DA.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.LL.A50Y.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.LL.A442.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.C8.A26Z.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.BH.A1FJ.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.E9.A3HO.01 2 0.2066 0.914 0.00 0.94 0.06
#> TCGA.E9.A1NA.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.BH.A0BS.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.B6.A0WT.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.B6.A0RN.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.D8.A1XJ.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.E2.A109.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.3C.AALI.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.BH.A1FL.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.E2.A15K.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.E2.A15K.06 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.E9.A1NI.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.AO.A12G.01 2 0.1529 0.929 0.00 0.96 0.04
#> TCGA.C8.A1HO.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.AN.A0XR.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.BH.A0HA.01 1 0.2959 0.867 0.90 0.00 0.10
#> TCGA.D8.A1XS.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.OL.A6VR.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.AR.A1AS.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.S3.A6ZG.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.AN.A0XP.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.D8.A1XD.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.AR.A24M.01 3 0.6126 0.443 0.40 0.00 0.60
#> TCGA.AC.A6NO.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.E2.A572.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.BH.A1ES.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.EW.A1PE.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.BH.A0H6.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.A7.A2KD.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.S3.A6ZH.01 3 0.5948 0.526 0.36 0.00 0.64
#> TCGA.BH.A1EX.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.AO.A125.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.UL.AAZ6.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.A2.A0CK.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.PE.A5DC.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.EW.A6SC.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.C8.A273.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.AR.A0U2.01 1 0.6244 0.062 0.56 0.00 0.44
#> TCGA.C8.A1HL.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.E2.A9RU.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.D8.A1JJ.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.E2.A1B4.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.B6.A1KC.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.E9.A5UP.01 2 0.1529 0.929 0.00 0.96 0.04
#> TCGA.A2.A1G4.01 2 0.6045 0.491 0.00 0.62 0.38
#> TCGA.A2.A1FV.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.D8.A1XC.01 3 0.5948 0.526 0.36 0.00 0.64
#> TCGA.E2.A15J.01 2 0.2537 0.896 0.00 0.92 0.08
#> TCGA.S3.AA11.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.AC.A3QQ.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.AQ.A54O.01 3 0.6045 0.486 0.38 0.00 0.62
#> TCGA.D8.A1JT.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.AR.A2LL.01 2 0.4291 0.792 0.00 0.82 0.18
#> TCGA.D8.A1X7.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.E9.A247.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.D8.A1X5.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.A8.A075.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.D8.A73X.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.E9.A3Q9.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.BH.A0E1.01 3 0.5948 0.526 0.36 0.00 0.64
#> TCGA.EW.A423.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.E2.A106.01 3 0.5948 0.526 0.36 0.00 0.64
#> TCGA.AR.A0TV.01 2 0.0892 0.942 0.00 0.98 0.02
#> TCGA.E2.A56Z.01 3 0.5948 0.526 0.36 0.00 0.64
#> TCGA.AC.A2FM.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.A7.A0D9.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.AC.A5XU.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.BH.A204.01 3 0.5948 0.526 0.36 0.00 0.64
#> TCGA.B6.A0WW.01 2 0.5948 0.532 0.00 0.64 0.36
#> TCGA.D8.A1XL.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.E9.A5UO.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.A2.A0SV.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.OL.A5RZ.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.AR.A24R.01 2 0.5948 0.532 0.00 0.64 0.36
#> TCGA.AO.A1KP.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.E9.A1RE.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.GM.A2DM.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.A2.A0YF.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.C8.A274.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.C8.A1HM.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.E9.A1RC.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.BH.A6R8.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.BH.A1FM.01 3 0.1529 0.865 0.04 0.00 0.96
#> TCGA.D8.A1JP.01 2 0.0892 0.942 0.00 0.98 0.02
#> TCGA.AO.A0JM.01 2 0.1529 0.929 0.00 0.96 0.04
#> TCGA.BH.A0DS.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.V7.A7HQ.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.EW.A1PA.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.AC.A3TM.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.AR.A2LE.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.GM.A3NY.01 2 0.2066 0.914 0.00 0.94 0.06
#> TCGA.BH.A5J0.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.BH.A0HK.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.AR.A24Z.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.S3.A6ZF.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.Z7.A8R6.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.OL.A66K.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.D8.A1JC.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.JL.A3YX.01 3 0.5948 0.526 0.36 0.00 0.64
#> TCGA.AN.A0XO.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.BH.A0DQ.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.B6.A2IU.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.AR.A250.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.OL.A5D8.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.AQ.A04H.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.D8.A1XG.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.AR.A0TZ.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.AR.A0U3.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.BH.A0HN.01 3 0.5948 0.526 0.36 0.00 0.64
#> TCGA.EW.A1OX.01 2 0.5948 0.532 0.00 0.64 0.36
#> TCGA.AR.A24V.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.AN.A0XS.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.LL.A6FP.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.E2.A1L8.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.A2.A1FW.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.AC.A62V.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.E2.A576.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.GM.A3NW.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.A7.A4SB.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.E9.A245.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.AO.A126.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.AC.A8OR.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.A7.A4SF.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.A7.A26J.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.A2.A25B.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.D8.A27W.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.E9.A2JS.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.C8.A3M8.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.D8.A1XU.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.BH.A1ES.06 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.D8.A1X6.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.PL.A8LX.01 1 0.0892 0.968 0.98 0.00 0.02
#> TCGA.EW.A6SA.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.E9.A1R5.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.E9.A54Y.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.AC.A3TN.01 2 0.5835 0.567 0.00 0.66 0.34
#> TCGA.EW.A1J3.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.BH.A1F8.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.B6.A0X5.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.AQ.A04L.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.B6.A0WV.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.BH.A1FD.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.A7.A13F.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.E2.A2P5.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.AO.A1KS.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.BH.A0DD.01 2 0.6192 0.397 0.00 0.58 0.42
#> TCGA.BH.A0HX.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.D8.A1X9.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.AR.A0TR.01 3 0.5948 0.526 0.36 0.00 0.64
#> TCGA.A7.A0DC.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.C8.A9FZ.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.AR.A24X.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.BH.A0GZ.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.B6.A0RM.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.AO.A12B.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.BH.A0DH.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.D8.A1JN.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.E2.A1IE.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.EW.A1P3.01 3 0.6302 0.225 0.48 0.00 0.52
#> TCGA.BH.A8FY.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.AO.A1KT.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.E2.A1IU.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.E9.A22H.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.D8.A3Z6.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.AR.A2LK.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.B6.A0RI.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.A8.A08O.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.EW.A1P6.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.D8.A1XF.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.A2.A0CT.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.E9.A1RG.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.BH.A1F2.01 3 0.5948 0.526 0.36 0.00 0.64
#> TCGA.AN.A0XT.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.BH.A0HI.01 3 0.5948 0.526 0.36 0.00 0.64
#> TCGA.B6.A0RL.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.E2.A1L9.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.A7.A26E.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.BH.A0W3.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.D8.A1J9.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.LL.A7T0.01 2 0.2066 0.914 0.00 0.94 0.06
#> TCGA.OL.A66O.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.AO.A03N.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.AR.A1AP.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.EW.A1PC.01 3 0.4291 0.684 0.00 0.18 0.82
#> TCGA.3C.AALJ.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.BH.A42T.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.C8.A26V.01 2 0.1529 0.929 0.00 0.96 0.04
#> TCGA.BH.A1EV.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.D8.A1JA.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.E2.A1IN.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.BH.A0H9.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.B6.A0RG.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.E9.A54X.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.C8.A1HN.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.BH.A0HB.01 3 0.5948 0.526 0.36 0.00 0.64
#> TCGA.A2.A25E.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.B6.A1KN.01 2 0.1529 0.929 0.00 0.96 0.04
#> TCGA.AR.A24K.01 3 0.6302 -0.111 0.00 0.48 0.52
#> TCGA.EW.A1OZ.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.S3.AA12.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.A2.A1FX.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.A7.A13G.01 1 0.0892 0.968 0.98 0.00 0.02
#> TCGA.LQ.A4E4.01 2 0.0892 0.942 0.00 0.98 0.02
#> TCGA.AQ.A1H2.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.D8.A27T.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.B6.A0X4.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.BH.A0HY.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.E2.A15I.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.A2.A0EU.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.BH.A0H7.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.A1.A0SG.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.EW.A1J5.01 3 0.5835 0.557 0.34 0.00 0.66
#> TCGA.D8.A1XR.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.AO.A0JB.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.C8.A27A.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.AC.A3EH.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.C8.A1HK.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.B6.A0WZ.01 3 0.2959 0.824 0.10 0.00 0.90
#> TCGA.A8.A0AD.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.AC.A3YJ.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.D8.A1Y1.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.E2.A105.01 3 0.0892 0.874 0.00 0.02 0.98
#> TCGA.BH.A0E2.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.E9.A1R7.01 2 0.0892 0.942 0.00 0.98 0.02
#> TCGA.E2.A10E.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.E9.A249.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.E2.A1BD.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.BH.A1ET.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.LD.A7W6.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.C8.A1HE.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.AC.A7VB.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.AO.A12C.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.D8.A73W.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.B6.A40B.01 3 0.1529 0.855 0.00 0.04 0.96
#> TCGA.AO.A0JI.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.PE.A5DD.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.A2.A04R.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.BH.A1F5.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.AC.A23E.01 3 0.5948 0.526 0.36 0.00 0.64
#> TCGA.D8.A1JS.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.WT.AB44.01 2 0.5948 0.532 0.00 0.64 0.36
#> TCGA.EW.A424.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.B6.A408.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.E2.A1L7.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.5T.A9QA.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.A2.A0SY.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.A2.A0YG.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.BH.A28Q.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.EW.A1J1.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.AQ.A0Y5.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.3C.AAAU.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.A2.A4S0.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.AR.A1AV.01 2 0.0000 0.954 0.00 1.00 0.00
#> TCGA.A7.A3J0.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.A7.A6VX.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.BH.A0BT.01 1 0.0000 0.990 1.00 0.00 0.00
#> TCGA.E2.A1IG.01 3 0.0000 0.891 0.00 0.00 1.00
#> TCGA.E9.A1NH.01 3 0.0000 0.891 0.00 0.00 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.EW.A2FW.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.D8.A1JD.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.D8.A1XA.01 3 0.0707 0.963 0.02 0.00 0.98 0.00
#> TCGA.AO.A1KQ.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A7.A3RF.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A2.A0SW.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.GM.A2D9.01 4 0.0000 0.983 0.00 0.00 0.00 1.00
#> TCGA.EW.A1P5.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.BH.A1EN.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.BH.A1FN.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EW.A1PD.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.E9.A1N5.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.D8.A1J8.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.BH.A0H0.01 1 0.0707 0.977 0.98 0.00 0.02 0.00
#> TCGA.A2.A0YC.01 3 0.0707 0.963 0.02 0.00 0.98 0.00
#> TCGA.GM.A2DC.01 4 0.0000 0.983 0.00 0.00 0.00 1.00
#> TCGA.AR.A24N.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.EW.A6S9.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.A1.A0SJ.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.BH.A1FG.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.E2.A1IL.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A7.A3IZ.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.E2.A570.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.LL.A5YM.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.AC.A4ZE.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.EW.A1P0.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.AR.A24H.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.D8.A1XV.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.AN.A0XV.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.A2.A0YT.01 3 0.0707 0.963 0.02 0.00 0.98 0.00
#> TCGA.BH.A0B5.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.D8.A1JI.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E9.A1R6.01 4 0.0000 0.983 0.00 0.00 0.00 1.00
#> TCGA.D8.A1XZ.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.BH.A0B8.01 3 0.0707 0.963 0.00 0.00 0.98 0.02
#> TCGA.LL.A6FQ.01 3 0.0707 0.963 0.00 0.00 0.98 0.02
#> TCGA.EW.A1OY.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B6.A0RP.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.LL.A9Q3.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.A1.A0SQ.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.E9.A1RB.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B6.A0RO.01 3 0.0707 0.963 0.00 0.00 0.98 0.02
#> TCGA.AC.A2BM.01 3 0.0707 0.963 0.00 0.00 0.98 0.02
#> TCGA.EW.A1J6.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.B6.A40C.01 4 0.1637 0.950 0.00 0.06 0.00 0.94
#> TCGA.A7.A26H.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.E2.A2P6.01 2 0.2921 0.835 0.00 0.86 0.00 0.14
#> TCGA.A2.A25C.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.OL.A5DA.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.LL.A50Y.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.LL.A442.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.C8.A26Z.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BH.A1FJ.01 4 0.1211 0.949 0.00 0.00 0.04 0.96
#> TCGA.E9.A3HO.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.E9.A1NA.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.BH.A0BS.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B6.A0WT.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B6.A0RN.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.D8.A1XJ.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.E2.A109.01 4 0.0000 0.983 0.00 0.00 0.00 1.00
#> TCGA.3C.AALI.01 3 0.4713 0.470 0.36 0.00 0.64 0.00
#> TCGA.BH.A1FL.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.E2.A15K.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E2.A15K.06 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E9.A1NI.01 3 0.0707 0.963 0.02 0.00 0.98 0.00
#> TCGA.AO.A12G.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.C8.A1HO.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.AN.A0XR.01 4 0.3172 0.827 0.00 0.16 0.00 0.84
#> TCGA.BH.A0HA.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.D8.A1XS.01 3 0.3975 0.702 0.24 0.00 0.76 0.00
#> TCGA.OL.A6VR.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AR.A1AS.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.S3.A6ZG.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.AN.A0XP.01 3 0.0707 0.963 0.02 0.00 0.98 0.00
#> TCGA.D8.A1XD.01 3 0.2011 0.894 0.00 0.00 0.92 0.08
#> TCGA.AR.A24M.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.AC.A6NO.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E2.A572.01 3 0.0707 0.963 0.02 0.00 0.98 0.00
#> TCGA.BH.A1ES.01 3 0.2345 0.871 0.00 0.00 0.90 0.10
#> TCGA.EW.A1PE.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.BH.A0H6.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A7.A2KD.01 3 0.0707 0.963 0.02 0.00 0.98 0.00
#> TCGA.S3.A6ZH.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.BH.A1EX.01 3 0.0707 0.963 0.02 0.00 0.98 0.00
#> TCGA.AO.A125.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.UL.AAZ6.01 4 0.0000 0.983 0.00 0.00 0.00 1.00
#> TCGA.A2.A0CK.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.PE.A5DC.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.EW.A6SC.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.C8.A273.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.AR.A0U2.01 3 0.0707 0.963 0.00 0.00 0.98 0.02
#> TCGA.C8.A1HL.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E2.A9RU.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.D8.A1JJ.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.E2.A1B4.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B6.A1KC.01 4 0.0000 0.983 0.00 0.00 0.00 1.00
#> TCGA.E9.A5UP.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.A2.A1G4.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.A2.A1FV.01 3 0.0707 0.963 0.00 0.00 0.98 0.02
#> TCGA.D8.A1XC.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.E2.A15J.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.S3.AA11.01 3 0.0707 0.963 0.00 0.00 0.98 0.02
#> TCGA.AC.A3QQ.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AQ.A54O.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.D8.A1JT.01 3 0.0707 0.963 0.02 0.00 0.98 0.00
#> TCGA.AR.A2LL.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.D8.A1X7.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E9.A247.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.D8.A1X5.01 3 0.0707 0.963 0.00 0.00 0.98 0.02
#> TCGA.A8.A075.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.D8.A73X.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.E9.A3Q9.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BH.A0E1.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.EW.A423.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.E2.A106.01 3 0.0707 0.963 0.00 0.00 0.98 0.02
#> TCGA.AR.A0TV.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.E2.A56Z.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.AC.A2FM.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.A7.A0D9.01 3 0.0707 0.963 0.02 0.00 0.98 0.00
#> TCGA.AC.A5XU.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.BH.A204.01 3 0.0707 0.963 0.00 0.00 0.98 0.02
#> TCGA.B6.A0WW.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.D8.A1XL.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.E9.A5UO.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.A2.A0SV.01 4 0.0000 0.983 0.00 0.00 0.00 1.00
#> TCGA.OL.A5RZ.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.AR.A24R.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.AO.A1KP.01 4 0.0000 0.983 0.00 0.00 0.00 1.00
#> TCGA.E9.A1RE.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.GM.A2DM.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A2.A0YF.01 3 0.0707 0.963 0.02 0.00 0.98 0.00
#> TCGA.C8.A274.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.C8.A1HM.01 3 0.4790 0.421 0.38 0.00 0.62 0.00
#> TCGA.E9.A1RC.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.BH.A6R8.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BH.A1FM.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.D8.A1JP.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.AO.A0JM.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.BH.A0DS.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.V7.A7HQ.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EW.A1PA.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.AC.A3TM.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.AR.A2LE.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.GM.A3NY.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.BH.A5J0.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BH.A0HK.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.AR.A24Z.01 3 0.0707 0.963 0.02 0.00 0.98 0.00
#> TCGA.S3.A6ZF.01 4 0.0000 0.983 0.00 0.00 0.00 1.00
#> TCGA.Z7.A8R6.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.OL.A66K.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.D8.A1JC.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.JL.A3YX.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.AN.A0XO.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.BH.A0DQ.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B6.A2IU.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AR.A250.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.OL.A5D8.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.AQ.A04H.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.D8.A1XG.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AR.A0TZ.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.AR.A0U3.01 4 0.0000 0.983 0.00 0.00 0.00 1.00
#> TCGA.BH.A0HN.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.EW.A1OX.01 4 0.0000 0.983 0.00 0.00 0.00 1.00
#> TCGA.AR.A24V.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AN.A0XS.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.LL.A6FP.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E2.A1L8.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A2.A1FW.01 4 0.0000 0.983 0.00 0.00 0.00 1.00
#> TCGA.AC.A62V.01 3 0.0707 0.963 0.00 0.00 0.98 0.02
#> TCGA.E2.A576.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.GM.A3NW.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.A7.A4SB.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E9.A245.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AO.A126.01 3 0.4522 0.520 0.00 0.00 0.68 0.32
#> TCGA.AC.A8OR.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A7.A4SF.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A7.A26J.01 3 0.0707 0.963 0.02 0.00 0.98 0.00
#> TCGA.A2.A25B.01 3 0.0707 0.963 0.02 0.00 0.98 0.00
#> TCGA.D8.A27W.01 4 0.0000 0.983 0.00 0.00 0.00 1.00
#> TCGA.E9.A2JS.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.C8.A3M8.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.D8.A1XU.01 4 0.0000 0.983 0.00 0.00 0.00 1.00
#> TCGA.BH.A1ES.06 4 0.0000 0.983 0.00 0.00 0.00 1.00
#> TCGA.D8.A1X6.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.PL.A8LX.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.EW.A6SA.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.E9.A1R5.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.E9.A54Y.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.AC.A3TN.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.EW.A1J3.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.BH.A1F8.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.B6.A0X5.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AQ.A04L.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.B6.A0WV.01 3 0.0707 0.963 0.02 0.00 0.98 0.00
#> TCGA.BH.A1FD.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.A7.A13F.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.E2.A2P5.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.AO.A1KS.01 4 0.0000 0.983 0.00 0.00 0.00 1.00
#> TCGA.BH.A0DD.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.BH.A0HX.01 3 0.0707 0.963 0.00 0.00 0.98 0.02
#> TCGA.D8.A1X9.01 4 0.0000 0.983 0.00 0.00 0.00 1.00
#> TCGA.AR.A0TR.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.A7.A0DC.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.C8.A9FZ.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.AR.A24X.01 4 0.1637 0.950 0.00 0.06 0.00 0.94
#> TCGA.BH.A0GZ.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.B6.A0RM.01 3 0.0707 0.963 0.02 0.00 0.98 0.00
#> TCGA.AO.A12B.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BH.A0DH.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.D8.A1JN.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.E2.A1IE.01 3 0.0707 0.963 0.00 0.00 0.98 0.02
#> TCGA.EW.A1P3.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.BH.A8FY.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.AO.A1KT.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.E2.A1IU.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E9.A22H.01 3 0.0707 0.963 0.02 0.00 0.98 0.00
#> TCGA.D8.A3Z6.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.AR.A2LK.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.B6.A0RI.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A8.A08O.01 3 0.4977 0.191 0.46 0.00 0.54 0.00
#> TCGA.EW.A1P6.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.D8.A1XF.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.A2.A0CT.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.E9.A1RG.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BH.A1F2.01 3 0.0707 0.963 0.00 0.00 0.98 0.02
#> TCGA.AN.A0XT.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BH.A0HI.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.B6.A0RL.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.E2.A1L9.01 3 0.0707 0.963 0.02 0.00 0.98 0.00
#> TCGA.A7.A26E.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.BH.A0W3.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.D8.A1J9.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.LL.A7T0.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.OL.A66O.01 4 0.0000 0.983 0.00 0.00 0.00 1.00
#> TCGA.AO.A03N.01 3 0.1637 0.928 0.06 0.00 0.94 0.00
#> TCGA.AR.A1AP.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.EW.A1PC.01 4 0.0000 0.983 0.00 0.00 0.00 1.00
#> TCGA.3C.AALJ.01 4 0.0000 0.983 0.00 0.00 0.00 1.00
#> TCGA.BH.A42T.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.C8.A26V.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.BH.A1EV.01 2 0.3610 0.747 0.00 0.80 0.00 0.20
#> TCGA.D8.A1JA.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.E2.A1IN.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BH.A0H9.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B6.A0RG.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E9.A54X.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.C8.A1HN.01 3 0.0707 0.963 0.00 0.00 0.98 0.02
#> TCGA.BH.A0HB.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.A2.A25E.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B6.A1KN.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.AR.A24K.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.EW.A1OZ.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.S3.AA12.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A2.A1FX.01 3 0.0707 0.963 0.02 0.00 0.98 0.00
#> TCGA.A7.A13G.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.LQ.A4E4.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.AQ.A1H2.01 3 0.0707 0.963 0.02 0.00 0.98 0.00
#> TCGA.D8.A27T.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B6.A0X4.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BH.A0HY.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.E2.A15I.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A2.A0EU.01 3 0.0707 0.963 0.02 0.00 0.98 0.00
#> TCGA.BH.A0H7.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A1.A0SG.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EW.A1J5.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.D8.A1XR.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AO.A0JB.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.C8.A27A.01 3 0.0707 0.963 0.00 0.00 0.98 0.02
#> TCGA.AC.A3EH.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.C8.A1HK.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.B6.A0WZ.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.A8.A0AD.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AC.A3YJ.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.D8.A1Y1.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.E2.A105.01 4 0.0000 0.983 0.00 0.00 0.00 1.00
#> TCGA.BH.A0E2.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.E9.A1R7.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.E2.A10E.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.E9.A249.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.E2.A1BD.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.BH.A1ET.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.LD.A7W6.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.C8.A1HE.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.AC.A7VB.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.AO.A12C.01 4 0.0000 0.983 0.00 0.00 0.00 1.00
#> TCGA.D8.A73W.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.B6.A40B.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.AO.A0JI.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.PE.A5DD.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.A2.A04R.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BH.A1F5.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AC.A23E.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.D8.A1JS.01 3 0.0707 0.963 0.02 0.00 0.98 0.00
#> TCGA.WT.AB44.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.EW.A424.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.B6.A408.01 3 0.0707 0.963 0.02 0.00 0.98 0.00
#> TCGA.E2.A1L7.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.5T.A9QA.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.A2.A0SY.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.A2.A0YG.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.BH.A28Q.01 4 0.0707 0.983 0.00 0.00 0.02 0.98
#> TCGA.EW.A1J1.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AQ.A0Y5.01 4 0.0707 0.984 0.00 0.02 0.00 0.98
#> TCGA.3C.AAAU.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A2.A4S0.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AR.A1AV.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.A7.A3J0.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A7.A6VX.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.BH.A0BT.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E2.A1IG.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
#> TCGA.E9.A1NH.01 3 0.0000 0.969 0.00 0.00 1.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.EW.A2FW.01 1 0.3513 0.8044 0.80 0.00 0.18 0.02 0.00
#> TCGA.D8.A1JD.01 1 0.3690 0.7809 0.78 0.00 0.20 0.02 0.00
#> TCGA.D8.A1XA.01 3 0.4262 0.5460 0.00 0.00 0.56 0.44 0.00
#> TCGA.AO.A1KQ.01 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A3RF.01 1 0.0609 0.9356 0.98 0.00 0.00 0.02 0.00
#> TCGA.A2.A0SW.01 3 0.3922 0.7264 0.00 0.00 0.78 0.04 0.18
#> TCGA.GM.A2D9.01 4 0.4302 0.8059 0.00 0.00 0.00 0.52 0.48
#> TCGA.EW.A1P5.01 3 0.1732 0.8044 0.00 0.00 0.92 0.00 0.08
#> TCGA.BH.A1EN.01 2 0.0000 0.9899 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A1FN.01 1 0.3999 0.7256 0.74 0.00 0.24 0.02 0.00
#> TCGA.EW.A1PD.01 4 0.4262 0.8693 0.00 0.00 0.00 0.56 0.44
#> TCGA.E9.A1N5.01 3 0.0000 0.8361 0.00 0.00 1.00 0.00 0.00
#> TCGA.D8.A1J8.01 2 0.0000 0.9899 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0H0.01 1 0.3690 0.7809 0.78 0.00 0.20 0.02 0.00
#> TCGA.A2.A0YC.01 3 0.0609 0.8335 0.00 0.00 0.98 0.02 0.00
#> TCGA.GM.A2DC.01 5 0.3983 -0.3818 0.00 0.00 0.00 0.34 0.66
#> TCGA.AR.A24N.01 2 0.0000 0.9899 0.00 1.00 0.00 0.00 0.00
#> TCGA.EW.A6S9.01 3 0.1043 0.8227 0.00 0.00 0.96 0.00 0.04
#> TCGA.A1.A0SJ.01 4 0.4262 0.8693 0.00 0.00 0.00 0.56 0.44
#> TCGA.BH.A1FG.01 3 0.0000 0.8361 0.00 0.00 1.00 0.00 0.00
#> TCGA.E2.A1IL.01 1 0.3513 0.8044 0.80 0.00 0.18 0.02 0.00
#> TCGA.A7.A3IZ.01 4 0.4302 0.8009 0.00 0.00 0.00 0.52 0.48
#> TCGA.E2.A570.01 3 0.0609 0.8335 0.00 0.00 0.98 0.02 0.00
#> TCGA.LL.A5YM.01 2 0.0000 0.9899 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A4ZE.01 2 0.0000 0.9899 0.00 1.00 0.00 0.00 0.00
#> TCGA.EW.A1P0.01 3 0.0000 0.8361 0.00 0.00 1.00 0.00 0.00
#> TCGA.AR.A24H.01 4 0.4262 0.8693 0.00 0.00 0.00 0.56 0.44
#> TCGA.D8.A1XV.01 4 0.4262 0.8693 0.00 0.00 0.00 0.56 0.44
#> TCGA.AN.A0XV.01 2 0.0000 0.9899 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A0YT.01 3 0.4262 0.5460 0.00 0.00 0.56 0.44 0.00
#> TCGA.BH.A0B5.01 3 0.5050 0.6748 0.00 0.00 0.70 0.12 0.18
#> TCGA.D8.A1JI.01 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1R6.01 5 0.0000 0.5169 0.00 0.00 0.00 0.00 1.00
#> TCGA.D8.A1XZ.01 4 0.4262 0.8693 0.00 0.00 0.00 0.56 0.44
#> TCGA.BH.A0B8.01 5 0.4767 0.5172 0.00 0.00 0.02 0.42 0.56
#> TCGA.LL.A6FQ.01 5 0.4767 0.5172 0.00 0.00 0.02 0.42 0.56
#> TCGA.EW.A1OY.01 1 0.0609 0.9356 0.98 0.00 0.00 0.02 0.00
#> TCGA.B6.A0RP.01 1 0.0609 0.9356 0.98 0.00 0.00 0.02 0.00
#> TCGA.LL.A9Q3.01 4 0.4262 0.8693 0.00 0.00 0.00 0.56 0.44
#> TCGA.A1.A0SQ.01 3 0.0000 0.8361 0.00 0.00 1.00 0.00 0.00
#> TCGA.E9.A1RB.01 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0RO.01 3 0.4227 0.5474 0.00 0.00 0.58 0.42 0.00
#> TCGA.AC.A2BM.01 4 0.6671 -0.4820 0.00 0.00 0.34 0.42 0.24
#> TCGA.EW.A1J6.01 3 0.0000 0.8361 0.00 0.00 1.00 0.00 0.00
#> TCGA.B6.A40C.01 4 0.4262 0.8693 0.00 0.00 0.00 0.56 0.44
#> TCGA.A7.A26H.01 5 0.0000 0.5169 0.00 0.00 0.00 0.00 1.00
#> TCGA.E2.A2P6.01 4 0.6111 0.5707 0.00 0.18 0.00 0.56 0.26
#> TCGA.A2.A25C.01 3 0.0000 0.8361 0.00 0.00 1.00 0.00 0.00
#> TCGA.OL.A5DA.01 4 0.4262 0.8693 0.00 0.00 0.00 0.56 0.44
#> TCGA.LL.A50Y.01 4 0.4262 0.8693 0.00 0.00 0.00 0.56 0.44
#> TCGA.LL.A442.01 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A26Z.01 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FJ.01 5 0.3852 0.5821 0.00 0.00 0.02 0.22 0.76
#> TCGA.E9.A3HO.01 4 0.4262 0.8693 0.00 0.00 0.00 0.56 0.44
#> TCGA.E9.A1NA.01 2 0.0000 0.9899 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0BS.01 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0WT.01 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0RN.01 5 0.4302 -0.7377 0.00 0.00 0.00 0.48 0.52
#> TCGA.D8.A1XJ.01 2 0.0000 0.9899 0.00 1.00 0.00 0.00 0.00
#> TCGA.E2.A109.01 5 0.4227 0.5338 0.00 0.00 0.00 0.42 0.58
#> TCGA.3C.AALI.01 1 0.6816 -0.0349 0.36 0.00 0.32 0.32 0.00
#> TCGA.BH.A1FL.01 4 0.4262 0.8693 0.00 0.00 0.00 0.56 0.44
#> TCGA.E2.A15K.01 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A15K.06 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1NI.01 3 0.4262 0.5460 0.00 0.00 0.56 0.44 0.00
#> TCGA.AO.A12G.01 4 0.4262 0.8693 0.00 0.00 0.00 0.56 0.44
#> TCGA.C8.A1HO.01 2 0.0000 0.9899 0.00 1.00 0.00 0.00 0.00
#> TCGA.AN.A0XR.01 4 0.4767 0.8386 0.00 0.02 0.00 0.56 0.42
#> TCGA.BH.A0HA.01 3 0.0000 0.8361 0.00 0.00 1.00 0.00 0.00
#> TCGA.D8.A1XS.01 3 0.0609 0.8335 0.00 0.00 0.98 0.02 0.00
#> TCGA.OL.A6VR.01 1 0.3690 0.7839 0.78 0.00 0.20 0.02 0.00
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#> TCGA.D8.A1JP.01 4 0.4262 0.8693 0.00 0.00 0.00 0.56 0.44
#> TCGA.AO.A0JM.01 4 0.4262 0.8693 0.00 0.00 0.00 0.56 0.44
#> TCGA.BH.A0DS.01 2 0.0000 0.9899 0.00 1.00 0.00 0.00 0.00
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#> TCGA.BH.A5J0.01 1 0.0609 0.9356 0.98 0.00 0.00 0.02 0.00
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#> TCGA.AR.A24Z.01 3 0.4262 0.5460 0.00 0.00 0.56 0.44 0.00
#> TCGA.S3.A6ZF.01 5 0.3561 -0.1029 0.00 0.00 0.00 0.26 0.74
#> TCGA.Z7.A8R6.01 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00
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#> TCGA.D8.A1JC.01 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00
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#> TCGA.BH.A0DD.01 4 0.4262 0.8693 0.00 0.00 0.00 0.56 0.44
#> TCGA.BH.A0HX.01 5 0.4767 0.5172 0.00 0.00 0.02 0.42 0.56
#> TCGA.D8.A1X9.01 5 0.3109 0.1305 0.00 0.00 0.00 0.20 0.80
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#> TCGA.AR.A24X.01 4 0.4262 0.8693 0.00 0.00 0.00 0.56 0.44
#> TCGA.BH.A0GZ.01 4 0.4262 0.8693 0.00 0.00 0.00 0.56 0.44
#> TCGA.B6.A0RM.01 3 0.0609 0.8335 0.00 0.00 0.98 0.02 0.00
#> TCGA.AO.A12B.01 1 0.2012 0.9040 0.92 0.00 0.06 0.02 0.00
#> TCGA.BH.A0DH.01 5 0.0609 0.4971 0.00 0.00 0.00 0.02 0.98
#> TCGA.D8.A1JN.01 2 0.0000 0.9899 0.00 1.00 0.00 0.00 0.00
#> TCGA.E2.A1IE.01 5 0.6064 0.3667 0.00 0.00 0.12 0.42 0.46
#> TCGA.EW.A1P3.01 3 0.0000 0.8361 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A8FY.01 5 0.3109 0.1314 0.00 0.00 0.00 0.20 0.80
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#> TCGA.D8.A3Z6.01 3 0.3922 0.7264 0.00 0.00 0.78 0.04 0.18
#> TCGA.AR.A2LK.01 4 0.4262 0.1164 0.00 0.44 0.00 0.56 0.00
#> TCGA.B6.A0RI.01 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00
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#> TCGA.BH.A1ET.01 1 0.0609 0.9356 0.98 0.00 0.00 0.02 0.00
#> TCGA.LD.A7W6.01 3 0.2929 0.7415 0.00 0.00 0.82 0.00 0.18
#> TCGA.C8.A1HE.01 4 0.4262 0.8693 0.00 0.00 0.00 0.56 0.44
#> TCGA.AC.A7VB.01 2 0.0000 0.9899 0.00 1.00 0.00 0.00 0.00
#> TCGA.AO.A12C.01 5 0.2280 0.5673 0.00 0.00 0.00 0.12 0.88
#> TCGA.D8.A73W.01 3 0.2929 0.7415 0.00 0.00 0.82 0.00 0.18
#> TCGA.B6.A40B.01 4 0.4262 0.8693 0.00 0.00 0.00 0.56 0.44
#> TCGA.AO.A0JI.01 2 0.0000 0.9899 0.00 1.00 0.00 0.00 0.00
#> TCGA.PE.A5DD.01 2 0.0000 0.9899 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A04R.01 1 0.2873 0.8600 0.86 0.00 0.12 0.02 0.00
#> TCGA.BH.A1F5.01 1 0.3106 0.8427 0.84 0.00 0.14 0.02 0.00
#> TCGA.AC.A23E.01 3 0.0000 0.8361 0.00 0.00 1.00 0.00 0.00
#> TCGA.D8.A1JS.01 3 0.0609 0.8335 0.00 0.00 0.98 0.02 0.00
#> TCGA.WT.AB44.01 4 0.4262 0.8693 0.00 0.00 0.00 0.56 0.44
#> TCGA.EW.A424.01 2 0.0000 0.9899 0.00 1.00 0.00 0.00 0.00
#> TCGA.B6.A408.01 3 0.0609 0.8335 0.00 0.00 0.98 0.02 0.00
#> TCGA.E2.A1L7.01 2 0.0000 0.9899 0.00 1.00 0.00 0.00 0.00
#> TCGA.5T.A9QA.01 2 0.0000 0.9899 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A0SY.01 2 0.1732 0.9052 0.00 0.92 0.00 0.08 0.00
#> TCGA.A2.A0YG.01 2 0.0000 0.9899 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A28Q.01 4 0.4262 0.8693 0.00 0.00 0.00 0.56 0.44
#> TCGA.EW.A1J1.01 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00
#> TCGA.AQ.A0Y5.01 4 0.4262 0.8693 0.00 0.00 0.00 0.56 0.44
#> TCGA.3C.AAAU.01 1 0.0609 0.9356 0.98 0.00 0.00 0.02 0.00
#> TCGA.A2.A4S0.01 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AV.01 2 0.0000 0.9899 0.00 1.00 0.00 0.00 0.00
#> TCGA.A7.A3J0.01 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A6VX.01 3 0.2929 0.7415 0.00 0.00 0.82 0.00 0.18
#> TCGA.BH.A0BT.01 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1IG.01 5 0.4767 0.5172 0.00 0.00 0.02 0.42 0.56
#> TCGA.E9.A1NH.01 3 0.1410 0.8143 0.00 0.00 0.94 0.00 0.06
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.EW.A2FW.01 6 0.5371 0.4312 0.36 0.00 0.12 0.00 0.00 0.52
#> TCGA.D8.A1JD.01 6 0.5120 0.5380 0.28 0.00 0.12 0.00 0.00 0.60
#> TCGA.D8.A1XA.01 6 0.2350 0.5157 0.00 0.00 0.02 0.00 0.10 0.88
#> TCGA.AO.A1KQ.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A3RF.01 1 0.2631 0.7852 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.A2.A0SW.01 3 0.3756 0.5996 0.00 0.00 0.60 0.00 0.40 0.00
#> TCGA.GM.A2D9.01 4 0.3198 0.6021 0.00 0.00 0.00 0.74 0.26 0.00
#> TCGA.EW.A1P5.01 3 0.4348 0.6633 0.00 0.00 0.64 0.00 0.32 0.04
#> TCGA.BH.A1EN.01 2 0.0000 0.9641 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FN.01 6 0.5324 0.4679 0.34 0.00 0.12 0.00 0.00 0.54
#> TCGA.EW.A1PD.01 4 0.0000 0.8974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E9.A1N5.01 3 0.3309 0.6222 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.D8.A1J8.01 2 0.0000 0.9641 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0H0.01 6 0.5029 0.5465 0.26 0.00 0.12 0.00 0.00 0.62
#> TCGA.A2.A0YC.01 6 0.3647 0.3824 0.00 0.00 0.36 0.00 0.00 0.64
#> TCGA.GM.A2DC.01 4 0.5095 -0.0671 0.00 0.00 0.08 0.50 0.42 0.00
#> TCGA.AR.A24N.01 2 0.0000 0.9641 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A6S9.01 3 0.4462 0.6647 0.00 0.00 0.66 0.00 0.28 0.06
#> TCGA.A1.A0SJ.01 4 0.0547 0.8893 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.BH.A1FG.01 3 0.3309 0.6222 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.E2.A1IL.01 6 0.5371 0.4312 0.36 0.00 0.12 0.00 0.00 0.52
#> TCGA.A7.A3IZ.01 5 0.3647 0.3328 0.00 0.00 0.00 0.36 0.64 0.00
#> TCGA.E2.A570.01 3 0.3309 0.6222 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.LL.A5YM.01 2 0.0000 0.9641 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A4ZE.01 2 0.0000 0.9641 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1P0.01 3 0.3647 0.4714 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.AR.A24H.01 4 0.2454 0.7503 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.D8.A1XV.01 4 0.0937 0.8849 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.AN.A0XV.01 2 0.2793 0.7454 0.00 0.80 0.00 0.20 0.00 0.00
#> TCGA.A2.A0YT.01 6 0.2350 0.5157 0.00 0.00 0.02 0.00 0.10 0.88
#> TCGA.BH.A0B5.01 3 0.4993 0.6153 0.00 0.00 0.56 0.00 0.36 0.08
#> TCGA.D8.A1JI.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1R6.01 5 0.1814 0.6567 0.00 0.00 0.00 0.10 0.90 0.00
#> TCGA.D8.A1XZ.01 4 0.3864 0.0653 0.00 0.00 0.00 0.52 0.48 0.00
#> TCGA.BH.A0B8.01 5 0.6070 0.4691 0.00 0.00 0.28 0.00 0.40 0.32
#> TCGA.LL.A6FQ.01 5 0.5575 0.4034 0.00 0.00 0.14 0.00 0.46 0.40
#> TCGA.EW.A1OY.01 1 0.3198 0.6688 0.74 0.00 0.00 0.00 0.00 0.26
#> TCGA.B6.A0RP.01 1 0.2631 0.7852 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.LL.A9Q3.01 4 0.0000 0.8974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A1.A0SQ.01 3 0.4144 0.4581 0.00 0.00 0.62 0.00 0.02 0.36
#> TCGA.E9.A1RB.01 1 0.1814 0.8596 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.B6.A0RO.01 6 0.2350 0.5157 0.00 0.00 0.02 0.00 0.10 0.88
#> TCGA.AC.A2BM.01 6 0.5992 -0.2065 0.00 0.00 0.24 0.00 0.34 0.42
#> TCGA.EW.A1J6.01 3 0.3409 0.5867 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.B6.A40C.01 4 0.0937 0.8696 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.A7.A26H.01 5 0.1814 0.6567 0.00 0.00 0.00 0.10 0.90 0.00
#> TCGA.E2.A2P6.01 4 0.1814 0.8060 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.A2.A25C.01 3 0.3309 0.6222 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.OL.A5DA.01 4 0.3198 0.5594 0.00 0.00 0.00 0.74 0.26 0.00
#> TCGA.LL.A50Y.01 4 0.1267 0.8588 0.00 0.00 0.00 0.94 0.06 0.00
#> TCGA.LL.A442.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A26Z.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FJ.01 5 0.0937 0.6496 0.00 0.00 0.00 0.04 0.96 0.00
#> TCGA.E9.A3HO.01 4 0.0000 0.8974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E9.A1NA.01 2 0.0547 0.9627 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BH.A0BS.01 1 0.0937 0.9003 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.B6.A0WT.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0RN.01 5 0.3756 0.2740 0.00 0.00 0.00 0.40 0.60 0.00
#> TCGA.D8.A1XJ.01 2 0.0547 0.9627 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.E2.A109.01 5 0.5438 0.5826 0.00 0.00 0.28 0.00 0.56 0.16
#> TCGA.3C.AALI.01 6 0.1480 0.5443 0.02 0.00 0.00 0.00 0.04 0.94
#> TCGA.BH.A1FL.01 4 0.0937 0.8759 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.E2.A15K.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A15K.06 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1NI.01 6 0.2350 0.5157 0.00 0.00 0.02 0.00 0.10 0.88
#> TCGA.AO.A12G.01 4 0.0000 0.8974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.C8.A1HO.01 2 0.0547 0.9627 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AN.A0XR.01 4 0.1092 0.8817 0.00 0.02 0.00 0.96 0.02 0.00
#> TCGA.BH.A0HA.01 3 0.3309 0.6222 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.D8.A1XS.01 6 0.3706 0.3528 0.00 0.00 0.38 0.00 0.00 0.62
#> TCGA.OL.A6VR.01 6 0.5371 0.4312 0.36 0.00 0.12 0.00 0.00 0.52
#> TCGA.AR.A1AS.01 6 0.5012 0.5154 0.30 0.00 0.10 0.00 0.00 0.60
#> TCGA.S3.A6ZG.01 2 0.0000 0.9641 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AN.A0XP.01 6 0.3647 0.3824 0.00 0.00 0.36 0.00 0.00 0.64
#> TCGA.D8.A1XD.01 3 0.4689 0.6019 0.00 0.00 0.58 0.02 0.38 0.02
#> TCGA.AR.A24M.01 3 0.3309 0.6222 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.AC.A6NO.01 6 0.5195 0.4296 0.36 0.00 0.10 0.00 0.00 0.54
#> TCGA.E2.A572.01 6 0.4078 0.4081 0.02 0.00 0.34 0.00 0.00 0.64
#> TCGA.BH.A1ES.01 3 0.4689 0.6019 0.00 0.00 0.58 0.02 0.38 0.02
#> TCGA.EW.A1PE.01 3 0.3309 0.6222 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.BH.A0H6.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A2KD.01 6 0.3706 0.3528 0.00 0.00 0.38 0.00 0.00 0.62
#> TCGA.S3.A6ZH.01 6 0.4420 0.2203 0.00 0.00 0.34 0.00 0.04 0.62
#> TCGA.BH.A1EX.01 6 0.3647 0.3824 0.00 0.00 0.36 0.00 0.00 0.64
#> TCGA.AO.A125.01 5 0.1814 0.6567 0.00 0.00 0.00 0.10 0.90 0.00
#> TCGA.UL.AAZ6.01 5 0.5438 0.5826 0.00 0.00 0.28 0.00 0.56 0.16
#> TCGA.A2.A0CK.01 3 0.4482 0.6390 0.00 0.00 0.60 0.00 0.36 0.04
#> TCGA.PE.A5DC.01 5 0.3797 0.2439 0.00 0.00 0.00 0.42 0.58 0.00
#> TCGA.EW.A6SC.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A273.01 3 0.3756 0.5996 0.00 0.00 0.60 0.00 0.40 0.00
#> TCGA.AR.A0U2.01 6 0.3985 0.3647 0.00 0.00 0.10 0.00 0.14 0.76
#> TCGA.C8.A1HL.01 6 0.4078 0.2327 0.34 0.00 0.00 0.00 0.02 0.64
#> TCGA.E2.A9RU.01 2 0.0547 0.9627 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.D8.A1JJ.01 4 0.0547 0.8893 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.E2.A1B4.01 1 0.2941 0.7322 0.78 0.00 0.00 0.00 0.00 0.22
#> TCGA.B6.A1KC.01 5 0.5783 0.5763 0.00 0.00 0.28 0.22 0.50 0.00
#> TCGA.E9.A5UP.01 4 0.0000 0.8974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A2.A1G4.01 4 0.0000 0.8974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A2.A1FV.01 5 0.5888 0.4843 0.00 0.00 0.22 0.00 0.46 0.32
#> TCGA.D8.A1XC.01 3 0.3309 0.6222 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.E2.A15J.01 4 0.0000 0.8974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.S3.AA11.01 5 0.6088 0.4501 0.00 0.00 0.28 0.00 0.38 0.34
#> TCGA.AC.A3QQ.01 6 0.5120 0.5380 0.28 0.00 0.12 0.00 0.00 0.60
#> TCGA.AQ.A54O.01 3 0.3309 0.6222 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.D8.A1JT.01 6 0.3309 0.4583 0.00 0.00 0.28 0.00 0.00 0.72
#> TCGA.AR.A2LL.01 4 0.0000 0.8974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D8.A1X7.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A247.01 2 0.0000 0.9641 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1X5.01 5 0.1267 0.6184 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.A8.A075.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A73X.01 4 0.0937 0.8767 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.E9.A3Q9.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0E1.01 3 0.3309 0.6222 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.EW.A423.01 2 0.0000 0.9641 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A106.01 6 0.2350 0.5157 0.00 0.00 0.02 0.00 0.10 0.88
#> TCGA.AR.A0TV.01 4 0.0547 0.8922 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.E2.A56Z.01 6 0.3321 0.4537 0.00 0.00 0.08 0.00 0.10 0.82
#> TCGA.AC.A2FM.01 2 0.0547 0.9627 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.A7.A0D9.01 6 0.3797 0.2681 0.00 0.00 0.42 0.00 0.00 0.58
#> TCGA.AC.A5XU.01 4 0.0547 0.8922 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.BH.A204.01 6 0.5419 -0.0341 0.00 0.00 0.20 0.00 0.22 0.58
#> TCGA.B6.A0WW.01 4 0.0547 0.8922 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.D8.A1XL.01 3 0.4420 0.6529 0.00 0.00 0.62 0.00 0.34 0.04
#> TCGA.E9.A5UO.01 5 0.2793 0.6012 0.00 0.00 0.00 0.20 0.80 0.00
#> TCGA.A2.A0SV.01 5 0.1814 0.6567 0.00 0.00 0.00 0.10 0.90 0.00
#> TCGA.OL.A5RZ.01 5 0.5235 0.3937 0.00 0.00 0.10 0.00 0.52 0.38
#> TCGA.AR.A24R.01 4 0.2793 0.6908 0.00 0.00 0.00 0.80 0.20 0.00
#> TCGA.AO.A1KP.01 5 0.2728 0.6660 0.00 0.00 0.04 0.10 0.86 0.00
#> TCGA.E9.A1RE.01 4 0.3578 0.4562 0.00 0.34 0.00 0.66 0.00 0.00
#> TCGA.GM.A2DM.01 1 0.2350 0.8455 0.88 0.00 0.02 0.00 0.00 0.10
#> TCGA.A2.A0YF.01 6 0.3647 0.3824 0.00 0.00 0.36 0.00 0.00 0.64
#> TCGA.C8.A274.01 2 0.0547 0.9627 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.C8.A1HM.01 6 0.1480 0.5443 0.02 0.00 0.00 0.00 0.04 0.94
#> TCGA.E9.A1RC.01 2 0.0547 0.9627 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BH.A6R8.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FM.01 6 0.4727 0.2667 0.00 0.00 0.10 0.00 0.24 0.66
#> TCGA.D8.A1JP.01 4 0.0000 0.8974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AO.A0JM.01 4 0.0547 0.8922 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.BH.A0DS.01 2 0.0000 0.9641 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.V7.A7HQ.01 1 0.4462 0.5143 0.66 0.00 0.06 0.00 0.00 0.28
#> TCGA.EW.A1PA.01 5 0.2581 0.6601 0.00 0.00 0.02 0.12 0.86 0.00
#> TCGA.AC.A3TM.01 5 0.5102 0.3005 0.00 0.00 0.24 0.14 0.62 0.00
#> TCGA.AR.A2LE.01 3 0.3756 0.5996 0.00 0.00 0.60 0.00 0.40 0.00
#> TCGA.GM.A3NY.01 4 0.0000 0.8974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A5J0.01 1 0.2793 0.7606 0.80 0.00 0.00 0.00 0.00 0.20
#> TCGA.BH.A0HK.01 2 0.0547 0.9627 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AR.A24Z.01 6 0.2350 0.5157 0.00 0.00 0.02 0.00 0.10 0.88
#> TCGA.S3.A6ZF.01 4 0.5586 -0.2511 0.00 0.00 0.14 0.44 0.42 0.00
#> TCGA.Z7.A8R6.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A66K.01 4 0.1814 0.8060 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.D8.A1JC.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.JL.A3YX.01 3 0.3409 0.5867 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.AN.A0XO.01 5 0.2048 0.6520 0.00 0.00 0.00 0.12 0.88 0.00
#> TCGA.BH.A0DQ.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A2IU.01 1 0.2631 0.7861 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.AR.A250.01 2 0.0000 0.9641 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5D8.01 2 0.0000 0.9641 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AQ.A04H.01 2 0.0000 0.9641 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1XG.01 6 0.5371 0.4312 0.36 0.00 0.12 0.00 0.00 0.52
#> TCGA.AR.A0TZ.01 2 0.0547 0.9627 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AR.A0U3.01 5 0.5438 0.6073 0.00 0.00 0.28 0.16 0.56 0.00
#> TCGA.BH.A0HN.01 3 0.3309 0.6222 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.EW.A1OX.01 5 0.5867 0.4972 0.00 0.00 0.24 0.28 0.48 0.00
#> TCGA.AR.A24V.01 1 0.3499 0.5645 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.AN.A0XS.01 6 0.5371 0.4312 0.36 0.00 0.12 0.00 0.00 0.52
#> TCGA.LL.A6FP.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1L8.01 6 0.5012 0.5154 0.30 0.00 0.10 0.00 0.00 0.60
#> TCGA.A2.A1FW.01 5 0.5692 0.4465 0.00 0.00 0.18 0.32 0.50 0.00
#> TCGA.AC.A62V.01 5 0.5428 0.4970 0.00 0.00 0.14 0.00 0.54 0.32
#> TCGA.E2.A576.01 2 0.0000 0.9641 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A3NW.01 4 0.0937 0.8849 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.A7.A4SB.01 6 0.5083 0.4905 0.32 0.00 0.10 0.00 0.00 0.58
#> TCGA.E9.A245.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A126.01 3 0.4246 0.5399 0.00 0.00 0.58 0.02 0.40 0.00
#> TCGA.AC.A8OR.01 1 0.2728 0.8270 0.86 0.00 0.04 0.00 0.00 0.10
#> TCGA.A7.A4SF.01 1 0.2260 0.8163 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.A7.A26J.01 6 0.2350 0.5157 0.00 0.00 0.02 0.00 0.10 0.88
#> TCGA.A2.A25B.01 6 0.1556 0.5470 0.00 0.00 0.08 0.00 0.00 0.92
#> TCGA.D8.A27W.01 5 0.5837 0.4304 0.00 0.00 0.20 0.34 0.46 0.00
#> TCGA.E9.A2JS.01 2 0.0547 0.9627 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.C8.A3M8.01 2 0.0547 0.9514 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.D8.A1XU.01 4 0.5195 0.0845 0.00 0.00 0.10 0.54 0.36 0.00
#> TCGA.BH.A1ES.06 5 0.4462 0.6691 0.00 0.00 0.28 0.06 0.66 0.00
#> TCGA.D8.A1X6.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PL.A8LX.01 3 0.3309 0.6222 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.EW.A6SA.01 2 0.0547 0.9627 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.E9.A1R5.01 2 0.0000 0.9641 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A54Y.01 5 0.0547 0.6431 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.AC.A3TN.01 4 0.0000 0.8974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EW.A1J3.01 3 0.3756 0.5996 0.00 0.00 0.60 0.00 0.40 0.00
#> TCGA.BH.A1F8.01 2 0.0547 0.9514 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.B6.A0X5.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AQ.A04L.01 4 0.0547 0.8922 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.B6.A0WV.01 6 0.2350 0.5157 0.00 0.00 0.02 0.00 0.10 0.88
#> TCGA.BH.A1FD.01 2 0.0000 0.9641 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A13F.01 4 0.3797 0.2454 0.00 0.00 0.00 0.58 0.42 0.00
#> TCGA.E2.A2P5.01 4 0.0547 0.8922 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.AO.A1KS.01 5 0.4613 0.6731 0.00 0.00 0.26 0.08 0.66 0.00
#> TCGA.BH.A0DD.01 4 0.0547 0.8922 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.BH.A0HX.01 5 0.6088 0.4501 0.00 0.00 0.28 0.00 0.38 0.34
#> TCGA.D8.A1X9.01 5 0.3309 0.5369 0.00 0.00 0.00 0.28 0.72 0.00
#> TCGA.AR.A0TR.01 3 0.3309 0.6222 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.A7.A0DC.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A9FZ.01 2 0.0547 0.9627 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AR.A24X.01 4 0.0000 0.8974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A0GZ.01 4 0.0000 0.8974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B6.A0RM.01 6 0.3851 0.1534 0.00 0.00 0.46 0.00 0.00 0.54
#> TCGA.AO.A12B.01 6 0.5115 0.1620 0.46 0.00 0.08 0.00 0.00 0.46
#> TCGA.BH.A0DH.01 5 0.2048 0.6520 0.00 0.00 0.00 0.12 0.88 0.00
#> TCGA.D8.A1JN.01 2 0.0000 0.9641 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1IE.01 5 0.5447 0.3828 0.00 0.00 0.12 0.00 0.46 0.42
#> TCGA.EW.A1P3.01 3 0.3409 0.5867 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.BH.A8FY.01 5 0.2631 0.6128 0.00 0.00 0.00 0.18 0.82 0.00
#> TCGA.AO.A1KT.01 5 0.1267 0.6539 0.00 0.00 0.00 0.06 0.94 0.00
#> TCGA.E2.A1IU.01 1 0.2793 0.7606 0.80 0.00 0.00 0.00 0.00 0.20
#> TCGA.E9.A22H.01 6 0.3706 0.3528 0.00 0.00 0.38 0.00 0.00 0.62
#> TCGA.D8.A3Z6.01 3 0.4199 0.6218 0.00 0.00 0.60 0.00 0.38 0.02
#> TCGA.AR.A2LK.01 4 0.2260 0.7527 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.B6.A0RI.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A8.A08O.01 6 0.5027 0.5355 0.20 0.00 0.16 0.00 0.00 0.64
#> TCGA.EW.A1P6.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1XF.01 2 0.0547 0.9627 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.A2.A0CT.01 2 0.0547 0.9627 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.E9.A1RG.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1F2.01 6 0.2350 0.5157 0.00 0.00 0.02 0.00 0.10 0.88
#> TCGA.AN.A0XT.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0HI.01 3 0.3309 0.6222 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.B6.A0RL.01 2 0.0547 0.9627 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.E2.A1L9.01 6 0.3851 0.1534 0.00 0.00 0.46 0.00 0.00 0.54
#> TCGA.A7.A26E.01 5 0.4172 0.5279 0.00 0.00 0.04 0.28 0.68 0.00
#> TCGA.BH.A0W3.01 3 0.3706 0.6207 0.00 0.00 0.62 0.00 0.38 0.00
#> TCGA.D8.A1J9.01 2 0.0547 0.9514 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.LL.A7T0.01 4 0.0000 0.8974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.OL.A66O.01 5 0.1092 0.6507 0.00 0.00 0.02 0.02 0.96 0.00
#> TCGA.AO.A03N.01 6 0.3706 0.3528 0.00 0.00 0.38 0.00 0.00 0.62
#> TCGA.AR.A1AP.01 2 0.0000 0.9641 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1PC.01 5 0.5783 0.5624 0.00 0.00 0.28 0.22 0.50 0.00
#> TCGA.3C.AALJ.01 5 0.5304 0.6545 0.00 0.00 0.28 0.04 0.62 0.06
#> TCGA.BH.A42T.01 2 0.0000 0.9641 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A26V.01 4 0.0000 0.8974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A1EV.01 4 0.0937 0.8633 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.D8.A1JA.01 4 0.0937 0.8849 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.E2.A1IN.01 6 0.5295 0.2345 0.44 0.00 0.10 0.00 0.00 0.46
#> TCGA.BH.A0H9.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0RG.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A54X.01 1 0.0547 0.9119 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.C8.A1HN.01 5 0.6070 0.4697 0.00 0.00 0.28 0.00 0.40 0.32
#> TCGA.BH.A0HB.01 3 0.3309 0.6222 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.A2.A25E.01 1 0.4282 0.2514 0.56 0.00 0.02 0.00 0.00 0.42
#> TCGA.B6.A1KN.01 4 0.0547 0.8922 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.AR.A24K.01 4 0.0000 0.8974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EW.A1OZ.01 2 0.0000 0.9641 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S3.AA12.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A1FX.01 6 0.2190 0.5408 0.00 0.00 0.06 0.00 0.04 0.90
#> TCGA.A7.A13G.01 3 0.3309 0.6222 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.LQ.A4E4.01 4 0.0000 0.8974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AQ.A1H2.01 6 0.2512 0.5361 0.00 0.00 0.06 0.00 0.06 0.88
#> TCGA.D8.A27T.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0X4.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0HY.01 2 0.0547 0.9627 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.E2.A15I.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0EU.01 6 0.3756 0.3130 0.00 0.00 0.40 0.00 0.00 0.60
#> TCGA.BH.A0H7.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A1.A0SG.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1J5.01 6 0.3321 0.4548 0.00 0.00 0.08 0.00 0.10 0.82
#> TCGA.D8.A1XR.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A0JB.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A27A.01 5 0.6088 0.4501 0.00 0.00 0.28 0.00 0.38 0.34
#> TCGA.AC.A3EH.01 2 0.3499 0.5393 0.00 0.68 0.00 0.32 0.00 0.00
#> TCGA.C8.A1HK.01 3 0.4482 0.6390 0.00 0.00 0.60 0.00 0.36 0.04
#> TCGA.B6.A0WZ.01 3 0.3309 0.6222 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.A8.A0AD.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A3YJ.01 3 0.3309 0.6222 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.D8.A1Y1.01 3 0.3756 0.5996 0.00 0.00 0.60 0.00 0.40 0.00
#> TCGA.E2.A105.01 5 0.5684 0.5827 0.00 0.00 0.28 0.20 0.52 0.00
#> TCGA.BH.A0E2.01 2 0.2260 0.8214 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.E9.A1R7.01 4 0.0000 0.8974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E2.A10E.01 4 0.0000 0.8974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E9.A249.01 3 0.4144 0.6392 0.00 0.00 0.62 0.00 0.36 0.02
#> TCGA.E2.A1BD.01 4 0.0000 0.8974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A1ET.01 1 0.2454 0.8069 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.LD.A7W6.01 3 0.4420 0.6529 0.00 0.00 0.62 0.00 0.34 0.04
#> TCGA.C8.A1HE.01 4 0.0000 0.8974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AC.A7VB.01 2 0.0547 0.9627 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AO.A12C.01 5 0.4711 0.6683 0.00 0.00 0.28 0.08 0.64 0.00
#> TCGA.D8.A73W.01 3 0.3756 0.5996 0.00 0.00 0.60 0.00 0.40 0.00
#> TCGA.B6.A40B.01 4 0.0937 0.8849 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.AO.A0JI.01 2 0.0547 0.9627 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.PE.A5DD.01 2 0.0547 0.9627 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.A2.A04R.01 6 0.4576 0.3250 0.40 0.00 0.04 0.00 0.00 0.56
#> TCGA.BH.A1F5.01 1 0.5095 -0.0437 0.50 0.00 0.08 0.00 0.00 0.42
#> TCGA.AC.A23E.01 3 0.3309 0.6222 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.D8.A1JS.01 6 0.3647 0.3824 0.00 0.00 0.36 0.00 0.00 0.64
#> TCGA.WT.AB44.01 4 0.0000 0.8974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EW.A424.01 2 0.0000 0.9641 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A408.01 6 0.3647 0.3824 0.00 0.00 0.36 0.00 0.00 0.64
#> TCGA.E2.A1L7.01 2 0.0000 0.9641 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.5T.A9QA.01 2 0.0547 0.9627 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.A2.A0SY.01 2 0.3797 0.2953 0.00 0.58 0.00 0.42 0.00 0.00
#> TCGA.A2.A0YG.01 2 0.1556 0.8914 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.BH.A28Q.01 4 0.0937 0.8767 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.EW.A1J1.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AQ.A0Y5.01 4 0.0000 0.8974 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.3C.AAAU.01 1 0.1814 0.8596 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.A2.A4S0.01 1 0.0547 0.9119 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.AR.A1AV.01 2 0.0000 0.9641 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A3J0.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A6VX.01 3 0.4482 0.6390 0.00 0.00 0.60 0.00 0.36 0.04
#> TCGA.BH.A0BT.01 1 0.0000 0.9220 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1IG.01 5 0.0000 0.6341 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.E9.A1NH.01 3 0.4348 0.6633 0.00 0.00 0.64 0.00 0.32 0.04
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.EW.A2FW.01 7 0.5542 0.5201 0.14 0.00 0.38 0.00 0.00 0.02 0.46
#> TCGA.D8.A1JD.01 7 0.5408 0.4994 0.04 0.00 0.42 0.00 0.00 0.08 0.46
#> TCGA.D8.A1XA.01 6 0.4429 0.6385 0.00 0.00 0.22 0.00 0.00 0.66 0.12
#> TCGA.AO.A1KQ.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A3RF.01 1 0.3525 0.3735 0.56 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.A2.A0SW.01 7 0.5408 -0.3253 0.00 0.00 0.42 0.00 0.08 0.04 0.46
#> TCGA.GM.A2D9.01 5 0.3546 0.1483 0.00 0.00 0.00 0.46 0.54 0.00 0.00
#> TCGA.EW.A1P5.01 3 0.3358 0.4643 0.00 0.00 0.64 0.00 0.00 0.00 0.36
#> TCGA.BH.A1EN.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FN.01 7 0.5132 0.4993 0.08 0.00 0.44 0.00 0.00 0.02 0.46
#> TCGA.EW.A1PD.01 4 0.0000 0.9000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E9.A1N5.01 3 0.0000 0.5617 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1J8.01 2 0.1006 0.9488 0.00 0.96 0.00 0.00 0.02 0.02 0.00
#> TCGA.BH.A0H0.01 7 0.5776 0.5159 0.06 0.00 0.38 0.00 0.00 0.10 0.46
#> TCGA.A2.A0YC.01 7 0.4875 0.4522 0.00 0.00 0.44 0.00 0.00 0.10 0.46
#> TCGA.GM.A2DC.01 5 0.2945 0.5457 0.00 0.00 0.00 0.26 0.74 0.00 0.00
#> TCGA.AR.A24N.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A6S9.01 3 0.2945 0.5090 0.00 0.00 0.74 0.00 0.00 0.00 0.26
#> TCGA.A1.A0SJ.01 4 0.1363 0.8680 0.00 0.00 0.00 0.94 0.02 0.00 0.04
#> TCGA.BH.A1FG.01 3 0.0863 0.5668 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.E2.A1IL.01 7 0.5429 0.5179 0.12 0.00 0.40 0.00 0.00 0.02 0.46
#> TCGA.A7.A3IZ.01 5 0.5293 0.6312 0.00 0.00 0.00 0.10 0.46 0.02 0.42
#> TCGA.E2.A570.01 3 0.0863 0.5244 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.LL.A5YM.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A4ZE.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1P0.01 3 0.1166 0.5312 0.00 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.AR.A24H.01 4 0.4421 0.1741 0.00 0.00 0.00 0.50 0.46 0.02 0.02
#> TCGA.D8.A1XV.01 4 0.3011 0.7857 0.00 0.00 0.00 0.82 0.12 0.00 0.06
#> TCGA.AN.A0XV.01 4 0.4657 0.2996 0.00 0.40 0.00 0.54 0.04 0.02 0.00
#> TCGA.A2.A0YT.01 6 0.4429 0.6385 0.00 0.00 0.22 0.00 0.00 0.66 0.12
#> TCGA.BH.A0B5.01 3 0.5240 0.3648 0.00 0.00 0.58 0.00 0.02 0.14 0.26
#> TCGA.D8.A1JI.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1R6.01 5 0.3867 0.6815 0.00 0.00 0.00 0.00 0.60 0.02 0.38
#> TCGA.D8.A1XZ.01 7 0.5665 -0.6352 0.00 0.00 0.00 0.16 0.40 0.02 0.42
#> TCGA.BH.A0B8.01 6 0.3052 0.4045 0.00 0.00 0.00 0.00 0.20 0.78 0.02
#> TCGA.LL.A6FQ.01 6 0.3011 0.4802 0.00 0.00 0.00 0.00 0.06 0.82 0.12
#> TCGA.EW.A1OY.01 1 0.3546 0.3254 0.54 0.00 0.00 0.00 0.00 0.00 0.46
#> TCGA.B6.A0RP.01 1 0.3525 0.3735 0.56 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.LL.A9Q3.01 4 0.0504 0.8928 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.A1.A0SQ.01 3 0.2569 0.4184 0.00 0.00 0.84 0.00 0.00 0.14 0.02
#> TCGA.E9.A1RB.01 1 0.3358 0.5110 0.64 0.00 0.00 0.00 0.00 0.00 0.36
#> TCGA.B6.A0RO.01 6 0.3519 0.6773 0.00 0.00 0.22 0.00 0.00 0.74 0.04
#> TCGA.AC.A2BM.01 6 0.2864 0.6078 0.00 0.00 0.12 0.00 0.02 0.84 0.02
#> TCGA.EW.A1J6.01 3 0.0000 0.5617 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A40C.01 4 0.1664 0.8934 0.00 0.00 0.00 0.92 0.06 0.02 0.00
#> TCGA.A7.A26H.01 5 0.3867 0.6777 0.00 0.00 0.00 0.00 0.60 0.02 0.38
#> TCGA.E2.A2P6.01 4 0.1664 0.8934 0.00 0.00 0.00 0.92 0.06 0.02 0.00
#> TCGA.A2.A25C.01 3 0.0000 0.5617 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5DA.01 4 0.3841 0.5272 0.00 0.00 0.00 0.68 0.04 0.00 0.28
#> TCGA.LL.A50Y.01 4 0.3086 0.7287 0.00 0.00 0.00 0.80 0.04 0.00 0.16
#> TCGA.LL.A442.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A26Z.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FJ.01 5 0.3943 0.6752 0.00 0.00 0.00 0.00 0.56 0.02 0.42
#> TCGA.E9.A3HO.01 4 0.0000 0.9000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E9.A1NA.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BS.01 1 0.2081 0.7670 0.86 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.B6.A0WT.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0RN.01 5 0.5040 0.6707 0.00 0.00 0.00 0.08 0.54 0.02 0.36
#> TCGA.D8.A1XJ.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A109.01 5 0.3755 0.4475 0.00 0.00 0.00 0.00 0.64 0.34 0.02
#> TCGA.3C.AALI.01 6 0.4873 0.5654 0.00 0.00 0.22 0.00 0.00 0.60 0.18
#> TCGA.BH.A1FL.01 4 0.2278 0.8233 0.00 0.00 0.00 0.88 0.04 0.00 0.08
#> TCGA.E2.A15K.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A15K.06 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1NI.01 6 0.4429 0.6385 0.00 0.00 0.22 0.00 0.00 0.66 0.12
#> TCGA.AO.A12G.01 4 0.0000 0.9000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.C8.A1HO.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AN.A0XR.01 4 0.1664 0.8934 0.00 0.00 0.00 0.92 0.06 0.02 0.00
#> TCGA.BH.A0HA.01 3 0.0000 0.5617 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1XS.01 3 0.4514 -0.4455 0.00 0.00 0.48 0.00 0.00 0.06 0.46
#> TCGA.OL.A6VR.01 7 0.5132 0.4993 0.08 0.00 0.44 0.00 0.00 0.02 0.46
#> TCGA.AR.A1AS.01 7 0.5776 0.5159 0.06 0.00 0.38 0.00 0.00 0.10 0.46
#> TCGA.S3.A6ZG.01 2 0.1006 0.9488 0.00 0.96 0.00 0.00 0.02 0.02 0.00
#> TCGA.AN.A0XP.01 7 0.4875 0.4522 0.00 0.00 0.44 0.00 0.00 0.10 0.46
#> TCGA.D8.A1XD.01 3 0.4622 0.3793 0.00 0.00 0.56 0.02 0.04 0.00 0.38
#> TCGA.AR.A24M.01 3 0.0000 0.5617 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A6NO.01 7 0.5542 0.5201 0.14 0.00 0.38 0.00 0.00 0.02 0.46
#> TCGA.E2.A572.01 7 0.4875 0.4522 0.00 0.00 0.44 0.00 0.00 0.10 0.46
#> TCGA.BH.A1ES.01 3 0.4778 0.4049 0.00 0.00 0.58 0.02 0.06 0.00 0.34
#> TCGA.EW.A1PE.01 3 0.0000 0.5617 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0H6.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A2KD.01 3 0.4514 -0.4455 0.00 0.00 0.48 0.00 0.00 0.06 0.46
#> TCGA.S3.A6ZH.01 6 0.4214 0.4967 0.00 0.00 0.40 0.00 0.00 0.56 0.04
#> TCGA.BH.A1EX.01 3 0.4710 -0.4689 0.00 0.00 0.46 0.00 0.00 0.08 0.46
#> TCGA.AO.A125.01 5 0.3968 0.6610 0.00 0.00 0.00 0.00 0.54 0.02 0.44
#> TCGA.UL.AAZ6.01 5 0.3755 0.4475 0.00 0.00 0.00 0.00 0.64 0.34 0.02
#> TCGA.A2.A0CK.01 3 0.4328 0.4283 0.00 0.00 0.60 0.00 0.06 0.00 0.34
#> TCGA.PE.A5DC.01 5 0.4869 0.6721 0.00 0.00 0.00 0.06 0.54 0.02 0.38
#> TCGA.EW.A6SC.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A273.01 3 0.3994 0.2890 0.00 0.00 0.50 0.00 0.02 0.00 0.48
#> TCGA.AR.A0U2.01 6 0.1718 0.6471 0.00 0.00 0.04 0.00 0.00 0.92 0.04
#> TCGA.C8.A1HL.01 6 0.5718 0.3903 0.18 0.00 0.04 0.00 0.00 0.54 0.24
#> TCGA.E2.A9RU.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JJ.01 4 0.0000 0.9000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E2.A1B4.01 1 0.3525 0.3735 0.56 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.B6.A1KC.01 5 0.2422 0.5796 0.00 0.00 0.00 0.00 0.82 0.18 0.00
#> TCGA.E9.A5UP.01 4 0.1006 0.8990 0.00 0.00 0.00 0.96 0.02 0.02 0.00
#> TCGA.A2.A1G4.01 4 0.0000 0.9000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A1FV.01 6 0.3199 0.4022 0.00 0.00 0.00 0.00 0.14 0.80 0.06
#> TCGA.D8.A1XC.01 3 0.0000 0.5617 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A15J.01 4 0.0000 0.9000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S3.AA11.01 6 0.3413 0.1898 0.00 0.00 0.00 0.00 0.38 0.62 0.00
#> TCGA.AC.A3QQ.01 7 0.5625 0.5168 0.06 0.00 0.40 0.00 0.00 0.08 0.46
#> TCGA.AQ.A54O.01 3 0.0863 0.5668 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.D8.A1JT.01 7 0.5134 0.4608 0.00 0.00 0.40 0.00 0.00 0.14 0.46
#> TCGA.AR.A2LL.01 4 0.0000 0.9000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A1X7.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A247.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1X5.01 7 0.5534 -0.6325 0.00 0.00 0.00 0.00 0.36 0.24 0.40
#> TCGA.A8.A075.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A73X.01 4 0.3011 0.7611 0.00 0.00 0.00 0.82 0.06 0.00 0.12
#> TCGA.E9.A3Q9.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0E1.01 3 0.0863 0.5668 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.EW.A423.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A106.01 6 0.3519 0.6773 0.00 0.00 0.22 0.00 0.00 0.74 0.04
#> TCGA.AR.A0TV.01 4 0.1928 0.8875 0.00 0.00 0.00 0.90 0.08 0.02 0.00
#> TCGA.E2.A56Z.01 6 0.3417 0.6664 0.00 0.00 0.26 0.00 0.00 0.72 0.02
#> TCGA.AC.A2FM.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A0D9.01 3 0.3985 -0.4015 0.00 0.00 0.52 0.00 0.00 0.02 0.46
#> TCGA.AC.A5XU.01 4 0.1928 0.8875 0.00 0.00 0.00 0.90 0.08 0.02 0.00
#> TCGA.BH.A204.01 6 0.1006 0.6019 0.00 0.00 0.00 0.00 0.02 0.96 0.02
#> TCGA.B6.A0WW.01 4 0.1928 0.8875 0.00 0.00 0.00 0.90 0.08 0.02 0.00
#> TCGA.D8.A1XL.01 3 0.4070 0.4452 0.00 0.00 0.62 0.00 0.04 0.00 0.34
#> TCGA.E9.A5UO.01 5 0.4869 0.6721 0.00 0.00 0.00 0.06 0.54 0.02 0.38
#> TCGA.A2.A0SV.01 5 0.3909 0.6759 0.00 0.00 0.00 0.00 0.58 0.02 0.40
#> TCGA.OL.A5RZ.01 6 0.4574 0.5139 0.00 0.00 0.06 0.00 0.10 0.72 0.12
#> TCGA.AR.A24R.01 4 0.3417 0.6370 0.00 0.00 0.00 0.72 0.26 0.02 0.00
#> TCGA.AO.A1KP.01 5 0.2832 0.6615 0.00 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.E9.A1RE.01 4 0.3061 0.8362 0.00 0.08 0.00 0.84 0.06 0.02 0.00
#> TCGA.GM.A2DM.01 1 0.3358 0.5110 0.64 0.00 0.00 0.00 0.00 0.00 0.36
#> TCGA.A2.A0YF.01 7 0.4710 0.4410 0.00 0.00 0.46 0.00 0.00 0.08 0.46
#> TCGA.C8.A274.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A1HM.01 6 0.4873 0.5654 0.00 0.00 0.22 0.00 0.00 0.60 0.18
#> TCGA.E9.A1RC.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A6R8.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FM.01 6 0.4308 0.6355 0.00 0.00 0.16 0.00 0.02 0.72 0.10
#> TCGA.D8.A1JP.01 4 0.0000 0.9000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AO.A0JM.01 4 0.1928 0.8875 0.00 0.00 0.00 0.90 0.08 0.02 0.00
#> TCGA.BH.A0DS.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V7.A7HQ.01 7 0.5709 0.2803 0.34 0.00 0.18 0.00 0.00 0.02 0.46
#> TCGA.EW.A1PA.01 5 0.3459 0.6325 0.00 0.00 0.00 0.00 0.60 0.00 0.40
#> TCGA.AC.A3TM.01 7 0.5665 -0.3457 0.00 0.00 0.40 0.02 0.16 0.00 0.42
#> TCGA.AR.A2LE.01 7 0.3985 -0.3786 0.00 0.00 0.46 0.00 0.02 0.00 0.52
#> TCGA.GM.A3NY.01 4 0.0000 0.9000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A5J0.01 1 0.3525 0.3735 0.56 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.BH.A0HK.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A24Z.01 6 0.4429 0.6385 0.00 0.00 0.22 0.00 0.00 0.66 0.12
#> TCGA.S3.A6ZF.01 5 0.2912 0.5849 0.00 0.00 0.00 0.14 0.82 0.04 0.00
#> TCGA.Z7.A8R6.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A66K.01 4 0.1860 0.8897 0.00 0.02 0.00 0.92 0.04 0.02 0.00
#> TCGA.D8.A1JC.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.JL.A3YX.01 3 0.0504 0.5586 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.AN.A0XO.01 5 0.3985 0.6503 0.00 0.00 0.00 0.00 0.52 0.02 0.46
#> TCGA.BH.A0DQ.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A2IU.01 1 0.3525 0.3735 0.56 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.AR.A250.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5D8.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AQ.A04H.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1XG.01 7 0.5132 0.4993 0.08 0.00 0.44 0.00 0.00 0.02 0.46
#> TCGA.AR.A0TZ.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A0U3.01 5 0.3186 0.5694 0.00 0.00 0.00 0.00 0.76 0.22 0.02
#> TCGA.BH.A0HN.01 3 0.0000 0.5617 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1OX.01 5 0.3541 0.6010 0.00 0.00 0.00 0.08 0.80 0.10 0.02
#> TCGA.AR.A24V.01 1 0.4710 0.1342 0.46 0.00 0.00 0.00 0.00 0.08 0.46
#> TCGA.AN.A0XS.01 7 0.5429 0.5180 0.12 0.00 0.40 0.00 0.00 0.02 0.46
#> TCGA.LL.A6FP.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1L8.01 7 0.5947 0.5230 0.08 0.00 0.36 0.00 0.00 0.10 0.46
#> TCGA.A2.A1FW.01 5 0.1363 0.6277 0.00 0.00 0.00 0.02 0.94 0.04 0.00
#> TCGA.AC.A62V.01 6 0.4045 0.3106 0.00 0.00 0.00 0.00 0.14 0.72 0.14
#> TCGA.E2.A576.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A3NW.01 4 0.1433 0.8733 0.00 0.00 0.00 0.92 0.08 0.00 0.00
#> TCGA.A7.A4SB.01 7 0.5625 0.5168 0.06 0.00 0.40 0.00 0.00 0.08 0.46
#> TCGA.E9.A245.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A126.01 3 0.4869 0.3563 0.00 0.00 0.54 0.02 0.06 0.00 0.38
#> TCGA.AC.A8OR.01 1 0.3358 0.5110 0.64 0.00 0.00 0.00 0.00 0.00 0.36
#> TCGA.A7.A4SF.01 1 0.1671 0.7946 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.A7.A26J.01 6 0.4243 0.6529 0.00 0.00 0.22 0.00 0.00 0.68 0.10
#> TCGA.A2.A25B.01 6 0.5421 0.2569 0.00 0.00 0.22 0.00 0.00 0.46 0.32
#> TCGA.D8.A27W.01 5 0.3058 0.5885 0.00 0.00 0.00 0.10 0.82 0.08 0.00
#> TCGA.E9.A2JS.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A3M8.01 2 0.2509 0.8740 0.00 0.88 0.00 0.06 0.04 0.02 0.00
#> TCGA.D8.A1XU.01 5 0.2945 0.5399 0.00 0.00 0.00 0.26 0.74 0.00 0.00
#> TCGA.BH.A1ES.06 5 0.2945 0.5184 0.00 0.00 0.00 0.00 0.74 0.26 0.00
#> TCGA.D8.A1X6.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PL.A8LX.01 3 0.0863 0.5244 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.EW.A6SA.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1R5.01 2 0.1006 0.9488 0.00 0.96 0.00 0.00 0.02 0.02 0.00
#> TCGA.E9.A54Y.01 5 0.4669 0.6513 0.00 0.00 0.00 0.00 0.52 0.08 0.40
#> TCGA.AC.A3TN.01 4 0.0000 0.9000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EW.A1J3.01 3 0.3546 0.3400 0.00 0.00 0.54 0.00 0.00 0.00 0.46
#> TCGA.BH.A1F8.01 2 0.2769 0.8508 0.00 0.86 0.00 0.08 0.04 0.02 0.00
#> TCGA.B6.A0X5.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AQ.A04L.01 4 0.1928 0.8875 0.00 0.00 0.00 0.90 0.08 0.02 0.00
#> TCGA.B6.A0WV.01 6 0.4243 0.6529 0.00 0.00 0.22 0.00 0.00 0.68 0.10
#> TCGA.BH.A1FD.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A13F.01 5 0.5451 0.6383 0.00 0.00 0.00 0.16 0.54 0.02 0.28
#> TCGA.E2.A2P5.01 4 0.1664 0.8934 0.00 0.00 0.00 0.92 0.06 0.02 0.00
#> TCGA.AO.A1KS.01 5 0.3086 0.5799 0.00 0.00 0.00 0.00 0.80 0.16 0.04
#> TCGA.BH.A0DD.01 4 0.3780 0.7168 0.00 0.00 0.00 0.72 0.24 0.02 0.02
#> TCGA.BH.A0HX.01 6 0.3417 0.3602 0.00 0.00 0.00 0.00 0.26 0.72 0.02
#> TCGA.D8.A1X9.01 5 0.4869 0.6721 0.00 0.00 0.00 0.06 0.54 0.02 0.38
#> TCGA.AR.A0TR.01 3 0.0000 0.5617 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A0DC.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A9FZ.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A24X.01 4 0.1363 0.8956 0.00 0.00 0.00 0.94 0.04 0.02 0.00
#> TCGA.BH.A0GZ.01 4 0.0000 0.9000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B6.A0RM.01 3 0.3968 -0.3745 0.00 0.00 0.54 0.00 0.00 0.02 0.44
#> TCGA.AO.A12B.01 7 0.5806 0.4794 0.22 0.00 0.30 0.00 0.00 0.02 0.46
#> TCGA.BH.A0DH.01 5 0.4869 0.6721 0.00 0.00 0.00 0.06 0.54 0.02 0.38
#> TCGA.D8.A1JN.01 2 0.1006 0.9488 0.00 0.96 0.00 0.00 0.02 0.02 0.00
#> TCGA.E2.A1IE.01 6 0.1664 0.6039 0.00 0.00 0.06 0.00 0.00 0.92 0.02
#> TCGA.EW.A1P3.01 3 0.0000 0.5617 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A8FY.01 5 0.4869 0.6721 0.00 0.00 0.00 0.06 0.54 0.02 0.38
#> TCGA.AO.A1KT.01 5 0.4669 0.6513 0.00 0.00 0.00 0.00 0.52 0.08 0.40
#> TCGA.E2.A1IU.01 1 0.3525 0.3735 0.56 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.E9.A22H.01 3 0.4514 -0.4455 0.00 0.00 0.48 0.00 0.00 0.06 0.46
#> TCGA.D8.A3Z6.01 3 0.3994 0.2890 0.00 0.00 0.50 0.00 0.02 0.00 0.48
#> TCGA.AR.A2LK.01 4 0.1860 0.8897 0.00 0.02 0.00 0.92 0.04 0.02 0.00
#> TCGA.B6.A0RI.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A8.A08O.01 7 0.5132 0.4747 0.02 0.00 0.44 0.00 0.00 0.08 0.46
#> TCGA.EW.A1P6.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1XF.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0CT.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RG.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1F2.01 6 0.3388 0.6816 0.00 0.00 0.20 0.00 0.00 0.76 0.04
#> TCGA.AN.A0XT.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0HI.01 3 0.0863 0.5668 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.B6.A0RL.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1L9.01 3 0.3525 -0.3443 0.00 0.00 0.56 0.00 0.00 0.00 0.44
#> TCGA.A7.A26E.01 5 0.4930 0.5857 0.00 0.00 0.00 0.16 0.58 0.00 0.26
#> TCGA.BH.A0W3.01 3 0.3525 0.3671 0.00 0.00 0.56 0.00 0.00 0.00 0.44
#> TCGA.D8.A1J9.01 2 0.2509 0.8740 0.00 0.88 0.00 0.06 0.04 0.02 0.00
#> TCGA.LL.A7T0.01 4 0.0000 0.9000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.OL.A66O.01 5 0.4175 0.6809 0.00 0.00 0.00 0.00 0.58 0.04 0.38
#> TCGA.AO.A03N.01 3 0.4278 -0.4258 0.00 0.00 0.50 0.00 0.00 0.04 0.46
#> TCGA.AR.A1AP.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1PC.01 5 0.2906 0.5878 0.00 0.00 0.00 0.00 0.80 0.18 0.02
#> TCGA.3C.AALJ.01 5 0.3139 0.5024 0.00 0.00 0.00 0.00 0.70 0.30 0.00
#> TCGA.BH.A42T.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A26V.01 4 0.1363 0.8956 0.00 0.00 0.00 0.94 0.04 0.02 0.00
#> TCGA.BH.A1EV.01 4 0.1006 0.8990 0.00 0.00 0.00 0.96 0.02 0.02 0.00
#> TCGA.D8.A1JA.01 4 0.1433 0.8733 0.00 0.00 0.00 0.92 0.08 0.00 0.00
#> TCGA.E2.A1IN.01 7 0.5635 0.5126 0.16 0.00 0.36 0.00 0.00 0.02 0.46
#> TCGA.BH.A0H9.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0RG.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A54X.01 1 0.0863 0.8488 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.C8.A1HN.01 6 0.3294 0.2941 0.00 0.00 0.00 0.00 0.34 0.66 0.00
#> TCGA.BH.A0HB.01 3 0.0000 0.5617 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A25E.01 7 0.5293 -0.0551 0.42 0.00 0.02 0.00 0.00 0.10 0.46
#> TCGA.B6.A1KN.01 4 0.1664 0.8934 0.00 0.00 0.00 0.92 0.06 0.02 0.00
#> TCGA.AR.A24K.01 4 0.0000 0.9000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EW.A1OZ.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S3.AA12.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A1FX.01 6 0.4873 0.5630 0.00 0.00 0.22 0.00 0.00 0.60 0.18
#> TCGA.A7.A13G.01 3 0.0863 0.5244 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.LQ.A4E4.01 4 0.1664 0.8934 0.00 0.00 0.00 0.92 0.06 0.02 0.00
#> TCGA.AQ.A1H2.01 6 0.4742 0.5916 0.00 0.00 0.22 0.00 0.00 0.62 0.16
#> TCGA.D8.A27T.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0X4.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0HY.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A15I.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0EU.01 3 0.3985 -0.4015 0.00 0.00 0.52 0.00 0.00 0.02 0.46
#> TCGA.BH.A0H7.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A1.A0SG.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1J5.01 6 0.3637 0.6719 0.00 0.00 0.24 0.00 0.00 0.72 0.04
#> TCGA.D8.A1XR.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A0JB.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A27A.01 6 0.3417 0.3602 0.00 0.00 0.00 0.00 0.26 0.72 0.02
#> TCGA.AC.A3EH.01 4 0.4388 0.5498 0.00 0.30 0.00 0.64 0.04 0.02 0.00
#> TCGA.C8.A1HK.01 3 0.4577 0.4249 0.00 0.00 0.58 0.00 0.02 0.04 0.36
#> TCGA.B6.A0WZ.01 3 0.0863 0.5670 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.A8.A0AD.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A3YJ.01 3 0.1433 0.5575 0.00 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.D8.A1Y1.01 7 0.5574 -0.3161 0.00 0.00 0.42 0.00 0.10 0.04 0.44
#> TCGA.E2.A105.01 5 0.3186 0.5694 0.00 0.00 0.00 0.00 0.76 0.22 0.02
#> TCGA.BH.A0E2.01 2 0.4388 0.4843 0.00 0.64 0.00 0.30 0.04 0.02 0.00
#> TCGA.E9.A1R7.01 4 0.1363 0.8973 0.00 0.00 0.00 0.94 0.04 0.02 0.00
#> TCGA.E2.A10E.01 4 0.0000 0.9000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E9.A249.01 3 0.3815 0.4442 0.00 0.00 0.62 0.00 0.02 0.00 0.36
#> TCGA.E2.A1BD.01 4 0.0504 0.9002 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.BH.A1ET.01 1 0.3459 0.4476 0.60 0.00 0.00 0.00 0.00 0.00 0.40
#> TCGA.LD.A7W6.01 3 0.3358 0.4643 0.00 0.00 0.64 0.00 0.00 0.00 0.36
#> TCGA.C8.A1HE.01 4 0.0000 0.9000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A7VB.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A12C.01 5 0.2945 0.5184 0.00 0.00 0.00 0.00 0.74 0.26 0.00
#> TCGA.D8.A73W.01 7 0.5132 -0.3357 0.00 0.00 0.44 0.00 0.08 0.02 0.46
#> TCGA.B6.A40B.01 4 0.0000 0.9000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AO.A0JI.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PE.A5DD.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A04R.01 7 0.6490 0.3874 0.24 0.00 0.18 0.00 0.00 0.12 0.46
#> TCGA.BH.A1F5.01 7 0.5766 0.4892 0.20 0.00 0.32 0.00 0.00 0.02 0.46
#> TCGA.AC.A23E.01 3 0.0863 0.5670 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.D8.A1JS.01 3 0.4514 -0.4455 0.00 0.00 0.48 0.00 0.00 0.06 0.46
#> TCGA.WT.AB44.01 4 0.0000 0.9000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EW.A424.01 2 0.1006 0.9488 0.00 0.96 0.00 0.00 0.02 0.02 0.00
#> TCGA.B6.A408.01 3 0.4514 -0.4455 0.00 0.00 0.48 0.00 0.00 0.06 0.46
#> TCGA.E2.A1L7.01 2 0.0504 0.9616 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.5T.A9QA.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0SY.01 4 0.3991 0.6708 0.00 0.22 0.00 0.72 0.04 0.02 0.00
#> TCGA.A2.A0YG.01 2 0.3000 0.8265 0.00 0.84 0.00 0.10 0.04 0.02 0.00
#> TCGA.BH.A28Q.01 4 0.1928 0.8361 0.00 0.00 0.00 0.90 0.02 0.00 0.08
#> TCGA.EW.A1J1.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AQ.A0Y5.01 4 0.1664 0.8934 0.00 0.00 0.00 0.92 0.06 0.02 0.00
#> TCGA.3C.AAAU.01 1 0.3459 0.4476 0.60 0.00 0.00 0.00 0.00 0.00 0.40
#> TCGA.A2.A4S0.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AV.01 2 0.0000 0.9740 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A3J0.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A6VX.01 3 0.4175 0.4040 0.00 0.00 0.58 0.00 0.04 0.00 0.38
#> TCGA.BH.A0BT.01 1 0.0000 0.8757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1IG.01 5 0.4692 0.6469 0.00 0.00 0.00 0.00 0.50 0.08 0.42
#> TCGA.E9.A1NH.01 3 0.3358 0.4643 0.00 0.00 0.64 0.00 0.00 0.00 0.36
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.EW.A2FW.01 7 0.1563 0.7777 0.10 0.00 0.00 0.00 0.00 0.00 0.90 0.00
#> TCGA.D8.A1JD.01 7 0.2407 0.7697 0.08 0.00 0.00 0.00 0.00 0.00 0.86 0.06
#> TCGA.D8.A1XA.01 6 0.2807 0.8281 0.00 0.00 0.02 0.00 0.00 0.84 0.10 0.04
#> TCGA.AO.A1KQ.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A3RF.01 7 0.3907 0.5245 0.38 0.00 0.00 0.00 0.00 0.00 0.58 0.04
#> TCGA.A2.A0SW.01 8 0.3737 0.1969 0.00 0.00 0.48 0.00 0.00 0.02 0.00 0.50
#> TCGA.GM.A2D9.01 5 0.4233 0.3564 0.00 0.00 0.00 0.34 0.60 0.00 0.02 0.04
#> TCGA.EW.A1P5.01 3 0.0941 0.7246 0.00 0.00 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.BH.A1EN.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FN.01 7 0.2348 0.7409 0.04 0.00 0.02 0.00 0.00 0.00 0.88 0.06
#> TCGA.EW.A1PD.01 4 0.2204 0.8314 0.00 0.00 0.02 0.90 0.02 0.00 0.02 0.04
#> TCGA.E9.A1N5.01 3 0.3757 0.7320 0.00 0.00 0.68 0.00 0.00 0.00 0.26 0.06
#> TCGA.D8.A1J8.01 2 0.1275 0.9185 0.00 0.94 0.00 0.04 0.00 0.00 0.00 0.02
#> TCGA.BH.A0H0.01 7 0.2947 0.7497 0.06 0.00 0.00 0.00 0.00 0.04 0.84 0.06
#> TCGA.A2.A0YC.01 7 0.2914 0.7267 0.00 0.00 0.04 0.00 0.00 0.04 0.84 0.08
#> TCGA.GM.A2DC.01 5 0.2807 0.6992 0.00 0.00 0.00 0.10 0.84 0.00 0.02 0.04
#> TCGA.AR.A24N.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A6S9.01 3 0.1557 0.7454 0.00 0.00 0.92 0.00 0.00 0.00 0.06 0.02
#> TCGA.A1.A0SJ.01 4 0.2532 0.8229 0.00 0.00 0.04 0.88 0.02 0.00 0.02 0.04
#> TCGA.BH.A1FG.01 3 0.3757 0.7346 0.00 0.00 0.68 0.00 0.00 0.00 0.26 0.06
#> TCGA.E2.A1IL.01 7 0.2407 0.7573 0.08 0.00 0.00 0.00 0.00 0.00 0.86 0.06
#> TCGA.A7.A3IZ.01 8 0.4428 0.7319 0.00 0.00 0.08 0.04 0.14 0.00 0.02 0.72
#> TCGA.E2.A570.01 3 0.4050 0.6494 0.00 0.00 0.60 0.00 0.00 0.00 0.34 0.06
#> TCGA.LL.A5YM.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A4ZE.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1P0.01 3 0.4180 0.7422 0.00 0.00 0.70 0.00 0.00 0.06 0.20 0.04
#> TCGA.AR.A24H.01 8 0.6011 0.0224 0.00 0.00 0.00 0.36 0.18 0.02 0.04 0.40
#> TCGA.D8.A1XV.01 8 0.3714 0.0358 0.00 0.00 0.02 0.44 0.00 0.00 0.00 0.54
#> TCGA.AN.A0XV.01 4 0.5355 0.4095 0.00 0.34 0.00 0.54 0.02 0.02 0.04 0.04
#> TCGA.A2.A0YT.01 6 0.3002 0.8257 0.00 0.00 0.02 0.00 0.00 0.82 0.12 0.04
#> TCGA.BH.A0B5.01 3 0.3941 0.4838 0.00 0.00 0.68 0.00 0.00 0.26 0.02 0.04
#> TCGA.D8.A1JI.01 1 0.1887 0.8844 0.90 0.00 0.00 0.00 0.00 0.00 0.06 0.04
#> TCGA.E9.A1R6.01 8 0.3594 0.6948 0.00 0.00 0.04 0.00 0.28 0.00 0.00 0.68
#> TCGA.D8.A1XZ.01 8 0.3687 0.6730 0.00 0.00 0.08 0.08 0.06 0.00 0.00 0.78
#> TCGA.BH.A0B8.01 6 0.2350 0.7062 0.00 0.00 0.00 0.00 0.10 0.86 0.00 0.04
#> TCGA.LL.A6FQ.01 6 0.1557 0.7768 0.00 0.00 0.02 0.00 0.00 0.92 0.00 0.06
#> TCGA.EW.A1OY.01 7 0.4050 0.5770 0.34 0.00 0.00 0.00 0.00 0.00 0.60 0.06
#> TCGA.B6.A0RP.01 7 0.3907 0.5245 0.38 0.00 0.00 0.00 0.00 0.00 0.58 0.04
#> TCGA.LL.A9Q3.01 4 0.1091 0.8390 0.00 0.00 0.00 0.94 0.06 0.00 0.00 0.00
#> TCGA.A1.A0SQ.01 3 0.4982 0.5573 0.00 0.00 0.58 0.00 0.00 0.18 0.22 0.02
#> TCGA.E9.A1RB.01 7 0.3729 0.3406 0.46 0.00 0.00 0.00 0.00 0.00 0.52 0.02
#> TCGA.B6.A0RO.01 6 0.2025 0.8271 0.00 0.00 0.02 0.00 0.00 0.88 0.10 0.00
#> TCGA.AC.A2BM.01 6 0.3402 0.7728 0.00 0.00 0.06 0.00 0.06 0.82 0.02 0.04
#> TCGA.EW.A1J6.01 3 0.3757 0.7346 0.00 0.00 0.68 0.00 0.00 0.00 0.26 0.06
#> TCGA.B6.A40C.01 4 0.3262 0.8186 0.00 0.00 0.00 0.82 0.02 0.02 0.04 0.10
#> TCGA.A7.A26H.01 8 0.4134 0.6848 0.00 0.00 0.08 0.00 0.30 0.00 0.00 0.62
#> TCGA.E2.A2P6.01 4 0.3262 0.8186 0.00 0.00 0.00 0.82 0.02 0.02 0.04 0.10
#> TCGA.A2.A25C.01 3 0.3660 0.7450 0.00 0.00 0.70 0.00 0.00 0.00 0.24 0.06
#> TCGA.OL.A5DA.01 4 0.4262 0.6923 0.00 0.00 0.12 0.74 0.04 0.00 0.02 0.08
#> TCGA.LL.A50Y.01 4 0.4110 0.7228 0.00 0.00 0.10 0.76 0.06 0.00 0.02 0.06
#> TCGA.LL.A442.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A26Z.01 1 0.0941 0.9452 0.96 0.00 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.BH.A1FJ.01 8 0.4314 0.7129 0.00 0.00 0.08 0.00 0.24 0.02 0.00 0.66
#> TCGA.E9.A3HO.01 4 0.0941 0.8477 0.00 0.00 0.02 0.96 0.00 0.00 0.02 0.00
#> TCGA.E9.A1NA.01 2 0.0471 0.9550 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.BH.A0BS.01 1 0.3095 0.5846 0.74 0.00 0.00 0.00 0.00 0.00 0.24 0.02
#> TCGA.B6.A0WT.01 1 0.1275 0.9290 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.B6.A0RN.01 8 0.4492 0.7171 0.00 0.00 0.04 0.06 0.18 0.00 0.02 0.70
#> TCGA.D8.A1XJ.01 2 0.0471 0.9550 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.E2.A109.01 5 0.2888 0.7192 0.00 0.00 0.00 0.00 0.80 0.16 0.00 0.04
#> TCGA.3C.AALI.01 6 0.3154 0.7965 0.00 0.00 0.00 0.00 0.00 0.78 0.16 0.06
#> TCGA.BH.A1FL.01 4 0.2940 0.7922 0.00 0.00 0.02 0.84 0.02 0.00 0.02 0.10
#> TCGA.E2.A15K.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A15K.06 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1NI.01 6 0.3002 0.8257 0.00 0.00 0.02 0.00 0.00 0.82 0.12 0.04
#> TCGA.AO.A12G.01 4 0.0471 0.8492 0.00 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.C8.A1HO.01 2 0.0471 0.9550 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.AN.A0XR.01 4 0.3262 0.8186 0.00 0.00 0.00 0.82 0.02 0.02 0.04 0.10
#> TCGA.BH.A0HA.01 3 0.3922 0.6990 0.00 0.00 0.64 0.00 0.00 0.00 0.30 0.06
#> TCGA.D8.A1XS.01 7 0.2165 0.7020 0.00 0.00 0.06 0.00 0.00 0.00 0.88 0.06
#> TCGA.OL.A6VR.01 7 0.2624 0.7461 0.06 0.00 0.02 0.00 0.00 0.00 0.86 0.06
#> TCGA.AR.A1AS.01 7 0.3454 0.7347 0.08 0.00 0.00 0.00 0.00 0.06 0.80 0.06
#> TCGA.S3.A6ZG.01 2 0.0471 0.9452 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.AN.A0XP.01 7 0.2674 0.7164 0.00 0.00 0.06 0.00 0.00 0.04 0.86 0.04
#> TCGA.D8.A1XD.01 3 0.2020 0.6941 0.00 0.00 0.90 0.00 0.06 0.00 0.02 0.02
#> TCGA.AR.A24M.01 3 0.3757 0.7320 0.00 0.00 0.68 0.00 0.00 0.00 0.26 0.06
#> TCGA.AC.A6NO.01 7 0.2547 0.7727 0.12 0.00 0.00 0.00 0.00 0.00 0.84 0.04
#> TCGA.E2.A572.01 7 0.2071 0.7346 0.00 0.00 0.04 0.00 0.00 0.02 0.90 0.04
#> TCGA.BH.A1ES.01 3 0.2265 0.6816 0.00 0.00 0.88 0.00 0.08 0.00 0.02 0.02
#> TCGA.EW.A1PE.01 3 0.3922 0.6990 0.00 0.00 0.64 0.00 0.00 0.00 0.30 0.06
#> TCGA.BH.A0H6.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A2KD.01 7 0.2165 0.7258 0.00 0.00 0.06 0.00 0.00 0.00 0.88 0.06
#> TCGA.S3.A6ZH.01 6 0.4727 0.6237 0.00 0.00 0.22 0.00 0.00 0.62 0.14 0.02
#> TCGA.BH.A1EX.01 7 0.2165 0.7258 0.00 0.00 0.06 0.00 0.00 0.00 0.88 0.06
#> TCGA.AO.A125.01 8 0.4575 0.7019 0.00 0.00 0.12 0.00 0.22 0.00 0.02 0.64
#> TCGA.UL.AAZ6.01 5 0.2888 0.7192 0.00 0.00 0.00 0.00 0.80 0.16 0.00 0.04
#> TCGA.A2.A0CK.01 3 0.2020 0.7200 0.00 0.00 0.90 0.00 0.06 0.00 0.02 0.02
#> TCGA.PE.A5DC.01 8 0.3675 0.7259 0.00 0.00 0.08 0.02 0.14 0.00 0.00 0.76
#> TCGA.EW.A6SC.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A273.01 3 0.2856 0.5081 0.00 0.00 0.78 0.00 0.00 0.02 0.00 0.20
#> TCGA.AR.A0U2.01 6 0.2204 0.7995 0.00 0.00 0.02 0.00 0.02 0.90 0.04 0.02
#> TCGA.C8.A1HL.01 6 0.4433 0.6843 0.06 0.00 0.00 0.00 0.00 0.68 0.20 0.06
#> TCGA.E2.A9RU.01 2 0.0471 0.9550 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.D8.A1JJ.01 4 0.2204 0.8314 0.00 0.00 0.02 0.90 0.02 0.00 0.02 0.04
#> TCGA.E2.A1B4.01 7 0.3746 0.6105 0.32 0.00 0.00 0.00 0.00 0.00 0.64 0.04
#> TCGA.B6.A1KC.01 5 0.0471 0.7856 0.00 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.E9.A5UP.01 4 0.0941 0.8495 0.00 0.00 0.02 0.96 0.00 0.00 0.00 0.02
#> TCGA.A2.A1G4.01 4 0.1408 0.8445 0.00 0.00 0.02 0.94 0.02 0.00 0.02 0.00
#> TCGA.A2.A1FV.01 6 0.3970 0.5182 0.00 0.00 0.00 0.00 0.10 0.68 0.00 0.22
#> TCGA.D8.A1XC.01 3 0.2534 0.7694 0.00 0.00 0.78 0.00 0.00 0.00 0.22 0.00
#> TCGA.E2.A15J.01 4 0.0941 0.8477 0.00 0.00 0.02 0.96 0.00 0.00 0.02 0.00
#> TCGA.S3.AA11.01 5 0.4008 0.1024 0.00 0.00 0.00 0.00 0.48 0.48 0.00 0.04
#> TCGA.AC.A3QQ.01 7 0.2407 0.7697 0.08 0.00 0.00 0.00 0.00 0.00 0.86 0.06
#> TCGA.AQ.A54O.01 3 0.3757 0.7346 0.00 0.00 0.68 0.00 0.00 0.00 0.26 0.06
#> TCGA.D8.A1JT.01 7 0.3185 0.6869 0.00 0.00 0.04 0.00 0.00 0.08 0.82 0.06
#> TCGA.AR.A2LL.01 4 0.0941 0.8473 0.00 0.00 0.02 0.96 0.02 0.00 0.00 0.00
#> TCGA.D8.A1X7.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A247.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1X5.01 8 0.6461 0.2707 0.00 0.00 0.24 0.00 0.14 0.30 0.00 0.32
#> TCGA.A8.A075.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A73X.01 4 0.4282 0.6969 0.00 0.00 0.10 0.74 0.10 0.00 0.02 0.04
#> TCGA.E9.A3Q9.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0E1.01 3 0.3757 0.7346 0.00 0.00 0.68 0.00 0.00 0.00 0.26 0.06
#> TCGA.EW.A423.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A106.01 6 0.2025 0.8271 0.00 0.00 0.02 0.00 0.00 0.88 0.10 0.00
#> TCGA.AR.A0TV.01 4 0.3627 0.8078 0.00 0.00 0.00 0.78 0.02 0.02 0.04 0.14
#> TCGA.E2.A56Z.01 6 0.2132 0.8199 0.00 0.00 0.04 0.00 0.00 0.88 0.08 0.00
#> TCGA.AC.A2FM.01 2 0.0471 0.9550 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.A7.A0D9.01 7 0.3299 0.5529 0.00 0.00 0.18 0.00 0.00 0.00 0.76 0.06
#> TCGA.AC.A5XU.01 4 0.3454 0.8107 0.00 0.00 0.00 0.80 0.02 0.02 0.04 0.12
#> TCGA.BH.A204.01 6 0.2071 0.7595 0.00 0.00 0.00 0.00 0.04 0.90 0.02 0.04
#> TCGA.B6.A0WW.01 4 0.3785 0.7973 0.00 0.00 0.00 0.76 0.02 0.02 0.04 0.16
#> TCGA.D8.A1XL.01 3 0.1408 0.7204 0.00 0.00 0.94 0.00 0.02 0.00 0.02 0.02
#> TCGA.E9.A5UO.01 8 0.4097 0.7433 0.00 0.00 0.08 0.02 0.20 0.00 0.00 0.70
#> TCGA.A2.A0SV.01 8 0.4247 0.6941 0.00 0.00 0.10 0.00 0.28 0.00 0.00 0.62
#> TCGA.OL.A5RZ.01 6 0.3471 0.7128 0.00 0.00 0.16 0.00 0.02 0.78 0.02 0.02
#> TCGA.AR.A24R.01 4 0.5533 0.4814 0.00 0.00 0.00 0.54 0.28 0.02 0.04 0.12
#> TCGA.AO.A1KP.01 5 0.2407 0.6994 0.00 0.00 0.06 0.00 0.86 0.00 0.00 0.08
#> TCGA.E9.A1RE.01 4 0.5080 0.7095 0.00 0.12 0.00 0.68 0.02 0.02 0.04 0.12
#> TCGA.GM.A2DM.01 7 0.3991 0.6211 0.32 0.00 0.00 0.00 0.00 0.00 0.62 0.06
#> TCGA.A2.A0YF.01 7 0.1887 0.7320 0.00 0.00 0.06 0.00 0.00 0.00 0.90 0.04
#> TCGA.C8.A274.01 2 0.0471 0.9550 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.C8.A1HM.01 6 0.3483 0.7896 0.00 0.00 0.02 0.00 0.00 0.76 0.18 0.04
#> TCGA.E9.A1RC.01 2 0.0471 0.9550 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.BH.A6R8.01 1 0.0471 0.9593 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.BH.A1FM.01 6 0.3758 0.7651 0.00 0.00 0.14 0.00 0.00 0.76 0.04 0.06
#> TCGA.D8.A1JP.01 4 0.0941 0.8473 0.00 0.00 0.02 0.96 0.02 0.00 0.00 0.00
#> TCGA.AO.A0JM.01 4 0.3627 0.8078 0.00 0.00 0.00 0.78 0.02 0.02 0.04 0.14
#> TCGA.BH.A0DS.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V7.A7HQ.01 7 0.2267 0.7551 0.18 0.00 0.00 0.00 0.00 0.00 0.82 0.00
#> TCGA.EW.A1PA.01 5 0.3434 0.5813 0.00 0.00 0.14 0.00 0.76 0.00 0.00 0.10
#> TCGA.AC.A3TM.01 3 0.5530 0.2971 0.00 0.00 0.60 0.08 0.12 0.00 0.02 0.18
#> TCGA.AR.A2LE.01 3 0.3449 0.2671 0.00 0.00 0.66 0.00 0.00 0.02 0.00 0.32
#> TCGA.GM.A3NY.01 4 0.0941 0.8473 0.00 0.00 0.02 0.96 0.02 0.00 0.00 0.00
#> TCGA.BH.A5J0.01 7 0.3907 0.5245 0.38 0.00 0.00 0.00 0.00 0.00 0.58 0.04
#> TCGA.BH.A0HK.01 2 0.0471 0.9550 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.AR.A24Z.01 6 0.3002 0.8257 0.00 0.00 0.02 0.00 0.00 0.82 0.12 0.04
#> TCGA.S3.A6ZF.01 5 0.0808 0.7752 0.00 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.Z7.A8R6.01 1 0.0471 0.9583 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.OL.A66K.01 4 0.3048 0.8203 0.00 0.00 0.00 0.84 0.02 0.02 0.04 0.08
#> TCGA.D8.A1JC.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.JL.A3YX.01 3 0.3426 0.7594 0.00 0.00 0.74 0.00 0.00 0.02 0.22 0.02
#> TCGA.AN.A0XO.01 8 0.4953 0.6464 0.00 0.00 0.16 0.00 0.24 0.00 0.02 0.58
#> TCGA.BH.A0DQ.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A2IU.01 7 0.3907 0.5245 0.38 0.00 0.00 0.00 0.00 0.00 0.58 0.04
#> TCGA.AR.A250.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5D8.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AQ.A04H.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1XG.01 7 0.2407 0.7573 0.08 0.00 0.00 0.00 0.00 0.00 0.86 0.06
#> TCGA.AR.A0TZ.01 2 0.0471 0.9550 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.AR.A0U3.01 5 0.2132 0.7688 0.00 0.00 0.00 0.00 0.88 0.08 0.00 0.04
#> TCGA.BH.A0HN.01 3 0.3404 0.7524 0.00 0.00 0.72 0.00 0.00 0.00 0.24 0.04
#> TCGA.EW.A1OX.01 5 0.2399 0.7605 0.00 0.00 0.00 0.04 0.88 0.04 0.00 0.04
#> TCGA.AR.A24V.01 7 0.4050 0.5770 0.34 0.00 0.00 0.00 0.00 0.00 0.60 0.06
#> TCGA.AN.A0XS.01 7 0.2623 0.7637 0.10 0.00 0.00 0.00 0.00 0.00 0.84 0.06
#> TCGA.LL.A6FP.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1L8.01 7 0.2623 0.7675 0.10 0.00 0.00 0.00 0.00 0.00 0.84 0.06
#> TCGA.A2.A1FW.01 5 0.1341 0.7639 0.00 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.AC.A62V.01 6 0.2856 0.6232 0.00 0.00 0.00 0.00 0.02 0.78 0.00 0.20
#> TCGA.E2.A576.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A3NW.01 4 0.3311 0.7650 0.00 0.00 0.02 0.80 0.02 0.00 0.02 0.14
#> TCGA.A7.A4SB.01 7 0.2407 0.7697 0.08 0.00 0.00 0.00 0.00 0.00 0.86 0.06
#> TCGA.E9.A245.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A126.01 3 0.2724 0.6635 0.00 0.00 0.86 0.02 0.08 0.00 0.02 0.02
#> TCGA.AC.A8OR.01 7 0.3991 0.6211 0.32 0.00 0.00 0.00 0.00 0.00 0.62 0.06
#> TCGA.A7.A4SF.01 1 0.3154 0.7061 0.78 0.00 0.00 0.00 0.00 0.00 0.16 0.06
#> TCGA.A7.A26J.01 6 0.2680 0.8282 0.00 0.00 0.02 0.00 0.00 0.84 0.12 0.02
#> TCGA.A2.A25B.01 6 0.4619 0.2801 0.00 0.00 0.02 0.00 0.00 0.48 0.44 0.06
#> TCGA.D8.A27W.01 5 0.0471 0.7832 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.E9.A2JS.01 2 0.0471 0.9550 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.C8.A3M8.01 2 0.3580 0.7805 0.00 0.80 0.00 0.10 0.00 0.02 0.04 0.04
#> TCGA.D8.A1XU.01 5 0.1887 0.7491 0.00 0.00 0.00 0.06 0.90 0.00 0.00 0.04
#> TCGA.BH.A1ES.06 5 0.1408 0.7818 0.00 0.00 0.02 0.00 0.94 0.02 0.00 0.02
#> TCGA.D8.A1X6.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PL.A8LX.01 3 0.3991 0.6728 0.00 0.00 0.62 0.00 0.00 0.00 0.32 0.06
#> TCGA.EW.A6SA.01 2 0.0471 0.9550 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.E9.A1R5.01 2 0.1275 0.9185 0.00 0.94 0.00 0.04 0.00 0.00 0.00 0.02
#> TCGA.E9.A54Y.01 8 0.4097 0.7348 0.00 0.00 0.08 0.00 0.20 0.02 0.00 0.70
#> TCGA.AC.A3TN.01 4 0.1874 0.8377 0.00 0.00 0.02 0.92 0.02 0.00 0.02 0.02
#> TCGA.EW.A1J3.01 3 0.1563 0.6609 0.00 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.BH.A1F8.01 2 0.4217 0.7312 0.00 0.76 0.00 0.12 0.02 0.02 0.04 0.04
#> TCGA.B6.A0X5.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AQ.A04L.01 4 0.3627 0.8078 0.00 0.00 0.00 0.78 0.02 0.02 0.04 0.14
#> TCGA.B6.A0WV.01 6 0.3002 0.8257 0.00 0.00 0.02 0.00 0.00 0.82 0.12 0.04
#> TCGA.BH.A1FD.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A13F.01 8 0.4097 0.7000 0.00 0.00 0.02 0.08 0.20 0.00 0.00 0.70
#> TCGA.E2.A2P5.01 4 0.3262 0.8186 0.00 0.00 0.00 0.82 0.02 0.02 0.04 0.10
#> TCGA.AO.A1KS.01 5 0.0471 0.7849 0.00 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.BH.A0DD.01 8 0.4458 -0.0184 0.00 0.00 0.00 0.38 0.02 0.02 0.02 0.56
#> TCGA.BH.A0HX.01 6 0.3675 0.3913 0.00 0.00 0.00 0.00 0.30 0.66 0.00 0.04
#> TCGA.D8.A1X9.01 8 0.4097 0.7433 0.00 0.00 0.08 0.02 0.20 0.00 0.00 0.70
#> TCGA.AR.A0TR.01 3 0.2981 0.7667 0.00 0.00 0.76 0.00 0.00 0.00 0.22 0.02
#> TCGA.A7.A0DC.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A9FZ.01 2 0.0471 0.9550 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.AR.A24X.01 4 0.2071 0.8373 0.00 0.00 0.00 0.90 0.00 0.02 0.04 0.04
#> TCGA.BH.A0GZ.01 4 0.0941 0.8473 0.00 0.00 0.02 0.96 0.02 0.00 0.00 0.00
#> TCGA.B6.A0RM.01 7 0.2623 0.6714 0.00 0.00 0.10 0.00 0.00 0.00 0.84 0.06
#> TCGA.AO.A12B.01 7 0.1947 0.7721 0.14 0.00 0.00 0.00 0.00 0.00 0.86 0.00
#> TCGA.BH.A0DH.01 8 0.4097 0.7433 0.00 0.00 0.08 0.02 0.20 0.00 0.00 0.70
#> TCGA.D8.A1JN.01 2 0.0471 0.9452 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.E2.A1IE.01 6 0.2532 0.7792 0.00 0.00 0.02 0.00 0.04 0.88 0.02 0.04
#> TCGA.EW.A1P3.01 3 0.3404 0.7524 0.00 0.00 0.72 0.00 0.00 0.00 0.24 0.04
#> TCGA.BH.A8FY.01 8 0.4097 0.7433 0.00 0.00 0.08 0.02 0.20 0.00 0.00 0.70
#> TCGA.AO.A1KT.01 8 0.4097 0.7348 0.00 0.00 0.08 0.00 0.20 0.02 0.00 0.70
#> TCGA.E2.A1IU.01 7 0.3862 0.5491 0.36 0.00 0.00 0.00 0.00 0.00 0.60 0.04
#> TCGA.E9.A22H.01 7 0.2407 0.6851 0.00 0.00 0.08 0.00 0.00 0.00 0.86 0.06
#> TCGA.D8.A3Z6.01 3 0.2404 0.6012 0.00 0.00 0.84 0.00 0.00 0.02 0.00 0.14
#> TCGA.AR.A2LK.01 4 0.3714 0.8113 0.00 0.02 0.00 0.80 0.02 0.02 0.04 0.10
#> TCGA.B6.A0RI.01 1 0.0471 0.9583 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.A8.A08O.01 7 0.1741 0.7583 0.04 0.00 0.02 0.00 0.00 0.00 0.92 0.02
#> TCGA.EW.A1P6.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1XF.01 2 0.0471 0.9550 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.A2.A0CT.01 2 0.0471 0.9550 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.E9.A1RG.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1F2.01 6 0.2265 0.8268 0.00 0.00 0.02 0.00 0.00 0.88 0.08 0.02
#> TCGA.AN.A0XT.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0HI.01 3 0.3757 0.7346 0.00 0.00 0.68 0.00 0.00 0.00 0.26 0.06
#> TCGA.B6.A0RL.01 2 0.0471 0.9550 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.E2.A1L9.01 7 0.3299 0.5542 0.00 0.00 0.18 0.00 0.00 0.00 0.76 0.06
#> TCGA.A7.A26E.01 5 0.5433 0.4480 0.00 0.00 0.12 0.20 0.60 0.00 0.02 0.06
#> TCGA.BH.A0W3.01 3 0.1765 0.6411 0.00 0.00 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.D8.A1J9.01 2 0.3580 0.7805 0.00 0.80 0.00 0.10 0.00 0.02 0.04 0.04
#> TCGA.LL.A7T0.01 4 0.0471 0.8494 0.00 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.OL.A66O.01 8 0.4314 0.7129 0.00 0.00 0.08 0.00 0.24 0.02 0.00 0.66
#> TCGA.AO.A03N.01 7 0.2165 0.7020 0.00 0.00 0.06 0.00 0.00 0.00 0.88 0.06
#> TCGA.AR.A1AP.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1PC.01 5 0.2132 0.7688 0.00 0.00 0.00 0.00 0.88 0.08 0.00 0.04
#> TCGA.3C.AALJ.01 5 0.1557 0.7819 0.00 0.00 0.02 0.00 0.92 0.06 0.00 0.00
#> TCGA.BH.A42T.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A26V.01 4 0.2591 0.8413 0.00 0.00 0.02 0.86 0.00 0.00 0.04 0.08
#> TCGA.BH.A1EV.01 4 0.1408 0.8482 0.00 0.00 0.00 0.94 0.02 0.02 0.00 0.02
#> TCGA.D8.A1JA.01 4 0.3514 0.5585 0.00 0.00 0.02 0.64 0.00 0.00 0.00 0.34
#> TCGA.E2.A1IN.01 7 0.1765 0.7773 0.12 0.00 0.00 0.00 0.00 0.00 0.88 0.00
#> TCGA.BH.A0H9.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0RG.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A54X.01 1 0.1341 0.8976 0.92 0.00 0.00 0.00 0.00 0.00 0.08 0.00
#> TCGA.C8.A1HN.01 5 0.4674 -0.0467 0.00 0.00 0.04 0.00 0.46 0.46 0.00 0.04
#> TCGA.BH.A0HB.01 3 0.2981 0.7667 0.00 0.00 0.76 0.00 0.00 0.00 0.22 0.02
#> TCGA.A2.A25E.01 7 0.4489 0.6589 0.26 0.00 0.00 0.00 0.00 0.04 0.64 0.06
#> TCGA.B6.A1KN.01 4 0.3454 0.8107 0.00 0.00 0.00 0.80 0.02 0.02 0.04 0.12
#> TCGA.AR.A24K.01 4 0.1741 0.8356 0.00 0.00 0.02 0.92 0.00 0.00 0.02 0.04
#> TCGA.EW.A1OZ.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S3.AA12.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A1FX.01 6 0.3337 0.8034 0.00 0.00 0.02 0.00 0.00 0.78 0.16 0.04
#> TCGA.A7.A13G.01 3 0.4050 0.6494 0.00 0.00 0.60 0.00 0.00 0.00 0.34 0.06
#> TCGA.LQ.A4E4.01 4 0.3580 0.8231 0.00 0.00 0.00 0.80 0.04 0.02 0.04 0.10
#> TCGA.AQ.A1H2.01 6 0.3002 0.8236 0.00 0.00 0.02 0.00 0.00 0.82 0.12 0.04
#> TCGA.D8.A27T.01 1 0.0471 0.9599 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.B6.A0X4.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0HY.01 2 0.0471 0.9550 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.E2.A15I.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0EU.01 7 0.2623 0.6714 0.00 0.00 0.10 0.00 0.00 0.00 0.84 0.06
#> TCGA.BH.A0H7.01 1 0.1275 0.9311 0.94 0.00 0.00 0.00 0.00 0.02 0.04 0.00
#> TCGA.A1.A0SG.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1J5.01 6 0.2484 0.8289 0.00 0.00 0.02 0.00 0.00 0.86 0.10 0.02
#> TCGA.D8.A1XR.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A0JB.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A27A.01 6 0.3675 0.3913 0.00 0.00 0.00 0.00 0.30 0.66 0.00 0.04
#> TCGA.AC.A3EH.01 4 0.5547 0.5363 0.00 0.26 0.00 0.58 0.02 0.02 0.04 0.08
#> TCGA.C8.A1HK.01 3 0.1557 0.6963 0.00 0.00 0.92 0.00 0.00 0.06 0.00 0.02
#> TCGA.B6.A0WZ.01 3 0.1947 0.7695 0.00 0.00 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.A8.A0AD.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A3YJ.01 3 0.1765 0.7659 0.00 0.00 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.D8.A1Y1.01 8 0.3570 0.4649 0.00 0.00 0.36 0.00 0.00 0.02 0.00 0.62
#> TCGA.E2.A105.01 5 0.1804 0.7688 0.00 0.00 0.00 0.00 0.90 0.08 0.00 0.02
#> TCGA.BH.A0E2.01 2 0.5395 0.1959 0.00 0.52 0.00 0.36 0.02 0.02 0.04 0.04
#> TCGA.E9.A1R7.01 4 0.3131 0.8296 0.00 0.00 0.00 0.84 0.04 0.02 0.04 0.06
#> TCGA.E2.A10E.01 4 0.0808 0.8458 0.00 0.00 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.E9.A249.01 3 0.0941 0.7246 0.00 0.00 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.E2.A1BD.01 4 0.0471 0.8494 0.00 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.BH.A1ET.01 7 0.3690 0.4430 0.42 0.00 0.00 0.00 0.00 0.00 0.56 0.02
#> TCGA.LD.A7W6.01 3 0.0941 0.7246 0.00 0.00 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.C8.A1HE.01 4 0.0941 0.8473 0.00 0.00 0.02 0.96 0.02 0.00 0.00 0.00
#> TCGA.AC.A7VB.01 2 0.0471 0.9550 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.AO.A12C.01 5 0.0941 0.7836 0.00 0.00 0.02 0.00 0.96 0.02 0.00 0.00
#> TCGA.D8.A73W.01 3 0.3690 0.0333 0.00 0.00 0.56 0.00 0.00 0.02 0.00 0.42
#> TCGA.B6.A40B.01 4 0.1741 0.8356 0.00 0.00 0.02 0.92 0.00 0.00 0.02 0.04
#> TCGA.AO.A0JI.01 2 0.0471 0.9550 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.PE.A5DD.01 2 0.0471 0.9550 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.A2.A04R.01 7 0.4053 0.7046 0.18 0.00 0.00 0.00 0.00 0.04 0.72 0.06
#> TCGA.BH.A1F5.01 7 0.1765 0.7771 0.12 0.00 0.00 0.00 0.00 0.00 0.88 0.00
#> TCGA.AC.A23E.01 3 0.2406 0.7738 0.00 0.00 0.80 0.00 0.00 0.00 0.20 0.00
#> TCGA.D8.A1JS.01 7 0.2407 0.6851 0.00 0.00 0.08 0.00 0.00 0.00 0.86 0.06
#> TCGA.WT.AB44.01 4 0.1741 0.8356 0.00 0.00 0.02 0.92 0.00 0.00 0.02 0.04
#> TCGA.EW.A424.01 2 0.0941 0.9337 0.00 0.96 0.00 0.02 0.00 0.00 0.00 0.02
#> TCGA.B6.A408.01 7 0.2648 0.6851 0.00 0.00 0.08 0.00 0.00 0.00 0.84 0.08
#> TCGA.E2.A1L7.01 2 0.1275 0.9185 0.00 0.94 0.00 0.04 0.00 0.00 0.00 0.02
#> TCGA.5T.A9QA.01 2 0.0471 0.9550 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.A2.A0SY.01 4 0.4912 0.6257 0.00 0.22 0.00 0.66 0.02 0.02 0.04 0.04
#> TCGA.A2.A0YG.01 2 0.4030 0.7574 0.00 0.78 0.00 0.10 0.02 0.02 0.04 0.04
#> TCGA.BH.A28Q.01 4 0.2532 0.8229 0.00 0.00 0.04 0.88 0.02 0.00 0.02 0.04
#> TCGA.EW.A1J1.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AQ.A0Y5.01 4 0.3369 0.8240 0.00 0.00 0.00 0.82 0.04 0.02 0.04 0.08
#> TCGA.3C.AAAU.01 7 0.3714 0.3934 0.44 0.00 0.00 0.00 0.00 0.00 0.54 0.02
#> TCGA.A2.A4S0.01 1 0.0808 0.9434 0.96 0.00 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.AR.A1AV.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A3J0.01 1 0.0000 0.9721 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A6VX.01 3 0.1408 0.7204 0.00 0.00 0.94 0.00 0.02 0.00 0.02 0.02
#> TCGA.BH.A0BT.01 1 0.1557 0.9058 0.92 0.00 0.00 0.00 0.00 0.00 0.06 0.02
#> TCGA.E2.A1IG.01 8 0.4646 0.7135 0.00 0.00 0.12 0.00 0.18 0.04 0.00 0.66
#> TCGA.E9.A1NH.01 3 0.0941 0.7246 0.00 0.00 0.96 0.00 0.00 0.00 0.02 0.02
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0115-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0151-leaf , Node0152-leaf , Node0153-leaf , Node0154-leaf , Node0211-leaf , Node0212 , Node0213 , Node0221 , Node0222 , Node0231-leaf , Node0232 , Node0233-leaf , Node0241-leaf , Node0242 , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0331-leaf , Node0332-leaf , Node0341-leaf , Node0342-leaf , Node0343-leaf , Node0411 , Node0412-leaf , Node0413 , Node0421-leaf , Node0422 , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["021"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 76 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.828 0.897 0.959 0.4802 0.536 0.536
#> 3 3 1.000 0.984 0.990 0.3720 0.665 0.447
#> 4 4 0.824 0.902 0.937 0.1324 0.818 0.526
#> 5 5 0.870 0.674 0.792 0.0546 0.931 0.746
#> 6 6 0.817 0.755 0.868 0.0338 0.955 0.807
#> 7 7 0.855 0.796 0.873 0.0272 0.971 0.858
#> 8 8 0.846 0.644 0.812 0.0177 0.954 0.757
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.EW.A2FW.01 2 0.000 0.996 0.00 1.00
#> TCGA.D8.A1JD.01 1 0.000 0.934 1.00 0.00
#> TCGA.AO.A1KQ.01 1 0.000 0.934 1.00 0.00
#> TCGA.A7.A3RF.01 1 0.855 0.614 0.72 0.28
#> TCGA.BH.A1FN.01 2 0.000 0.996 0.00 1.00
#> TCGA.BH.A0H0.01 1 0.000 0.934 1.00 0.00
#> TCGA.E2.A1IL.01 2 0.000 0.996 0.00 1.00
#> TCGA.D8.A1JI.01 1 0.000 0.934 1.00 0.00
#> TCGA.EW.A1OY.01 1 0.000 0.934 1.00 0.00
#> TCGA.B6.A0RP.01 1 0.000 0.934 1.00 0.00
#> TCGA.E9.A1RB.01 2 0.000 0.996 0.00 1.00
#> TCGA.LL.A442.01 2 0.000 0.996 0.00 1.00
#> TCGA.C8.A26Z.01 1 0.000 0.934 1.00 0.00
#> TCGA.BH.A0BS.01 2 0.000 0.996 0.00 1.00
#> TCGA.B6.A0WT.01 1 0.000 0.934 1.00 0.00
#> TCGA.E2.A15K.01 1 0.000 0.934 1.00 0.00
#> TCGA.E2.A15K.06 1 0.000 0.934 1.00 0.00
#> TCGA.OL.A6VR.01 2 0.000 0.996 0.00 1.00
#> TCGA.AR.A1AS.01 1 0.000 0.934 1.00 0.00
#> TCGA.AC.A6NO.01 1 0.995 0.244 0.54 0.46
#> TCGA.BH.A0H6.01 2 0.000 0.996 0.00 1.00
#> TCGA.EW.A6SC.01 1 0.000 0.934 1.00 0.00
#> TCGA.C8.A1HL.01 1 0.000 0.934 1.00 0.00
#> TCGA.E2.A1B4.01 2 0.000 0.996 0.00 1.00
#> TCGA.AC.A3QQ.01 1 0.000 0.934 1.00 0.00
#> TCGA.D8.A1X7.01 1 0.000 0.934 1.00 0.00
#> TCGA.A8.A075.01 2 0.000 0.996 0.00 1.00
#> TCGA.E9.A3Q9.01 1 0.000 0.934 1.00 0.00
#> TCGA.GM.A2DM.01 2 0.000 0.996 0.00 1.00
#> TCGA.BH.A6R8.01 1 0.000 0.934 1.00 0.00
#> TCGA.V7.A7HQ.01 2 0.000 0.996 0.00 1.00
#> TCGA.BH.A5J0.01 1 0.000 0.934 1.00 0.00
#> TCGA.Z7.A8R6.01 1 0.995 0.244 0.54 0.46
#> TCGA.D8.A1JC.01 1 0.000 0.934 1.00 0.00
#> TCGA.BH.A0DQ.01 1 0.000 0.934 1.00 0.00
#> TCGA.B6.A2IU.01 1 0.000 0.934 1.00 0.00
#> TCGA.D8.A1XG.01 2 0.000 0.996 0.00 1.00
#> TCGA.AR.A24V.01 1 0.000 0.934 1.00 0.00
#> TCGA.AN.A0XS.01 2 0.000 0.996 0.00 1.00
#> TCGA.LL.A6FP.01 1 0.000 0.934 1.00 0.00
#> TCGA.E2.A1L8.01 1 0.000 0.934 1.00 0.00
#> TCGA.A7.A4SB.01 1 0.000 0.934 1.00 0.00
#> TCGA.E9.A245.01 2 0.000 0.996 0.00 1.00
#> TCGA.AC.A8OR.01 2 0.000 0.996 0.00 1.00
#> TCGA.A7.A4SF.01 1 0.000 0.934 1.00 0.00
#> TCGA.D8.A1X6.01 1 0.000 0.934 1.00 0.00
#> TCGA.B6.A0X5.01 1 0.000 0.934 1.00 0.00
#> TCGA.A7.A0DC.01 2 0.000 0.996 0.00 1.00
#> TCGA.AO.A12B.01 2 0.000 0.996 0.00 1.00
#> TCGA.E2.A1IU.01 1 0.990 0.296 0.56 0.44
#> TCGA.B6.A0RI.01 1 0.995 0.244 0.54 0.46
#> TCGA.EW.A1P6.01 1 0.995 0.244 0.54 0.46
#> TCGA.E9.A1RG.01 1 0.000 0.934 1.00 0.00
#> TCGA.AN.A0XT.01 2 0.141 0.975 0.02 0.98
#> TCGA.E2.A1IN.01 2 0.000 0.996 0.00 1.00
#> TCGA.BH.A0H9.01 1 0.000 0.934 1.00 0.00
#> TCGA.B6.A0RG.01 1 0.000 0.934 1.00 0.00
#> TCGA.E9.A54X.01 2 0.000 0.996 0.00 1.00
#> TCGA.A2.A25E.01 1 0.000 0.934 1.00 0.00
#> TCGA.S3.AA12.01 1 0.000 0.934 1.00 0.00
#> TCGA.D8.A27T.01 1 0.000 0.934 1.00 0.00
#> TCGA.B6.A0X4.01 2 0.000 0.996 0.00 1.00
#> TCGA.E2.A15I.01 1 0.000 0.934 1.00 0.00
#> TCGA.BH.A0H7.01 1 0.000 0.934 1.00 0.00
#> TCGA.A1.A0SG.01 1 0.000 0.934 1.00 0.00
#> TCGA.D8.A1XR.01 1 0.995 0.244 0.54 0.46
#> TCGA.AO.A0JB.01 1 0.000 0.934 1.00 0.00
#> TCGA.A8.A0AD.01 1 0.000 0.934 1.00 0.00
#> TCGA.BH.A1ET.01 2 0.000 0.996 0.00 1.00
#> TCGA.A2.A04R.01 1 0.000 0.934 1.00 0.00
#> TCGA.BH.A1F5.01 2 0.000 0.996 0.00 1.00
#> TCGA.EW.A1J1.01 1 0.000 0.934 1.00 0.00
#> TCGA.3C.AAAU.01 2 0.402 0.904 0.08 0.92
#> TCGA.A2.A4S0.01 2 0.000 0.996 0.00 1.00
#> TCGA.A7.A3J0.01 2 0.000 0.996 0.00 1.00
#> TCGA.BH.A0BT.01 1 0.000 0.934 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.EW.A2FW.01 2 0.0000 0.989 0.00 1.00 0.00
#> TCGA.D8.A1JD.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.AO.A1KQ.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.A7.A3RF.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.BH.A1FN.01 2 0.0000 0.989 0.00 1.00 0.00
#> TCGA.BH.A0H0.01 3 0.0892 0.972 0.02 0.00 0.98
#> TCGA.E2.A1IL.01 2 0.0000 0.989 0.00 1.00 0.00
#> TCGA.D8.A1JI.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.EW.A1OY.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.B6.A0RP.01 3 0.0892 0.972 0.02 0.00 0.98
#> TCGA.E9.A1RB.01 2 0.2537 0.929 0.00 0.92 0.08
#> TCGA.LL.A442.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.C8.A26Z.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.BH.A0BS.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.B6.A0WT.01 3 0.2066 0.950 0.06 0.00 0.94
#> TCGA.E2.A15K.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.E2.A15K.06 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.OL.A6VR.01 2 0.0000 0.989 0.00 1.00 0.00
#> TCGA.AR.A1AS.01 3 0.2066 0.950 0.06 0.00 0.94
#> TCGA.AC.A6NO.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.BH.A0H6.01 2 0.0000 0.989 0.00 1.00 0.00
#> TCGA.EW.A6SC.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.C8.A1HL.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.E2.A1B4.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.AC.A3QQ.01 3 0.2066 0.950 0.06 0.00 0.94
#> TCGA.D8.A1X7.01 3 0.2066 0.950 0.06 0.00 0.94
#> TCGA.A8.A075.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.E9.A3Q9.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.GM.A2DM.01 2 0.0000 0.989 0.00 1.00 0.00
#> TCGA.BH.A6R8.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.V7.A7HQ.01 2 0.0000 0.989 0.00 1.00 0.00
#> TCGA.BH.A5J0.01 3 0.2066 0.950 0.06 0.00 0.94
#> TCGA.Z7.A8R6.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.D8.A1JC.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.BH.A0DQ.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.B6.A2IU.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.D8.A1XG.01 2 0.0000 0.989 0.00 1.00 0.00
#> TCGA.AR.A24V.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.AN.A0XS.01 2 0.2066 0.948 0.00 0.94 0.06
#> TCGA.LL.A6FP.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.E2.A1L8.01 3 0.2066 0.950 0.06 0.00 0.94
#> TCGA.A7.A4SB.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.E9.A245.01 2 0.0000 0.989 0.00 1.00 0.00
#> TCGA.AC.A8OR.01 2 0.0000 0.989 0.00 1.00 0.00
#> TCGA.A7.A4SF.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.D8.A1X6.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.B6.A0X5.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.A7.A0DC.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.AO.A12B.01 2 0.0000 0.989 0.00 1.00 0.00
#> TCGA.E2.A1IU.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.B6.A0RI.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.EW.A1P6.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.E9.A1RG.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.AN.A0XT.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.E2.A1IN.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.BH.A0H9.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.B6.A0RG.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.E9.A54X.01 2 0.0000 0.989 0.00 1.00 0.00
#> TCGA.A2.A25E.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.S3.AA12.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.D8.A27T.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.B6.A0X4.01 2 0.0000 0.989 0.00 1.00 0.00
#> TCGA.E2.A15I.01 3 0.2066 0.950 0.06 0.00 0.94
#> TCGA.BH.A0H7.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.A1.A0SG.01 3 0.2066 0.950 0.06 0.00 0.94
#> TCGA.D8.A1XR.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.AO.A0JB.01 3 0.0892 0.972 0.02 0.00 0.98
#> TCGA.A8.A0AD.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.BH.A1ET.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.A2.A04R.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.BH.A1F5.01 2 0.2066 0.948 0.00 0.94 0.06
#> TCGA.EW.A1J1.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.3C.AAAU.01 3 0.0000 0.980 0.00 0.00 1.00
#> TCGA.A2.A4S0.01 2 0.0000 0.989 0.00 1.00 0.00
#> TCGA.A7.A3J0.01 2 0.0000 0.989 0.00 1.00 0.00
#> TCGA.BH.A0BT.01 1 0.0000 1.000 1.00 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.EW.A2FW.01 2 0.4134 0.806 0.00 0.74 0.00 0.26
#> TCGA.D8.A1JD.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.AO.A1KQ.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A7.A3RF.01 3 0.0707 0.904 0.00 0.00 0.98 0.02
#> TCGA.BH.A1FN.01 2 0.4134 0.806 0.00 0.74 0.00 0.26
#> TCGA.BH.A0H0.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.E2.A1IL.01 2 0.2345 0.901 0.00 0.90 0.00 0.10
#> TCGA.D8.A1JI.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EW.A1OY.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B6.A0RP.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.E9.A1RB.01 4 0.0000 0.850 0.00 0.00 0.00 1.00
#> TCGA.LL.A442.01 4 0.0000 0.850 0.00 0.00 0.00 1.00
#> TCGA.C8.A26Z.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BH.A0BS.01 4 0.2345 0.910 0.00 0.00 0.10 0.90
#> TCGA.B6.A0WT.01 3 0.0707 0.904 0.00 0.00 0.98 0.02
#> TCGA.E2.A15K.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E2.A15K.06 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.OL.A6VR.01 2 0.0000 0.919 0.00 1.00 0.00 0.00
#> TCGA.AR.A1AS.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.AC.A6NO.01 4 0.4134 0.812 0.00 0.00 0.26 0.74
#> TCGA.BH.A0H6.01 2 0.4134 0.806 0.00 0.74 0.00 0.26
#> TCGA.EW.A6SC.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.C8.A1HL.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E2.A1B4.01 4 0.2345 0.910 0.00 0.00 0.10 0.90
#> TCGA.AC.A3QQ.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.D8.A1X7.01 3 0.0707 0.904 0.00 0.00 0.98 0.02
#> TCGA.A8.A075.01 4 0.2345 0.910 0.00 0.00 0.10 0.90
#> TCGA.E9.A3Q9.01 3 0.3975 0.709 0.24 0.00 0.76 0.00
#> TCGA.GM.A2DM.01 2 0.0000 0.919 0.00 1.00 0.00 0.00
#> TCGA.BH.A6R8.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.V7.A7HQ.01 2 0.4134 0.806 0.00 0.74 0.00 0.26
#> TCGA.BH.A5J0.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.Z7.A8R6.01 4 0.3801 0.856 0.00 0.00 0.22 0.78
#> TCGA.D8.A1JC.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BH.A0DQ.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B6.A2IU.01 3 0.2921 0.809 0.14 0.00 0.86 0.00
#> TCGA.D8.A1XG.01 2 0.0000 0.919 0.00 1.00 0.00 0.00
#> TCGA.AR.A24V.01 3 0.3975 0.709 0.24 0.00 0.76 0.00
#> TCGA.AN.A0XS.01 4 0.0707 0.841 0.00 0.02 0.00 0.98
#> TCGA.LL.A6FP.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E2.A1L8.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.A7.A4SB.01 3 0.0707 0.904 0.00 0.00 0.98 0.02
#> TCGA.E9.A245.01 2 0.2011 0.906 0.00 0.92 0.00 0.08
#> TCGA.AC.A8OR.01 2 0.0000 0.919 0.00 1.00 0.00 0.00
#> TCGA.A7.A4SF.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.D8.A1X6.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B6.A0X5.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A7.A0DC.01 4 0.2345 0.910 0.00 0.00 0.10 0.90
#> TCGA.AO.A12B.01 2 0.2011 0.906 0.00 0.92 0.00 0.08
#> TCGA.E2.A1IU.01 3 0.4790 0.141 0.00 0.00 0.62 0.38
#> TCGA.B6.A0RI.01 4 0.3975 0.838 0.00 0.00 0.24 0.76
#> TCGA.EW.A1P6.01 4 0.3610 0.872 0.00 0.00 0.20 0.80
#> TCGA.E9.A1RG.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AN.A0XT.01 4 0.3400 0.884 0.00 0.00 0.18 0.82
#> TCGA.E2.A1IN.01 4 0.2345 0.910 0.00 0.00 0.10 0.90
#> TCGA.BH.A0H9.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.B6.A0RG.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E9.A54X.01 2 0.0000 0.919 0.00 1.00 0.00 0.00
#> TCGA.A2.A25E.01 3 0.2647 0.826 0.12 0.00 0.88 0.00
#> TCGA.S3.AA12.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.D8.A27T.01 3 0.3975 0.709 0.24 0.00 0.76 0.00
#> TCGA.B6.A0X4.01 2 0.0000 0.919 0.00 1.00 0.00 0.00
#> TCGA.E2.A15I.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.BH.A0H7.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A1.A0SG.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.D8.A1XR.01 4 0.3975 0.838 0.00 0.00 0.24 0.76
#> TCGA.AO.A0JB.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.A8.A0AD.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BH.A1ET.01 4 0.2011 0.904 0.00 0.00 0.08 0.92
#> TCGA.A2.A04R.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BH.A1F5.01 4 0.0707 0.841 0.00 0.02 0.00 0.98
#> TCGA.EW.A1J1.01 3 0.0707 0.904 0.00 0.00 0.98 0.02
#> TCGA.3C.AAAU.01 4 0.2345 0.904 0.00 0.00 0.10 0.90
#> TCGA.A2.A4S0.01 2 0.0000 0.919 0.00 1.00 0.00 0.00
#> TCGA.A7.A3J0.01 2 0.0000 0.919 0.00 1.00 0.00 0.00
#> TCGA.BH.A0BT.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.EW.A2FW.01 2 0.1043 0.49554 0.00 0.96 0.00 0.04 0.00
#> TCGA.D8.A1JD.01 3 0.2331 0.82212 0.00 0.00 0.90 0.08 0.02
#> TCGA.AO.A1KQ.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A3RF.01 5 0.6350 -0.47767 0.00 0.00 0.16 0.42 0.42
#> TCGA.BH.A1FN.01 2 0.1043 0.49554 0.00 0.96 0.00 0.04 0.00
#> TCGA.BH.A0H0.01 3 0.0609 0.88410 0.00 0.00 0.98 0.00 0.02
#> TCGA.E2.A1IL.01 2 0.0000 0.48617 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A1JI.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1OY.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0RP.01 3 0.0000 0.89013 0.00 0.00 1.00 0.00 0.00
#> TCGA.E9.A1RB.01 2 0.5173 0.00358 0.00 0.50 0.00 0.46 0.04
#> TCGA.LL.A442.01 4 0.2020 0.77229 0.00 0.10 0.00 0.90 0.00
#> TCGA.C8.A26Z.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BS.01 4 0.0000 0.85417 0.00 0.00 0.00 1.00 0.00
#> TCGA.B6.A0WT.01 3 0.3895 0.70670 0.00 0.00 0.68 0.00 0.32
#> TCGA.E2.A15K.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A15K.06 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A6VR.01 2 0.4307 -0.22867 0.00 0.50 0.00 0.00 0.50
#> TCGA.AR.A1AS.01 3 0.0000 0.89013 0.00 0.00 1.00 0.00 0.00
#> TCGA.AC.A6NO.01 4 0.3513 0.76158 0.00 0.00 0.02 0.80 0.18
#> TCGA.BH.A0H6.01 2 0.1043 0.49554 0.00 0.96 0.00 0.04 0.00
#> TCGA.EW.A6SC.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A1HL.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1B4.01 4 0.0609 0.85457 0.00 0.00 0.00 0.98 0.02
#> TCGA.AC.A3QQ.01 3 0.0000 0.89013 0.00 0.00 1.00 0.00 0.00
#> TCGA.D8.A1X7.01 3 0.3983 0.69948 0.00 0.00 0.66 0.00 0.34
#> TCGA.A8.A075.01 4 0.0609 0.85457 0.00 0.00 0.00 0.98 0.02
#> TCGA.E9.A3Q9.01 3 0.1648 0.87341 0.02 0.00 0.94 0.00 0.04
#> TCGA.GM.A2DM.01 2 0.4307 -0.22867 0.00 0.50 0.00 0.00 0.50
#> TCGA.BH.A6R8.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.V7.A7HQ.01 2 0.1043 0.49554 0.00 0.96 0.00 0.04 0.00
#> TCGA.BH.A5J0.01 3 0.0000 0.89013 0.00 0.00 1.00 0.00 0.00
#> TCGA.Z7.A8R6.01 4 0.2012 0.85402 0.00 0.00 0.02 0.92 0.06
#> TCGA.D8.A1JC.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DQ.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A2IU.01 3 0.0609 0.88321 0.02 0.00 0.98 0.00 0.00
#> TCGA.D8.A1XG.01 2 0.4307 -0.22867 0.00 0.50 0.00 0.00 0.50
#> TCGA.AR.A24V.01 3 0.0609 0.88321 0.02 0.00 0.98 0.00 0.00
#> TCGA.AN.A0XS.01 2 0.4829 -0.03411 0.00 0.50 0.00 0.48 0.02
#> TCGA.LL.A6FP.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1L8.01 3 0.0000 0.89013 0.00 0.00 1.00 0.00 0.00
#> TCGA.A7.A4SB.01 3 0.5888 0.55379 0.00 0.00 0.58 0.14 0.28
#> TCGA.E9.A245.01 2 0.0000 0.48617 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A8OR.01 5 0.4307 -0.18971 0.00 0.50 0.00 0.00 0.50
#> TCGA.A7.A4SF.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1X6.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0X5.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A0DC.01 4 0.0609 0.85457 0.00 0.00 0.00 0.98 0.02
#> TCGA.AO.A12B.01 2 0.0000 0.48617 0.00 1.00 0.00 0.00 0.00
#> TCGA.E2.A1IU.01 4 0.4982 0.65700 0.00 0.00 0.10 0.70 0.20
#> TCGA.B6.A0RI.01 4 0.2012 0.84757 0.00 0.00 0.02 0.92 0.06
#> TCGA.EW.A1P6.01 4 0.1648 0.85599 0.00 0.00 0.02 0.94 0.04
#> TCGA.E9.A1RG.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.AN.A0XT.01 4 0.1648 0.85340 0.00 0.00 0.02 0.94 0.04
#> TCGA.E2.A1IN.01 4 0.0609 0.85457 0.00 0.00 0.00 0.98 0.02
#> TCGA.BH.A0H9.01 4 0.6766 0.19631 0.00 0.00 0.30 0.40 0.30
#> TCGA.B6.A0RG.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A54X.01 2 0.4307 -0.22867 0.00 0.50 0.00 0.00 0.50
#> TCGA.A2.A25E.01 3 0.3684 0.73887 0.00 0.00 0.72 0.00 0.28
#> TCGA.S3.AA12.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A27T.01 3 0.0609 0.88321 0.02 0.00 0.98 0.00 0.00
#> TCGA.B6.A0X4.01 2 0.4307 -0.22867 0.00 0.50 0.00 0.00 0.50
#> TCGA.E2.A15I.01 3 0.0000 0.89013 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A0H7.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.A1.A0SG.01 3 0.0000 0.89013 0.00 0.00 1.00 0.00 0.00
#> TCGA.D8.A1XR.01 4 0.2012 0.84757 0.00 0.00 0.02 0.92 0.06
#> TCGA.AO.A0JB.01 3 0.1732 0.86247 0.00 0.00 0.92 0.00 0.08
#> TCGA.A8.A0AD.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1ET.01 4 0.1043 0.84451 0.00 0.00 0.00 0.96 0.04
#> TCGA.A2.A04R.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1F5.01 2 0.5173 -0.01047 0.00 0.50 0.00 0.46 0.04
#> TCGA.EW.A1J1.01 3 0.4060 0.67060 0.00 0.00 0.64 0.00 0.36
#> TCGA.3C.AAAU.01 4 0.4060 0.56130 0.00 0.00 0.00 0.64 0.36
#> TCGA.A2.A4S0.01 2 0.4307 -0.22867 0.00 0.50 0.00 0.00 0.50
#> TCGA.A7.A3J0.01 5 0.4307 -0.18971 0.00 0.50 0.00 0.00 0.50
#> TCGA.BH.A0BT.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.EW.A2FW.01 2 0.4042 0.8594 0.00 0.76 0.00 0.02 0.18 0.04
#> TCGA.D8.A1JD.01 3 0.1814 0.6652 0.00 0.00 0.90 0.10 0.00 0.00
#> TCGA.AO.A1KQ.01 1 0.3475 0.8456 0.80 0.14 0.00 0.00 0.00 0.06
#> TCGA.A7.A3RF.01 6 0.5643 0.5334 0.00 0.02 0.16 0.22 0.00 0.60
#> TCGA.BH.A1FN.01 2 0.3678 0.8631 0.00 0.78 0.00 0.02 0.18 0.02
#> TCGA.BH.A0H0.01 3 0.0547 0.7568 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.E2.A1IL.01 2 0.3460 0.8397 0.00 0.76 0.00 0.00 0.22 0.02
#> TCGA.D8.A1JI.01 1 0.0000 0.9271 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1OY.01 1 0.3475 0.8456 0.80 0.14 0.00 0.00 0.00 0.06
#> TCGA.B6.A0RP.01 3 0.0000 0.7618 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E9.A1RB.01 2 0.4244 0.7012 0.00 0.72 0.00 0.20 0.00 0.08
#> TCGA.LL.A442.01 4 0.3679 0.6576 0.00 0.20 0.00 0.76 0.00 0.04
#> TCGA.C8.A26Z.01 1 0.0547 0.9235 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.BH.A0BS.01 4 0.1267 0.8261 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.B6.A0WT.01 3 0.3869 -0.3474 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.E2.A15K.01 1 0.0000 0.9271 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A15K.06 1 0.0000 0.9271 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A6VR.01 5 0.0000 1.0000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AR.A1AS.01 3 0.0000 0.7618 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A6NO.01 4 0.2512 0.7843 0.00 0.00 0.06 0.88 0.00 0.06
#> TCGA.BH.A0H6.01 2 0.3156 0.8629 0.00 0.80 0.00 0.02 0.18 0.00
#> TCGA.EW.A6SC.01 1 0.3523 0.8268 0.78 0.18 0.00 0.00 0.00 0.04
#> TCGA.C8.A1HL.01 1 0.0000 0.9271 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1B4.01 4 0.1480 0.8215 0.00 0.02 0.00 0.94 0.00 0.04
#> TCGA.AC.A3QQ.01 3 0.1092 0.7621 0.00 0.02 0.96 0.00 0.00 0.02
#> TCGA.D8.A1X7.01 3 0.3797 -0.0701 0.00 0.00 0.58 0.00 0.00 0.42
#> TCGA.A8.A075.01 4 0.1480 0.8215 0.00 0.02 0.00 0.94 0.00 0.04
#> TCGA.E9.A3Q9.01 3 0.3523 0.6562 0.00 0.18 0.78 0.00 0.00 0.04
#> TCGA.GM.A2DM.01 5 0.0000 1.0000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BH.A6R8.01 1 0.0000 0.9271 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V7.A7HQ.01 2 0.3156 0.8629 0.00 0.80 0.00 0.02 0.18 0.00
#> TCGA.BH.A5J0.01 3 0.1480 0.7558 0.00 0.04 0.94 0.00 0.00 0.02
#> TCGA.Z7.A8R6.01 4 0.0547 0.8274 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.D8.A1JC.01 1 0.0547 0.9235 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.BH.A0DQ.01 1 0.3523 0.8268 0.78 0.18 0.00 0.00 0.00 0.04
#> TCGA.B6.A2IU.01 3 0.3523 0.6562 0.00 0.18 0.78 0.00 0.00 0.04
#> TCGA.D8.A1XG.01 5 0.0000 1.0000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AR.A24V.01 3 0.3523 0.6562 0.00 0.18 0.78 0.00 0.00 0.04
#> TCGA.AN.A0XS.01 2 0.2793 0.7513 0.00 0.80 0.00 0.20 0.00 0.00
#> TCGA.LL.A6FP.01 1 0.0000 0.9271 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1L8.01 3 0.0000 0.7618 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A7.A4SB.01 3 0.5692 -0.2082 0.00 0.00 0.50 0.18 0.00 0.32
#> TCGA.E9.A245.01 2 0.4121 0.8301 0.00 0.72 0.00 0.00 0.22 0.06
#> TCGA.AC.A8OR.01 5 0.0000 1.0000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A7.A4SF.01 1 0.0000 0.9271 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1X6.01 1 0.3523 0.8268 0.78 0.18 0.00 0.00 0.00 0.04
#> TCGA.B6.A0X5.01 1 0.0000 0.9271 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A0DC.01 4 0.1480 0.8215 0.00 0.02 0.00 0.94 0.00 0.04
#> TCGA.AO.A12B.01 2 0.4380 0.8209 0.00 0.70 0.00 0.00 0.22 0.08
#> TCGA.E2.A1IU.01 4 0.4503 0.4736 0.00 0.00 0.24 0.68 0.00 0.08
#> TCGA.B6.A0RI.01 4 0.1865 0.8085 0.00 0.00 0.04 0.92 0.00 0.04
#> TCGA.EW.A1P6.01 4 0.0547 0.8274 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.E9.A1RG.01 1 0.3475 0.8456 0.80 0.14 0.00 0.00 0.00 0.06
#> TCGA.AN.A0XT.01 4 0.1267 0.8178 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.E2.A1IN.01 4 0.1480 0.8215 0.00 0.02 0.00 0.94 0.00 0.04
#> TCGA.BH.A0H9.01 4 0.6394 -0.2052 0.00 0.02 0.36 0.40 0.00 0.22
#> TCGA.B6.A0RG.01 1 0.0000 0.9271 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A54X.01 5 0.0000 1.0000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A2.A25E.01 6 0.4337 0.0915 0.00 0.02 0.48 0.00 0.00 0.50
#> TCGA.S3.AA12.01 1 0.0000 0.9271 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A27T.01 3 0.3351 0.6698 0.00 0.16 0.80 0.00 0.00 0.04
#> TCGA.B6.A0X4.01 5 0.0000 1.0000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.E2.A15I.01 3 0.0000 0.7618 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0H7.01 1 0.0547 0.9235 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.A1.A0SG.01 3 0.1092 0.7621 0.00 0.02 0.96 0.00 0.00 0.02
#> TCGA.D8.A1XR.01 4 0.1865 0.8085 0.00 0.00 0.04 0.92 0.00 0.04
#> TCGA.AO.A0JB.01 3 0.0937 0.7487 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.A8.A0AD.01 1 0.3523 0.8268 0.78 0.18 0.00 0.00 0.00 0.04
#> TCGA.BH.A1ET.01 4 0.3711 0.6619 0.00 0.02 0.00 0.72 0.00 0.26
#> TCGA.A2.A04R.01 1 0.0000 0.9271 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1F5.01 2 0.2793 0.7513 0.00 0.80 0.00 0.20 0.00 0.00
#> TCGA.EW.A1J1.01 6 0.3499 0.4823 0.00 0.00 0.32 0.00 0.00 0.68
#> TCGA.3C.AAAU.01 6 0.3592 0.3107 0.00 0.02 0.00 0.24 0.00 0.74
#> TCGA.A2.A4S0.01 5 0.0000 1.0000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A7.A3J0.01 5 0.0000 1.0000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BH.A0BT.01 1 0.0547 0.9235 0.98 0.00 0.00 0.00 0.00 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.EW.A2FW.01 2 0.1860 0.938 0.00 0.92 0.00 0.02 0.04 0.00 0.02
#> TCGA.D8.A1JD.01 3 0.2512 0.695 0.00 0.00 0.86 0.10 0.00 0.04 0.00
#> TCGA.AO.A1KQ.01 1 0.3047 0.743 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.A7.A3RF.01 6 0.4079 0.707 0.00 0.00 0.04 0.08 0.00 0.76 0.12
#> TCGA.BH.A1FN.01 2 0.1860 0.938 0.00 0.92 0.00 0.02 0.04 0.00 0.02
#> TCGA.BH.A0H0.01 3 0.2159 0.734 0.00 0.02 0.90 0.00 0.00 0.02 0.06
#> TCGA.E2.A1IL.01 2 0.2278 0.920 0.00 0.88 0.00 0.00 0.08 0.00 0.04
#> TCGA.D8.A1JI.01 1 0.0000 0.887 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1OY.01 1 0.3047 0.743 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.B6.A0RP.01 3 0.1006 0.758 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.E9.A1RB.01 2 0.2569 0.797 0.00 0.84 0.00 0.02 0.00 0.00 0.14
#> TCGA.LL.A442.01 4 0.4177 0.655 0.00 0.18 0.00 0.70 0.00 0.00 0.12
#> TCGA.C8.A26Z.01 1 0.0000 0.887 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BS.01 4 0.1433 0.833 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.B6.A0WT.01 6 0.1886 0.742 0.00 0.00 0.12 0.00 0.00 0.88 0.00
#> TCGA.E2.A15K.01 1 0.0000 0.887 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A15K.06 1 0.0000 0.887 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A6VR.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AR.A1AS.01 3 0.1006 0.758 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.AC.A6NO.01 4 0.2509 0.817 0.00 0.00 0.02 0.88 0.00 0.04 0.06
#> TCGA.BH.A0H6.01 2 0.1363 0.938 0.00 0.94 0.00 0.02 0.04 0.00 0.00
#> TCGA.EW.A6SC.01 1 0.4003 0.672 0.64 0.00 0.04 0.00 0.00 0.00 0.32
#> TCGA.C8.A1HL.01 1 0.0000 0.887 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1B4.01 4 0.2163 0.837 0.00 0.02 0.00 0.88 0.00 0.00 0.10
#> TCGA.AC.A3QQ.01 3 0.1363 0.770 0.00 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.D8.A1X7.01 6 0.2906 0.705 0.00 0.00 0.18 0.00 0.00 0.80 0.02
#> TCGA.A8.A075.01 4 0.1664 0.845 0.00 0.02 0.00 0.92 0.00 0.00 0.06
#> TCGA.E9.A3Q9.01 3 0.4524 0.541 0.02 0.00 0.60 0.00 0.00 0.04 0.34
#> TCGA.GM.A2DM.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A6R8.01 1 0.0000 0.887 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V7.A7HQ.01 2 0.1363 0.938 0.00 0.94 0.00 0.02 0.04 0.00 0.00
#> TCGA.BH.A5J0.01 3 0.1363 0.770 0.00 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.Z7.A8R6.01 4 0.1928 0.841 0.00 0.00 0.02 0.90 0.00 0.00 0.08
#> TCGA.D8.A1JC.01 1 0.0000 0.887 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DQ.01 1 0.3139 0.727 0.70 0.00 0.00 0.00 0.00 0.00 0.30
#> TCGA.B6.A2IU.01 3 0.3685 0.597 0.00 0.00 0.66 0.00 0.00 0.02 0.32
#> TCGA.D8.A1XG.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AR.A24V.01 3 0.4146 0.581 0.02 0.00 0.64 0.00 0.00 0.02 0.32
#> TCGA.AN.A0XS.01 2 0.1166 0.910 0.00 0.94 0.00 0.06 0.00 0.00 0.00
#> TCGA.LL.A6FP.01 1 0.0000 0.887 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1L8.01 3 0.0000 0.771 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A4SB.01 6 0.5047 0.415 0.00 0.00 0.34 0.14 0.00 0.52 0.00
#> TCGA.E9.A245.01 2 0.2278 0.920 0.00 0.88 0.00 0.00 0.08 0.00 0.04
#> TCGA.AC.A8OR.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A7.A4SF.01 1 0.0000 0.887 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1X6.01 1 0.4264 0.649 0.62 0.00 0.06 0.00 0.00 0.00 0.32
#> TCGA.B6.A0X5.01 1 0.0000 0.887 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A0DC.01 4 0.1664 0.845 0.00 0.02 0.00 0.92 0.00 0.00 0.06
#> TCGA.AO.A12B.01 2 0.2278 0.920 0.00 0.88 0.00 0.00 0.08 0.00 0.04
#> TCGA.E2.A1IU.01 4 0.4963 0.496 0.00 0.00 0.24 0.64 0.00 0.06 0.06
#> TCGA.B6.A0RI.01 4 0.1006 0.845 0.00 0.00 0.02 0.96 0.00 0.00 0.02
#> TCGA.EW.A1P6.01 4 0.1928 0.841 0.00 0.00 0.02 0.90 0.00 0.00 0.08
#> TCGA.E9.A1RG.01 1 0.3047 0.743 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.AN.A0XT.01 4 0.1166 0.841 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.E2.A1IN.01 4 0.1664 0.845 0.00 0.02 0.00 0.92 0.00 0.00 0.06
#> TCGA.BH.A0H9.01 3 0.6196 0.101 0.00 0.00 0.50 0.26 0.00 0.12 0.12
#> TCGA.B6.A0RG.01 1 0.0000 0.887 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A54X.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A2.A25E.01 6 0.2912 0.717 0.00 0.00 0.14 0.00 0.00 0.82 0.04
#> TCGA.S3.AA12.01 1 0.0000 0.887 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A27T.01 3 0.4146 0.581 0.02 0.00 0.64 0.00 0.00 0.02 0.32
#> TCGA.B6.A0X4.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E2.A15I.01 3 0.0000 0.771 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0H7.01 1 0.0000 0.887 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A1.A0SG.01 3 0.1363 0.770 0.00 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.D8.A1XR.01 4 0.1664 0.834 0.00 0.00 0.02 0.92 0.00 0.00 0.06
#> TCGA.AO.A0JB.01 3 0.2509 0.716 0.00 0.02 0.88 0.00 0.00 0.04 0.06
#> TCGA.A8.A0AD.01 1 0.4264 0.649 0.62 0.00 0.06 0.00 0.00 0.00 0.32
#> TCGA.BH.A1ET.01 4 0.5406 0.392 0.00 0.06 0.00 0.50 0.00 0.06 0.38
#> TCGA.A2.A04R.01 1 0.0000 0.887 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1F5.01 2 0.0863 0.917 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.EW.A1J1.01 6 0.1166 0.730 0.00 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.3C.AAAU.01 6 0.5413 0.463 0.00 0.04 0.00 0.08 0.00 0.44 0.44
#> TCGA.A2.A4S0.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A7.A3J0.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A0BT.01 1 0.0000 0.887 1.00 0.00 0.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.EW.A2FW.01 2 0.0941 0.9251 0.00 0.96 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.D8.A1JD.01 3 0.5103 0.4456 0.00 0.00 0.44 0.22 0.00 0.00 0.34 0.00
#> TCGA.AO.A1KQ.01 1 0.4308 0.5470 0.62 0.02 0.00 0.00 0.00 0.02 0.32 0.02
#> TCGA.A7.A3RF.01 6 0.4779 0.3106 0.00 0.00 0.28 0.04 0.00 0.60 0.00 0.08
#> TCGA.BH.A1FN.01 2 0.1275 0.9245 0.00 0.94 0.04 0.00 0.02 0.00 0.00 0.00
#> TCGA.BH.A0H0.01 3 0.3318 0.7100 0.00 0.00 0.54 0.00 0.00 0.00 0.46 0.00
#> TCGA.E2.A1IL.01 2 0.1275 0.9245 0.00 0.94 0.04 0.00 0.02 0.00 0.00 0.00
#> TCGA.D8.A1JI.01 1 0.0000 0.8643 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1OY.01 1 0.4308 0.5470 0.62 0.02 0.00 0.00 0.00 0.02 0.32 0.02
#> TCGA.B6.A0RP.01 3 0.3329 0.7175 0.00 0.00 0.52 0.00 0.00 0.00 0.48 0.00
#> TCGA.E9.A1RB.01 2 0.3514 0.4656 0.00 0.64 0.02 0.00 0.00 0.00 0.00 0.34
#> TCGA.LL.A442.01 4 0.6698 0.2983 0.00 0.18 0.12 0.48 0.00 0.08 0.00 0.14
#> TCGA.C8.A26Z.01 1 0.1408 0.8468 0.94 0.02 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.BH.A0BS.01 4 0.3687 0.7438 0.00 0.00 0.06 0.78 0.00 0.08 0.00 0.08
#> TCGA.B6.A0WT.01 6 0.3337 0.6623 0.00 0.00 0.02 0.00 0.00 0.78 0.16 0.04
#> TCGA.E2.A15K.01 1 0.0000 0.8643 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A15K.06 1 0.0000 0.8643 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A6VR.01 5 0.0000 1.0000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A1AS.01 3 0.3329 0.7175 0.00 0.00 0.52 0.00 0.00 0.00 0.48 0.00
#> TCGA.AC.A6NO.01 4 0.4138 0.7162 0.00 0.00 0.16 0.72 0.00 0.08 0.00 0.04
#> TCGA.BH.A0H6.01 2 0.0471 0.9254 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.EW.A6SC.01 7 0.3333 -0.3562 0.50 0.00 0.00 0.00 0.00 0.00 0.50 0.00
#> TCGA.C8.A1HL.01 1 0.0000 0.8643 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1B4.01 4 0.1557 0.7458 0.00 0.00 0.00 0.92 0.00 0.02 0.00 0.06
#> TCGA.AC.A3QQ.01 7 0.3193 -0.5300 0.00 0.00 0.38 0.00 0.00 0.00 0.62 0.00
#> TCGA.D8.A1X7.01 6 0.2888 0.6610 0.00 0.00 0.04 0.00 0.00 0.80 0.16 0.00
#> TCGA.A8.A075.01 4 0.0808 0.7545 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.E9.A3Q9.01 7 0.0808 0.3554 0.00 0.00 0.04 0.00 0.00 0.00 0.96 0.00
#> TCGA.GM.A2DM.01 5 0.0000 1.0000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A6R8.01 1 0.0000 0.8643 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.V7.A7HQ.01 2 0.0471 0.9254 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.BH.A5J0.01 7 0.3374 -0.3992 0.00 0.00 0.30 0.00 0.00 0.00 0.68 0.02
#> TCGA.Z7.A8R6.01 4 0.0808 0.7656 0.00 0.00 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JC.01 1 0.1408 0.8468 0.94 0.02 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.BH.A0DQ.01 1 0.3329 0.2912 0.52 0.00 0.00 0.00 0.00 0.00 0.48 0.00
#> TCGA.B6.A2IU.01 7 0.0000 0.3713 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D8.A1XG.01 5 0.0000 1.0000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A24V.01 7 0.0000 0.3713 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AN.A0XS.01 2 0.0471 0.9158 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.LL.A6FP.01 1 0.0000 0.8643 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1L8.01 3 0.3737 0.7053 0.00 0.00 0.50 0.00 0.00 0.00 0.48 0.02
#> TCGA.A7.A4SB.01 6 0.6652 0.3007 0.00 0.00 0.24 0.18 0.00 0.44 0.08 0.06
#> TCGA.E9.A245.01 2 0.2020 0.9105 0.00 0.90 0.06 0.00 0.02 0.02 0.00 0.00
#> TCGA.AC.A8OR.01 5 0.0000 1.0000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A7.A4SF.01 1 0.0000 0.8643 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1X6.01 7 0.3333 -0.3562 0.50 0.00 0.00 0.00 0.00 0.00 0.50 0.00
#> TCGA.B6.A0X5.01 1 0.0000 0.8643 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A0DC.01 4 0.0808 0.7545 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.AO.A12B.01 2 0.2482 0.8994 0.00 0.88 0.06 0.00 0.02 0.02 0.00 0.02
#> TCGA.E2.A1IU.01 4 0.5804 0.5047 0.00 0.00 0.24 0.56 0.00 0.06 0.06 0.08
#> TCGA.B6.A0RI.01 4 0.3270 0.7490 0.00 0.00 0.12 0.80 0.00 0.06 0.00 0.02
#> TCGA.EW.A1P6.01 4 0.1091 0.7621 0.00 0.00 0.06 0.94 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RG.01 1 0.4308 0.5470 0.62 0.02 0.00 0.00 0.00 0.02 0.32 0.02
#> TCGA.AN.A0XT.01 4 0.4898 0.5186 0.00 0.00 0.30 0.56 0.00 0.12 0.00 0.02
#> TCGA.E2.A1IN.01 4 0.0808 0.7545 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.BH.A0H9.01 3 0.5583 -0.0885 0.00 0.00 0.62 0.14 0.00 0.10 0.04 0.10
#> TCGA.B6.A0RG.01 1 0.0000 0.8643 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A54X.01 5 0.0000 1.0000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A25E.01 6 0.2569 0.6608 0.00 0.00 0.00 0.00 0.00 0.82 0.16 0.02
#> TCGA.S3.AA12.01 1 0.0000 0.8643 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A27T.01 7 0.0000 0.3713 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.B6.A0X4.01 5 0.0000 1.0000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E2.A15I.01 3 0.3329 0.7175 0.00 0.00 0.52 0.00 0.00 0.00 0.48 0.00
#> TCGA.BH.A0H7.01 1 0.1408 0.8468 0.94 0.02 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.A1.A0SG.01 7 0.3570 -0.5224 0.00 0.00 0.36 0.00 0.00 0.00 0.62 0.02
#> TCGA.D8.A1XR.01 4 0.3337 0.7387 0.00 0.00 0.16 0.78 0.00 0.04 0.00 0.02
#> TCGA.AO.A0JB.01 3 0.3690 0.6666 0.00 0.00 0.56 0.00 0.00 0.00 0.42 0.02
#> TCGA.A8.A0AD.01 1 0.3333 0.2376 0.50 0.00 0.00 0.00 0.00 0.00 0.50 0.00
#> TCGA.BH.A1ET.01 8 0.2406 0.6813 0.00 0.00 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.A2.A04R.01 1 0.0000 0.8643 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1F5.01 2 0.0471 0.9181 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.EW.A1J1.01 6 0.2981 0.5028 0.00 0.00 0.00 0.00 0.00 0.76 0.02 0.22
#> TCGA.3C.AAAU.01 8 0.1091 0.6531 0.00 0.00 0.00 0.00 0.00 0.06 0.00 0.94
#> TCGA.A2.A4S0.01 5 0.0000 1.0000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A7.A3J0.01 5 0.0000 1.0000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0BT.01 1 0.1408 0.8468 0.94 0.02 0.00 0.00 0.00 0.02 0.00 0.02
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node021. Child nodes: Node02121-leaf , Node02122-leaf , Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02214-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02321-leaf , Node02322-leaf , Node02421-leaf , Node02422-leaf , Node02423-leaf , Node04111-leaf , Node04112-leaf , Node04113 , Node04131-leaf , Node04132-leaf , Node04133-leaf , Node04221-leaf , Node04222-leaf , Node04331-leaf , Node04332-leaf , Node04333-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0212"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 18 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.889 0.952 0.981 0.5256 0.477 0.477
#> 3 3 1.000 0.991 0.996 0.2547 0.824 0.645
#> 4 4 0.850 0.638 0.898 0.1054 0.948 0.846
#> 5 5 0.902 0.844 0.949 0.0553 0.889 0.630
#> 6 6 0.856 0.799 0.908 0.0417 0.987 0.935
#> 7 7 0.869 0.700 0.913 0.0258 0.987 0.931
#> 8 8 0.915 0.637 0.941 0.0248 0.993 0.963
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 3
There is also optional best \(k\) = 3 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.EW.A2FW.01 2 0.000 0.961 0.00 1.00
#> TCGA.BH.A1FN.01 2 0.000 0.961 0.00 1.00
#> TCGA.E2.A1IL.01 2 0.000 0.961 0.00 1.00
#> TCGA.E9.A1RB.01 2 0.000 0.961 0.00 1.00
#> TCGA.OL.A6VR.01 2 0.000 0.961 0.00 1.00
#> TCGA.BH.A0H6.01 2 0.000 0.961 0.00 1.00
#> TCGA.GM.A2DM.01 1 0.000 1.000 1.00 0.00
#> TCGA.V7.A7HQ.01 2 0.000 0.961 0.00 1.00
#> TCGA.D8.A1XG.01 1 0.000 1.000 1.00 0.00
#> TCGA.AN.A0XS.01 2 0.000 0.961 0.00 1.00
#> TCGA.E9.A245.01 1 0.000 1.000 1.00 0.00
#> TCGA.AC.A8OR.01 1 0.000 1.000 1.00 0.00
#> TCGA.AO.A12B.01 2 0.925 0.485 0.34 0.66
#> TCGA.E9.A54X.01 1 0.000 1.000 1.00 0.00
#> TCGA.B6.A0X4.01 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A1F5.01 2 0.000 0.961 0.00 1.00
#> TCGA.A2.A4S0.01 1 0.000 1.000 1.00 0.00
#> TCGA.A7.A3J0.01 1 0.000 1.000 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.EW.A2FW.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.BH.A1FN.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.E2.A1IL.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.E9.A1RB.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.OL.A6VR.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.BH.A0H6.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.GM.A2DM.01 3 0.254 0.913 0.08 0 0.92
#> TCGA.V7.A7HQ.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.D8.A1XG.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.AN.A0XS.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.E9.A245.01 3 0.000 0.973 0.00 0 1.00
#> TCGA.AC.A8OR.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.AO.A12B.01 3 0.000 0.973 0.00 0 1.00
#> TCGA.E9.A54X.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.B6.A0X4.01 3 0.000 0.973 0.00 0 1.00
#> TCGA.BH.A1F5.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.A2.A4S0.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.A7.A3J0.01 1 0.000 1.000 1.00 0 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.EW.A2FW.01 2 0.000 0.769 0.00 1.00 0.00 0.00
#> TCGA.BH.A1FN.01 4 0.626 0.000 0.00 0.40 0.06 0.54
#> TCGA.E2.A1IL.01 2 0.499 -0.703 0.00 0.52 0.00 0.48
#> TCGA.E9.A1RB.01 2 0.491 -0.533 0.00 0.58 0.00 0.42
#> TCGA.OL.A6VR.01 2 0.000 0.769 0.00 1.00 0.00 0.00
#> TCGA.BH.A0H6.01 2 0.000 0.769 0.00 1.00 0.00 0.00
#> TCGA.GM.A2DM.01 3 0.634 0.836 0.06 0.00 0.48 0.46
#> TCGA.V7.A7HQ.01 2 0.000 0.769 0.00 1.00 0.00 0.00
#> TCGA.D8.A1XG.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AN.A0XS.01 2 0.000 0.769 0.00 1.00 0.00 0.00
#> TCGA.E9.A245.01 3 0.559 0.853 0.02 0.00 0.52 0.46
#> TCGA.AC.A8OR.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AO.A12B.01 3 0.000 0.578 0.00 0.00 1.00 0.00
#> TCGA.E9.A54X.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B6.A0X4.01 3 0.498 0.849 0.00 0.00 0.54 0.46
#> TCGA.BH.A1F5.01 2 0.000 0.769 0.00 1.00 0.00 0.00
#> TCGA.A2.A4S0.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A7.A3J0.01 1 0.000 1.000 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.EW.A2FW.01 2 0.000 1.000 0.00 1.00 0.00 0.00 0
#> TCGA.BH.A1FN.01 4 0.000 0.232 0.00 0.00 0.00 1.00 0
#> TCGA.E2.A1IL.01 4 0.426 0.550 0.00 0.44 0.00 0.56 0
#> TCGA.E9.A1RB.01 4 0.423 0.578 0.00 0.42 0.00 0.58 0
#> TCGA.OL.A6VR.01 2 0.000 1.000 0.00 1.00 0.00 0.00 0
#> TCGA.BH.A0H6.01 2 0.000 1.000 0.00 1.00 0.00 0.00 0
#> TCGA.GM.A2DM.01 3 0.141 0.913 0.06 0.00 0.94 0.00 0
#> TCGA.V7.A7HQ.01 2 0.000 1.000 0.00 1.00 0.00 0.00 0
#> TCGA.D8.A1XG.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0
#> TCGA.AN.A0XS.01 2 0.000 1.000 0.00 1.00 0.00 0.00 0
#> TCGA.E9.A245.01 3 0.000 0.957 0.00 0.00 1.00 0.00 0
#> TCGA.AC.A8OR.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0
#> TCGA.AO.A12B.01 5 0.000 0.000 0.00 0.00 0.00 0.00 1
#> TCGA.E9.A54X.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0
#> TCGA.B6.A0X4.01 3 0.000 0.957 0.00 0.00 1.00 0.00 0
#> TCGA.BH.A1F5.01 2 0.000 1.000 0.00 1.00 0.00 0.00 0
#> TCGA.A2.A4S0.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0
#> TCGA.A7.A3J0.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.EW.A2FW.01 2 0.0547 0.974 0.00 0.98 0.00 0.02 0 0.00
#> TCGA.BH.A1FN.01 6 0.2941 0.000 0.00 0.00 0.00 0.22 0 0.78
#> TCGA.E2.A1IL.01 4 0.4810 0.743 0.00 0.22 0.00 0.66 0 0.12
#> TCGA.E9.A1RB.01 4 0.2454 0.750 0.00 0.16 0.00 0.84 0 0.00
#> TCGA.OL.A6VR.01 2 0.0000 0.995 0.00 1.00 0.00 0.00 0 0.00
#> TCGA.BH.A0H6.01 2 0.0000 0.995 0.00 1.00 0.00 0.00 0 0.00
#> TCGA.GM.A2DM.01 3 0.5027 0.615 0.00 0.00 0.64 0.16 0 0.20
#> TCGA.V7.A7HQ.01 2 0.0000 0.995 0.00 1.00 0.00 0.00 0 0.00
#> TCGA.D8.A1XG.01 1 0.0000 0.964 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.AN.A0XS.01 2 0.0000 0.995 0.00 1.00 0.00 0.00 0 0.00
#> TCGA.E9.A245.01 3 0.0000 0.817 0.00 0.00 1.00 0.00 0 0.00
#> TCGA.AC.A8OR.01 1 0.0000 0.964 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.AO.A12B.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1 0.00
#> TCGA.E9.A54X.01 1 0.2794 0.846 0.86 0.00 0.00 0.06 0 0.08
#> TCGA.B6.A0X4.01 3 0.0547 0.813 0.00 0.00 0.98 0.00 0 0.02
#> TCGA.BH.A1F5.01 2 0.0000 0.995 0.00 1.00 0.00 0.00 0 0.00
#> TCGA.A2.A4S0.01 1 0.0000 0.964 1.00 0.00 0.00 0.00 0 0.00
#> TCGA.A7.A3J0.01 1 0.0000 0.964 1.00 0.00 0.00 0.00 0 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.EW.A2FW.01 2 0.216 0.860 0.00 0.88 0.00 0.02 0 0.00 0.10
#> TCGA.BH.A1FN.01 6 0.000 0.000 0.00 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.E2.A1IL.01 4 0.670 0.297 0.00 0.20 0.00 0.42 0 0.14 0.24
#> TCGA.E9.A1RB.01 4 0.000 0.324 0.00 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.OL.A6VR.01 2 0.000 0.974 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.BH.A0H6.01 2 0.000 0.974 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.GM.A2DM.01 7 0.336 0.000 0.00 0.00 0.36 0.00 0 0.00 0.64
#> TCGA.V7.A7HQ.01 2 0.000 0.974 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.D8.A1XG.01 1 0.000 0.945 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.AN.A0XS.01 2 0.000 0.974 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.E9.A245.01 3 0.143 0.857 0.00 0.00 0.92 0.00 0 0.00 0.08
#> TCGA.AC.A8OR.01 1 0.000 0.945 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.AO.A12B.01 5 0.000 0.000 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.E9.A54X.01 1 0.271 0.746 0.78 0.00 0.00 0.00 0 0.00 0.22
#> TCGA.B6.A0X4.01 3 0.000 0.865 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.BH.A1F5.01 2 0.000 0.974 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.A2.A4S0.01 1 0.000 0.945 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.A7.A3J0.01 1 0.000 0.945 1.00 0.00 0.00 0.00 0 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.EW.A2FW.01 2 0.3991 0.659 0.00 0.70 0.00 0.22 0 0.00 0.06 0.02
#> TCGA.BH.A1FN.01 6 0.0000 0.000 0.00 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.E2.A1IL.01 4 0.3873 0.000 0.00 0.02 0.00 0.72 0 0.06 0.00 0.20
#> TCGA.E9.A1RB.01 8 0.0000 0.000 0.00 0.00 0.00 0.00 0 0.00 0.00 1.00
#> TCGA.OL.A6VR.01 2 0.0471 0.928 0.00 0.98 0.00 0.00 0 0.00 0.00 0.02
#> TCGA.BH.A0H6.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.GM.A2DM.01 7 0.1341 0.000 0.00 0.00 0.08 0.00 0 0.00 0.92 0.00
#> TCGA.V7.A7HQ.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.D8.A1XG.01 1 0.0000 0.934 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.AN.A0XS.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.E9.A245.01 3 0.1765 0.851 0.00 0.00 0.88 0.00 0 0.00 0.12 0.00
#> TCGA.AC.A8OR.01 1 0.0000 0.934 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.AO.A12B.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.E9.A54X.01 1 0.3431 0.678 0.74 0.00 0.00 0.06 0 0.00 0.20 0.00
#> TCGA.B6.A0X4.01 3 0.0000 0.859 0.00 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.BH.A1F5.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.A2.A4S0.01 1 0.0000 0.934 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.A7.A3J0.01 1 0.0000 0.934 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node021. Child nodes: Node02121-leaf , Node02122-leaf , Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02214-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02321-leaf , Node02322-leaf , Node02421-leaf , Node02422-leaf , Node02423-leaf , Node04111-leaf , Node04112-leaf , Node04113 , Node04131-leaf , Node04132-leaf , Node04133-leaf , Node04221-leaf , Node04222-leaf , Node04331-leaf , Node04332-leaf , Node04333-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0213"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 31 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4736 0.527 0.527
#> 3 3 0.832 0.936 0.963 0.3905 0.643 0.418
#> 4 4 0.835 0.808 0.927 0.1368 0.781 0.455
#> 5 5 0.791 0.758 0.889 0.0837 0.847 0.470
#> 6 6 0.803 0.750 0.841 0.0348 0.948 0.747
#> 7 7 0.877 0.730 0.885 0.0281 0.955 0.750
#> 8 8 0.887 0.691 0.818 0.0151 0.953 0.686
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.D8.A1JD.01 1 0 1 1 0
#> TCGA.A7.A3RF.01 2 0 1 0 1
#> TCGA.BH.A0H0.01 1 0 1 1 0
#> TCGA.B6.A0RP.01 1 0 1 1 0
#> TCGA.LL.A442.01 2 0 1 0 1
#> TCGA.BH.A0BS.01 1 0 1 1 0
#> TCGA.B6.A0WT.01 1 0 1 1 0
#> TCGA.AR.A1AS.01 1 0 1 1 0
#> TCGA.AC.A6NO.01 1 0 1 1 0
#> TCGA.E2.A1B4.01 1 0 1 1 0
#> TCGA.AC.A3QQ.01 1 0 1 1 0
#> TCGA.D8.A1X7.01 1 0 1 1 0
#> TCGA.A8.A075.01 2 0 1 0 1
#> TCGA.BH.A5J0.01 2 0 1 0 1
#> TCGA.Z7.A8R6.01 1 0 1 1 0
#> TCGA.E2.A1L8.01 1 0 1 1 0
#> TCGA.A7.A4SB.01 1 0 1 1 0
#> TCGA.A7.A0DC.01 1 0 1 1 0
#> TCGA.E2.A1IU.01 1 0 1 1 0
#> TCGA.B6.A0RI.01 1 0 1 1 0
#> TCGA.EW.A1P6.01 2 0 1 0 1
#> TCGA.AN.A0XT.01 2 0 1 0 1
#> TCGA.E2.A1IN.01 2 0 1 0 1
#> TCGA.BH.A0H9.01 2 0 1 0 1
#> TCGA.E2.A15I.01 1 0 1 1 0
#> TCGA.A1.A0SG.01 1 0 1 1 0
#> TCGA.D8.A1XR.01 2 0 1 0 1
#> TCGA.AO.A0JB.01 2 0 1 0 1
#> TCGA.BH.A1ET.01 1 0 1 1 0
#> TCGA.EW.A1J1.01 2 0 1 0 1
#> TCGA.3C.AAAU.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.D8.A1JD.01 1 0.334 0.888 0.88 0.00 0.12
#> TCGA.A7.A3RF.01 3 0.254 0.927 0.00 0.08 0.92
#> TCGA.BH.A0H0.01 1 0.000 0.932 1.00 0.00 0.00
#> TCGA.B6.A0RP.01 1 0.000 0.932 1.00 0.00 0.00
#> TCGA.LL.A442.01 3 0.334 0.892 0.00 0.12 0.88
#> TCGA.BH.A0BS.01 1 0.207 0.916 0.94 0.00 0.06
#> TCGA.B6.A0WT.01 3 0.000 0.958 0.00 0.00 1.00
#> TCGA.AR.A1AS.01 1 0.000 0.932 1.00 0.00 0.00
#> TCGA.AC.A6NO.01 1 0.334 0.888 0.88 0.00 0.12
#> TCGA.E2.A1B4.01 1 0.000 0.932 1.00 0.00 0.00
#> TCGA.AC.A3QQ.01 1 0.000 0.932 1.00 0.00 0.00
#> TCGA.D8.A1X7.01 1 0.296 0.900 0.90 0.00 0.10
#> TCGA.A8.A075.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.BH.A5J0.01 3 0.334 0.892 0.00 0.12 0.88
#> TCGA.Z7.A8R6.01 3 0.000 0.958 0.00 0.00 1.00
#> TCGA.E2.A1L8.01 1 0.000 0.932 1.00 0.00 0.00
#> TCGA.A7.A4SB.01 3 0.000 0.958 0.00 0.00 1.00
#> TCGA.A7.A0DC.01 3 0.000 0.958 0.00 0.00 1.00
#> TCGA.E2.A1IU.01 1 0.000 0.932 1.00 0.00 0.00
#> TCGA.B6.A0RI.01 3 0.000 0.958 0.00 0.00 1.00
#> TCGA.EW.A1P6.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.AN.A0XT.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.E2.A1IN.01 3 0.207 0.936 0.00 0.06 0.94
#> TCGA.BH.A0H9.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.E2.A15I.01 3 0.000 0.958 0.00 0.00 1.00
#> TCGA.A1.A0SG.01 3 0.000 0.958 0.00 0.00 1.00
#> TCGA.D8.A1XR.01 3 0.254 0.927 0.00 0.08 0.92
#> TCGA.AO.A0JB.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.BH.A1ET.01 1 0.556 0.662 0.70 0.00 0.30
#> TCGA.EW.A1J1.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.3C.AAAU.01 3 0.000 0.958 0.00 0.00 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.D8.A1JD.01 3 0.4713 0.47458 0.36 0.00 0.64 0.00
#> TCGA.A7.A3RF.01 4 0.0000 0.86875 0.00 0.00 0.00 1.00
#> TCGA.BH.A0H0.01 1 0.0000 0.91906 1.00 0.00 0.00 0.00
#> TCGA.B6.A0RP.01 1 0.0000 0.91906 1.00 0.00 0.00 0.00
#> TCGA.LL.A442.01 4 0.0000 0.86875 0.00 0.00 0.00 1.00
#> TCGA.BH.A0BS.01 1 0.4948 -0.00318 0.56 0.00 0.44 0.00
#> TCGA.B6.A0WT.01 3 0.0000 0.85156 0.00 0.00 1.00 0.00
#> TCGA.AR.A1AS.01 1 0.0000 0.91906 1.00 0.00 0.00 0.00
#> TCGA.AC.A6NO.01 3 0.4713 0.47458 0.36 0.00 0.64 0.00
#> TCGA.E2.A1B4.01 1 0.0000 0.91906 1.00 0.00 0.00 0.00
#> TCGA.AC.A3QQ.01 1 0.0000 0.91906 1.00 0.00 0.00 0.00
#> TCGA.D8.A1X7.01 3 0.4790 0.43198 0.38 0.00 0.62 0.00
#> TCGA.A8.A075.01 2 0.0000 0.97525 0.00 1.00 0.00 0.00
#> TCGA.BH.A5J0.01 4 0.0000 0.86875 0.00 0.00 0.00 1.00
#> TCGA.Z7.A8R6.01 3 0.0707 0.83745 0.00 0.00 0.98 0.02
#> TCGA.E2.A1L8.01 1 0.0000 0.91906 1.00 0.00 0.00 0.00
#> TCGA.A7.A4SB.01 3 0.0000 0.85156 0.00 0.00 1.00 0.00
#> TCGA.A7.A0DC.01 3 0.0000 0.85156 0.00 0.00 1.00 0.00
#> TCGA.E2.A1IU.01 1 0.0707 0.90449 0.98 0.00 0.02 0.00
#> TCGA.B6.A0RI.01 3 0.0000 0.85156 0.00 0.00 1.00 0.00
#> TCGA.EW.A1P6.01 2 0.2647 0.86313 0.00 0.88 0.00 0.12
#> TCGA.AN.A0XT.01 2 0.0000 0.97525 0.00 1.00 0.00 0.00
#> TCGA.E2.A1IN.01 4 0.4624 0.54916 0.00 0.00 0.34 0.66
#> TCGA.BH.A0H9.01 2 0.0000 0.97525 0.00 1.00 0.00 0.00
#> TCGA.E2.A15I.01 4 0.3610 0.70647 0.00 0.00 0.20 0.80
#> TCGA.A1.A0SG.01 3 0.0707 0.83745 0.00 0.00 0.98 0.02
#> TCGA.D8.A1XR.01 4 0.0000 0.86875 0.00 0.00 0.00 1.00
#> TCGA.AO.A0JB.01 2 0.0000 0.97525 0.00 1.00 0.00 0.00
#> TCGA.BH.A1ET.01 3 0.0000 0.85156 0.00 0.00 1.00 0.00
#> TCGA.EW.A1J1.01 2 0.0000 0.97525 0.00 1.00 0.00 0.00
#> TCGA.3C.AAAU.01 3 0.0000 0.85156 0.00 0.00 1.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.D8.A1JD.01 5 0.3421 0.710 0.08 0.00 0.08 0.00 0.84
#> TCGA.A7.A3RF.01 4 0.0000 0.930 0.00 0.00 0.00 1.00 0.00
#> TCGA.BH.A0H0.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0RP.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.LL.A442.01 4 0.0000 0.930 0.00 0.00 0.00 1.00 0.00
#> TCGA.BH.A0BS.01 5 0.1732 0.724 0.08 0.00 0.00 0.00 0.92
#> TCGA.B6.A0WT.01 3 0.2280 0.771 0.00 0.00 0.88 0.00 0.12
#> TCGA.AR.A1AS.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A6NO.01 5 0.2754 0.725 0.08 0.00 0.04 0.00 0.88
#> TCGA.E2.A1B4.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A3QQ.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1X7.01 5 0.1043 0.709 0.04 0.00 0.00 0.00 0.96
#> TCGA.A8.A075.01 2 0.0000 0.958 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A5J0.01 4 0.3291 0.835 0.00 0.00 0.12 0.84 0.04
#> TCGA.Z7.A8R6.01 3 0.0609 0.765 0.00 0.00 0.98 0.00 0.02
#> TCGA.E2.A1L8.01 5 0.4302 0.152 0.48 0.00 0.00 0.00 0.52
#> TCGA.A7.A4SB.01 3 0.3983 0.546 0.00 0.00 0.66 0.00 0.34
#> TCGA.A7.A0DC.01 3 0.2280 0.771 0.00 0.00 0.88 0.00 0.12
#> TCGA.E2.A1IU.01 5 0.3684 0.586 0.28 0.00 0.00 0.00 0.72
#> TCGA.B6.A0RI.01 3 0.4126 0.470 0.00 0.00 0.62 0.00 0.38
#> TCGA.EW.A1P6.01 2 0.4634 0.762 0.00 0.78 0.12 0.06 0.04
#> TCGA.AN.A0XT.01 2 0.0000 0.958 0.00 1.00 0.00 0.00 0.00
#> TCGA.E2.A1IN.01 3 0.3291 0.622 0.00 0.00 0.84 0.12 0.04
#> TCGA.BH.A0H9.01 2 0.0000 0.958 0.00 1.00 0.00 0.00 0.00
#> TCGA.E2.A15I.01 4 0.2754 0.835 0.00 0.00 0.08 0.88 0.04
#> TCGA.A1.A0SG.01 3 0.0000 0.756 0.00 0.00 1.00 0.00 0.00
#> TCGA.D8.A1XR.01 4 0.0000 0.930 0.00 0.00 0.00 1.00 0.00
#> TCGA.AO.A0JB.01 2 0.0000 0.958 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A1ET.01 5 0.3109 0.579 0.00 0.00 0.20 0.00 0.80
#> TCGA.EW.A1J1.01 2 0.0000 0.958 0.00 1.00 0.00 0.00 0.00
#> TCGA.3C.AAAU.01 5 0.4302 -0.407 0.00 0.00 0.48 0.00 0.52
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.D8.A1JD.01 5 0.2981 0.819 0.00 0.00 0.16 0.02 0.82 0.00
#> TCGA.A7.A3RF.01 6 0.3756 0.705 0.00 0.00 0.00 0.40 0.00 0.60
#> TCGA.BH.A0H0.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0RP.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LL.A442.01 6 0.3756 0.705 0.00 0.00 0.00 0.40 0.00 0.60
#> TCGA.BH.A0BS.01 5 0.1807 0.833 0.02 0.00 0.06 0.00 0.92 0.00
#> TCGA.B6.A0WT.01 3 0.0547 0.768 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.AR.A1AS.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A6NO.01 5 0.2454 0.825 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.E2.A1B4.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A3QQ.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1X7.01 5 0.2190 0.790 0.00 0.00 0.04 0.06 0.90 0.00
#> TCGA.A8.A075.01 2 0.0000 0.908 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A5J0.01 6 0.0000 0.539 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.Z7.A8R6.01 3 0.2793 0.743 0.00 0.00 0.80 0.20 0.00 0.00
#> TCGA.E2.A1L8.01 5 0.3076 0.726 0.24 0.00 0.00 0.00 0.76 0.00
#> TCGA.A7.A4SB.01 3 0.1865 0.763 0.00 0.00 0.92 0.04 0.04 0.00
#> TCGA.A7.A0DC.01 3 0.2941 0.750 0.00 0.00 0.78 0.22 0.00 0.00
#> TCGA.E2.A1IU.01 5 0.2793 0.769 0.20 0.00 0.00 0.00 0.80 0.00
#> TCGA.B6.A0RI.01 3 0.1814 0.732 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.EW.A1P6.01 2 0.4609 0.421 0.00 0.54 0.00 0.04 0.00 0.42
#> TCGA.AN.A0XT.01 2 0.0000 0.908 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1IN.01 6 0.5963 -0.277 0.00 0.00 0.32 0.24 0.00 0.44
#> TCGA.BH.A0H9.01 2 0.0000 0.908 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A15I.01 6 0.6525 0.545 0.00 0.00 0.20 0.30 0.04 0.46
#> TCGA.A1.A0SG.01 3 0.4244 0.683 0.00 0.00 0.72 0.20 0.00 0.08
#> TCGA.D8.A1XR.01 6 0.4246 0.701 0.00 0.00 0.00 0.40 0.02 0.58
#> TCGA.AO.A0JB.01 2 0.0000 0.908 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1ET.01 5 0.3076 0.768 0.00 0.00 0.24 0.00 0.76 0.00
#> TCGA.EW.A1J1.01 2 0.0547 0.900 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.3C.AAAU.01 3 0.5428 0.420 0.00 0.00 0.54 0.32 0.14 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.D8.A1JD.01 5 0.0863 0.908 0.00 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.A7.A3RF.01 6 0.0504 0.801 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.BH.A0H0.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0RP.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LL.A442.01 6 0.0000 0.805 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BH.A0BS.01 5 0.0000 0.919 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B6.A0WT.01 3 0.3396 0.487 0.00 0.00 0.80 0.14 0.02 0.00 0.04
#> TCGA.AR.A1AS.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A6NO.01 5 0.0000 0.919 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E2.A1B4.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A3QQ.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1X7.01 5 0.1928 0.871 0.00 0.00 0.00 0.08 0.90 0.00 0.02
#> TCGA.A8.A075.01 2 0.0000 0.971 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A5J0.01 7 0.3413 0.274 0.00 0.00 0.00 0.00 0.00 0.38 0.62
#> TCGA.Z7.A8R6.01 3 0.3139 0.552 0.00 0.00 0.70 0.00 0.00 0.00 0.30
#> TCGA.E2.A1L8.01 5 0.0504 0.918 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.A7.A4SB.01 3 0.3052 0.419 0.00 0.00 0.78 0.20 0.00 0.00 0.02
#> TCGA.A7.A0DC.01 3 0.3908 0.518 0.00 0.00 0.72 0.08 0.00 0.00 0.20
#> TCGA.E2.A1IU.01 5 0.0504 0.918 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.B6.A0RI.01 3 0.3244 0.406 0.00 0.00 0.78 0.18 0.04 0.00 0.00
#> TCGA.EW.A1P6.01 7 0.3358 0.316 0.00 0.36 0.00 0.00 0.00 0.00 0.64
#> TCGA.AN.A0XT.01 2 0.0000 0.971 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1IN.01 7 0.1433 0.391 0.00 0.00 0.08 0.00 0.00 0.00 0.92
#> TCGA.BH.A0H9.01 2 0.0000 0.971 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A15I.01 6 0.5218 0.473 0.00 0.00 0.20 0.18 0.02 0.60 0.00
#> TCGA.A1.A0SG.01 3 0.2945 0.577 0.00 0.00 0.74 0.00 0.00 0.00 0.26
#> TCGA.D8.A1XR.01 6 0.1671 0.791 0.00 0.00 0.00 0.10 0.00 0.90 0.00
#> TCGA.AO.A0JB.01 2 0.0000 0.971 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1ET.01 5 0.3667 0.620 0.00 0.00 0.20 0.06 0.74 0.00 0.00
#> TCGA.EW.A1J1.01 2 0.2163 0.874 0.00 0.88 0.00 0.10 0.00 0.00 0.02
#> TCGA.3C.AAAU.01 4 0.2708 0.000 0.00 0.00 0.22 0.78 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.D8.A1JD.01 5 0.0808 0.90733 0.00 0.00 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.A7.A3RF.01 6 0.1741 0.83375 0.00 0.00 0.00 0.02 0.02 0.92 0.04 0.00
#> TCGA.BH.A0H0.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0RP.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LL.A442.01 6 0.0000 0.85979 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A0BS.01 5 0.0471 0.91758 0.02 0.00 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.B6.A0WT.01 8 0.3272 0.00550 0.00 0.00 0.42 0.00 0.00 0.00 0.00 0.58
#> TCGA.AR.A1AS.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A6NO.01 5 0.0471 0.91167 0.00 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.E2.A1B4.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A3QQ.01 1 0.0000 1.00000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1X7.01 5 0.4245 0.64918 0.00 0.00 0.00 0.08 0.72 0.00 0.06 0.14
#> TCGA.A8.A075.01 2 0.0000 0.96746 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A5J0.01 7 0.2650 0.62720 0.00 0.00 0.00 0.00 0.00 0.24 0.76 0.00
#> TCGA.Z7.A8R6.01 3 0.3880 0.53725 0.00 0.00 0.68 0.00 0.00 0.00 0.08 0.24
#> TCGA.E2.A1L8.01 5 0.0808 0.91582 0.04 0.00 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.A7.A4SB.01 3 0.3431 0.39503 0.00 0.00 0.74 0.06 0.00 0.00 0.00 0.20
#> TCGA.A7.A0DC.01 3 0.1091 0.56183 0.00 0.00 0.94 0.06 0.00 0.00 0.00 0.00
#> TCGA.E2.A1IU.01 5 0.0808 0.91582 0.04 0.00 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.B6.A0RI.01 8 0.3237 0.05159 0.00 0.00 0.40 0.00 0.00 0.00 0.00 0.60
#> TCGA.EW.A1P6.01 7 0.2406 0.63740 0.00 0.20 0.00 0.00 0.00 0.00 0.80 0.00
#> TCGA.AN.A0XT.01 2 0.0000 0.96746 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1IN.01 7 0.2648 0.63748 0.00 0.00 0.08 0.00 0.00 0.00 0.84 0.08
#> TCGA.BH.A0H9.01 2 0.0000 0.96746 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A15I.01 8 0.3083 0.00194 0.00 0.00 0.00 0.00 0.00 0.34 0.00 0.66
#> TCGA.A1.A0SG.01 3 0.3293 0.55479 0.00 0.00 0.74 0.00 0.00 0.00 0.04 0.22
#> TCGA.D8.A1XR.01 6 0.3178 0.77476 0.00 0.00 0.00 0.04 0.00 0.80 0.02 0.14
#> TCGA.AO.A0JB.01 2 0.0000 0.96746 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1ET.01 8 0.4008 -0.00984 0.00 0.00 0.04 0.00 0.48 0.00 0.00 0.48
#> TCGA.EW.A1J1.01 2 0.2591 0.86025 0.00 0.86 0.00 0.04 0.00 0.00 0.02 0.08
#> TCGA.3C.AAAU.01 4 0.2348 0.00000 0.00 0.00 0.04 0.88 0.02 0.00 0.00 0.06
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0115-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0151-leaf , Node0152-leaf , Node0153-leaf , Node0154-leaf , Node0211-leaf , Node0212 , Node0213 , Node0221 , Node0222 , Node0231-leaf , Node0232 , Node0233-leaf , Node0241-leaf , Node0242 , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0331-leaf , Node0332-leaf , Node0341-leaf , Node0342-leaf , Node0343-leaf , Node0411 , Node0412-leaf , Node0413 , Node0421-leaf , Node0422 , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["022"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 55 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.987 0.994 0.4964 0.504 0.504
#> 3 3 0.795 0.833 0.917 0.3317 0.733 0.522
#> 4 4 0.783 0.804 0.902 0.1393 0.865 0.628
#> 5 5 0.705 0.639 0.795 0.0643 0.936 0.747
#> 6 6 0.736 0.511 0.663 0.0404 0.924 0.653
#> 7 7 0.773 0.511 0.681 0.0267 0.884 0.471
#> 8 8 0.803 0.659 0.816 0.0211 0.937 0.640
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.BH.A1EN.01 2 0.000 0.993 0.00 1.00
#> TCGA.D8.A1J8.01 1 0.000 0.994 1.00 0.00
#> TCGA.AR.A24N.01 2 0.000 0.993 0.00 1.00
#> TCGA.LL.A5YM.01 1 0.000 0.994 1.00 0.00
#> TCGA.AC.A4ZE.01 2 0.000 0.993 0.00 1.00
#> TCGA.AN.A0XV.01 2 0.000 0.993 0.00 1.00
#> TCGA.E2.A2P6.01 2 0.000 0.993 0.00 1.00
#> TCGA.E9.A1NA.01 1 0.000 0.994 1.00 0.00
#> TCGA.D8.A1XJ.01 2 0.000 0.993 0.00 1.00
#> TCGA.C8.A1HO.01 1 0.000 0.994 1.00 0.00
#> TCGA.S3.A6ZG.01 2 0.000 0.993 0.00 1.00
#> TCGA.E2.A9RU.01 2 0.000 0.993 0.00 1.00
#> TCGA.E9.A247.01 1 0.000 0.994 1.00 0.00
#> TCGA.EW.A423.01 2 0.000 0.993 0.00 1.00
#> TCGA.AC.A2FM.01 1 0.000 0.994 1.00 0.00
#> TCGA.E9.A1RE.01 1 0.000 0.994 1.00 0.00
#> TCGA.C8.A274.01 2 0.000 0.993 0.00 1.00
#> TCGA.E9.A1RC.01 2 0.000 0.993 0.00 1.00
#> TCGA.BH.A0DS.01 2 0.000 0.993 0.00 1.00
#> TCGA.BH.A0HK.01 2 0.000 0.993 0.00 1.00
#> TCGA.OL.A66K.01 2 0.000 0.993 0.00 1.00
#> TCGA.AR.A250.01 1 0.000 0.994 1.00 0.00
#> TCGA.OL.A5D8.01 2 0.000 0.993 0.00 1.00
#> TCGA.AQ.A04H.01 1 0.000 0.994 1.00 0.00
#> TCGA.AR.A0TZ.01 1 0.000 0.994 1.00 0.00
#> TCGA.E2.A576.01 1 0.000 0.994 1.00 0.00
#> TCGA.E9.A2JS.01 1 0.000 0.994 1.00 0.00
#> TCGA.C8.A3M8.01 1 0.000 0.994 1.00 0.00
#> TCGA.EW.A6SA.01 1 0.000 0.994 1.00 0.00
#> TCGA.E9.A1R5.01 2 0.000 0.993 0.00 1.00
#> TCGA.BH.A1F8.01 2 0.000 0.993 0.00 1.00
#> TCGA.BH.A1FD.01 2 0.000 0.993 0.00 1.00
#> TCGA.C8.A9FZ.01 1 0.529 0.862 0.88 0.12
#> TCGA.D8.A1JN.01 2 0.000 0.993 0.00 1.00
#> TCGA.AR.A2LK.01 2 0.000 0.993 0.00 1.00
#> TCGA.D8.A1XF.01 1 0.000 0.994 1.00 0.00
#> TCGA.A2.A0CT.01 1 0.000 0.994 1.00 0.00
#> TCGA.B6.A0RL.01 1 0.000 0.994 1.00 0.00
#> TCGA.D8.A1J9.01 2 0.000 0.993 0.00 1.00
#> TCGA.AR.A1AP.01 2 0.000 0.993 0.00 1.00
#> TCGA.BH.A42T.01 2 0.000 0.993 0.00 1.00
#> TCGA.BH.A1EV.01 2 0.000 0.993 0.00 1.00
#> TCGA.EW.A1OZ.01 1 0.000 0.994 1.00 0.00
#> TCGA.BH.A0HY.01 2 0.000 0.993 0.00 1.00
#> TCGA.AC.A3EH.01 2 0.000 0.993 0.00 1.00
#> TCGA.BH.A0E2.01 1 0.000 0.994 1.00 0.00
#> TCGA.AC.A7VB.01 1 0.000 0.994 1.00 0.00
#> TCGA.AO.A0JI.01 1 0.000 0.994 1.00 0.00
#> TCGA.PE.A5DD.01 2 0.000 0.993 0.00 1.00
#> TCGA.EW.A424.01 2 0.000 0.993 0.00 1.00
#> TCGA.E2.A1L7.01 2 0.000 0.993 0.00 1.00
#> TCGA.5T.A9QA.01 1 0.000 0.994 1.00 0.00
#> TCGA.A2.A0SY.01 2 0.000 0.993 0.00 1.00
#> TCGA.A2.A0YG.01 2 0.722 0.747 0.20 0.80
#> TCGA.AR.A1AV.01 2 0.000 0.993 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.BH.A1EN.01 2 0.0892 0.859 0.00 0.98 0.02
#> TCGA.D8.A1J8.01 2 0.0000 0.849 0.00 1.00 0.00
#> TCGA.AR.A24N.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.LL.A5YM.01 1 0.0000 0.911 1.00 0.00 0.00
#> TCGA.AC.A4ZE.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.AN.A0XV.01 2 0.5948 0.552 0.00 0.64 0.36
#> TCGA.E2.A2P6.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.E9.A1NA.01 1 0.0892 0.911 0.98 0.02 0.00
#> TCGA.D8.A1XJ.01 2 0.5948 0.552 0.00 0.64 0.36
#> TCGA.C8.A1HO.01 1 0.0892 0.911 0.98 0.02 0.00
#> TCGA.S3.A6ZG.01 2 0.0892 0.859 0.00 0.98 0.02
#> TCGA.E2.A9RU.01 2 0.1529 0.857 0.00 0.96 0.04
#> TCGA.E9.A247.01 2 0.5835 0.335 0.34 0.66 0.00
#> TCGA.EW.A423.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.AC.A2FM.01 1 0.0892 0.911 0.98 0.02 0.00
#> TCGA.E9.A1RE.01 1 0.5835 0.575 0.66 0.34 0.00
#> TCGA.C8.A274.01 2 0.5948 0.552 0.00 0.64 0.36
#> TCGA.E9.A1RC.01 2 0.1529 0.857 0.00 0.96 0.04
#> TCGA.BH.A0DS.01 2 0.5948 0.552 0.00 0.64 0.36
#> TCGA.BH.A0HK.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.OL.A66K.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.AR.A250.01 1 0.5835 0.575 0.66 0.34 0.00
#> TCGA.OL.A5D8.01 2 0.0892 0.859 0.00 0.98 0.02
#> TCGA.AQ.A04H.01 1 0.0000 0.911 1.00 0.00 0.00
#> TCGA.AR.A0TZ.01 1 0.0892 0.911 0.98 0.02 0.00
#> TCGA.E2.A576.01 2 0.3686 0.727 0.14 0.86 0.00
#> TCGA.E9.A2JS.01 1 0.0892 0.911 0.98 0.02 0.00
#> TCGA.C8.A3M8.01 1 0.0000 0.911 1.00 0.00 0.00
#> TCGA.EW.A6SA.01 1 0.0000 0.911 1.00 0.00 0.00
#> TCGA.E9.A1R5.01 2 0.5948 0.552 0.00 0.64 0.36
#> TCGA.BH.A1F8.01 2 0.0892 0.859 0.00 0.98 0.02
#> TCGA.BH.A1FD.01 2 0.1529 0.857 0.00 0.96 0.04
#> TCGA.C8.A9FZ.01 2 0.0000 0.849 0.00 1.00 0.00
#> TCGA.D8.A1JN.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.AR.A2LK.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.D8.A1XF.01 1 0.0892 0.911 0.98 0.02 0.00
#> TCGA.A2.A0CT.01 1 0.0000 0.911 1.00 0.00 0.00
#> TCGA.B6.A0RL.01 1 0.0000 0.911 1.00 0.00 0.00
#> TCGA.D8.A1J9.01 2 0.2066 0.847 0.00 0.94 0.06
#> TCGA.AR.A1AP.01 2 0.6280 0.334 0.00 0.54 0.46
#> TCGA.BH.A42T.01 2 0.0892 0.859 0.00 0.98 0.02
#> TCGA.BH.A1EV.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.EW.A1OZ.01 1 0.5216 0.684 0.74 0.26 0.00
#> TCGA.BH.A0HY.01 2 0.0892 0.859 0.00 0.98 0.02
#> TCGA.AC.A3EH.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.BH.A0E2.01 1 0.6192 0.452 0.58 0.42 0.00
#> TCGA.AC.A7VB.01 1 0.0000 0.911 1.00 0.00 0.00
#> TCGA.AO.A0JI.01 1 0.0892 0.911 0.98 0.02 0.00
#> TCGA.PE.A5DD.01 2 0.0892 0.859 0.00 0.98 0.02
#> TCGA.EW.A424.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.E2.A1L7.01 2 0.1529 0.857 0.00 0.96 0.04
#> TCGA.5T.A9QA.01 1 0.0892 0.911 0.98 0.02 0.00
#> TCGA.A2.A0SY.01 2 0.1529 0.857 0.00 0.96 0.04
#> TCGA.A2.A0YG.01 2 0.0000 0.849 0.00 1.00 0.00
#> TCGA.AR.A1AV.01 3 0.0000 1.000 0.00 0.00 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.BH.A1EN.01 4 0.361 0.811 0.00 0.20 0.00 0.80
#> TCGA.D8.A1J8.01 4 0.380 0.790 0.00 0.22 0.00 0.78
#> TCGA.AR.A24N.01 3 0.000 0.945 0.00 0.00 1.00 0.00
#> TCGA.LL.A5YM.01 1 0.317 0.828 0.84 0.00 0.00 0.16
#> TCGA.AC.A4ZE.01 3 0.234 0.847 0.00 0.00 0.90 0.10
#> TCGA.AN.A0XV.01 2 0.164 0.885 0.00 0.94 0.06 0.00
#> TCGA.E2.A2P6.01 3 0.000 0.945 0.00 0.00 1.00 0.00
#> TCGA.E9.A1NA.01 1 0.000 0.859 1.00 0.00 0.00 0.00
#> TCGA.D8.A1XJ.01 2 0.000 0.893 0.00 1.00 0.00 0.00
#> TCGA.C8.A1HO.01 1 0.000 0.859 1.00 0.00 0.00 0.00
#> TCGA.S3.A6ZG.01 4 0.292 0.829 0.00 0.14 0.00 0.86
#> TCGA.E2.A9RU.01 2 0.201 0.856 0.00 0.92 0.00 0.08
#> TCGA.E9.A247.01 4 0.000 0.820 0.00 0.00 0.00 1.00
#> TCGA.EW.A423.01 3 0.000 0.945 0.00 0.00 1.00 0.00
#> TCGA.AC.A2FM.01 1 0.000 0.859 1.00 0.00 0.00 0.00
#> TCGA.E9.A1RE.01 4 0.000 0.820 0.00 0.00 0.00 1.00
#> TCGA.C8.A274.01 2 0.164 0.885 0.00 0.94 0.06 0.00
#> TCGA.E9.A1RC.01 2 0.000 0.893 0.00 1.00 0.00 0.00
#> TCGA.BH.A0DS.01 2 0.549 0.305 0.00 0.58 0.40 0.02
#> TCGA.BH.A0HK.01 3 0.000 0.945 0.00 0.00 1.00 0.00
#> TCGA.OL.A66K.01 3 0.000 0.945 0.00 0.00 1.00 0.00
#> TCGA.AR.A250.01 4 0.000 0.820 0.00 0.00 0.00 1.00
#> TCGA.OL.A5D8.01 4 0.361 0.811 0.00 0.20 0.00 0.80
#> TCGA.AQ.A04H.01 1 0.479 0.617 0.62 0.00 0.00 0.38
#> TCGA.AR.A0TZ.01 1 0.000 0.859 1.00 0.00 0.00 0.00
#> TCGA.E2.A576.01 4 0.000 0.820 0.00 0.00 0.00 1.00
#> TCGA.E9.A2JS.01 1 0.000 0.859 1.00 0.00 0.00 0.00
#> TCGA.C8.A3M8.01 1 0.361 0.809 0.80 0.00 0.00 0.20
#> TCGA.EW.A6SA.01 1 0.361 0.809 0.80 0.00 0.00 0.20
#> TCGA.E9.A1R5.01 2 0.164 0.885 0.00 0.94 0.06 0.00
#> TCGA.BH.A1F8.01 4 0.471 0.544 0.00 0.36 0.00 0.64
#> TCGA.BH.A1FD.01 2 0.201 0.856 0.00 0.92 0.00 0.08
#> TCGA.C8.A9FZ.01 2 0.471 0.217 0.00 0.64 0.00 0.36
#> TCGA.D8.A1JN.01 3 0.000 0.945 0.00 0.00 1.00 0.00
#> TCGA.AR.A2LK.01 3 0.000 0.945 0.00 0.00 1.00 0.00
#> TCGA.D8.A1XF.01 1 0.000 0.859 1.00 0.00 0.00 0.00
#> TCGA.A2.A0CT.01 1 0.292 0.836 0.86 0.00 0.00 0.14
#> TCGA.B6.A0RL.01 1 0.292 0.836 0.86 0.00 0.00 0.14
#> TCGA.D8.A1J9.01 2 0.191 0.887 0.00 0.94 0.04 0.02
#> TCGA.AR.A1AP.01 2 0.164 0.885 0.00 0.94 0.06 0.00
#> TCGA.BH.A42T.01 2 0.000 0.893 0.00 1.00 0.00 0.00
#> TCGA.BH.A1EV.01 3 0.201 0.880 0.00 0.08 0.92 0.00
#> TCGA.EW.A1OZ.01 4 0.000 0.820 0.00 0.00 0.00 1.00
#> TCGA.BH.A0HY.01 2 0.000 0.893 0.00 1.00 0.00 0.00
#> TCGA.AC.A3EH.01 3 0.000 0.945 0.00 0.00 1.00 0.00
#> TCGA.BH.A0E2.01 1 0.761 -0.201 0.40 0.20 0.00 0.40
#> TCGA.AC.A7VB.01 1 0.479 0.617 0.62 0.00 0.00 0.38
#> TCGA.AO.A0JI.01 1 0.000 0.859 1.00 0.00 0.00 0.00
#> TCGA.PE.A5DD.01 4 0.361 0.811 0.00 0.20 0.00 0.80
#> TCGA.EW.A424.01 3 0.471 0.411 0.00 0.36 0.64 0.00
#> TCGA.E2.A1L7.01 2 0.000 0.893 0.00 1.00 0.00 0.00
#> TCGA.5T.A9QA.01 1 0.000 0.859 1.00 0.00 0.00 0.00
#> TCGA.A2.A0SY.01 2 0.000 0.893 0.00 1.00 0.00 0.00
#> TCGA.A2.A0YG.01 2 0.201 0.827 0.00 0.92 0.00 0.08
#> TCGA.AR.A1AV.01 3 0.000 0.945 0.00 0.00 1.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.BH.A1EN.01 4 0.0609 0.772 0.00 0.02 0.00 0.98 0.00
#> TCGA.D8.A1J8.01 4 0.2438 0.732 0.04 0.06 0.00 0.90 0.00
#> TCGA.AR.A24N.01 3 0.1043 0.873 0.04 0.00 0.96 0.00 0.00
#> TCGA.LL.A5YM.01 5 0.2280 0.597 0.12 0.00 0.00 0.00 0.88
#> TCGA.AC.A4ZE.01 3 0.4588 0.664 0.06 0.00 0.72 0.22 0.00
#> TCGA.AN.A0XV.01 2 0.3903 0.694 0.02 0.80 0.02 0.16 0.00
#> TCGA.E2.A2P6.01 3 0.0000 0.882 0.00 0.00 1.00 0.00 0.00
#> TCGA.E9.A1NA.01 1 0.4132 0.842 0.72 0.00 0.00 0.02 0.26
#> TCGA.D8.A1XJ.01 2 0.0000 0.696 0.00 1.00 0.00 0.00 0.00
#> TCGA.C8.A1HO.01 1 0.3561 0.856 0.74 0.00 0.00 0.00 0.26
#> TCGA.S3.A6ZG.01 4 0.1648 0.752 0.04 0.02 0.00 0.94 0.00
#> TCGA.E2.A9RU.01 2 0.4675 0.554 0.02 0.60 0.00 0.38 0.00
#> TCGA.E9.A247.01 4 0.4252 0.557 0.02 0.00 0.00 0.70 0.28
#> TCGA.EW.A423.01 3 0.0000 0.882 0.00 0.00 1.00 0.00 0.00
#> TCGA.AC.A2FM.01 1 0.3561 0.856 0.74 0.00 0.00 0.00 0.26
#> TCGA.E9.A1RE.01 5 0.3561 0.384 0.00 0.00 0.00 0.26 0.74
#> TCGA.C8.A274.01 2 0.3291 0.706 0.00 0.84 0.04 0.12 0.00
#> TCGA.E9.A1RC.01 2 0.2516 0.660 0.14 0.86 0.00 0.00 0.00
#> TCGA.BH.A0DS.01 2 0.7536 0.297 0.06 0.38 0.18 0.38 0.00
#> TCGA.BH.A0HK.01 3 0.1043 0.873 0.04 0.00 0.96 0.00 0.00
#> TCGA.OL.A66K.01 3 0.0000 0.882 0.00 0.00 1.00 0.00 0.00
#> TCGA.AR.A250.01 4 0.4798 0.241 0.02 0.00 0.00 0.54 0.44
#> TCGA.OL.A5D8.01 4 0.1216 0.764 0.02 0.02 0.00 0.96 0.00
#> TCGA.AQ.A04H.01 5 0.1043 0.693 0.00 0.00 0.00 0.04 0.96
#> TCGA.AR.A0TZ.01 1 0.4132 0.842 0.72 0.00 0.00 0.02 0.26
#> TCGA.E2.A576.01 4 0.3796 0.554 0.00 0.00 0.00 0.70 0.30
#> TCGA.E9.A2JS.01 1 0.3561 0.856 0.74 0.00 0.00 0.00 0.26
#> TCGA.C8.A3M8.01 5 0.0609 0.687 0.02 0.00 0.00 0.00 0.98
#> TCGA.EW.A6SA.01 5 0.0609 0.687 0.02 0.00 0.00 0.00 0.98
#> TCGA.E9.A1R5.01 2 0.3291 0.706 0.00 0.84 0.04 0.12 0.00
#> TCGA.BH.A1F8.01 4 0.3291 0.654 0.04 0.12 0.00 0.84 0.00
#> TCGA.BH.A1FD.01 2 0.4675 0.554 0.02 0.60 0.00 0.38 0.00
#> TCGA.C8.A9FZ.01 2 0.6146 0.336 0.20 0.56 0.00 0.24 0.00
#> TCGA.D8.A1JN.01 3 0.0000 0.882 0.00 0.00 1.00 0.00 0.00
#> TCGA.AR.A2LK.01 3 0.0000 0.882 0.00 0.00 1.00 0.00 0.00
#> TCGA.D8.A1XF.01 1 0.3561 0.856 0.74 0.00 0.00 0.00 0.26
#> TCGA.A2.A0CT.01 5 0.4456 0.200 0.32 0.00 0.00 0.02 0.66
#> TCGA.B6.A0RL.01 5 0.4456 0.200 0.32 0.00 0.00 0.02 0.66
#> TCGA.D8.A1J9.01 2 0.4675 0.554 0.02 0.60 0.00 0.38 0.00
#> TCGA.AR.A1AP.01 2 0.1043 0.694 0.00 0.96 0.04 0.00 0.00
#> TCGA.BH.A42T.01 2 0.3106 0.660 0.14 0.84 0.00 0.02 0.00
#> TCGA.BH.A1EV.01 3 0.3895 0.531 0.00 0.32 0.68 0.00 0.00
#> TCGA.EW.A1OZ.01 5 0.4818 -0.143 0.02 0.00 0.00 0.46 0.52
#> TCGA.BH.A0HY.01 2 0.5979 0.557 0.12 0.52 0.00 0.36 0.00
#> TCGA.AC.A3EH.01 3 0.0000 0.882 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A0E2.01 1 0.7222 -0.196 0.40 0.30 0.00 0.28 0.02
#> TCGA.AC.A7VB.01 5 0.1043 0.693 0.00 0.00 0.00 0.04 0.96
#> TCGA.AO.A0JI.01 1 0.3561 0.856 0.74 0.00 0.00 0.00 0.26
#> TCGA.PE.A5DD.01 4 0.0609 0.772 0.00 0.02 0.00 0.98 0.00
#> TCGA.EW.A424.01 3 0.5447 0.211 0.06 0.44 0.50 0.00 0.00
#> TCGA.E2.A1L7.01 2 0.2516 0.660 0.14 0.86 0.00 0.00 0.00
#> TCGA.5T.A9QA.01 1 0.3561 0.856 0.74 0.00 0.00 0.00 0.26
#> TCGA.A2.A0SY.01 2 0.2732 0.708 0.00 0.84 0.00 0.16 0.00
#> TCGA.A2.A0YG.01 2 0.6111 0.434 0.18 0.56 0.00 0.26 0.00
#> TCGA.AR.A1AV.01 3 0.2797 0.832 0.06 0.00 0.88 0.06 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.BH.A1EN.01 4 0.4360 0.4938 0.00 0.00 0.00 0.68 0.06 0.26
#> TCGA.D8.A1J8.01 4 0.2581 0.5780 0.00 0.00 0.00 0.86 0.02 0.12
#> TCGA.AR.A24N.01 3 0.2631 0.7731 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.LL.A5YM.01 5 0.4002 0.5309 0.32 0.00 0.00 0.00 0.66 0.02
#> TCGA.AC.A4ZE.01 3 0.5071 0.4306 0.00 0.00 0.52 0.08 0.00 0.40
#> TCGA.AN.A0XV.01 2 0.4328 0.1246 0.00 0.52 0.00 0.02 0.00 0.46
#> TCGA.E2.A2P6.01 3 0.0000 0.8310 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E9.A1NA.01 1 0.0547 0.8878 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.D8.A1XJ.01 2 0.4348 0.3309 0.00 0.64 0.00 0.00 0.04 0.32
#> TCGA.C8.A1HO.01 1 0.0000 0.8964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S3.A6ZG.01 4 0.3819 0.5108 0.00 0.00 0.00 0.70 0.02 0.28
#> TCGA.E2.A9RU.01 6 0.6513 0.5265 0.00 0.28 0.00 0.32 0.02 0.38
#> TCGA.E9.A247.01 4 0.3198 0.3880 0.00 0.00 0.00 0.74 0.26 0.00
#> TCGA.EW.A423.01 3 0.0000 0.8310 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A2FM.01 1 0.0000 0.8964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RE.01 5 0.3309 0.4642 0.00 0.00 0.00 0.28 0.72 0.00
#> TCGA.C8.A274.01 2 0.4576 0.2647 0.00 0.56 0.00 0.00 0.04 0.40
#> TCGA.E9.A1RC.01 2 0.0937 0.3993 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.BH.A0DS.01 6 0.4812 0.3599 0.00 0.04 0.04 0.24 0.00 0.68
#> TCGA.BH.A0HK.01 3 0.2631 0.7731 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.OL.A66K.01 3 0.0000 0.8310 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A250.01 4 0.3869 -0.1397 0.00 0.00 0.00 0.50 0.50 0.00
#> TCGA.OL.A5D8.01 4 0.3499 0.4720 0.00 0.00 0.00 0.68 0.00 0.32
#> TCGA.AQ.A04H.01 5 0.2790 0.7659 0.14 0.00 0.00 0.02 0.84 0.00
#> TCGA.AR.A0TZ.01 1 0.0547 0.8878 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.E2.A576.01 4 0.4348 0.3451 0.00 0.00 0.00 0.64 0.32 0.04
#> TCGA.E9.A2JS.01 1 0.0000 0.8964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A3M8.01 5 0.3315 0.7360 0.20 0.00 0.00 0.00 0.78 0.02
#> TCGA.EW.A6SA.01 5 0.2793 0.7416 0.20 0.00 0.00 0.00 0.80 0.00
#> TCGA.E9.A1R5.01 2 0.5020 0.2735 0.00 0.56 0.00 0.02 0.04 0.38
#> TCGA.BH.A1F8.01 4 0.2350 0.5819 0.00 0.00 0.00 0.88 0.02 0.10
#> TCGA.BH.A1FD.01 6 0.6397 0.5515 0.00 0.26 0.00 0.28 0.02 0.44
#> TCGA.C8.A9FZ.01 2 0.6365 0.1663 0.00 0.52 0.00 0.28 0.06 0.14
#> TCGA.D8.A1JN.01 3 0.0000 0.8310 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A2LK.01 3 0.0000 0.8310 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A1XF.01 1 0.0000 0.8964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0CT.01 1 0.4078 0.4157 0.64 0.00 0.00 0.00 0.34 0.02
#> TCGA.B6.A0RL.01 1 0.4078 0.4157 0.64 0.00 0.00 0.00 0.34 0.02
#> TCGA.D8.A1J9.01 6 0.5888 0.4053 0.00 0.32 0.00 0.22 0.00 0.46
#> TCGA.AR.A1AP.01 2 0.4420 0.3234 0.00 0.62 0.00 0.00 0.04 0.34
#> TCGA.BH.A42T.01 2 0.0547 0.3922 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BH.A1EV.01 3 0.6356 0.0401 0.00 0.16 0.48 0.00 0.04 0.32
#> TCGA.EW.A1OZ.01 5 0.4282 0.1664 0.00 0.00 0.00 0.42 0.56 0.02
#> TCGA.BH.A0HY.01 2 0.6380 -0.4069 0.00 0.44 0.00 0.30 0.02 0.24
#> TCGA.AC.A3EH.01 3 0.0000 0.8310 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0E2.01 2 0.7218 0.1417 0.04 0.48 0.00 0.26 0.06 0.16
#> TCGA.AC.A7VB.01 5 0.2790 0.7659 0.14 0.00 0.00 0.02 0.84 0.00
#> TCGA.AO.A0JI.01 1 0.0000 0.8964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PE.A5DD.01 4 0.3592 0.5578 0.00 0.00 0.00 0.74 0.02 0.24
#> TCGA.EW.A424.01 6 0.5481 -0.0885 0.00 0.34 0.14 0.00 0.00 0.52
#> TCGA.E2.A1L7.01 2 0.0547 0.3956 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.5T.A9QA.01 1 0.0000 0.8964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0SY.01 2 0.4310 0.1597 0.00 0.54 0.00 0.02 0.00 0.44
#> TCGA.A2.A0YG.01 2 0.4637 0.1471 0.00 0.60 0.00 0.36 0.02 0.02
#> TCGA.AR.A1AV.01 3 0.3819 0.6818 0.00 0.00 0.70 0.02 0.00 0.28
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.BH.A1EN.01 4 0.1006 0.4047 0.00 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.D8.A1J8.01 4 0.2278 0.4207 0.00 0.00 0.00 0.88 0.00 0.08 0.04
#> TCGA.AR.A24N.01 3 0.3047 0.5749 0.00 0.00 0.72 0.00 0.00 0.28 0.00
#> TCGA.LL.A5YM.01 5 0.1166 0.6706 0.06 0.00 0.00 0.00 0.94 0.00 0.00
#> TCGA.AC.A4ZE.01 6 0.4866 -0.1894 0.00 0.00 0.42 0.10 0.00 0.48 0.00
#> TCGA.AN.A0XV.01 2 0.2722 0.6044 0.00 0.84 0.00 0.00 0.00 0.12 0.04
#> TCGA.E2.A2P6.01 3 0.0000 0.8216 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1NA.01 1 0.2376 0.8554 0.86 0.00 0.00 0.00 0.12 0.02 0.00
#> TCGA.D8.A1XJ.01 2 0.2769 0.6170 0.00 0.86 0.00 0.00 0.02 0.08 0.04
#> TCGA.C8.A1HO.01 1 0.0000 0.9582 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S3.A6ZG.01 6 0.3496 0.0992 0.00 0.00 0.00 0.42 0.00 0.58 0.00
#> TCGA.E2.A9RU.01 4 0.5772 0.1172 0.00 0.34 0.00 0.48 0.00 0.14 0.04
#> TCGA.E9.A247.01 4 0.6126 0.2641 0.00 0.00 0.00 0.50 0.16 0.26 0.08
#> TCGA.EW.A423.01 3 0.0000 0.8216 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A2FM.01 1 0.0000 0.9582 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RE.01 5 0.5431 0.4168 0.00 0.00 0.00 0.08 0.56 0.30 0.06
#> TCGA.C8.A274.01 2 0.1006 0.6500 0.00 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.E9.A1RC.01 2 0.4938 0.2991 0.00 0.58 0.00 0.00 0.02 0.08 0.32
#> TCGA.BH.A0DS.01 6 0.6480 0.1818 0.00 0.26 0.04 0.24 0.00 0.44 0.02
#> TCGA.BH.A0HK.01 3 0.3413 0.4359 0.00 0.00 0.62 0.00 0.00 0.38 0.00
#> TCGA.OL.A66K.01 3 0.0000 0.8216 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A250.01 4 0.6110 0.1090 0.00 0.00 0.00 0.44 0.28 0.24 0.04
#> TCGA.OL.A5D8.01 4 0.3086 0.2921 0.00 0.00 0.00 0.80 0.00 0.16 0.04
#> TCGA.AQ.A04H.01 5 0.3000 0.6816 0.04 0.00 0.00 0.00 0.84 0.10 0.02
#> TCGA.AR.A0TZ.01 1 0.1886 0.8684 0.88 0.00 0.00 0.00 0.12 0.00 0.00
#> TCGA.E2.A576.01 4 0.5897 0.2460 0.00 0.00 0.00 0.50 0.20 0.26 0.04
#> TCGA.E9.A2JS.01 1 0.0000 0.9582 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A3M8.01 5 0.0863 0.6747 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.EW.A6SA.01 5 0.3000 0.6816 0.04 0.00 0.00 0.00 0.84 0.10 0.02
#> TCGA.E9.A1R5.01 2 0.0000 0.6535 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1F8.01 4 0.3940 0.4190 0.00 0.08 0.00 0.78 0.00 0.08 0.06
#> TCGA.BH.A1FD.01 4 0.5709 0.0310 0.00 0.40 0.00 0.44 0.00 0.12 0.04
#> TCGA.C8.A9FZ.01 7 0.2509 0.8392 0.00 0.06 0.00 0.04 0.02 0.00 0.88
#> TCGA.D8.A1JN.01 3 0.0000 0.8216 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A2LK.01 3 0.0000 0.8216 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1XF.01 1 0.0000 0.9582 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0CT.01 5 0.3358 0.3521 0.36 0.00 0.00 0.00 0.64 0.00 0.00
#> TCGA.B6.A0RL.01 5 0.3358 0.3521 0.36 0.00 0.00 0.00 0.64 0.00 0.00
#> TCGA.D8.A1J9.01 2 0.5132 -0.0999 0.00 0.46 0.00 0.44 0.00 0.08 0.02
#> TCGA.AR.A1AP.01 2 0.1363 0.6452 0.00 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.BH.A42T.01 2 0.4547 0.3876 0.00 0.58 0.00 0.00 0.00 0.08 0.34
#> TCGA.BH.A1EV.01 2 0.4317 0.2984 0.00 0.58 0.38 0.00 0.00 0.02 0.02
#> TCGA.EW.A1OZ.01 5 0.6057 0.0752 0.00 0.00 0.00 0.26 0.46 0.24 0.04
#> TCGA.BH.A0HY.01 4 0.6695 0.1680 0.00 0.24 0.00 0.48 0.02 0.12 0.14
#> TCGA.AC.A3EH.01 3 0.0000 0.8216 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0E2.01 7 0.3257 0.8420 0.02 0.00 0.00 0.04 0.08 0.02 0.84
#> TCGA.AC.A7VB.01 5 0.3000 0.6816 0.04 0.00 0.00 0.00 0.84 0.10 0.02
#> TCGA.AO.A0JI.01 1 0.0000 0.9582 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PE.A5DD.01 4 0.0504 0.4106 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.EW.A424.01 2 0.4305 0.3994 0.00 0.66 0.04 0.00 0.00 0.28 0.02
#> TCGA.E2.A1L7.01 2 0.5105 0.1867 0.00 0.50 0.00 0.00 0.02 0.08 0.40
#> TCGA.5T.A9QA.01 1 0.0000 0.9582 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0SY.01 2 0.2512 0.6167 0.00 0.86 0.00 0.00 0.00 0.10 0.04
#> TCGA.A2.A0YG.01 4 0.6881 -0.0472 0.00 0.14 0.00 0.40 0.02 0.12 0.32
#> TCGA.AR.A1AV.01 3 0.3546 0.2277 0.00 0.00 0.54 0.00 0.00 0.46 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.BH.A1EN.01 4 0.4487 0.50899 0.00 0.00 0.00 0.62 0.02 0.08 0.00 0.28
#> TCGA.D8.A1J8.01 8 0.4008 -0.44950 0.00 0.00 0.00 0.48 0.00 0.04 0.00 0.48
#> TCGA.AR.A24N.01 3 0.3272 0.00905 0.00 0.00 0.58 0.00 0.00 0.42 0.00 0.00
#> TCGA.LL.A5YM.01 5 0.1557 0.82293 0.06 0.00 0.00 0.00 0.92 0.00 0.00 0.02
#> TCGA.AC.A4ZE.01 6 0.2265 0.70626 0.00 0.00 0.08 0.00 0.02 0.88 0.00 0.02
#> TCGA.AN.A0XV.01 2 0.2994 0.66633 0.00 0.80 0.00 0.14 0.00 0.06 0.00 0.00
#> TCGA.E2.A2P6.01 3 0.0000 0.90968 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1NA.01 1 0.2940 0.84269 0.84 0.00 0.00 0.02 0.10 0.02 0.00 0.02
#> TCGA.D8.A1XJ.01 2 0.1874 0.67394 0.00 0.92 0.00 0.02 0.00 0.02 0.02 0.02
#> TCGA.C8.A1HO.01 1 0.0000 0.95388 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S3.A6ZG.01 6 0.2859 0.62787 0.00 0.00 0.00 0.02 0.02 0.82 0.00 0.14
#> TCGA.E2.A9RU.01 4 0.2224 0.64982 0.00 0.12 0.00 0.86 0.00 0.02 0.00 0.00
#> TCGA.E9.A247.01 8 0.1887 0.65432 0.00 0.00 0.00 0.04 0.06 0.00 0.00 0.90
#> TCGA.EW.A423.01 3 0.0000 0.90968 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A2FM.01 1 0.0000 0.95388 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RE.01 8 0.4995 0.25302 0.00 0.00 0.00 0.04 0.36 0.08 0.00 0.52
#> TCGA.C8.A274.01 2 0.0000 0.69675 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RC.01 2 0.4162 0.45670 0.00 0.66 0.00 0.02 0.00 0.02 0.28 0.02
#> TCGA.BH.A0DS.01 6 0.4504 0.43696 0.00 0.10 0.02 0.24 0.00 0.64 0.00 0.00
#> TCGA.BH.A0HK.01 6 0.3142 0.43816 0.00 0.00 0.36 0.00 0.00 0.64 0.00 0.00
#> TCGA.OL.A66K.01 3 0.0000 0.90968 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A250.01 8 0.2025 0.66570 0.00 0.00 0.00 0.02 0.10 0.00 0.00 0.88
#> TCGA.OL.A5D8.01 4 0.4953 0.49297 0.00 0.00 0.00 0.58 0.02 0.24 0.00 0.16
#> TCGA.AQ.A04H.01 5 0.2204 0.82317 0.02 0.00 0.00 0.04 0.90 0.02 0.00 0.02
#> TCGA.AR.A0TZ.01 1 0.2484 0.85616 0.86 0.00 0.00 0.02 0.10 0.00 0.00 0.02
#> TCGA.E2.A576.01 8 0.2132 0.64987 0.00 0.00 0.00 0.04 0.08 0.00 0.00 0.88
#> TCGA.E9.A2JS.01 1 0.0000 0.95388 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A3M8.01 5 0.0941 0.82196 0.02 0.00 0.00 0.00 0.96 0.00 0.00 0.02
#> TCGA.EW.A6SA.01 5 0.2204 0.82317 0.02 0.00 0.00 0.04 0.90 0.02 0.00 0.02
#> TCGA.E9.A1R5.01 2 0.2132 0.69394 0.00 0.88 0.00 0.08 0.00 0.04 0.00 0.00
#> TCGA.BH.A1F8.01 4 0.3971 0.37953 0.00 0.00 0.00 0.54 0.00 0.04 0.00 0.42
#> TCGA.BH.A1FD.01 4 0.3657 0.56821 0.00 0.20 0.00 0.72 0.00 0.08 0.00 0.00
#> TCGA.C8.A9FZ.01 7 0.0471 1.00000 0.00 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.D8.A1JN.01 3 0.0000 0.90968 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A2LK.01 3 0.0000 0.90968 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1XF.01 1 0.0000 0.95388 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0CT.01 5 0.3426 0.71955 0.22 0.00 0.00 0.02 0.74 0.00 0.00 0.02
#> TCGA.B6.A0RL.01 5 0.3426 0.71955 0.22 0.00 0.00 0.02 0.74 0.00 0.00 0.02
#> TCGA.D8.A1J9.01 4 0.4512 0.56816 0.00 0.22 0.00 0.66 0.00 0.08 0.00 0.04
#> TCGA.AR.A1AP.01 2 0.0000 0.69675 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A42T.01 2 0.5206 0.41042 0.00 0.50 0.00 0.16 0.00 0.02 0.32 0.00
#> TCGA.BH.A1EV.01 2 0.3299 0.15144 0.00 0.56 0.44 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1OZ.01 8 0.3291 0.55713 0.00 0.00 0.00 0.00 0.28 0.02 0.00 0.70
#> TCGA.BH.A0HY.01 4 0.1887 0.64772 0.00 0.06 0.00 0.90 0.00 0.00 0.04 0.00
#> TCGA.AC.A3EH.01 3 0.0000 0.90968 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0E2.01 7 0.0471 1.00000 0.00 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.AC.A7VB.01 5 0.2204 0.82317 0.02 0.00 0.00 0.04 0.90 0.02 0.00 0.02
#> TCGA.AO.A0JI.01 1 0.0000 0.95388 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PE.A5DD.01 4 0.4803 0.30912 0.00 0.00 0.00 0.46 0.02 0.08 0.00 0.44
#> TCGA.EW.A424.01 2 0.4612 0.48273 0.00 0.64 0.04 0.08 0.00 0.24 0.00 0.00
#> TCGA.E2.A1L7.01 2 0.4367 0.38997 0.00 0.60 0.00 0.02 0.00 0.02 0.34 0.02
#> TCGA.5T.A9QA.01 1 0.0000 0.95388 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0SY.01 2 0.3154 0.64866 0.00 0.78 0.00 0.16 0.00 0.06 0.00 0.00
#> TCGA.A2.A0YG.01 4 0.4713 0.50758 0.00 0.02 0.00 0.68 0.00 0.04 0.18 0.08
#> TCGA.AR.A1AV.01 6 0.2267 0.68857 0.00 0.00 0.18 0.00 0.00 0.82 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node022. Child nodes: Node02121-leaf , Node02122-leaf , Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02214-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02321-leaf , Node02322-leaf , Node02421-leaf , Node02422-leaf , Node02423-leaf , Node04111-leaf , Node04112-leaf , Node04113 , Node04131-leaf , Node04132-leaf , Node04133-leaf , Node04221-leaf , Node04222-leaf , Node04331-leaf , Node04332-leaf , Node04333-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0221"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 23 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.980 0.991 0.4938 0.502 0.502
#> 3 3 0.636 0.550 0.562 0.2804 0.755 0.534
#> 4 4 0.905 0.963 0.948 0.1868 0.897 0.679
#> 5 5 0.881 0.834 0.900 0.0860 0.901 0.609
#> 6 6 0.848 0.628 0.837 0.0364 0.953 0.745
#> 7 7 0.843 0.841 0.891 0.0272 0.968 0.795
#> 8 8 0.929 0.836 0.895 0.0176 1.000 1.000
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.D8.A1J8.01 1 0.000 1.000 1.0 0.0
#> TCGA.LL.A5YM.01 2 0.722 0.750 0.2 0.8
#> TCGA.E9.A1NA.01 1 0.000 1.000 1.0 0.0
#> TCGA.C8.A1HO.01 1 0.000 1.000 1.0 0.0
#> TCGA.E9.A247.01 1 0.000 1.000 1.0 0.0
#> TCGA.AC.A2FM.01 1 0.000 1.000 1.0 0.0
#> TCGA.E9.A1RE.01 2 0.000 0.975 0.0 1.0
#> TCGA.AR.A250.01 2 0.000 0.975 0.0 1.0
#> TCGA.AQ.A04H.01 2 0.000 0.975 0.0 1.0
#> TCGA.AR.A0TZ.01 1 0.000 1.000 1.0 0.0
#> TCGA.E2.A576.01 2 0.000 0.975 0.0 1.0
#> TCGA.E9.A2JS.01 1 0.000 1.000 1.0 0.0
#> TCGA.C8.A3M8.01 2 0.000 0.975 0.0 1.0
#> TCGA.EW.A6SA.01 2 0.000 0.975 0.0 1.0
#> TCGA.C8.A9FZ.01 1 0.000 1.000 1.0 0.0
#> TCGA.D8.A1XF.01 1 0.000 1.000 1.0 0.0
#> TCGA.A2.A0CT.01 1 0.000 1.000 1.0 0.0
#> TCGA.B6.A0RL.01 1 0.000 1.000 1.0 0.0
#> TCGA.EW.A1OZ.01 2 0.000 0.975 0.0 1.0
#> TCGA.BH.A0E2.01 1 0.000 1.000 1.0 0.0
#> TCGA.AC.A7VB.01 2 0.000 0.975 0.0 1.0
#> TCGA.AO.A0JI.01 1 0.000 1.000 1.0 0.0
#> TCGA.5T.A9QA.01 1 0.000 1.000 1.0 0.0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.D8.A1J8.01 3 0.583 0.607 0.34 0.00 0.66
#> TCGA.LL.A5YM.01 3 1.000 -0.385 0.32 0.34 0.34
#> TCGA.E9.A1NA.01 1 0.583 0.636 0.66 0.00 0.34
#> TCGA.C8.A1HO.01 1 0.583 0.349 0.66 0.34 0.00
#> TCGA.E9.A247.01 1 0.583 0.349 0.66 0.34 0.00
#> TCGA.AC.A2FM.01 3 0.583 0.607 0.34 0.00 0.66
#> TCGA.E9.A1RE.01 2 0.583 0.662 0.34 0.66 0.00
#> TCGA.AR.A250.01 2 0.583 0.643 0.00 0.66 0.34
#> TCGA.AQ.A04H.01 2 0.583 0.662 0.34 0.66 0.00
#> TCGA.AR.A0TZ.01 1 0.583 0.636 0.66 0.00 0.34
#> TCGA.E2.A576.01 2 0.583 0.643 0.00 0.66 0.34
#> TCGA.E9.A2JS.01 3 0.583 0.607 0.34 0.00 0.66
#> TCGA.C8.A3M8.01 2 0.583 0.643 0.00 0.66 0.34
#> TCGA.EW.A6SA.01 2 0.583 0.662 0.34 0.66 0.00
#> TCGA.C8.A9FZ.01 1 0.619 0.469 0.58 0.00 0.42
#> TCGA.D8.A1XF.01 3 0.583 0.607 0.34 0.00 0.66
#> TCGA.A2.A0CT.01 1 0.583 0.636 0.66 0.00 0.34
#> TCGA.B6.A0RL.01 1 0.583 0.636 0.66 0.00 0.34
#> TCGA.EW.A1OZ.01 2 0.583 0.643 0.00 0.66 0.34
#> TCGA.BH.A0E2.01 1 0.619 0.469 0.58 0.00 0.42
#> TCGA.AC.A7VB.01 2 0.583 0.662 0.34 0.66 0.00
#> TCGA.AO.A0JI.01 3 0.583 0.607 0.34 0.00 0.66
#> TCGA.5T.A9QA.01 3 0.583 0.607 0.34 0.00 0.66
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.D8.A1J8.01 3 0.3610 0.844 0.20 0.00 0.80 0.00
#> TCGA.LL.A5YM.01 4 0.1211 0.911 0.04 0.00 0.00 0.96
#> TCGA.E9.A1NA.01 1 0.0000 0.972 1.00 0.00 0.00 0.00
#> TCGA.C8.A1HO.01 1 0.0707 0.969 0.98 0.00 0.00 0.02
#> TCGA.E9.A247.01 1 0.0707 0.969 0.98 0.00 0.00 0.02
#> TCGA.AC.A2FM.01 3 0.2011 0.971 0.08 0.00 0.92 0.00
#> TCGA.E9.A1RE.01 2 0.0707 0.975 0.00 0.98 0.02 0.00
#> TCGA.AR.A250.01 4 0.1637 0.978 0.00 0.06 0.00 0.94
#> TCGA.AQ.A04H.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.AR.A0TZ.01 1 0.0707 0.970 0.98 0.00 0.02 0.00
#> TCGA.E2.A576.01 4 0.1637 0.978 0.00 0.06 0.00 0.94
#> TCGA.E9.A2JS.01 3 0.2011 0.971 0.08 0.00 0.92 0.00
#> TCGA.C8.A3M8.01 4 0.1637 0.978 0.00 0.06 0.00 0.94
#> TCGA.EW.A6SA.01 2 0.1637 0.956 0.00 0.94 0.06 0.00
#> TCGA.C8.A9FZ.01 1 0.1913 0.961 0.94 0.00 0.02 0.04
#> TCGA.D8.A1XF.01 3 0.2011 0.971 0.08 0.00 0.92 0.00
#> TCGA.A2.A0CT.01 1 0.1411 0.969 0.96 0.00 0.02 0.02
#> TCGA.B6.A0RL.01 1 0.0707 0.969 0.98 0.00 0.00 0.02
#> TCGA.EW.A1OZ.01 4 0.1637 0.978 0.00 0.06 0.00 0.94
#> TCGA.BH.A0E2.01 1 0.1913 0.961 0.94 0.00 0.02 0.04
#> TCGA.AC.A7VB.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.AO.A0JI.01 3 0.2011 0.971 0.08 0.00 0.92 0.00
#> TCGA.5T.A9QA.01 3 0.2011 0.971 0.08 0.00 0.92 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.D8.A1J8.01 1 0.4126 0.311 0.62 0.00 0.38 0.0 0.00
#> TCGA.LL.A5YM.01 4 0.3796 0.741 0.00 0.00 0.00 0.7 0.30
#> TCGA.E9.A1NA.01 1 0.1043 0.720 0.96 0.00 0.00 0.0 0.04
#> TCGA.C8.A1HO.01 5 0.3424 0.656 0.24 0.00 0.00 0.0 0.76
#> TCGA.E9.A247.01 1 0.3274 0.494 0.78 0.00 0.00 0.0 0.22
#> TCGA.AC.A2FM.01 3 0.0000 1.000 0.00 0.00 1.00 0.0 0.00
#> TCGA.E9.A1RE.01 2 0.2020 0.922 0.00 0.90 0.00 0.0 0.10
#> TCGA.AR.A250.01 4 0.0000 0.919 0.00 0.00 0.00 1.0 0.00
#> TCGA.AQ.A04H.01 2 0.0000 0.970 0.00 1.00 0.00 0.0 0.00
#> TCGA.AR.A0TZ.01 1 0.1043 0.720 0.96 0.00 0.00 0.0 0.04
#> TCGA.E2.A576.01 4 0.0000 0.919 0.00 0.00 0.00 1.0 0.00
#> TCGA.E9.A2JS.01 3 0.0000 1.000 0.00 0.00 1.00 0.0 0.00
#> TCGA.C8.A3M8.01 4 0.2020 0.889 0.00 0.00 0.00 0.9 0.10
#> TCGA.EW.A6SA.01 2 0.0609 0.964 0.00 0.98 0.00 0.0 0.02
#> TCGA.C8.A9FZ.01 5 0.4262 0.804 0.44 0.00 0.00 0.0 0.56
#> TCGA.D8.A1XF.01 3 0.0000 1.000 0.00 0.00 1.00 0.0 0.00
#> TCGA.A2.A0CT.01 1 0.0000 0.733 1.00 0.00 0.00 0.0 0.00
#> TCGA.B6.A0RL.01 1 0.0609 0.730 0.98 0.00 0.00 0.0 0.02
#> TCGA.EW.A1OZ.01 4 0.0000 0.919 0.00 0.00 0.00 1.0 0.00
#> TCGA.BH.A0E2.01 5 0.4262 0.804 0.44 0.00 0.00 0.0 0.56
#> TCGA.AC.A7VB.01 2 0.0000 0.970 0.00 1.00 0.00 0.0 0.00
#> TCGA.AO.A0JI.01 3 0.0000 1.000 0.00 0.00 1.00 0.0 0.00
#> TCGA.5T.A9QA.01 3 0.0000 1.000 0.00 0.00 1.00 0.0 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.D8.A1J8.01 1 0.383 0.240 0.56 0.00 0.44 0.00 0.00 0.00
#> TCGA.LL.A5YM.01 6 0.599 0.000 0.00 0.00 0.00 0.34 0.24 0.42
#> TCGA.E9.A1NA.01 1 0.000 0.609 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A1HO.01 5 0.320 0.434 0.26 0.00 0.00 0.00 0.74 0.00
#> TCGA.E9.A247.01 5 0.489 -0.356 0.44 0.00 0.00 0.00 0.50 0.06
#> TCGA.AC.A2FM.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E9.A1RE.01 2 0.375 0.801 0.00 0.78 0.00 0.00 0.08 0.14
#> TCGA.AR.A250.01 4 0.000 0.772 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AQ.A04H.01 2 0.000 0.917 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A0TZ.01 1 0.000 0.609 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A576.01 4 0.000 0.772 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E9.A2JS.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.C8.A3M8.01 4 0.380 -0.324 0.00 0.00 0.00 0.58 0.00 0.42
#> TCGA.EW.A6SA.01 2 0.156 0.892 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.C8.A9FZ.01 5 0.604 0.568 0.28 0.00 0.00 0.00 0.42 0.30
#> TCGA.D8.A1XF.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A0CT.01 1 0.383 0.631 0.76 0.00 0.00 0.00 0.18 0.06
#> TCGA.B6.A0RL.01 1 0.409 0.619 0.74 0.00 0.00 0.00 0.18 0.08
#> TCGA.EW.A1OZ.01 4 0.000 0.772 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A0E2.01 5 0.604 0.568 0.28 0.00 0.00 0.00 0.42 0.30
#> TCGA.AC.A7VB.01 2 0.000 0.917 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A0JI.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.5T.A9QA.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.D8.A1J8.01 1 0.294 0.593 0.74 0.00 0.26 0.00 0.00 0.00 0.00
#> TCGA.LL.A5YM.01 6 0.367 0.866 0.00 0.00 0.00 0.14 0.10 0.76 0.00
#> TCGA.E9.A1NA.01 1 0.337 0.723 0.78 0.00 0.00 0.00 0.16 0.00 0.06
#> TCGA.C8.A1HO.01 5 0.305 0.408 0.00 0.00 0.00 0.00 0.72 0.00 0.28
#> TCGA.E9.A247.01 5 0.369 0.536 0.32 0.00 0.00 0.00 0.66 0.00 0.02
#> TCGA.AC.A2FM.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RE.01 2 0.340 0.799 0.00 0.82 0.00 0.00 0.08 0.06 0.04
#> TCGA.AR.A250.01 4 0.000 0.980 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AQ.A04H.01 2 0.000 0.886 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A0TZ.01 1 0.337 0.723 0.78 0.00 0.00 0.00 0.16 0.00 0.06
#> TCGA.E2.A576.01 4 0.101 0.959 0.00 0.00 0.00 0.96 0.02 0.02 0.00
#> TCGA.E9.A2JS.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A3M8.01 6 0.271 0.861 0.00 0.00 0.00 0.22 0.00 0.78 0.00
#> TCGA.EW.A6SA.01 2 0.363 0.785 0.00 0.80 0.00 0.00 0.06 0.10 0.04
#> TCGA.C8.A9FZ.01 7 0.143 0.971 0.08 0.00 0.00 0.00 0.00 0.00 0.92
#> TCGA.D8.A1XF.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0CT.01 1 0.166 0.708 0.92 0.00 0.00 0.00 0.00 0.06 0.02
#> TCGA.B6.A0RL.01 1 0.166 0.708 0.92 0.00 0.00 0.00 0.00 0.06 0.02
#> TCGA.EW.A1OZ.01 4 0.000 0.980 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0E2.01 7 0.193 0.971 0.08 0.00 0.00 0.00 0.02 0.00 0.90
#> TCGA.AC.A7VB.01 2 0.000 0.886 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A0JI.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.5T.A9QA.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.D8.A1J8.01 8 0.473 0.563 0.18 0.00 0.26 0.00 0.00 0.00 0.00 0.56
#> TCGA.LL.A5YM.01 6 0.109 0.867 0.00 0.00 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.E9.A1NA.01 8 0.373 0.634 0.46 0.00 0.00 0.00 0.00 0.00 0.02 0.52
#> TCGA.C8.A1HO.01 5 0.485 0.493 0.24 0.00 0.00 0.00 0.54 0.00 0.22 0.00
#> TCGA.E9.A247.01 5 0.156 0.576 0.00 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.AC.A2FM.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RE.01 2 0.363 0.791 0.08 0.78 0.00 0.00 0.10 0.04 0.00 0.00
#> TCGA.AR.A250.01 4 0.000 0.954 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AQ.A04H.01 2 0.000 0.897 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A0TZ.01 8 0.362 0.676 0.38 0.00 0.00 0.00 0.00 0.00 0.02 0.60
#> TCGA.E2.A576.01 4 0.156 0.904 0.10 0.00 0.00 0.90 0.00 0.00 0.00 0.00
#> TCGA.E9.A2JS.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A3M8.01 6 0.315 0.867 0.16 0.00 0.00 0.06 0.00 0.78 0.00 0.00
#> TCGA.EW.A6SA.01 2 0.222 0.848 0.12 0.86 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.C8.A9FZ.01 7 0.000 1.000 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D8.A1XF.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0CT.01 8 0.000 0.650 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.B6.A0RL.01 8 0.000 0.650 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EW.A1OZ.01 4 0.000 0.954 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0E2.01 7 0.000 1.000 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AC.A7VB.01 2 0.000 0.897 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A0JI.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5T.A9QA.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node022. Child nodes: Node02121-leaf , Node02122-leaf , Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02214-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02321-leaf , Node02322-leaf , Node02421-leaf , Node02422-leaf , Node02423-leaf , Node04111-leaf , Node04112-leaf , Node04113 , Node04131-leaf , Node04132-leaf , Node04133-leaf , Node04221-leaf , Node04222-leaf , Node04331-leaf , Node04332-leaf , Node04333-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0222"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 32 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.933 0.977 0.988 0.5030 0.492 0.492
#> 3 3 1.000 0.999 0.999 0.3631 0.694 0.449
#> 4 4 0.811 0.813 0.887 0.0974 0.901 0.701
#> 5 5 0.761 0.643 0.714 0.0470 0.923 0.705
#> 6 6 0.726 0.670 0.787 0.0364 0.952 0.778
#> 7 7 0.805 0.552 0.770 0.0313 0.982 0.905
#> 8 8 0.784 0.753 0.804 0.0151 0.954 0.739
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.BH.A1EN.01 2 0.584 0.862 0.14 0.86
#> TCGA.AR.A24N.01 2 0.000 0.969 0.00 1.00
#> TCGA.AC.A4ZE.01 2 0.000 0.969 0.00 1.00
#> TCGA.AN.A0XV.01 1 0.000 1.000 1.00 0.00
#> TCGA.E2.A2P6.01 2 0.000 0.969 0.00 1.00
#> TCGA.D8.A1XJ.01 1 0.000 1.000 1.00 0.00
#> TCGA.S3.A6ZG.01 2 0.000 0.969 0.00 1.00
#> TCGA.E2.A9RU.01 1 0.000 1.000 1.00 0.00
#> TCGA.EW.A423.01 2 0.000 0.969 0.00 1.00
#> TCGA.C8.A274.01 1 0.000 1.000 1.00 0.00
#> TCGA.E9.A1RC.01 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A0DS.01 2 0.584 0.862 0.14 0.86
#> TCGA.BH.A0HK.01 2 0.000 0.969 0.00 1.00
#> TCGA.OL.A66K.01 2 0.000 0.969 0.00 1.00
#> TCGA.OL.A5D8.01 1 0.000 1.000 1.00 0.00
#> TCGA.E9.A1R5.01 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A1F8.01 2 0.529 0.881 0.12 0.88
#> TCGA.BH.A1FD.01 1 0.000 1.000 1.00 0.00
#> TCGA.D8.A1JN.01 2 0.000 0.969 0.00 1.00
#> TCGA.AR.A2LK.01 2 0.000 0.969 0.00 1.00
#> TCGA.D8.A1J9.01 1 0.000 1.000 1.00 0.00
#> TCGA.AR.A1AP.01 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A42T.01 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A1EV.01 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A0HY.01 1 0.000 1.000 1.00 0.00
#> TCGA.AC.A3EH.01 2 0.000 0.969 0.00 1.00
#> TCGA.PE.A5DD.01 1 0.000 1.000 1.00 0.00
#> TCGA.EW.A424.01 1 0.000 1.000 1.00 0.00
#> TCGA.E2.A1L7.01 1 0.000 1.000 1.00 0.00
#> TCGA.A2.A0SY.01 1 0.000 1.000 1.00 0.00
#> TCGA.A2.A0YG.01 1 0.000 1.000 1.00 0.00
#> TCGA.AR.A1AV.01 2 0.000 0.969 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.BH.A1EN.01 3 0.0000 1.000 0.00 0 1.00
#> TCGA.AR.A24N.01 3 0.0000 1.000 0.00 0 1.00
#> TCGA.AC.A4ZE.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.AN.A0XV.01 3 0.0000 1.000 0.00 0 1.00
#> TCGA.E2.A2P6.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.D8.A1XJ.01 1 0.0000 0.998 1.00 0 0.00
#> TCGA.S3.A6ZG.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.E2.A9RU.01 3 0.0000 1.000 0.00 0 1.00
#> TCGA.EW.A423.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.C8.A274.01 1 0.0000 0.998 1.00 0 0.00
#> TCGA.E9.A1RC.01 1 0.0000 0.998 1.00 0 0.00
#> TCGA.BH.A0DS.01 3 0.0000 1.000 0.00 0 1.00
#> TCGA.BH.A0HK.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.OL.A66K.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.OL.A5D8.01 3 0.0000 1.000 0.00 0 1.00
#> TCGA.E9.A1R5.01 1 0.0892 0.979 0.98 0 0.02
#> TCGA.BH.A1F8.01 3 0.0000 1.000 0.00 0 1.00
#> TCGA.BH.A1FD.01 3 0.0000 1.000 0.00 0 1.00
#> TCGA.D8.A1JN.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.AR.A2LK.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.D8.A1J9.01 3 0.0000 1.000 0.00 0 1.00
#> TCGA.AR.A1AP.01 1 0.0000 0.998 1.00 0 0.00
#> TCGA.BH.A42T.01 1 0.0000 0.998 1.00 0 0.00
#> TCGA.BH.A1EV.01 1 0.0000 0.998 1.00 0 0.00
#> TCGA.BH.A0HY.01 1 0.0000 0.998 1.00 0 0.00
#> TCGA.AC.A3EH.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.PE.A5DD.01 3 0.0000 1.000 0.00 0 1.00
#> TCGA.EW.A424.01 3 0.0000 1.000 0.00 0 1.00
#> TCGA.E2.A1L7.01 1 0.0000 0.998 1.00 0 0.00
#> TCGA.A2.A0SY.01 3 0.0000 1.000 0.00 0 1.00
#> TCGA.A2.A0YG.01 1 0.0000 0.998 1.00 0 0.00
#> TCGA.AR.A1AV.01 2 0.0000 1.000 0.00 1 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.BH.A1EN.01 4 0.1637 0.950 0.00 0.00 0.06 0.94
#> TCGA.AR.A24N.01 4 0.1211 0.952 0.00 0.00 0.04 0.96
#> TCGA.AC.A4ZE.01 2 0.0707 0.973 0.00 0.98 0.00 0.02
#> TCGA.AN.A0XV.01 3 0.3975 0.739 0.00 0.00 0.76 0.24
#> TCGA.E2.A2P6.01 2 0.0707 0.973 0.00 0.98 0.00 0.02
#> TCGA.D8.A1XJ.01 1 0.0000 0.789 1.00 0.00 0.00 0.00
#> TCGA.S3.A6ZG.01 2 0.2011 0.924 0.00 0.92 0.00 0.08
#> TCGA.E2.A9RU.01 3 0.3975 0.739 0.00 0.00 0.76 0.24
#> TCGA.EW.A423.01 2 0.0000 0.973 0.00 1.00 0.00 0.00
#> TCGA.C8.A274.01 1 0.4713 0.648 0.64 0.00 0.36 0.00
#> TCGA.E9.A1RC.01 1 0.0000 0.789 1.00 0.00 0.00 0.00
#> TCGA.BH.A0DS.01 4 0.1211 0.952 0.00 0.00 0.04 0.96
#> TCGA.BH.A0HK.01 2 0.0707 0.973 0.00 0.98 0.00 0.02
#> TCGA.OL.A66K.01 2 0.2011 0.924 0.00 0.92 0.00 0.08
#> TCGA.OL.A5D8.01 4 0.2647 0.884 0.00 0.00 0.12 0.88
#> TCGA.E9.A1R5.01 3 0.1637 0.682 0.06 0.00 0.94 0.00
#> TCGA.BH.A1F8.01 3 0.4624 0.646 0.00 0.00 0.66 0.34
#> TCGA.BH.A1FD.01 3 0.4713 0.573 0.00 0.00 0.64 0.36
#> TCGA.D8.A1JN.01 2 0.0707 0.966 0.00 0.98 0.00 0.02
#> TCGA.AR.A2LK.01 2 0.0000 0.973 0.00 1.00 0.00 0.00
#> TCGA.D8.A1J9.01 3 0.0000 0.748 0.00 0.00 1.00 0.00
#> TCGA.AR.A1AP.01 1 0.0000 0.789 1.00 0.00 0.00 0.00
#> TCGA.BH.A42T.01 1 0.4994 0.497 0.52 0.00 0.48 0.00
#> TCGA.BH.A1EV.01 1 0.4994 0.497 0.52 0.00 0.48 0.00
#> TCGA.BH.A0HY.01 1 0.4134 0.719 0.74 0.00 0.26 0.00
#> TCGA.AC.A3EH.01 2 0.0707 0.973 0.00 0.98 0.00 0.02
#> TCGA.PE.A5DD.01 3 0.4134 0.721 0.00 0.00 0.74 0.26
#> TCGA.EW.A424.01 3 0.0000 0.748 0.00 0.00 1.00 0.00
#> TCGA.E2.A1L7.01 1 0.0000 0.789 1.00 0.00 0.00 0.00
#> TCGA.A2.A0SY.01 3 0.0000 0.748 0.00 0.00 1.00 0.00
#> TCGA.A2.A0YG.01 1 0.0000 0.789 1.00 0.00 0.00 0.00
#> TCGA.AR.A1AV.01 2 0.0000 0.973 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.BH.A1EN.01 4 0.473 0.730 0.00 0.00 0.24 0.70 0.06
#> TCGA.AR.A24N.01 4 0.104 0.767 0.00 0.00 0.04 0.96 0.00
#> TCGA.AC.A4ZE.01 2 0.122 0.873 0.00 0.96 0.02 0.00 0.02
#> TCGA.AN.A0XV.01 3 0.418 0.693 0.00 0.00 0.60 0.00 0.40
#> TCGA.E2.A2P6.01 2 0.122 0.873 0.00 0.96 0.02 0.00 0.02
#> TCGA.D8.A1XJ.01 1 0.000 0.866 1.00 0.00 0.00 0.00 0.00
#> TCGA.S3.A6ZG.01 2 0.580 0.591 0.00 0.64 0.06 0.26 0.04
#> TCGA.E2.A9RU.01 3 0.413 0.695 0.00 0.00 0.62 0.00 0.38
#> TCGA.EW.A423.01 2 0.000 0.873 0.00 1.00 0.00 0.00 0.00
#> TCGA.C8.A274.01 5 0.473 0.292 0.40 0.00 0.02 0.00 0.58
#> TCGA.E9.A1RC.01 1 0.000 0.866 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DS.01 4 0.104 0.767 0.00 0.00 0.04 0.96 0.00
#> TCGA.BH.A0HK.01 2 0.122 0.873 0.00 0.96 0.02 0.00 0.02
#> TCGA.OL.A66K.01 2 0.590 0.563 0.00 0.62 0.06 0.28 0.04
#> TCGA.OL.A5D8.01 4 0.418 0.593 0.00 0.00 0.40 0.60 0.00
#> TCGA.E9.A1R5.01 5 0.356 0.167 0.00 0.00 0.26 0.00 0.74
#> TCGA.BH.A1F8.01 3 0.646 0.271 0.00 0.00 0.50 0.26 0.24
#> TCGA.BH.A1FD.01 3 0.422 0.440 0.00 0.00 0.78 0.10 0.12
#> TCGA.D8.A1JN.01 2 0.464 0.724 0.00 0.74 0.10 0.00 0.16
#> TCGA.AR.A2LK.01 2 0.000 0.873 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A1J9.01 5 0.413 -0.278 0.00 0.00 0.38 0.00 0.62
#> TCGA.AR.A1AP.01 1 0.173 0.812 0.92 0.00 0.00 0.00 0.08
#> TCGA.BH.A42T.01 5 0.356 0.612 0.26 0.00 0.00 0.00 0.74
#> TCGA.BH.A1EV.01 5 0.356 0.612 0.26 0.00 0.00 0.00 0.74
#> TCGA.BH.A0HY.01 1 0.429 -0.026 0.54 0.00 0.00 0.00 0.46
#> TCGA.AC.A3EH.01 2 0.122 0.873 0.00 0.96 0.02 0.00 0.02
#> TCGA.PE.A5DD.01 3 0.398 0.684 0.00 0.00 0.66 0.00 0.34
#> TCGA.EW.A424.01 3 0.423 0.674 0.00 0.00 0.58 0.00 0.42
#> TCGA.E2.A1L7.01 1 0.000 0.866 1.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0SY.01 3 0.429 0.607 0.00 0.00 0.54 0.00 0.46
#> TCGA.A2.A0YG.01 1 0.000 0.866 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AV.01 2 0.000 0.873 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.BH.A1EN.01 6 0.5361 0.183 0.00 0.00 0.02 0.44 0.06 0.48
#> TCGA.AR.A24N.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AC.A4ZE.01 2 0.0000 0.830 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AN.A0XV.01 3 0.0000 0.712 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E2.A2P6.01 2 0.0000 0.830 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1XJ.01 1 0.0000 0.936 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S3.A6ZG.01 2 0.6873 0.362 0.00 0.46 0.00 0.20 0.26 0.08
#> TCGA.E2.A9RU.01 3 0.1267 0.689 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.EW.A423.01 2 0.0000 0.830 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A274.01 5 0.6167 0.730 0.26 0.00 0.16 0.00 0.54 0.04
#> TCGA.E9.A1RC.01 1 0.0000 0.936 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DS.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A0HK.01 2 0.0000 0.830 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A66K.01 2 0.6873 0.362 0.00 0.46 0.00 0.20 0.26 0.08
#> TCGA.OL.A5D8.01 6 0.5987 0.444 0.00 0.00 0.30 0.26 0.00 0.44
#> TCGA.E9.A1R5.01 5 0.3797 0.516 0.00 0.00 0.42 0.00 0.58 0.00
#> TCGA.BH.A1F8.01 3 0.6554 0.233 0.00 0.00 0.50 0.06 0.26 0.18
#> TCGA.BH.A1FD.01 3 0.3864 -0.120 0.00 0.00 0.52 0.00 0.00 0.48
#> TCGA.D8.A1JN.01 2 0.5712 0.469 0.00 0.52 0.00 0.00 0.22 0.26
#> TCGA.AR.A2LK.01 2 0.0000 0.830 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1J9.01 3 0.3679 0.433 0.00 0.00 0.76 0.00 0.20 0.04
#> TCGA.AR.A1AP.01 1 0.3156 0.683 0.80 0.00 0.00 0.00 0.18 0.02
#> TCGA.BH.A42T.01 5 0.6167 0.796 0.16 0.00 0.26 0.00 0.54 0.04
#> TCGA.BH.A1EV.01 5 0.5354 0.795 0.16 0.00 0.26 0.00 0.58 0.00
#> TCGA.BH.A0HY.01 5 0.6382 0.617 0.32 0.00 0.10 0.00 0.50 0.08
#> TCGA.AC.A3EH.01 2 0.0000 0.830 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.PE.A5DD.01 3 0.2454 0.589 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.EW.A424.01 3 0.0937 0.702 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.E2.A1L7.01 1 0.0000 0.936 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0SY.01 3 0.0937 0.702 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.A2.A0YG.01 1 0.0000 0.936 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AV.01 2 0.0000 0.830 0.00 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.BH.A1EN.01 6 0.668 0.141 0.00 0.00 0.06 0.32 0.02 0.40 0.20
#> TCGA.AR.A24N.01 4 0.000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A4ZE.01 2 0.000 0.675 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AN.A0XV.01 3 0.117 0.630 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.E2.A2P6.01 2 0.000 0.675 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1XJ.01 1 0.000 0.916 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S3.A6ZG.01 2 0.679 -0.424 0.00 0.36 0.00 0.24 0.00 0.28 0.12
#> TCGA.E2.A9RU.01 3 0.228 0.590 0.00 0.00 0.88 0.00 0.04 0.08 0.00
#> TCGA.EW.A423.01 2 0.151 0.655 0.00 0.94 0.00 0.00 0.02 0.02 0.02
#> TCGA.C8.A274.01 5 0.277 0.830 0.08 0.00 0.02 0.00 0.86 0.00 0.04
#> TCGA.E9.A1RC.01 1 0.000 0.916 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DS.01 4 0.000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0HK.01 2 0.000 0.675 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A66K.01 2 0.682 -0.422 0.00 0.34 0.00 0.26 0.00 0.28 0.12
#> TCGA.OL.A5D8.01 6 0.485 0.258 0.00 0.00 0.40 0.10 0.00 0.50 0.00
#> TCGA.E9.A1R5.01 5 0.167 0.811 0.00 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.BH.A1F8.01 3 0.586 0.229 0.00 0.00 0.46 0.02 0.06 0.40 0.06
#> TCGA.BH.A1FD.01 3 0.356 -0.450 0.00 0.00 0.50 0.00 0.00 0.50 0.00
#> TCGA.D8.A1JN.01 7 0.534 0.000 0.00 0.40 0.00 0.00 0.00 0.18 0.42
#> TCGA.AR.A2LK.01 2 0.101 0.664 0.00 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.D8.A1J9.01 3 0.494 0.316 0.00 0.00 0.56 0.00 0.30 0.00 0.14
#> TCGA.AR.A1AP.01 1 0.403 0.564 0.70 0.00 0.00 0.00 0.22 0.00 0.08
#> TCGA.BH.A42T.01 5 0.390 0.830 0.04 0.00 0.04 0.00 0.76 0.00 0.16
#> TCGA.BH.A1EV.01 5 0.221 0.852 0.04 0.00 0.04 0.00 0.90 0.00 0.02
#> TCGA.BH.A0HY.01 5 0.488 0.758 0.06 0.00 0.04 0.00 0.62 0.00 0.28
#> TCGA.AC.A3EH.01 2 0.000 0.675 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PE.A5DD.01 3 0.143 0.548 0.00 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.EW.A424.01 3 0.226 0.636 0.00 0.00 0.84 0.00 0.16 0.00 0.00
#> TCGA.E2.A1L7.01 1 0.000 0.916 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0SY.01 3 0.226 0.636 0.00 0.00 0.84 0.00 0.16 0.00 0.00
#> TCGA.A2.A0YG.01 1 0.000 0.916 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AV.01 2 0.151 0.655 0.00 0.94 0.00 0.00 0.02 0.02 0.02
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.BH.A1EN.01 6 0.518 0.368 0.00 0.00 0.00 0.20 0.02 0.60 0.16 0.02
#> TCGA.AR.A24N.01 4 0.265 1.000 0.00 0.00 0.00 0.76 0.00 0.00 0.00 0.24
#> TCGA.AC.A4ZE.01 2 0.000 0.934 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AN.A0XV.01 3 0.176 0.725 0.00 0.00 0.88 0.00 0.12 0.00 0.00 0.00
#> TCGA.E2.A2P6.01 2 0.000 0.934 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1XJ.01 1 0.000 0.920 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S3.A6ZG.01 8 0.294 1.000 0.00 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.E2.A9RU.01 3 0.326 0.657 0.00 0.00 0.78 0.00 0.10 0.12 0.00 0.00
#> TCGA.EW.A423.01 2 0.267 0.876 0.00 0.88 0.02 0.00 0.02 0.04 0.02 0.02
#> TCGA.C8.A274.01 5 0.235 0.761 0.06 0.00 0.02 0.00 0.88 0.00 0.00 0.04
#> TCGA.E9.A1RC.01 1 0.000 0.920 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DS.01 4 0.265 1.000 0.00 0.00 0.00 0.76 0.00 0.00 0.00 0.24
#> TCGA.BH.A0HK.01 2 0.000 0.934 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A66K.01 8 0.294 1.000 0.00 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.OL.A5D8.01 6 0.304 0.718 0.00 0.00 0.18 0.04 0.00 0.78 0.00 0.00
#> TCGA.E9.A1R5.01 5 0.176 0.717 0.00 0.00 0.12 0.00 0.88 0.00 0.00 0.00
#> TCGA.BH.A1F8.01 3 0.479 0.182 0.00 0.00 0.48 0.08 0.00 0.00 0.02 0.42
#> TCGA.BH.A1FD.01 6 0.253 0.697 0.00 0.00 0.22 0.00 0.00 0.78 0.00 0.00
#> TCGA.D8.A1JN.01 7 0.629 0.000 0.00 0.30 0.00 0.06 0.00 0.02 0.40 0.22
#> TCGA.AR.A2LK.01 2 0.141 0.914 0.00 0.94 0.02 0.00 0.00 0.00 0.02 0.02
#> TCGA.D8.A1J9.01 3 0.473 0.409 0.00 0.00 0.56 0.00 0.26 0.00 0.18 0.00
#> TCGA.AR.A1AP.01 1 0.422 0.615 0.70 0.00 0.00 0.02 0.14 0.00 0.14 0.00
#> TCGA.BH.A42T.01 5 0.373 0.717 0.02 0.00 0.02 0.00 0.68 0.00 0.28 0.00
#> TCGA.BH.A1EV.01 5 0.128 0.774 0.02 0.00 0.04 0.00 0.94 0.00 0.00 0.00
#> TCGA.BH.A0HY.01 5 0.394 0.640 0.04 0.00 0.00 0.00 0.56 0.00 0.40 0.00
#> TCGA.AC.A3EH.01 2 0.000 0.934 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PE.A5DD.01 3 0.315 0.608 0.00 0.00 0.78 0.00 0.06 0.16 0.00 0.00
#> TCGA.EW.A424.01 3 0.227 0.716 0.00 0.00 0.82 0.00 0.18 0.00 0.00 0.00
#> TCGA.E2.A1L7.01 1 0.000 0.920 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0SY.01 3 0.227 0.716 0.00 0.00 0.82 0.00 0.18 0.00 0.00 0.00
#> TCGA.A2.A0YG.01 1 0.000 0.920 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AV.01 2 0.267 0.876 0.00 0.88 0.02 0.00 0.02 0.04 0.02 0.02
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0115-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0151-leaf , Node0152-leaf , Node0153-leaf , Node0154-leaf , Node0211-leaf , Node0212 , Node0213 , Node0221 , Node0222 , Node0231-leaf , Node0232 , Node0233-leaf , Node0241-leaf , Node0242 , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0331-leaf , Node0332-leaf , Node0341-leaf , Node0342-leaf , Node0343-leaf , Node0411 , Node0412-leaf , Node0413 , Node0421-leaf , Node0422 , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["023"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 95 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.956 0.933 0.972 0.5032 0.497 0.497
#> 3 3 1.000 0.959 0.983 0.3233 0.784 0.589
#> 4 4 0.752 0.710 0.863 0.1229 0.851 0.590
#> 5 5 0.751 0.707 0.808 0.0575 0.871 0.546
#> 6 6 0.777 0.743 0.836 0.0360 0.900 0.582
#> 7 7 0.786 0.625 0.805 0.0274 0.957 0.778
#> 8 8 0.781 0.561 0.774 0.0179 0.984 0.906
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.D8.A1XA.01 2 0.000 0.944 0.00 1.00
#> TCGA.A2.A0SW.01 2 0.000 0.944 0.00 1.00
#> TCGA.EW.A1P5.01 1 0.000 1.000 1.00 0.00
#> TCGA.E9.A1N5.01 1 0.000 1.000 1.00 0.00
#> TCGA.A2.A0YC.01 2 0.971 0.413 0.40 0.60
#> TCGA.EW.A6S9.01 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A1FG.01 1 0.000 1.000 1.00 0.00
#> TCGA.E2.A570.01 1 0.000 1.000 1.00 0.00
#> TCGA.EW.A1P0.01 2 0.000 0.944 0.00 1.00
#> TCGA.A2.A0YT.01 2 0.000 0.944 0.00 1.00
#> TCGA.BH.A0B5.01 2 0.000 0.944 0.00 1.00
#> TCGA.BH.A0B8.01 2 0.000 0.944 0.00 1.00
#> TCGA.LL.A6FQ.01 2 0.000 0.944 0.00 1.00
#> TCGA.A1.A0SQ.01 2 0.000 0.944 0.00 1.00
#> TCGA.B6.A0RO.01 2 0.000 0.944 0.00 1.00
#> TCGA.AC.A2BM.01 2 0.000 0.944 0.00 1.00
#> TCGA.EW.A1J6.01 2 0.958 0.455 0.38 0.62
#> TCGA.A2.A25C.01 1 0.000 1.000 1.00 0.00
#> TCGA.3C.AALI.01 2 0.000 0.944 0.00 1.00
#> TCGA.E9.A1NI.01 2 0.000 0.944 0.00 1.00
#> TCGA.BH.A0HA.01 1 0.000 1.000 1.00 0.00
#> TCGA.D8.A1XS.01 1 0.000 1.000 1.00 0.00
#> TCGA.AN.A0XP.01 2 0.971 0.413 0.40 0.60
#> TCGA.D8.A1XD.01 1 0.000 1.000 1.00 0.00
#> TCGA.AR.A24M.01 1 0.000 1.000 1.00 0.00
#> TCGA.E2.A572.01 2 0.000 0.944 0.00 1.00
#> TCGA.BH.A1ES.01 1 0.000 1.000 1.00 0.00
#> TCGA.EW.A1PE.01 1 0.000 1.000 1.00 0.00
#> TCGA.A7.A2KD.01 2 0.000 0.944 0.00 1.00
#> TCGA.S3.A6ZH.01 2 0.000 0.944 0.00 1.00
#> TCGA.BH.A1EX.01 2 0.000 0.944 0.00 1.00
#> TCGA.A2.A0CK.01 1 0.000 1.000 1.00 0.00
#> TCGA.C8.A273.01 2 0.971 0.413 0.40 0.60
#> TCGA.AR.A0U2.01 2 0.000 0.944 0.00 1.00
#> TCGA.A2.A1FV.01 2 0.000 0.944 0.00 1.00
#> TCGA.D8.A1XC.01 1 0.000 1.000 1.00 0.00
#> TCGA.S3.AA11.01 2 0.000 0.944 0.00 1.00
#> TCGA.AQ.A54O.01 1 0.000 1.000 1.00 0.00
#> TCGA.D8.A1JT.01 2 0.000 0.944 0.00 1.00
#> TCGA.D8.A1X5.01 2 0.000 0.944 0.00 1.00
#> TCGA.BH.A0E1.01 1 0.000 1.000 1.00 0.00
#> TCGA.E2.A106.01 2 0.000 0.944 0.00 1.00
#> TCGA.E2.A56Z.01 2 0.000 0.944 0.00 1.00
#> TCGA.A7.A0D9.01 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A204.01 2 0.000 0.944 0.00 1.00
#> TCGA.D8.A1XL.01 1 0.000 1.000 1.00 0.00
#> TCGA.OL.A5RZ.01 2 0.000 0.944 0.00 1.00
#> TCGA.A2.A0YF.01 2 0.000 0.944 0.00 1.00
#> TCGA.C8.A1HM.01 2 0.000 0.944 0.00 1.00
#> TCGA.BH.A1FM.01 2 0.000 0.944 0.00 1.00
#> TCGA.AR.A2LE.01 1 0.000 1.000 1.00 0.00
#> TCGA.AR.A24Z.01 2 0.000 0.944 0.00 1.00
#> TCGA.JL.A3YX.01 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A0HN.01 1 0.000 1.000 1.00 0.00
#> TCGA.AC.A62V.01 2 0.000 0.944 0.00 1.00
#> TCGA.AO.A126.01 1 0.000 1.000 1.00 0.00
#> TCGA.A7.A26J.01 2 0.000 0.944 0.00 1.00
#> TCGA.A2.A25B.01 2 0.000 0.944 0.00 1.00
#> TCGA.PL.A8LX.01 1 0.000 1.000 1.00 0.00
#> TCGA.EW.A1J3.01 1 0.000 1.000 1.00 0.00
#> TCGA.B6.A0WV.01 2 0.000 0.944 0.00 1.00
#> TCGA.BH.A0HX.01 2 0.000 0.944 0.00 1.00
#> TCGA.AR.A0TR.01 1 0.000 1.000 1.00 0.00
#> TCGA.B6.A0RM.01 1 0.000 1.000 1.00 0.00
#> TCGA.E2.A1IE.01 2 0.000 0.944 0.00 1.00
#> TCGA.EW.A1P3.01 2 0.000 0.944 0.00 1.00
#> TCGA.E9.A22H.01 2 0.971 0.413 0.40 0.60
#> TCGA.D8.A3Z6.01 1 0.000 1.000 1.00 0.00
#> TCGA.A8.A08O.01 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A1F2.01 2 0.000 0.944 0.00 1.00
#> TCGA.BH.A0HI.01 1 0.000 1.000 1.00 0.00
#> TCGA.E2.A1L9.01 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A0W3.01 1 0.000 1.000 1.00 0.00
#> TCGA.AO.A03N.01 1 0.000 1.000 1.00 0.00
#> TCGA.C8.A1HN.01 2 0.000 0.944 0.00 1.00
#> TCGA.BH.A0HB.01 1 0.000 1.000 1.00 0.00
#> TCGA.A2.A1FX.01 2 0.000 0.944 0.00 1.00
#> TCGA.A7.A13G.01 1 0.000 1.000 1.00 0.00
#> TCGA.AQ.A1H2.01 2 0.000 0.944 0.00 1.00
#> TCGA.A2.A0EU.01 1 0.000 1.000 1.00 0.00
#> TCGA.EW.A1J5.01 2 0.000 0.944 0.00 1.00
#> TCGA.C8.A27A.01 2 0.000 0.944 0.00 1.00
#> TCGA.C8.A1HK.01 2 0.000 0.944 0.00 1.00
#> TCGA.B6.A0WZ.01 1 0.000 1.000 1.00 0.00
#> TCGA.AC.A3YJ.01 1 0.000 1.000 1.00 0.00
#> TCGA.D8.A1Y1.01 2 0.904 0.567 0.32 0.68
#> TCGA.E9.A249.01 1 0.000 1.000 1.00 0.00
#> TCGA.LD.A7W6.01 1 0.000 1.000 1.00 0.00
#> TCGA.D8.A73W.01 1 0.000 1.000 1.00 0.00
#> TCGA.AC.A23E.01 1 0.000 1.000 1.00 0.00
#> TCGA.D8.A1JS.01 1 0.000 1.000 1.00 0.00
#> TCGA.B6.A408.01 2 0.971 0.413 0.40 0.60
#> TCGA.A7.A6VX.01 1 0.000 1.000 1.00 0.00
#> TCGA.E2.A1IG.01 2 0.000 0.944 0.00 1.00
#> TCGA.E9.A1NH.01 1 0.000 1.000 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.D8.A1XA.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.A2.A0SW.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.EW.A1P5.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.E9.A1N5.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.A2.A0YC.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.EW.A6S9.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.BH.A1FG.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.E2.A570.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.EW.A1P0.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.A2.A0YT.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.BH.A0B5.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.BH.A0B8.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.LL.A6FQ.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.A1.A0SQ.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.B6.A0RO.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.AC.A2BM.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.EW.A1J6.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.A2.A25C.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.3C.AALI.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.E9.A1NI.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.BH.A0HA.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.D8.A1XS.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.AN.A0XP.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.D8.A1XD.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.AR.A24M.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.E2.A572.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.BH.A1ES.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.EW.A1PE.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.A7.A2KD.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.S3.A6ZH.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.BH.A1EX.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.A2.A0CK.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.C8.A273.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.AR.A0U2.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.A2.A1FV.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.D8.A1XC.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.S3.AA11.01 3 0.207 0.911 0.00 0.06 0.94
#> TCGA.AQ.A54O.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.D8.A1JT.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.D8.A1X5.01 3 0.429 0.776 0.00 0.18 0.82
#> TCGA.BH.A0E1.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.E2.A106.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.E2.A56Z.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.A7.A0D9.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.BH.A204.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.D8.A1XL.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.OL.A5RZ.01 2 0.153 0.958 0.00 0.96 0.04
#> TCGA.A2.A0YF.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.C8.A1HM.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.BH.A1FM.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.AR.A2LE.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.AR.A24Z.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.JL.A3YX.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.BH.A0HN.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.AC.A62V.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.AO.A126.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.A7.A26J.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.A2.A25B.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.PL.A8LX.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.EW.A1J3.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.B6.A0WV.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.BH.A0HX.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.AR.A0TR.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.B6.A0RM.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.E2.A1IE.01 3 0.624 0.253 0.00 0.44 0.56
#> TCGA.EW.A1P3.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.E9.A22H.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.D8.A3Z6.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.A8.A08O.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.BH.A1F2.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.BH.A0HI.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.E2.A1L9.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.BH.A0W3.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.AO.A03N.01 1 0.254 0.908 0.92 0.00 0.08
#> TCGA.C8.A1HN.01 2 0.153 0.958 0.00 0.96 0.04
#> TCGA.BH.A0HB.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.A2.A1FX.01 3 0.571 0.549 0.00 0.32 0.68
#> TCGA.A7.A13G.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.AQ.A1H2.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.A2.A0EU.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.EW.A1J5.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.C8.A27A.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.C8.A1HK.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.B6.A0WZ.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.AC.A3YJ.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.D8.A1Y1.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.E9.A249.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.LD.A7W6.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.D8.A73W.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.AC.A23E.01 1 0.153 0.950 0.96 0.00 0.04
#> TCGA.D8.A1JS.01 1 0.000 0.986 1.00 0.00 0.00
#> TCGA.B6.A408.01 3 0.000 0.963 0.00 0.00 1.00
#> TCGA.A7.A6VX.01 1 0.613 0.351 0.60 0.00 0.40
#> TCGA.E2.A1IG.01 2 0.000 0.997 0.00 1.00 0.00
#> TCGA.E9.A1NH.01 1 0.000 0.986 1.00 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.D8.A1XA.01 2 0.0000 0.9648 0.00 1.00 0.00 0.00
#> TCGA.A2.A0SW.01 3 0.2921 0.8242 0.00 0.00 0.86 0.14
#> TCGA.EW.A1P5.01 1 0.0000 0.8553 1.00 0.00 0.00 0.00
#> TCGA.E9.A1N5.01 1 0.3975 0.6615 0.76 0.00 0.00 0.24
#> TCGA.A2.A0YC.01 3 0.4994 0.5273 0.00 0.00 0.52 0.48
#> TCGA.EW.A6S9.01 1 0.3975 0.6615 0.76 0.00 0.00 0.24
#> TCGA.BH.A1FG.01 1 0.0000 0.8553 1.00 0.00 0.00 0.00
#> TCGA.E2.A570.01 1 0.4713 0.4092 0.64 0.00 0.00 0.36
#> TCGA.EW.A1P0.01 3 0.2011 0.8237 0.00 0.00 0.92 0.08
#> TCGA.A2.A0YT.01 2 0.0000 0.9648 0.00 1.00 0.00 0.00
#> TCGA.BH.A0B5.01 3 0.2921 0.8263 0.00 0.00 0.86 0.14
#> TCGA.BH.A0B8.01 2 0.0000 0.9648 0.00 1.00 0.00 0.00
#> TCGA.LL.A6FQ.01 2 0.0000 0.9648 0.00 1.00 0.00 0.00
#> TCGA.A1.A0SQ.01 2 0.4994 0.1750 0.00 0.52 0.48 0.00
#> TCGA.B6.A0RO.01 3 0.2011 0.8237 0.00 0.00 0.92 0.08
#> TCGA.AC.A2BM.01 3 0.0000 0.7997 0.00 0.00 1.00 0.00
#> TCGA.EW.A1J6.01 3 0.2921 0.8263 0.00 0.00 0.86 0.14
#> TCGA.A2.A25C.01 1 0.0000 0.8553 1.00 0.00 0.00 0.00
#> TCGA.3C.AALI.01 2 0.0000 0.9648 0.00 1.00 0.00 0.00
#> TCGA.E9.A1NI.01 2 0.0000 0.9648 0.00 1.00 0.00 0.00
#> TCGA.BH.A0HA.01 1 0.0000 0.8553 1.00 0.00 0.00 0.00
#> TCGA.D8.A1XS.01 4 0.3172 0.6173 0.16 0.00 0.00 0.84
#> TCGA.AN.A0XP.01 3 0.4907 0.6009 0.00 0.00 0.58 0.42
#> TCGA.D8.A1XD.01 1 0.0000 0.8553 1.00 0.00 0.00 0.00
#> TCGA.AR.A24M.01 4 0.3975 0.5670 0.24 0.00 0.00 0.76
#> TCGA.E2.A572.01 3 0.2921 0.8263 0.00 0.00 0.86 0.14
#> TCGA.BH.A1ES.01 1 0.0000 0.8553 1.00 0.00 0.00 0.00
#> TCGA.EW.A1PE.01 1 0.4134 0.6335 0.74 0.00 0.00 0.26
#> TCGA.A7.A2KD.01 3 0.3172 0.8195 0.00 0.00 0.84 0.16
#> TCGA.S3.A6ZH.01 2 0.2011 0.9211 0.00 0.92 0.08 0.00
#> TCGA.BH.A1EX.01 3 0.3172 0.8195 0.00 0.00 0.84 0.16
#> TCGA.A2.A0CK.01 1 0.0000 0.8553 1.00 0.00 0.00 0.00
#> TCGA.C8.A273.01 3 0.4994 0.5273 0.00 0.00 0.52 0.48
#> TCGA.AR.A0U2.01 2 0.0000 0.9648 0.00 1.00 0.00 0.00
#> TCGA.A2.A1FV.01 2 0.0000 0.9648 0.00 1.00 0.00 0.00
#> TCGA.D8.A1XC.01 1 0.4134 0.6335 0.74 0.00 0.00 0.26
#> TCGA.S3.AA11.01 3 0.0000 0.7997 0.00 0.00 1.00 0.00
#> TCGA.AQ.A54O.01 1 0.3400 0.7234 0.82 0.00 0.00 0.18
#> TCGA.D8.A1JT.01 2 0.2011 0.9211 0.00 0.92 0.08 0.00
#> TCGA.D8.A1X5.01 3 0.0707 0.7907 0.00 0.02 0.98 0.00
#> TCGA.BH.A0E1.01 1 0.0000 0.8553 1.00 0.00 0.00 0.00
#> TCGA.E2.A106.01 3 0.0000 0.7997 0.00 0.00 1.00 0.00
#> TCGA.E2.A56Z.01 3 0.2011 0.8237 0.00 0.00 0.92 0.08
#> TCGA.A7.A0D9.01 4 0.4994 0.1238 0.48 0.00 0.00 0.52
#> TCGA.BH.A204.01 2 0.0000 0.9648 0.00 1.00 0.00 0.00
#> TCGA.D8.A1XL.01 1 0.0000 0.8553 1.00 0.00 0.00 0.00
#> TCGA.OL.A5RZ.01 3 0.3801 0.5655 0.00 0.22 0.78 0.00
#> TCGA.A2.A0YF.01 3 0.2921 0.8263 0.00 0.00 0.86 0.14
#> TCGA.C8.A1HM.01 2 0.2011 0.9211 0.00 0.92 0.08 0.00
#> TCGA.BH.A1FM.01 2 0.0000 0.9648 0.00 1.00 0.00 0.00
#> TCGA.AR.A2LE.01 4 0.0000 0.6213 0.00 0.00 0.00 1.00
#> TCGA.AR.A24Z.01 2 0.0000 0.9648 0.00 1.00 0.00 0.00
#> TCGA.JL.A3YX.01 4 0.4522 -0.0413 0.00 0.00 0.32 0.68
#> TCGA.BH.A0HN.01 4 0.2345 0.4971 0.00 0.00 0.10 0.90
#> TCGA.AC.A62V.01 2 0.0000 0.9648 0.00 1.00 0.00 0.00
#> TCGA.AO.A126.01 1 0.0000 0.8553 1.00 0.00 0.00 0.00
#> TCGA.A7.A26J.01 2 0.0000 0.9648 0.00 1.00 0.00 0.00
#> TCGA.A2.A25B.01 2 0.0000 0.9648 0.00 1.00 0.00 0.00
#> TCGA.PL.A8LX.01 1 0.4977 0.0505 0.54 0.00 0.00 0.46
#> TCGA.EW.A1J3.01 4 0.4994 0.1238 0.48 0.00 0.00 0.52
#> TCGA.B6.A0WV.01 2 0.0000 0.9648 0.00 1.00 0.00 0.00
#> TCGA.BH.A0HX.01 2 0.0000 0.9648 0.00 1.00 0.00 0.00
#> TCGA.AR.A0TR.01 4 0.4406 0.4941 0.30 0.00 0.00 0.70
#> TCGA.B6.A0RM.01 1 0.0000 0.8553 1.00 0.00 0.00 0.00
#> TCGA.E2.A1IE.01 3 0.0707 0.7907 0.00 0.02 0.98 0.00
#> TCGA.EW.A1P3.01 3 0.2921 0.8263 0.00 0.00 0.86 0.14
#> TCGA.E9.A22H.01 3 0.4994 0.5273 0.00 0.00 0.52 0.48
#> TCGA.D8.A3Z6.01 4 0.3975 0.2011 0.00 0.00 0.24 0.76
#> TCGA.A8.A08O.01 4 0.4522 -0.0413 0.00 0.00 0.32 0.68
#> TCGA.BH.A1F2.01 2 0.0000 0.9648 0.00 1.00 0.00 0.00
#> TCGA.BH.A0HI.01 1 0.0000 0.8553 1.00 0.00 0.00 0.00
#> TCGA.E2.A1L9.01 4 0.4994 0.1238 0.48 0.00 0.00 0.52
#> TCGA.BH.A0W3.01 1 0.4277 0.5982 0.72 0.00 0.00 0.28
#> TCGA.AO.A03N.01 4 0.0000 0.6213 0.00 0.00 0.00 1.00
#> TCGA.C8.A1HN.01 3 0.3400 0.6329 0.00 0.18 0.82 0.00
#> TCGA.BH.A0HB.01 4 0.3400 0.6084 0.18 0.00 0.00 0.82
#> TCGA.A2.A1FX.01 3 0.0707 0.7907 0.00 0.02 0.98 0.00
#> TCGA.A7.A13G.01 1 0.0000 0.8553 1.00 0.00 0.00 0.00
#> TCGA.AQ.A1H2.01 2 0.0000 0.9648 0.00 1.00 0.00 0.00
#> TCGA.A2.A0EU.01 4 0.4994 0.1238 0.48 0.00 0.00 0.52
#> TCGA.EW.A1J5.01 2 0.2011 0.9211 0.00 0.92 0.08 0.00
#> TCGA.C8.A27A.01 2 0.0000 0.9648 0.00 1.00 0.00 0.00
#> TCGA.C8.A1HK.01 3 0.2345 0.8260 0.00 0.00 0.90 0.10
#> TCGA.B6.A0WZ.01 4 0.1637 0.6405 0.06 0.00 0.00 0.94
#> TCGA.AC.A3YJ.01 4 0.4994 0.1238 0.48 0.00 0.00 0.52
#> TCGA.D8.A1Y1.01 3 0.4994 0.5273 0.00 0.00 0.52 0.48
#> TCGA.E9.A249.01 1 0.0000 0.8553 1.00 0.00 0.00 0.00
#> TCGA.LD.A7W6.01 4 0.3975 0.5670 0.24 0.00 0.00 0.76
#> TCGA.D8.A73W.01 4 0.2647 0.6313 0.12 0.00 0.00 0.88
#> TCGA.AC.A23E.01 4 0.0707 0.6381 0.02 0.00 0.00 0.98
#> TCGA.D8.A1JS.01 4 0.4977 0.1790 0.46 0.00 0.00 0.54
#> TCGA.B6.A408.01 3 0.4994 0.5273 0.00 0.00 0.52 0.48
#> TCGA.A7.A6VX.01 4 0.0000 0.6213 0.00 0.00 0.00 1.00
#> TCGA.E2.A1IG.01 2 0.2011 0.9211 0.00 0.92 0.08 0.00
#> TCGA.E9.A1NH.01 1 0.0000 0.8553 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.D8.A1XA.01 2 0.0000 0.9263 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A0SW.01 5 0.6691 -0.3835 0.00 0.00 0.36 0.24 0.40
#> TCGA.EW.A1P5.01 1 0.0000 0.9683 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1N5.01 4 0.4227 0.6921 0.42 0.00 0.00 0.58 0.00
#> TCGA.A2.A0YC.01 5 0.0609 0.7074 0.00 0.00 0.02 0.00 0.98
#> TCGA.EW.A6S9.01 4 0.4227 0.6921 0.42 0.00 0.00 0.58 0.00
#> TCGA.BH.A1FG.01 1 0.0000 0.9683 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A570.01 4 0.3895 0.7902 0.32 0.00 0.00 0.68 0.00
#> TCGA.EW.A1P0.01 3 0.3731 0.6289 0.00 0.00 0.80 0.04 0.16
#> TCGA.A2.A0YT.01 2 0.0000 0.9263 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0B5.01 3 0.4227 0.4212 0.00 0.00 0.58 0.00 0.42
#> TCGA.BH.A0B8.01 2 0.2012 0.8923 0.00 0.92 0.02 0.06 0.00
#> TCGA.LL.A6FQ.01 2 0.0000 0.9263 0.00 1.00 0.00 0.00 0.00
#> TCGA.A1.A0SQ.01 3 0.6691 0.0942 0.00 0.36 0.40 0.24 0.00
#> TCGA.B6.A0RO.01 3 0.2280 0.6561 0.00 0.00 0.88 0.00 0.12
#> TCGA.AC.A2BM.01 3 0.2012 0.6649 0.00 0.00 0.92 0.06 0.02
#> TCGA.EW.A1J6.01 3 0.4262 0.3910 0.00 0.00 0.56 0.00 0.44
#> TCGA.A2.A25C.01 1 0.3424 0.4907 0.76 0.00 0.00 0.24 0.00
#> TCGA.3C.AALI.01 2 0.0000 0.9263 0.00 1.00 0.00 0.00 0.00
#> TCGA.E9.A1NI.01 2 0.0000 0.9263 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0HA.01 1 0.0000 0.9683 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1XS.01 4 0.4644 0.5806 0.04 0.00 0.00 0.68 0.28
#> TCGA.AN.A0XP.01 5 0.2732 0.5498 0.00 0.00 0.16 0.00 0.84
#> TCGA.D8.A1XD.01 1 0.1410 0.8898 0.94 0.00 0.00 0.06 0.00
#> TCGA.AR.A24M.01 4 0.5130 0.6698 0.10 0.00 0.00 0.68 0.22
#> TCGA.E2.A572.01 3 0.5646 0.4269 0.00 0.00 0.52 0.08 0.40
#> TCGA.BH.A1ES.01 1 0.0000 0.9683 1.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1PE.01 4 0.4182 0.7195 0.40 0.00 0.00 0.60 0.00
#> TCGA.A7.A2KD.01 3 0.6548 0.4237 0.00 0.00 0.42 0.20 0.38
#> TCGA.S3.A6ZH.01 2 0.4263 0.7856 0.00 0.76 0.06 0.18 0.00
#> TCGA.BH.A1EX.01 5 0.5457 -0.3623 0.00 0.00 0.46 0.06 0.48
#> TCGA.A2.A0CK.01 1 0.0000 0.9683 1.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A273.01 5 0.0609 0.7074 0.00 0.00 0.02 0.00 0.98
#> TCGA.AR.A0U2.01 2 0.0000 0.9263 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A1FV.01 2 0.0000 0.9263 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A1XC.01 4 0.4227 0.6921 0.42 0.00 0.00 0.58 0.00
#> TCGA.S3.AA11.01 3 0.2012 0.6649 0.00 0.00 0.92 0.06 0.02
#> TCGA.AQ.A54O.01 4 0.4302 0.5640 0.48 0.00 0.00 0.52 0.00
#> TCGA.D8.A1JT.01 2 0.5013 0.6978 0.00 0.68 0.08 0.24 0.00
#> TCGA.D8.A1X5.01 3 0.3561 0.6224 0.00 0.00 0.74 0.26 0.00
#> TCGA.BH.A0E1.01 1 0.0000 0.9683 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A106.01 3 0.1043 0.6705 0.00 0.00 0.96 0.00 0.04
#> TCGA.E2.A56Z.01 3 0.1410 0.6682 0.00 0.00 0.94 0.00 0.06
#> TCGA.A7.A0D9.01 4 0.4644 0.7834 0.28 0.00 0.00 0.68 0.04
#> TCGA.BH.A204.01 2 0.0000 0.9263 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A1XL.01 1 0.0000 0.9683 1.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5RZ.01 3 0.4252 0.6065 0.00 0.02 0.70 0.28 0.00
#> TCGA.A2.A0YF.01 3 0.5607 0.4495 0.00 0.00 0.54 0.08 0.38
#> TCGA.C8.A1HM.01 2 0.4263 0.7856 0.00 0.76 0.06 0.18 0.00
#> TCGA.BH.A1FM.01 2 0.0000 0.9263 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A2LE.01 5 0.3424 0.5511 0.00 0.00 0.00 0.24 0.76
#> TCGA.AR.A24Z.01 2 0.0000 0.9263 0.00 1.00 0.00 0.00 0.00
#> TCGA.JL.A3YX.01 5 0.0609 0.7074 0.00 0.00 0.02 0.00 0.98
#> TCGA.BH.A0HN.01 5 0.1043 0.6959 0.00 0.00 0.00 0.04 0.96
#> TCGA.AC.A62V.01 2 0.0000 0.9263 0.00 1.00 0.00 0.00 0.00
#> TCGA.AO.A126.01 1 0.0000 0.9683 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A26J.01 2 0.0000 0.9263 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A25B.01 2 0.0000 0.9263 0.00 1.00 0.00 0.00 0.00
#> TCGA.PL.A8LX.01 4 0.3895 0.7902 0.32 0.00 0.00 0.68 0.00
#> TCGA.EW.A1J3.01 4 0.3895 0.7902 0.32 0.00 0.00 0.68 0.00
#> TCGA.B6.A0WV.01 2 0.0000 0.9263 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0HX.01 2 0.0000 0.9263 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A0TR.01 4 0.5258 0.7468 0.18 0.00 0.00 0.68 0.14
#> TCGA.B6.A0RM.01 1 0.0000 0.9683 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1IE.01 3 0.2929 0.6368 0.00 0.00 0.82 0.18 0.00
#> TCGA.EW.A1P3.01 3 0.4262 0.3910 0.00 0.00 0.56 0.00 0.44
#> TCGA.E9.A22H.01 5 0.2280 0.6046 0.00 0.00 0.12 0.00 0.88
#> TCGA.D8.A3Z6.01 5 0.0609 0.7034 0.00 0.00 0.00 0.02 0.98
#> TCGA.A8.A08O.01 5 0.0609 0.7074 0.00 0.00 0.02 0.00 0.98
#> TCGA.BH.A1F2.01 2 0.3319 0.8315 0.00 0.82 0.02 0.16 0.00
#> TCGA.BH.A0HI.01 1 0.0000 0.9683 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1L9.01 4 0.3895 0.7902 0.32 0.00 0.00 0.68 0.00
#> TCGA.BH.A0W3.01 4 0.4126 0.7417 0.38 0.00 0.00 0.62 0.00
#> TCGA.AO.A03N.01 5 0.4227 0.1894 0.00 0.00 0.00 0.42 0.58
#> TCGA.C8.A1HN.01 3 0.2929 0.6368 0.00 0.00 0.82 0.18 0.00
#> TCGA.BH.A0HB.01 4 0.4644 0.5806 0.04 0.00 0.00 0.68 0.28
#> TCGA.A2.A1FX.01 3 0.3561 0.6224 0.00 0.00 0.74 0.26 0.00
#> TCGA.A7.A13G.01 1 0.0000 0.9683 1.00 0.00 0.00 0.00 0.00
#> TCGA.AQ.A1H2.01 2 0.2331 0.8821 0.00 0.90 0.02 0.08 0.00
#> TCGA.A2.A0EU.01 4 0.3895 0.7902 0.32 0.00 0.00 0.68 0.00
#> TCGA.EW.A1J5.01 2 0.4263 0.7856 0.00 0.76 0.06 0.18 0.00
#> TCGA.C8.A27A.01 2 0.0000 0.9263 0.00 1.00 0.00 0.00 0.00
#> TCGA.C8.A1HK.01 3 0.5263 0.5829 0.00 0.00 0.66 0.10 0.24
#> TCGA.B6.A0WZ.01 4 0.3983 0.4477 0.00 0.00 0.00 0.66 0.34
#> TCGA.AC.A3YJ.01 4 0.3895 0.7902 0.32 0.00 0.00 0.68 0.00
#> TCGA.D8.A1Y1.01 5 0.0609 0.7074 0.00 0.00 0.02 0.00 0.98
#> TCGA.E9.A249.01 1 0.0000 0.9683 1.00 0.00 0.00 0.00 0.00
#> TCGA.LD.A7W6.01 4 0.5130 0.6698 0.10 0.00 0.00 0.68 0.22
#> TCGA.D8.A73W.01 4 0.4644 0.5806 0.04 0.00 0.00 0.68 0.28
#> TCGA.AC.A23E.01 5 0.4227 0.1894 0.00 0.00 0.00 0.42 0.58
#> TCGA.D8.A1JS.01 4 0.4456 0.7830 0.32 0.00 0.00 0.66 0.02
#> TCGA.B6.A408.01 5 0.0609 0.7074 0.00 0.00 0.02 0.00 0.98
#> TCGA.A7.A6VX.01 5 0.4227 0.1894 0.00 0.00 0.00 0.42 0.58
#> TCGA.E2.A1IG.01 2 0.5484 0.6370 0.00 0.64 0.12 0.24 0.00
#> TCGA.E9.A1NH.01 1 0.0000 0.9683 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.D8.A1XA.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0SW.01 5 0.4938 0.441 0.00 0.00 0.08 0.00 0.58 0.34
#> TCGA.EW.A1P5.01 1 0.1480 0.935 0.94 0.00 0.00 0.04 0.00 0.02
#> TCGA.E9.A1N5.01 4 0.3318 0.821 0.14 0.00 0.02 0.82 0.00 0.02
#> TCGA.A2.A0YC.01 5 0.2094 0.800 0.00 0.00 0.00 0.08 0.90 0.02
#> TCGA.EW.A6S9.01 4 0.3163 0.826 0.14 0.00 0.00 0.82 0.00 0.04
#> TCGA.BH.A1FG.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A570.01 4 0.2474 0.855 0.08 0.00 0.00 0.88 0.00 0.04
#> TCGA.EW.A1P0.01 3 0.3950 0.647 0.00 0.00 0.72 0.00 0.24 0.04
#> TCGA.A2.A0YT.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0B5.01 5 0.2581 0.755 0.00 0.00 0.12 0.00 0.86 0.02
#> TCGA.BH.A0B8.01 2 0.4609 -0.184 0.00 0.54 0.04 0.00 0.00 0.42
#> TCGA.LL.A6FQ.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A1.A0SQ.01 6 0.5027 0.629 0.00 0.20 0.16 0.00 0.00 0.64
#> TCGA.B6.A0RO.01 3 0.5195 0.339 0.00 0.00 0.54 0.00 0.36 0.10
#> TCGA.AC.A2BM.01 3 0.2728 0.756 0.00 0.00 0.86 0.00 0.04 0.10
#> TCGA.EW.A1J6.01 5 0.3270 0.749 0.00 0.00 0.12 0.00 0.82 0.06
#> TCGA.A2.A25C.01 1 0.4195 0.706 0.74 0.00 0.04 0.20 0.00 0.02
#> TCGA.3C.AALI.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1NI.01 2 0.0547 0.862 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.BH.A0HA.01 1 0.1480 0.935 0.94 0.00 0.00 0.04 0.00 0.02
#> TCGA.D8.A1XS.01 4 0.2350 0.806 0.00 0.00 0.02 0.88 0.00 0.10
#> TCGA.AN.A0XP.01 5 0.2784 0.790 0.00 0.00 0.04 0.04 0.88 0.04
#> TCGA.D8.A1XD.01 1 0.2094 0.899 0.90 0.00 0.00 0.08 0.00 0.02
#> TCGA.AR.A24M.01 4 0.1092 0.838 0.00 0.00 0.02 0.96 0.00 0.02
#> TCGA.E2.A572.01 5 0.3321 0.711 0.00 0.00 0.10 0.00 0.82 0.08
#> TCGA.BH.A1ES.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1PE.01 4 0.3163 0.818 0.14 0.00 0.04 0.82 0.00 0.00
#> TCGA.A7.A2KD.01 5 0.4475 0.616 0.00 0.00 0.10 0.00 0.70 0.20
#> TCGA.S3.A6ZH.01 6 0.4282 0.488 0.00 0.42 0.02 0.00 0.00 0.56
#> TCGA.BH.A1EX.01 5 0.2474 0.765 0.00 0.00 0.04 0.00 0.88 0.08
#> TCGA.A2.A0CK.01 1 0.1480 0.935 0.94 0.00 0.00 0.04 0.00 0.02
#> TCGA.C8.A273.01 5 0.2094 0.800 0.00 0.00 0.00 0.08 0.90 0.02
#> TCGA.AR.A0U2.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A1FV.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1XC.01 4 0.2790 0.826 0.14 0.00 0.02 0.84 0.00 0.00
#> TCGA.S3.AA11.01 3 0.1814 0.738 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.AQ.A54O.01 4 0.4460 0.691 0.24 0.00 0.04 0.70 0.00 0.02
#> TCGA.D8.A1JT.01 6 0.4078 0.594 0.00 0.34 0.02 0.00 0.00 0.64
#> TCGA.D8.A1X5.01 6 0.4631 0.272 0.00 0.00 0.32 0.00 0.06 0.62
#> TCGA.BH.A0E1.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A106.01 3 0.3787 0.747 0.00 0.00 0.78 0.00 0.12 0.10
#> TCGA.E2.A56Z.01 3 0.3660 0.733 0.00 0.00 0.78 0.00 0.16 0.06
#> TCGA.A7.A0D9.01 4 0.4066 0.843 0.08 0.00 0.02 0.78 0.00 0.12
#> TCGA.BH.A204.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1XL.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5RZ.01 6 0.4962 0.324 0.00 0.02 0.28 0.00 0.06 0.64
#> TCGA.A2.A0YF.01 5 0.4377 0.623 0.00 0.00 0.12 0.00 0.72 0.16
#> TCGA.C8.A1HM.01 6 0.4328 0.392 0.00 0.46 0.02 0.00 0.00 0.52
#> TCGA.BH.A1FM.01 2 0.0547 0.863 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AR.A2LE.01 4 0.5672 0.244 0.00 0.00 0.02 0.52 0.36 0.10
#> TCGA.AR.A24Z.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.JL.A3YX.01 5 0.3324 0.792 0.00 0.00 0.02 0.08 0.84 0.06
#> TCGA.BH.A0HN.01 5 0.4306 0.685 0.00 0.00 0.02 0.12 0.76 0.10
#> TCGA.AC.A62V.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A126.01 1 0.1092 0.943 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.A7.A26J.01 2 0.2581 0.720 0.00 0.86 0.02 0.00 0.00 0.12
#> TCGA.A2.A25B.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.PL.A8LX.01 4 0.2474 0.851 0.08 0.00 0.04 0.88 0.00 0.00
#> TCGA.EW.A1J3.01 4 0.2474 0.855 0.08 0.00 0.00 0.88 0.00 0.04
#> TCGA.B6.A0WV.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0HX.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A0TR.01 4 0.3420 0.845 0.06 0.00 0.04 0.84 0.00 0.06
#> TCGA.B6.A0RM.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1IE.01 3 0.2454 0.705 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.EW.A1P3.01 5 0.2474 0.771 0.00 0.00 0.08 0.00 0.88 0.04
#> TCGA.E9.A22H.01 5 0.1807 0.803 0.00 0.00 0.02 0.06 0.92 0.00
#> TCGA.D8.A3Z6.01 5 0.3324 0.765 0.00 0.00 0.02 0.08 0.84 0.06
#> TCGA.A8.A08O.01 5 0.3324 0.765 0.00 0.00 0.02 0.08 0.84 0.06
#> TCGA.BH.A1F2.01 2 0.4310 -0.201 0.00 0.54 0.02 0.00 0.00 0.44
#> TCGA.BH.A0HI.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1L9.01 4 0.2094 0.853 0.08 0.00 0.02 0.90 0.00 0.00
#> TCGA.BH.A0W3.01 4 0.2728 0.850 0.10 0.00 0.00 0.86 0.00 0.04
#> TCGA.AO.A03N.01 4 0.4066 0.742 0.00 0.00 0.02 0.78 0.08 0.12
#> TCGA.C8.A1HN.01 3 0.2454 0.705 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.BH.A0HB.01 4 0.2581 0.808 0.00 0.00 0.02 0.86 0.00 0.12
#> TCGA.A2.A1FX.01 6 0.3916 0.330 0.00 0.00 0.30 0.00 0.02 0.68
#> TCGA.A7.A13G.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AQ.A1H2.01 2 0.3828 -0.127 0.00 0.56 0.00 0.00 0.00 0.44
#> TCGA.A2.A0EU.01 4 0.2474 0.855 0.08 0.00 0.00 0.88 0.00 0.04
#> TCGA.EW.A1J5.01 6 0.4609 0.487 0.00 0.42 0.04 0.00 0.00 0.54
#> TCGA.C8.A27A.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A1HK.01 5 0.4475 0.618 0.00 0.00 0.10 0.00 0.70 0.20
#> TCGA.B6.A0WZ.01 4 0.3258 0.787 0.00 0.00 0.02 0.84 0.04 0.10
#> TCGA.AC.A3YJ.01 4 0.2474 0.851 0.08 0.00 0.04 0.88 0.00 0.00
#> TCGA.D8.A1Y1.01 5 0.2094 0.800 0.00 0.00 0.00 0.08 0.90 0.02
#> TCGA.E9.A249.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LD.A7W6.01 4 0.1092 0.838 0.00 0.00 0.02 0.96 0.00 0.02
#> TCGA.D8.A73W.01 4 0.1865 0.826 0.00 0.00 0.04 0.92 0.00 0.04
#> TCGA.AC.A23E.01 4 0.4066 0.742 0.00 0.00 0.02 0.78 0.08 0.12
#> TCGA.D8.A1JS.01 4 0.2345 0.855 0.06 0.00 0.02 0.90 0.00 0.02
#> TCGA.B6.A408.01 5 0.2474 0.801 0.00 0.00 0.00 0.08 0.88 0.04
#> TCGA.A7.A6VX.01 4 0.4066 0.742 0.00 0.00 0.02 0.78 0.08 0.12
#> TCGA.E2.A1IG.01 6 0.4834 0.656 0.00 0.26 0.10 0.00 0.00 0.64
#> TCGA.E9.A1NH.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.D8.A1XA.01 2 0.0000 0.9336 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0SW.01 5 0.5931 0.1774 0.00 0.00 0.12 0.00 0.42 0.40 0.06
#> TCGA.EW.A1P5.01 1 0.2832 0.7835 0.76 0.00 0.00 0.24 0.00 0.00 0.00
#> TCGA.E9.A1N5.01 4 0.0000 0.6663 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A0YC.01 5 0.0863 0.6857 0.00 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.EW.A6S9.01 4 0.0504 0.6623 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.BH.A1FG.01 1 0.0000 0.8901 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A570.01 4 0.0504 0.6623 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EW.A1P0.01 3 0.5091 0.5687 0.00 0.00 0.66 0.00 0.12 0.06 0.16
#> TCGA.A2.A0YT.01 2 0.0000 0.9336 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0B5.01 5 0.2376 0.6406 0.00 0.00 0.12 0.00 0.86 0.00 0.02
#> TCGA.BH.A0B8.01 2 0.4278 -0.4328 0.00 0.50 0.00 0.00 0.00 0.46 0.04
#> TCGA.LL.A6FQ.01 2 0.0000 0.9336 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A1.A0SQ.01 6 0.4340 0.5992 0.00 0.14 0.12 0.00 0.00 0.72 0.02
#> TCGA.B6.A0RO.01 3 0.5853 0.1702 0.00 0.00 0.48 0.00 0.32 0.04 0.16
#> TCGA.AC.A2BM.01 3 0.0000 0.8104 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1J6.01 5 0.5509 0.5031 0.00 0.00 0.08 0.00 0.60 0.10 0.22
#> TCGA.A2.A25C.01 4 0.4923 -0.1914 0.42 0.00 0.00 0.50 0.00 0.02 0.06
#> TCGA.3C.AALI.01 2 0.0000 0.9336 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1NI.01 2 0.0000 0.9336 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0HA.01 1 0.2832 0.7835 0.76 0.00 0.00 0.24 0.00 0.00 0.00
#> TCGA.D8.A1XS.01 4 0.3815 -0.1037 0.00 0.00 0.00 0.62 0.00 0.02 0.36
#> TCGA.AN.A0XP.01 5 0.4016 0.6109 0.00 0.00 0.04 0.00 0.76 0.06 0.14
#> TCGA.D8.A1XD.01 1 0.3685 0.6589 0.66 0.00 0.00 0.32 0.00 0.00 0.02
#> TCGA.AR.A24M.01 4 0.2912 0.5677 0.00 0.00 0.00 0.82 0.00 0.04 0.14
#> TCGA.E2.A572.01 5 0.4422 0.5673 0.00 0.00 0.16 0.00 0.72 0.04 0.08
#> TCGA.BH.A1ES.01 1 0.0000 0.8901 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1PE.01 4 0.1166 0.6597 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.A7.A2KD.01 5 0.6385 0.3187 0.00 0.00 0.16 0.00 0.48 0.24 0.12
#> TCGA.S3.A6ZH.01 6 0.3909 0.5646 0.00 0.40 0.00 0.00 0.00 0.58 0.02
#> TCGA.BH.A1EX.01 5 0.3011 0.6248 0.00 0.00 0.12 0.00 0.82 0.00 0.06
#> TCGA.A2.A0CK.01 1 0.2832 0.7835 0.76 0.00 0.00 0.24 0.00 0.00 0.00
#> TCGA.C8.A273.01 5 0.1166 0.6810 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.AR.A0U2.01 2 0.0000 0.9336 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A1FV.01 2 0.0000 0.9336 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1XC.01 4 0.1363 0.6672 0.00 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.S3.AA11.01 3 0.0504 0.8075 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.AQ.A54O.01 4 0.2804 0.5703 0.06 0.00 0.00 0.86 0.00 0.02 0.06
#> TCGA.D8.A1JT.01 6 0.3417 0.6457 0.00 0.26 0.00 0.00 0.00 0.72 0.02
#> TCGA.D8.A1X5.01 6 0.4538 0.2735 0.00 0.00 0.28 0.00 0.00 0.62 0.10
#> TCGA.BH.A0E1.01 1 0.0000 0.8901 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A106.01 3 0.2016 0.7991 0.00 0.00 0.90 0.00 0.00 0.04 0.06
#> TCGA.E2.A56Z.01 3 0.2016 0.7991 0.00 0.00 0.90 0.00 0.00 0.04 0.06
#> TCGA.A7.A0D9.01 4 0.3526 0.5317 0.00 0.00 0.00 0.76 0.00 0.06 0.18
#> TCGA.BH.A204.01 2 0.0000 0.9336 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1XL.01 1 0.0000 0.8901 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5RZ.01 6 0.4698 0.2240 0.00 0.00 0.24 0.00 0.00 0.62 0.14
#> TCGA.A2.A0YF.01 5 0.6661 0.2626 0.00 0.00 0.18 0.00 0.44 0.22 0.16
#> TCGA.C8.A1HM.01 6 0.3496 0.5447 0.00 0.42 0.00 0.00 0.00 0.58 0.00
#> TCGA.BH.A1FM.01 2 0.1928 0.8190 0.00 0.90 0.00 0.00 0.00 0.08 0.02
#> TCGA.AR.A2LE.01 5 0.5438 -0.2059 0.00 0.00 0.00 0.12 0.44 0.02 0.42
#> TCGA.AR.A24Z.01 2 0.0000 0.9336 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.JL.A3YX.01 5 0.4377 0.5870 0.00 0.00 0.02 0.00 0.68 0.06 0.24
#> TCGA.BH.A0HN.01 5 0.3139 0.5225 0.00 0.00 0.00 0.00 0.70 0.00 0.30
#> TCGA.AC.A62V.01 2 0.0000 0.9336 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A126.01 1 0.2422 0.8166 0.82 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.A7.A26J.01 2 0.2259 0.7154 0.00 0.84 0.00 0.00 0.00 0.16 0.00
#> TCGA.A2.A25B.01 2 0.0000 0.9336 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PL.A8LX.01 4 0.1928 0.6389 0.00 0.00 0.00 0.90 0.00 0.02 0.08
#> TCGA.EW.A1J3.01 4 0.1928 0.6362 0.00 0.00 0.00 0.90 0.00 0.02 0.08
#> TCGA.B6.A0WV.01 2 0.0000 0.9336 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0HX.01 2 0.0000 0.9336 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A0TR.01 4 0.4243 0.4748 0.00 0.00 0.00 0.68 0.00 0.10 0.22
#> TCGA.B6.A0RM.01 1 0.0000 0.8901 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1IE.01 3 0.1433 0.7702 0.00 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.EW.A1P3.01 5 0.4536 0.5902 0.00 0.00 0.08 0.00 0.72 0.06 0.14
#> TCGA.E9.A22H.01 5 0.0000 0.6858 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D8.A3Z6.01 5 0.2572 0.6209 0.00 0.00 0.00 0.00 0.80 0.00 0.20
#> TCGA.A8.A08O.01 5 0.2572 0.6209 0.00 0.00 0.00 0.00 0.80 0.00 0.20
#> TCGA.BH.A1F2.01 6 0.3525 0.5080 0.00 0.44 0.00 0.00 0.00 0.56 0.00
#> TCGA.BH.A0HI.01 1 0.0000 0.8901 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1L9.01 4 0.0504 0.6686 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.BH.A0W3.01 4 0.1006 0.6648 0.00 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.AO.A03N.01 7 0.5016 1.0000 0.00 0.00 0.00 0.42 0.12 0.00 0.46
#> TCGA.C8.A1HN.01 3 0.1886 0.7601 0.00 0.00 0.88 0.00 0.00 0.12 0.00
#> TCGA.BH.A0HB.01 4 0.3755 -0.0741 0.00 0.00 0.00 0.64 0.00 0.02 0.34
#> TCGA.A2.A1FX.01 6 0.4353 0.3197 0.00 0.00 0.24 0.00 0.00 0.66 0.10
#> TCGA.A7.A13G.01 1 0.0000 0.8901 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AQ.A1H2.01 6 0.3994 0.4060 0.00 0.48 0.00 0.00 0.00 0.50 0.02
#> TCGA.A2.A0EU.01 4 0.2906 0.5219 0.00 0.00 0.00 0.80 0.00 0.02 0.18
#> TCGA.EW.A1J5.01 6 0.3496 0.5447 0.00 0.42 0.00 0.00 0.00 0.58 0.00
#> TCGA.C8.A27A.01 2 0.0000 0.9336 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A1HK.01 5 0.6846 0.2066 0.00 0.00 0.20 0.00 0.40 0.20 0.20
#> TCGA.B6.A0WZ.01 4 0.4505 -0.7460 0.00 0.00 0.00 0.50 0.06 0.00 0.44
#> TCGA.AC.A3YJ.01 4 0.2278 0.6396 0.00 0.00 0.00 0.88 0.00 0.04 0.08
#> TCGA.D8.A1Y1.01 5 0.0863 0.6857 0.00 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.E9.A249.01 1 0.0000 0.8901 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LD.A7W6.01 4 0.2912 0.5677 0.00 0.00 0.00 0.82 0.00 0.04 0.14
#> TCGA.D8.A73W.01 4 0.3637 0.3239 0.00 0.00 0.00 0.72 0.00 0.04 0.24
#> TCGA.AC.A23E.01 7 0.5016 1.0000 0.00 0.00 0.00 0.42 0.12 0.00 0.46
#> TCGA.D8.A1JS.01 4 0.3526 0.5477 0.00 0.00 0.00 0.76 0.00 0.06 0.18
#> TCGA.B6.A408.01 5 0.0504 0.6866 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.A7.A6VX.01 7 0.5016 1.0000 0.00 0.00 0.00 0.42 0.12 0.00 0.46
#> TCGA.E2.A1IG.01 6 0.4242 0.6365 0.00 0.18 0.08 0.00 0.00 0.72 0.02
#> TCGA.E9.A1NH.01 1 0.0000 0.8901 1.00 0.00 0.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.D8.A1XA.01 2 0.0000 0.9529 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0SW.01 5 0.7014 -0.4604 0.00 0.00 0.10 0.00 0.34 0.26 0.06 0.24
#> TCGA.EW.A1P5.01 1 0.2719 0.7940 0.80 0.00 0.00 0.18 0.00 0.02 0.00 0.00
#> TCGA.E9.A1N5.01 4 0.1408 0.6691 0.02 0.00 0.00 0.94 0.00 0.02 0.02 0.00
#> TCGA.A2.A0YC.01 5 0.0000 0.4933 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EW.A6S9.01 4 0.2484 0.6355 0.02 0.00 0.00 0.86 0.00 0.02 0.10 0.00
#> TCGA.BH.A1FG.01 1 0.0000 0.8843 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A570.01 4 0.2025 0.6367 0.00 0.00 0.00 0.88 0.00 0.02 0.10 0.00
#> TCGA.EW.A1P0.01 3 0.4559 0.3464 0.00 0.00 0.60 0.00 0.08 0.00 0.02 0.30
#> TCGA.A2.A0YT.01 2 0.0000 0.9529 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0B5.01 5 0.4069 0.2146 0.00 0.00 0.18 0.00 0.68 0.00 0.00 0.14
#> TCGA.BH.A0B8.01 6 0.4340 0.4854 0.00 0.38 0.00 0.00 0.00 0.54 0.08 0.00
#> TCGA.LL.A6FQ.01 2 0.0000 0.9529 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A1.A0SQ.01 6 0.4880 0.6053 0.00 0.10 0.06 0.00 0.02 0.68 0.14 0.00
#> TCGA.B6.A0RO.01 3 0.6080 -0.3121 0.00 0.00 0.38 0.00 0.20 0.02 0.04 0.36
#> TCGA.AC.A2BM.01 3 0.0471 0.6744 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.EW.A1J6.01 5 0.5273 0.0688 0.00 0.00 0.06 0.00 0.44 0.00 0.08 0.42
#> TCGA.A2.A25C.01 4 0.5465 0.3144 0.26 0.00 0.00 0.56 0.00 0.02 0.12 0.04
#> TCGA.3C.AALI.01 2 0.0000 0.9529 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1NI.01 2 0.1341 0.8724 0.00 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.BH.A0HA.01 1 0.2856 0.7786 0.78 0.00 0.00 0.20 0.00 0.02 0.00 0.00
#> TCGA.D8.A1XS.01 4 0.3658 -0.0477 0.00 0.00 0.00 0.58 0.00 0.02 0.40 0.00
#> TCGA.AN.A0XP.01 5 0.3880 0.3406 0.00 0.00 0.02 0.00 0.64 0.00 0.02 0.32
#> TCGA.D8.A1XD.01 1 0.4325 0.4267 0.56 0.00 0.00 0.38 0.00 0.02 0.04 0.00
#> TCGA.AR.A24M.01 4 0.2725 0.5800 0.00 0.00 0.00 0.82 0.00 0.00 0.14 0.04
#> TCGA.E2.A572.01 5 0.5351 -0.1707 0.00 0.00 0.18 0.00 0.54 0.04 0.00 0.24
#> TCGA.BH.A1ES.01 1 0.0000 0.8843 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1PE.01 4 0.1557 0.6598 0.02 0.00 0.00 0.92 0.00 0.00 0.06 0.00
#> TCGA.A7.A2KD.01 5 0.6968 -0.4996 0.00 0.00 0.10 0.00 0.34 0.20 0.06 0.30
#> TCGA.S3.A6ZH.01 6 0.4504 0.6827 0.00 0.24 0.02 0.00 0.00 0.64 0.10 0.00
#> TCGA.BH.A1EX.01 5 0.4557 -0.0837 0.00 0.00 0.14 0.00 0.58 0.00 0.00 0.28
#> TCGA.A2.A0CK.01 1 0.2856 0.7786 0.78 0.00 0.00 0.20 0.00 0.02 0.00 0.00
#> TCGA.C8.A273.01 5 0.0471 0.4923 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.AR.A0U2.01 2 0.0000 0.9529 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A1FV.01 2 0.0000 0.9529 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1XC.01 4 0.0941 0.6734 0.02 0.00 0.00 0.96 0.00 0.02 0.00 0.00
#> TCGA.S3.AA11.01 3 0.0000 0.6711 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AQ.A54O.01 4 0.4034 0.5708 0.06 0.00 0.00 0.76 0.00 0.02 0.12 0.04
#> TCGA.D8.A1JT.01 6 0.4371 0.6520 0.00 0.16 0.02 0.00 0.00 0.68 0.14 0.00
#> TCGA.D8.A1X5.01 6 0.5155 0.2705 0.00 0.00 0.22 0.00 0.00 0.60 0.08 0.10
#> TCGA.BH.A0E1.01 1 0.0000 0.8843 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A106.01 3 0.3337 0.5790 0.00 0.00 0.78 0.00 0.00 0.02 0.04 0.16
#> TCGA.E2.A56Z.01 3 0.3337 0.5790 0.00 0.00 0.78 0.00 0.00 0.02 0.04 0.16
#> TCGA.A7.A0D9.01 4 0.4995 0.3682 0.00 0.00 0.00 0.52 0.00 0.04 0.36 0.08
#> TCGA.BH.A204.01 2 0.0000 0.9529 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1XL.01 1 0.0000 0.8843 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5RZ.01 6 0.6124 -0.0788 0.00 0.00 0.18 0.00 0.00 0.38 0.10 0.34
#> TCGA.A2.A0YF.01 5 0.6638 -0.5570 0.00 0.00 0.14 0.00 0.34 0.16 0.02 0.34
#> TCGA.C8.A1HM.01 6 0.2756 0.6868 0.00 0.26 0.00 0.00 0.00 0.74 0.00 0.00
#> TCGA.BH.A1FM.01 2 0.2623 0.7564 0.00 0.84 0.00 0.00 0.00 0.10 0.06 0.00
#> TCGA.AR.A2LE.01 5 0.4673 -0.1171 0.00 0.00 0.00 0.08 0.56 0.00 0.34 0.02
#> TCGA.AR.A24Z.01 2 0.0000 0.9529 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.JL.A3YX.01 5 0.4199 0.3551 0.00 0.00 0.00 0.00 0.60 0.00 0.08 0.32
#> TCGA.BH.A0HN.01 5 0.3095 0.4160 0.00 0.00 0.00 0.00 0.74 0.00 0.24 0.02
#> TCGA.AC.A62V.01 2 0.0000 0.9529 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A126.01 1 0.2569 0.8049 0.82 0.00 0.00 0.16 0.00 0.02 0.00 0.00
#> TCGA.A7.A26J.01 2 0.3015 0.4066 0.00 0.68 0.00 0.00 0.00 0.32 0.00 0.00
#> TCGA.A2.A25B.01 2 0.0000 0.9529 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.PL.A8LX.01 4 0.1341 0.6591 0.00 0.00 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.EW.A1J3.01 4 0.3170 0.5550 0.00 0.00 0.00 0.76 0.00 0.04 0.20 0.00
#> TCGA.B6.A0WV.01 2 0.0000 0.9529 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0HX.01 2 0.0000 0.9529 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A0TR.01 4 0.4165 0.4898 0.00 0.00 0.00 0.64 0.00 0.00 0.26 0.10
#> TCGA.B6.A0RM.01 1 0.0000 0.8843 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1IE.01 3 0.1765 0.6417 0.00 0.00 0.88 0.00 0.00 0.12 0.00 0.00
#> TCGA.EW.A1P3.01 5 0.4621 0.2793 0.00 0.00 0.08 0.00 0.58 0.00 0.02 0.32
#> TCGA.E9.A22H.01 5 0.0808 0.4928 0.00 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.D8.A3Z6.01 5 0.2267 0.4545 0.00 0.00 0.00 0.00 0.82 0.00 0.18 0.00
#> TCGA.A8.A08O.01 5 0.2719 0.4551 0.00 0.00 0.00 0.00 0.80 0.00 0.18 0.02
#> TCGA.BH.A1F2.01 6 0.2938 0.6503 0.00 0.30 0.00 0.00 0.00 0.70 0.00 0.00
#> TCGA.BH.A0HI.01 1 0.0000 0.8843 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1L9.01 4 0.0000 0.6742 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0W3.01 4 0.2591 0.6484 0.02 0.00 0.00 0.86 0.00 0.04 0.08 0.00
#> TCGA.AO.A03N.01 7 0.5073 0.8864 0.00 0.00 0.00 0.32 0.22 0.00 0.46 0.00
#> TCGA.C8.A1HN.01 3 0.2224 0.6280 0.00 0.00 0.86 0.00 0.00 0.12 0.00 0.02
#> TCGA.BH.A0HB.01 4 0.3193 0.1302 0.00 0.00 0.00 0.62 0.00 0.00 0.38 0.00
#> TCGA.A2.A1FX.01 6 0.4937 0.3251 0.00 0.00 0.18 0.00 0.00 0.64 0.10 0.08
#> TCGA.A7.A13G.01 1 0.0000 0.8843 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AQ.A1H2.01 6 0.4302 0.5583 0.00 0.36 0.00 0.00 0.00 0.56 0.08 0.00
#> TCGA.A2.A0EU.01 4 0.3293 0.5250 0.00 0.00 0.00 0.74 0.00 0.04 0.22 0.00
#> TCGA.EW.A1J5.01 6 0.2756 0.6868 0.00 0.26 0.00 0.00 0.00 0.74 0.00 0.00
#> TCGA.C8.A27A.01 2 0.0000 0.9529 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A1HK.01 8 0.5660 0.0000 0.00 0.00 0.10 0.00 0.22 0.04 0.06 0.58
#> TCGA.B6.A0WZ.01 7 0.4693 0.6663 0.00 0.00 0.00 0.42 0.12 0.00 0.46 0.00
#> TCGA.AC.A3YJ.01 4 0.2818 0.6167 0.00 0.00 0.00 0.82 0.00 0.00 0.12 0.06
#> TCGA.D8.A1Y1.01 5 0.1091 0.4667 0.00 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.E9.A249.01 1 0.0000 0.8843 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LD.A7W6.01 4 0.2569 0.5641 0.00 0.00 0.00 0.82 0.00 0.00 0.16 0.02
#> TCGA.D8.A73W.01 4 0.2719 0.5314 0.00 0.00 0.00 0.80 0.00 0.00 0.18 0.02
#> TCGA.AC.A23E.01 7 0.5073 0.8864 0.00 0.00 0.00 0.32 0.22 0.00 0.46 0.00
#> TCGA.D8.A1JS.01 4 0.3894 0.5584 0.00 0.00 0.00 0.76 0.00 0.08 0.10 0.06
#> TCGA.B6.A408.01 5 0.0808 0.4788 0.00 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.A7.A6VX.01 7 0.5116 0.8349 0.00 0.00 0.00 0.28 0.26 0.00 0.46 0.00
#> TCGA.E2.A1IG.01 6 0.4620 0.6283 0.00 0.12 0.06 0.00 0.00 0.68 0.14 0.00
#> TCGA.E9.A1NH.01 1 0.0000 0.8843 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node023. Child nodes: Node02121-leaf , Node02122-leaf , Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02214-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02321-leaf , Node02322-leaf , Node02421-leaf , Node02422-leaf , Node02423-leaf , Node04111-leaf , Node04112-leaf , Node04113 , Node04131-leaf , Node04132-leaf , Node04133-leaf , Node04221-leaf , Node04222-leaf , Node04331-leaf , Node04332-leaf , Node04333-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0232"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 27 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.971 0.985 0.4190 0.567 0.567
#> 3 3 0.883 0.828 0.941 0.4682 0.752 0.588
#> 4 4 0.770 0.860 0.893 0.1612 0.781 0.490
#> 5 5 0.797 0.850 0.861 0.1064 0.843 0.471
#> 6 6 0.827 0.824 0.904 0.0463 0.980 0.891
#> 7 7 0.937 0.812 0.918 0.0332 1.000 1.000
#> 8 8 0.917 0.801 0.890 0.0206 0.983 0.895
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.D8.A1XA.01 1 0.00 1.000 1.00 0.00
#> TCGA.A2.A0YT.01 1 0.00 1.000 1.00 0.00
#> TCGA.BH.A0B8.01 2 0.00 0.942 0.00 1.00
#> TCGA.LL.A6FQ.01 1 0.00 1.000 1.00 0.00
#> TCGA.A1.A0SQ.01 1 0.00 1.000 1.00 0.00
#> TCGA.3C.AALI.01 1 0.00 1.000 1.00 0.00
#> TCGA.E9.A1NI.01 1 0.00 1.000 1.00 0.00
#> TCGA.S3.A6ZH.01 1 0.00 1.000 1.00 0.00
#> TCGA.AR.A0U2.01 1 0.00 1.000 1.00 0.00
#> TCGA.A2.A1FV.01 2 0.00 0.942 0.00 1.00
#> TCGA.D8.A1JT.01 1 0.00 1.000 1.00 0.00
#> TCGA.BH.A204.01 2 0.00 0.942 0.00 1.00
#> TCGA.OL.A5RZ.01 1 0.00 1.000 1.00 0.00
#> TCGA.C8.A1HM.01 1 0.00 1.000 1.00 0.00
#> TCGA.BH.A1FM.01 1 0.00 1.000 1.00 0.00
#> TCGA.AR.A24Z.01 1 0.00 1.000 1.00 0.00
#> TCGA.AC.A62V.01 2 0.00 0.942 0.00 1.00
#> TCGA.A7.A26J.01 2 0.00 0.942 0.00 1.00
#> TCGA.A2.A25B.01 2 0.76 0.754 0.22 0.78
#> TCGA.B6.A0WV.01 1 0.00 1.000 1.00 0.00
#> TCGA.BH.A0HX.01 2 0.68 0.804 0.18 0.82
#> TCGA.BH.A1F2.01 1 0.00 1.000 1.00 0.00
#> TCGA.C8.A1HN.01 1 0.00 1.000 1.00 0.00
#> TCGA.AQ.A1H2.01 1 0.00 1.000 1.00 0.00
#> TCGA.EW.A1J5.01 1 0.00 1.000 1.00 0.00
#> TCGA.C8.A27A.01 2 0.00 0.942 0.00 1.00
#> TCGA.E2.A1IG.01 1 0.00 1.000 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.D8.A1XA.01 1 0.0892 0.918 0.98 0.00 0.02
#> TCGA.A2.A0YT.01 1 0.0892 0.918 0.98 0.00 0.02
#> TCGA.BH.A0B8.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.LL.A6FQ.01 1 0.6280 0.124 0.54 0.00 0.46
#> TCGA.A1.A0SQ.01 1 0.0000 0.912 1.00 0.00 0.00
#> TCGA.3C.AALI.01 3 0.0000 0.885 0.00 0.00 1.00
#> TCGA.E9.A1NI.01 1 0.6280 0.124 0.54 0.00 0.46
#> TCGA.S3.A6ZH.01 1 0.0000 0.912 1.00 0.00 0.00
#> TCGA.AR.A0U2.01 1 0.0892 0.918 0.98 0.00 0.02
#> TCGA.A2.A1FV.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.D8.A1JT.01 1 0.0892 0.918 0.98 0.00 0.02
#> TCGA.BH.A204.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.OL.A5RZ.01 1 0.0000 0.912 1.00 0.00 0.00
#> TCGA.C8.A1HM.01 1 0.0892 0.918 0.98 0.00 0.02
#> TCGA.BH.A1FM.01 1 0.0000 0.912 1.00 0.00 0.00
#> TCGA.AR.A24Z.01 1 0.0892 0.918 0.98 0.00 0.02
#> TCGA.AC.A62V.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.A7.A26J.01 3 0.0892 0.863 0.00 0.02 0.98
#> TCGA.A2.A25B.01 3 0.0000 0.885 0.00 0.00 1.00
#> TCGA.B6.A0WV.01 3 0.0000 0.885 0.00 0.00 1.00
#> TCGA.BH.A0HX.01 3 0.0000 0.885 0.00 0.00 1.00
#> TCGA.BH.A1F2.01 3 0.6302 -0.097 0.48 0.00 0.52
#> TCGA.C8.A1HN.01 1 0.0892 0.918 0.98 0.00 0.02
#> TCGA.AQ.A1H2.01 1 0.0000 0.912 1.00 0.00 0.00
#> TCGA.EW.A1J5.01 3 0.0000 0.885 0.00 0.00 1.00
#> TCGA.C8.A27A.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.E2.A1IG.01 1 0.0892 0.918 0.98 0.00 0.02
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.D8.A1XA.01 4 0.380 0.753 0.22 0.00 0.00 0.78
#> TCGA.A2.A0YT.01 4 0.491 0.467 0.42 0.00 0.00 0.58
#> TCGA.BH.A0B8.01 2 0.000 0.970 0.00 1.00 0.00 0.00
#> TCGA.LL.A6FQ.01 4 0.455 0.780 0.18 0.00 0.04 0.78
#> TCGA.A1.A0SQ.01 1 0.000 0.937 1.00 0.00 0.00 0.00
#> TCGA.3C.AALI.01 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.E9.A1NI.01 4 0.455 0.780 0.18 0.00 0.04 0.78
#> TCGA.S3.A6ZH.01 1 0.121 0.952 0.96 0.00 0.00 0.04
#> TCGA.AR.A0U2.01 1 0.164 0.929 0.94 0.00 0.00 0.06
#> TCGA.A2.A1FV.01 2 0.000 0.970 0.00 1.00 0.00 0.00
#> TCGA.D8.A1JT.01 1 0.201 0.912 0.92 0.00 0.00 0.08
#> TCGA.BH.A204.01 2 0.000 0.970 0.00 1.00 0.00 0.00
#> TCGA.OL.A5RZ.01 1 0.121 0.952 0.96 0.00 0.00 0.04
#> TCGA.C8.A1HM.01 4 0.491 0.467 0.42 0.00 0.00 0.58
#> TCGA.BH.A1FM.01 1 0.121 0.952 0.96 0.00 0.00 0.04
#> TCGA.AR.A24Z.01 1 0.201 0.941 0.92 0.00 0.00 0.08
#> TCGA.AC.A62V.01 2 0.000 0.970 0.00 1.00 0.00 0.00
#> TCGA.A7.A26J.01 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.A2.A25B.01 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.B6.A0WV.01 4 0.413 0.557 0.00 0.00 0.26 0.74
#> TCGA.BH.A0HX.01 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.BH.A1F2.01 4 0.484 0.759 0.14 0.00 0.08 0.78
#> TCGA.C8.A1HN.01 1 0.201 0.941 0.92 0.00 0.00 0.08
#> TCGA.AQ.A1H2.01 1 0.121 0.952 0.96 0.00 0.00 0.04
#> TCGA.EW.A1J5.01 4 0.441 0.491 0.00 0.00 0.30 0.70
#> TCGA.C8.A27A.01 2 0.317 0.873 0.00 0.84 0.00 0.16
#> TCGA.E2.A1IG.01 1 0.121 0.939 0.96 0.00 0.00 0.04
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.D8.A1XA.01 4 0.1043 0.970 0.04 0.00 0.00 0.96 0.00
#> TCGA.A2.A0YT.01 1 0.3796 0.588 0.70 0.00 0.00 0.30 0.00
#> TCGA.BH.A0B8.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00
#> TCGA.LL.A6FQ.01 4 0.1043 0.970 0.04 0.00 0.00 0.96 0.00
#> TCGA.A1.A0SQ.01 5 0.4182 0.938 0.40 0.00 0.00 0.00 0.60
#> TCGA.3C.AALI.01 3 0.2331 0.927 0.00 0.00 0.90 0.02 0.08
#> TCGA.E9.A1NI.01 4 0.1043 0.970 0.04 0.00 0.00 0.96 0.00
#> TCGA.S3.A6ZH.01 5 0.4262 0.984 0.44 0.00 0.00 0.00 0.56
#> TCGA.AR.A0U2.01 1 0.0000 0.642 1.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A1FV.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A1JT.01 1 0.3274 0.591 0.78 0.00 0.00 0.00 0.22
#> TCGA.BH.A204.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00
#> TCGA.OL.A5RZ.01 5 0.4262 0.984 0.44 0.00 0.00 0.00 0.56
#> TCGA.C8.A1HM.01 1 0.3796 0.588 0.70 0.00 0.00 0.30 0.00
#> TCGA.BH.A1FM.01 5 0.4262 0.984 0.44 0.00 0.00 0.00 0.56
#> TCGA.AR.A24Z.01 1 0.0609 0.630 0.98 0.00 0.00 0.00 0.02
#> TCGA.AC.A62V.01 2 0.0000 0.969 0.00 1.00 0.00 0.00 0.00
#> TCGA.A7.A26J.01 3 0.0000 0.976 0.00 0.00 1.00 0.00 0.00
#> TCGA.A2.A25B.01 3 0.0000 0.976 0.00 0.00 1.00 0.00 0.00
#> TCGA.B6.A0WV.01 4 0.1820 0.957 0.02 0.00 0.02 0.94 0.02
#> TCGA.BH.A0HX.01 3 0.0000 0.976 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A1F2.01 1 0.5048 0.383 0.58 0.00 0.00 0.38 0.04
#> TCGA.C8.A1HN.01 1 0.0609 0.630 0.98 0.00 0.00 0.00 0.02
#> TCGA.AQ.A1H2.01 5 0.4262 0.984 0.44 0.00 0.00 0.00 0.56
#> TCGA.EW.A1J5.01 4 0.1648 0.940 0.00 0.00 0.04 0.94 0.02
#> TCGA.C8.A27A.01 2 0.3106 0.870 0.00 0.84 0.00 0.02 0.14
#> TCGA.E2.A1IG.01 1 0.1410 0.626 0.94 0.00 0.00 0.00 0.06
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.D8.A1XA.01 4 0.0547 0.936 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.A2.A0YT.01 1 0.3045 0.710 0.84 0.00 0.00 0.10 0.06 0.00
#> TCGA.BH.A0B8.01 2 0.0547 0.937 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.LL.A6FQ.01 4 0.0547 0.936 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.A1.A0SQ.01 5 0.1480 0.924 0.02 0.00 0.00 0.00 0.94 0.04
#> TCGA.3C.AALI.01 3 0.2728 0.874 0.04 0.00 0.86 0.00 0.00 0.10
#> TCGA.E9.A1NI.01 4 0.0547 0.936 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.S3.A6ZH.01 5 0.0000 0.982 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AR.A0U2.01 1 0.2631 0.730 0.82 0.00 0.00 0.00 0.18 0.00
#> TCGA.A2.A1FV.01 2 0.0000 0.944 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JT.01 6 0.4798 0.000 0.30 0.00 0.00 0.00 0.08 0.62
#> TCGA.BH.A204.01 2 0.0000 0.944 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5RZ.01 5 0.0000 0.982 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.C8.A1HM.01 1 0.3045 0.710 0.84 0.00 0.00 0.10 0.06 0.00
#> TCGA.BH.A1FM.01 5 0.0000 0.982 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AR.A24Z.01 1 0.2793 0.725 0.80 0.00 0.00 0.00 0.20 0.00
#> TCGA.AC.A62V.01 2 0.0000 0.944 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A26J.01 3 0.0000 0.960 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A25B.01 3 0.0000 0.960 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B6.A0WV.01 4 0.2048 0.903 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.BH.A0HX.01 3 0.0000 0.960 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A1F2.01 1 0.2048 0.624 0.88 0.00 0.00 0.12 0.00 0.00
#> TCGA.C8.A1HN.01 1 0.2941 0.707 0.78 0.00 0.00 0.00 0.22 0.00
#> TCGA.AQ.A1H2.01 5 0.0000 0.982 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EW.A1J5.01 4 0.2048 0.903 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.C8.A27A.01 2 0.3928 0.770 0.08 0.76 0.00 0.00 0.00 0.16
#> TCGA.E2.A1IG.01 1 0.4758 0.273 0.58 0.00 0.00 0.00 0.36 0.06
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.D8.A1XA.01 7 0.0000 0.813 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.A2.A0YT.01 1 0.0000 0.888 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0B8.01 2 0.0863 0.893 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.LL.A6FQ.01 7 0.0000 0.813 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.A1.A0SQ.01 5 0.1928 0.885 0.00 0.00 0.00 0.02 0.90 0.08 0.00
#> TCGA.3C.AALI.01 3 0.3186 0.756 0.00 0.00 0.76 0.22 0.00 0.02 0.00
#> TCGA.E9.A1NI.01 7 0.0000 0.813 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.S3.A6ZH.01 5 0.0000 0.973 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AR.A0U2.01 1 0.0000 0.888 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A1FV.01 2 0.0000 0.908 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JT.01 6 0.2081 0.000 0.14 0.00 0.00 0.00 0.00 0.86 0.00
#> TCGA.BH.A204.01 2 0.0000 0.908 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5RZ.01 5 0.0000 0.973 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.C8.A1HM.01 1 0.0504 0.883 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.BH.A1FM.01 5 0.0000 0.973 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AR.A24Z.01 1 0.1433 0.854 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.AC.A62V.01 2 0.0000 0.908 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A26J.01 3 0.0504 0.912 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.A2.A25B.01 3 0.0000 0.920 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0WV.01 7 0.3358 0.699 0.00 0.00 0.00 0.36 0.00 0.00 0.64
#> TCGA.BH.A0HX.01 3 0.0000 0.920 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1F2.01 1 0.0504 0.883 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.C8.A1HN.01 1 0.0863 0.877 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.AQ.A1H2.01 5 0.0000 0.973 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EW.A1J5.01 7 0.3459 0.672 0.00 0.00 0.00 0.40 0.00 0.00 0.60
#> TCGA.C8.A27A.01 2 0.4338 0.602 0.00 0.64 0.00 0.28 0.00 0.08 0.00
#> TCGA.E2.A1IG.01 1 0.5652 0.345 0.60 0.00 0.00 0.10 0.18 0.12 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.D8.A1XA.01 7 0.3514 0.947 0.00 0.00 0.00 0.34 0.00 0.00 0.64 0.02
#> TCGA.A2.A0YT.01 1 0.0000 0.821 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0B8.01 2 0.1607 0.857 0.00 0.92 0.00 0.00 0.00 0.04 0.04 0.00
#> TCGA.LL.A6FQ.01 7 0.3142 0.974 0.00 0.00 0.00 0.36 0.00 0.00 0.64 0.00
#> TCGA.A1.A0SQ.01 5 0.3154 0.737 0.00 0.00 0.00 0.00 0.78 0.06 0.00 0.16
#> TCGA.3C.AALI.01 3 0.4614 0.518 0.00 0.00 0.58 0.00 0.00 0.00 0.16 0.26
#> TCGA.E9.A1NI.01 7 0.3142 0.974 0.00 0.00 0.00 0.36 0.00 0.00 0.64 0.00
#> TCGA.S3.A6ZH.01 5 0.0000 0.942 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A0U2.01 1 0.1275 0.803 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.A2.A1FV.01 2 0.0000 0.888 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JT.01 6 0.0808 0.000 0.04 0.00 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.BH.A204.01 2 0.0000 0.888 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5RZ.01 5 0.0000 0.942 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.C8.A1HM.01 1 0.0000 0.821 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FM.01 5 0.0000 0.942 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A24Z.01 1 0.2981 0.735 0.76 0.00 0.00 0.00 0.00 0.00 0.02 0.22
#> TCGA.AC.A62V.01 2 0.0000 0.888 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A26J.01 3 0.0000 0.866 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A25B.01 3 0.0000 0.866 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0WV.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0HX.01 3 0.0000 0.866 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1F2.01 1 0.0471 0.815 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.C8.A1HN.01 1 0.2114 0.780 0.84 0.00 0.00 0.00 0.00 0.00 0.00 0.16
#> TCGA.AQ.A1H2.01 5 0.0000 0.942 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EW.A1J5.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A27A.01 2 0.4199 0.547 0.00 0.60 0.00 0.00 0.00 0.00 0.08 0.32
#> TCGA.E2.A1IG.01 1 0.5594 0.276 0.42 0.00 0.00 0.00 0.10 0.08 0.00 0.40
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0115-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0151-leaf , Node0152-leaf , Node0153-leaf , Node0154-leaf , Node0211-leaf , Node0212 , Node0213 , Node0221 , Node0222 , Node0231-leaf , Node0232 , Node0233-leaf , Node0241-leaf , Node0242 , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0331-leaf , Node0332-leaf , Node0341-leaf , Node0342-leaf , Node0343-leaf , Node0411 , Node0412-leaf , Node0413 , Node0421-leaf , Node0422 , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["024"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 85 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.998 0.999 0.5057 0.495 0.495
#> 3 3 0.970 0.921 0.970 0.3087 0.686 0.453
#> 4 4 0.906 0.893 0.938 0.1308 0.865 0.627
#> 5 5 0.871 0.827 0.888 0.0519 0.960 0.840
#> 6 6 0.853 0.663 0.796 0.0361 0.959 0.815
#> 7 7 0.813 0.653 0.816 0.0329 0.933 0.685
#> 8 8 0.799 0.637 0.761 0.0153 0.955 0.740
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.GM.A2D9.01 1 0.000 1.000 1.00 0.00
#> TCGA.EW.A1PD.01 1 0.000 1.000 1.00 0.00
#> TCGA.GM.A2DC.01 1 0.000 1.000 1.00 0.00
#> TCGA.A1.A0SJ.01 1 0.000 1.000 1.00 0.00
#> TCGA.A7.A3IZ.01 2 0.000 0.998 0.00 1.00
#> TCGA.AR.A24H.01 2 0.000 0.998 0.00 1.00
#> TCGA.D8.A1XV.01 1 0.000 1.000 1.00 0.00
#> TCGA.E9.A1R6.01 2 0.000 0.998 0.00 1.00
#> TCGA.D8.A1XZ.01 2 0.000 0.998 0.00 1.00
#> TCGA.LL.A9Q3.01 1 0.000 1.000 1.00 0.00
#> TCGA.B6.A40C.01 1 0.000 1.000 1.00 0.00
#> TCGA.A7.A26H.01 1 0.000 1.000 1.00 0.00
#> TCGA.OL.A5DA.01 1 0.000 1.000 1.00 0.00
#> TCGA.LL.A50Y.01 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A1FJ.01 2 0.000 0.998 0.00 1.00
#> TCGA.E9.A3HO.01 1 0.000 1.000 1.00 0.00
#> TCGA.B6.A0RN.01 2 0.000 0.998 0.00 1.00
#> TCGA.E2.A109.01 2 0.000 0.998 0.00 1.00
#> TCGA.BH.A1FL.01 1 0.000 1.000 1.00 0.00
#> TCGA.AO.A12G.01 1 0.000 1.000 1.00 0.00
#> TCGA.AN.A0XR.01 2 0.000 0.998 0.00 1.00
#> TCGA.AO.A125.01 2 0.000 0.998 0.00 1.00
#> TCGA.UL.AAZ6.01 2 0.000 0.998 0.00 1.00
#> TCGA.PE.A5DC.01 2 0.000 0.998 0.00 1.00
#> TCGA.D8.A1JJ.01 1 0.000 1.000 1.00 0.00
#> TCGA.B6.A1KC.01 2 0.000 0.998 0.00 1.00
#> TCGA.E9.A5UP.01 1 0.000 1.000 1.00 0.00
#> TCGA.A2.A1G4.01 1 0.000 1.000 1.00 0.00
#> TCGA.E2.A15J.01 1 0.000 1.000 1.00 0.00
#> TCGA.AR.A2LL.01 1 0.000 1.000 1.00 0.00
#> TCGA.D8.A73X.01 1 0.000 1.000 1.00 0.00
#> TCGA.AR.A0TV.01 1 0.000 1.000 1.00 0.00
#> TCGA.AC.A5XU.01 2 0.000 0.998 0.00 1.00
#> TCGA.B6.A0WW.01 2 0.000 0.998 0.00 1.00
#> TCGA.E9.A5UO.01 2 0.000 0.998 0.00 1.00
#> TCGA.A2.A0SV.01 2 0.141 0.980 0.02 0.98
#> TCGA.AR.A24R.01 2 0.000 0.998 0.00 1.00
#> TCGA.AO.A1KP.01 2 0.000 0.998 0.00 1.00
#> TCGA.D8.A1JP.01 1 0.000 1.000 1.00 0.00
#> TCGA.AO.A0JM.01 2 0.000 0.998 0.00 1.00
#> TCGA.EW.A1PA.01 2 0.242 0.960 0.04 0.96
#> TCGA.AC.A3TM.01 1 0.000 1.000 1.00 0.00
#> TCGA.GM.A3NY.01 1 0.000 1.000 1.00 0.00
#> TCGA.S3.A6ZF.01 1 0.000 1.000 1.00 0.00
#> TCGA.AN.A0XO.01 1 0.000 1.000 1.00 0.00
#> TCGA.AR.A0U3.01 2 0.000 0.998 0.00 1.00
#> TCGA.EW.A1OX.01 2 0.000 0.998 0.00 1.00
#> TCGA.A2.A1FW.01 2 0.000 0.998 0.00 1.00
#> TCGA.GM.A3NW.01 2 0.141 0.980 0.02 0.98
#> TCGA.D8.A27W.01 1 0.000 1.000 1.00 0.00
#> TCGA.D8.A1XU.01 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A1ES.06 1 0.000 1.000 1.00 0.00
#> TCGA.E9.A54Y.01 2 0.000 0.998 0.00 1.00
#> TCGA.AC.A3TN.01 1 0.000 1.000 1.00 0.00
#> TCGA.AQ.A04L.01 2 0.000 0.998 0.00 1.00
#> TCGA.A7.A13F.01 2 0.000 0.998 0.00 1.00
#> TCGA.E2.A2P5.01 2 0.000 0.998 0.00 1.00
#> TCGA.AO.A1KS.01 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A0DD.01 2 0.000 0.998 0.00 1.00
#> TCGA.D8.A1X9.01 2 0.000 0.998 0.00 1.00
#> TCGA.AR.A24X.01 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A0GZ.01 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A0DH.01 2 0.000 0.998 0.00 1.00
#> TCGA.BH.A8FY.01 2 0.000 0.998 0.00 1.00
#> TCGA.AO.A1KT.01 2 0.000 0.998 0.00 1.00
#> TCGA.A7.A26E.01 1 0.000 1.000 1.00 0.00
#> TCGA.LL.A7T0.01 1 0.000 1.000 1.00 0.00
#> TCGA.OL.A66O.01 2 0.000 0.998 0.00 1.00
#> TCGA.EW.A1PC.01 2 0.000 0.998 0.00 1.00
#> TCGA.3C.AALJ.01 2 0.000 0.998 0.00 1.00
#> TCGA.C8.A26V.01 1 0.000 1.000 1.00 0.00
#> TCGA.D8.A1JA.01 2 0.000 0.998 0.00 1.00
#> TCGA.B6.A1KN.01 2 0.000 0.998 0.00 1.00
#> TCGA.AR.A24K.01 1 0.000 1.000 1.00 0.00
#> TCGA.LQ.A4E4.01 2 0.000 0.998 0.00 1.00
#> TCGA.E2.A105.01 2 0.000 0.998 0.00 1.00
#> TCGA.E9.A1R7.01 1 0.000 1.000 1.00 0.00
#> TCGA.E2.A10E.01 1 0.000 1.000 1.00 0.00
#> TCGA.E2.A1BD.01 1 0.000 1.000 1.00 0.00
#> TCGA.C8.A1HE.01 1 0.000 1.000 1.00 0.00
#> TCGA.AO.A12C.01 2 0.000 0.998 0.00 1.00
#> TCGA.B6.A40B.01 1 0.000 1.000 1.00 0.00
#> TCGA.WT.AB44.01 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A28Q.01 1 0.000 1.000 1.00 0.00
#> TCGA.AQ.A0Y5.01 1 0.000 1.000 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.GM.A2D9.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.EW.A1PD.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.GM.A2DC.01 3 0.6126 0.3332 0.40 0.00 0.60
#> TCGA.A1.A0SJ.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.A7.A3IZ.01 3 0.0892 0.9371 0.00 0.02 0.98
#> TCGA.AR.A24H.01 2 0.0000 0.9887 0.00 1.00 0.00
#> TCGA.D8.A1XV.01 1 0.6192 0.2506 0.58 0.00 0.42
#> TCGA.E9.A1R6.01 3 0.1529 0.9229 0.00 0.04 0.96
#> TCGA.D8.A1XZ.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.LL.A9Q3.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.B6.A40C.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.A7.A26H.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.OL.A5DA.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.LL.A50Y.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.BH.A1FJ.01 2 0.0000 0.9887 0.00 1.00 0.00
#> TCGA.E9.A3HO.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.B6.A0RN.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.E2.A109.01 2 0.0000 0.9887 0.00 1.00 0.00
#> TCGA.BH.A1FL.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.AO.A12G.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.AN.A0XR.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.AO.A125.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.UL.AAZ6.01 2 0.0000 0.9887 0.00 1.00 0.00
#> TCGA.PE.A5DC.01 2 0.0000 0.9887 0.00 1.00 0.00
#> TCGA.D8.A1JJ.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.B6.A1KC.01 3 0.1529 0.9229 0.00 0.04 0.96
#> TCGA.E9.A5UP.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.A2.A1G4.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.E2.A15J.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.AR.A2LL.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.D8.A73X.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.AR.A0TV.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.AC.A5XU.01 2 0.4796 0.7151 0.00 0.78 0.22
#> TCGA.B6.A0WW.01 2 0.0000 0.9887 0.00 1.00 0.00
#> TCGA.E9.A5UO.01 2 0.0000 0.9887 0.00 1.00 0.00
#> TCGA.A2.A0SV.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.AR.A24R.01 3 0.1529 0.9229 0.00 0.04 0.96
#> TCGA.AO.A1KP.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.D8.A1JP.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.AO.A0JM.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.EW.A1PA.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.AC.A3TM.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.GM.A3NY.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.S3.A6ZF.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.AN.A0XO.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.AR.A0U3.01 2 0.0000 0.9887 0.00 1.00 0.00
#> TCGA.EW.A1OX.01 2 0.0000 0.9887 0.00 1.00 0.00
#> TCGA.A2.A1FW.01 2 0.0000 0.9887 0.00 1.00 0.00
#> TCGA.GM.A3NW.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.D8.A27W.01 3 0.5835 0.4730 0.34 0.00 0.66
#> TCGA.D8.A1XU.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.BH.A1ES.06 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.E9.A54Y.01 2 0.0000 0.9887 0.00 1.00 0.00
#> TCGA.AC.A3TN.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.AQ.A04L.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.A7.A13F.01 3 0.2959 0.8611 0.00 0.10 0.90
#> TCGA.E2.A2P5.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.AO.A1KS.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.BH.A0DD.01 2 0.0000 0.9887 0.00 1.00 0.00
#> TCGA.D8.A1X9.01 2 0.0000 0.9887 0.00 1.00 0.00
#> TCGA.AR.A24X.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.BH.A0GZ.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.BH.A0DH.01 2 0.0000 0.9887 0.00 1.00 0.00
#> TCGA.BH.A8FY.01 2 0.0000 0.9887 0.00 1.00 0.00
#> TCGA.AO.A1KT.01 2 0.0000 0.9887 0.00 1.00 0.00
#> TCGA.A7.A26E.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.LL.A7T0.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.OL.A66O.01 2 0.0000 0.9887 0.00 1.00 0.00
#> TCGA.EW.A1PC.01 2 0.0000 0.9887 0.00 1.00 0.00
#> TCGA.3C.AALJ.01 2 0.0000 0.9887 0.00 1.00 0.00
#> TCGA.C8.A26V.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.D8.A1JA.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.B6.A1KN.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.AR.A24K.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.LQ.A4E4.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.E2.A105.01 2 0.0000 0.9887 0.00 1.00 0.00
#> TCGA.E9.A1R7.01 3 0.6302 0.0683 0.48 0.00 0.52
#> TCGA.E2.A10E.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.E2.A1BD.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.C8.A1HE.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.AO.A12C.01 3 0.1529 0.9229 0.00 0.04 0.96
#> TCGA.B6.A40B.01 3 0.0000 0.9501 0.00 0.00 1.00
#> TCGA.WT.AB44.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.BH.A28Q.01 1 0.0000 0.9685 1.00 0.00 0.00
#> TCGA.AQ.A0Y5.01 1 0.6126 0.3077 0.60 0.00 0.40
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.GM.A2D9.01 4 0.1211 0.919 0.00 0.00 0.04 0.96
#> TCGA.EW.A1PD.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.GM.A2DC.01 4 0.1211 0.901 0.00 0.00 0.04 0.96
#> TCGA.A1.A0SJ.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.A7.A3IZ.01 3 0.0000 0.818 0.00 0.00 1.00 0.00
#> TCGA.AR.A24H.01 2 0.0000 0.974 0.00 1.00 0.00 0.00
#> TCGA.D8.A1XV.01 4 0.1913 0.906 0.02 0.00 0.04 0.94
#> TCGA.E9.A1R6.01 3 0.1637 0.815 0.00 0.00 0.94 0.06
#> TCGA.D8.A1XZ.01 3 0.3975 0.773 0.00 0.00 0.76 0.24
#> TCGA.LL.A9Q3.01 4 0.0707 0.919 0.00 0.00 0.02 0.98
#> TCGA.B6.A40C.01 4 0.1637 0.903 0.00 0.00 0.06 0.94
#> TCGA.A7.A26H.01 4 0.0707 0.919 0.00 0.00 0.02 0.98
#> TCGA.OL.A5DA.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.LL.A50Y.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.BH.A1FJ.01 2 0.4855 0.431 0.00 0.60 0.40 0.00
#> TCGA.E9.A3HO.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.B6.A0RN.01 3 0.1637 0.815 0.00 0.00 0.94 0.06
#> TCGA.E2.A109.01 2 0.0000 0.974 0.00 1.00 0.00 0.00
#> TCGA.BH.A1FL.01 4 0.0707 0.919 0.00 0.00 0.02 0.98
#> TCGA.AO.A12G.01 1 0.2921 0.837 0.86 0.00 0.00 0.14
#> TCGA.AN.A0XR.01 3 0.1211 0.816 0.00 0.00 0.96 0.04
#> TCGA.AO.A125.01 3 0.0707 0.821 0.00 0.00 0.98 0.02
#> TCGA.UL.AAZ6.01 2 0.0000 0.974 0.00 1.00 0.00 0.00
#> TCGA.PE.A5DC.01 2 0.0000 0.974 0.00 1.00 0.00 0.00
#> TCGA.D8.A1JJ.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.B6.A1KC.01 3 0.1637 0.815 0.00 0.00 0.94 0.06
#> TCGA.E9.A5UP.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.A2.A1G4.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.E2.A15J.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.AR.A2LL.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.D8.A73X.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.AR.A0TV.01 3 0.4948 0.435 0.00 0.00 0.56 0.44
#> TCGA.AC.A5XU.01 3 0.2921 0.765 0.00 0.14 0.86 0.00
#> TCGA.B6.A0WW.01 3 0.3400 0.730 0.00 0.18 0.82 0.00
#> TCGA.E9.A5UO.01 2 0.0000 0.974 0.00 1.00 0.00 0.00
#> TCGA.A2.A0SV.01 4 0.0707 0.919 0.00 0.00 0.02 0.98
#> TCGA.AR.A24R.01 3 0.1637 0.815 0.00 0.00 0.94 0.06
#> TCGA.AO.A1KP.01 3 0.0707 0.821 0.00 0.00 0.98 0.02
#> TCGA.D8.A1JP.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.AO.A0JM.01 3 0.3975 0.773 0.00 0.00 0.76 0.24
#> TCGA.EW.A1PA.01 3 0.4948 0.435 0.00 0.00 0.56 0.44
#> TCGA.AC.A3TM.01 1 0.0707 0.973 0.98 0.00 0.00 0.02
#> TCGA.GM.A3NY.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.S3.A6ZF.01 4 0.1637 0.903 0.00 0.00 0.06 0.94
#> TCGA.AN.A0XO.01 4 0.0707 0.919 0.00 0.00 0.02 0.98
#> TCGA.AR.A0U3.01 2 0.0000 0.974 0.00 1.00 0.00 0.00
#> TCGA.EW.A1OX.01 2 0.1211 0.944 0.00 0.96 0.04 0.00
#> TCGA.A2.A1FW.01 2 0.0000 0.974 0.00 1.00 0.00 0.00
#> TCGA.GM.A3NW.01 3 0.3801 0.779 0.00 0.00 0.78 0.22
#> TCGA.D8.A27W.01 4 0.1211 0.914 0.00 0.00 0.04 0.96
#> TCGA.D8.A1XU.01 4 0.1211 0.914 0.00 0.00 0.04 0.96
#> TCGA.BH.A1ES.06 4 0.0707 0.919 0.00 0.00 0.02 0.98
#> TCGA.E9.A54Y.01 2 0.0000 0.974 0.00 1.00 0.00 0.00
#> TCGA.AC.A3TN.01 1 0.2011 0.911 0.92 0.00 0.00 0.08
#> TCGA.AQ.A04L.01 3 0.3975 0.773 0.00 0.00 0.76 0.24
#> TCGA.A7.A13F.01 3 0.1637 0.815 0.00 0.00 0.94 0.06
#> TCGA.E2.A2P5.01 3 0.3801 0.779 0.00 0.00 0.78 0.22
#> TCGA.AO.A1KS.01 4 0.4948 0.180 0.44 0.00 0.00 0.56
#> TCGA.BH.A0DD.01 2 0.0000 0.974 0.00 1.00 0.00 0.00
#> TCGA.D8.A1X9.01 2 0.0000 0.974 0.00 1.00 0.00 0.00
#> TCGA.AR.A24X.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.BH.A0GZ.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.BH.A0DH.01 2 0.0000 0.974 0.00 1.00 0.00 0.00
#> TCGA.BH.A8FY.01 2 0.0000 0.974 0.00 1.00 0.00 0.00
#> TCGA.AO.A1KT.01 2 0.0000 0.974 0.00 1.00 0.00 0.00
#> TCGA.A7.A26E.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.LL.A7T0.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.OL.A66O.01 2 0.0000 0.974 0.00 1.00 0.00 0.00
#> TCGA.EW.A1PC.01 2 0.0000 0.974 0.00 1.00 0.00 0.00
#> TCGA.3C.AALJ.01 2 0.1637 0.928 0.00 0.94 0.06 0.00
#> TCGA.C8.A26V.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.D8.A1JA.01 3 0.3801 0.779 0.00 0.00 0.78 0.22
#> TCGA.B6.A1KN.01 3 0.3975 0.773 0.00 0.00 0.76 0.24
#> TCGA.AR.A24K.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.LQ.A4E4.01 3 0.3801 0.784 0.00 0.00 0.78 0.22
#> TCGA.E2.A105.01 2 0.0000 0.974 0.00 1.00 0.00 0.00
#> TCGA.E9.A1R7.01 4 0.0000 0.918 0.00 0.00 0.00 1.00
#> TCGA.E2.A10E.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.E2.A1BD.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.C8.A1HE.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.AO.A12C.01 3 0.1637 0.815 0.00 0.00 0.94 0.06
#> TCGA.B6.A40B.01 4 0.1637 0.903 0.00 0.00 0.06 0.94
#> TCGA.WT.AB44.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.BH.A28Q.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.AQ.A0Y5.01 4 0.1913 0.906 0.02 0.00 0.04 0.94
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.GM.A2D9.01 4 0.1732 0.8959 0.00 0.00 0.08 0.92 0.00
#> TCGA.EW.A1PD.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A2DC.01 4 0.2020 0.8626 0.00 0.00 0.10 0.90 0.00
#> TCGA.A1.A0SJ.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A3IZ.01 5 0.4060 -0.0734 0.00 0.00 0.36 0.00 0.64
#> TCGA.AR.A24H.01 2 0.0000 0.9536 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A1XV.01 4 0.3424 0.8376 0.00 0.00 0.24 0.76 0.00
#> TCGA.E9.A1R6.01 5 0.0000 0.6755 0.00 0.00 0.00 0.00 1.00
#> TCGA.D8.A1XZ.01 3 0.4060 0.8717 0.00 0.00 0.64 0.00 0.36
#> TCGA.LL.A9Q3.01 4 0.1732 0.8742 0.00 0.00 0.08 0.92 0.00
#> TCGA.B6.A40C.01 4 0.3424 0.8376 0.00 0.00 0.24 0.76 0.00
#> TCGA.A7.A26H.01 4 0.0000 0.8991 0.00 0.00 0.00 1.00 0.00
#> TCGA.OL.A5DA.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00
#> TCGA.LL.A50Y.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FJ.01 5 0.3690 0.4834 0.00 0.20 0.02 0.00 0.78
#> TCGA.E9.A3HO.01 1 0.2516 0.8758 0.86 0.00 0.14 0.00 0.00
#> TCGA.B6.A0RN.01 5 0.2280 0.5661 0.00 0.00 0.12 0.00 0.88
#> TCGA.E2.A109.01 2 0.0000 0.9536 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A1FL.01 4 0.0000 0.8991 0.00 0.00 0.00 1.00 0.00
#> TCGA.AO.A12G.01 1 0.5680 0.5964 0.62 0.00 0.24 0.14 0.00
#> TCGA.AN.A0XR.01 5 0.3983 0.0127 0.00 0.00 0.34 0.00 0.66
#> TCGA.AO.A125.01 5 0.4227 -0.3271 0.00 0.00 0.42 0.00 0.58
#> TCGA.UL.AAZ6.01 2 0.0609 0.9480 0.00 0.98 0.02 0.00 0.00
#> TCGA.PE.A5DC.01 2 0.0000 0.9536 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A1JJ.01 1 0.1732 0.9168 0.92 0.00 0.08 0.00 0.00
#> TCGA.B6.A1KC.01 5 0.0000 0.6755 0.00 0.00 0.00 0.00 1.00
#> TCGA.E9.A5UP.01 1 0.1732 0.9168 0.92 0.00 0.08 0.00 0.00
#> TCGA.A2.A1G4.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A15J.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A2LL.01 1 0.1043 0.9398 0.96 0.00 0.04 0.00 0.00
#> TCGA.D8.A73X.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A0TV.01 3 0.3390 0.4666 0.00 0.00 0.84 0.10 0.06
#> TCGA.AC.A5XU.01 3 0.4060 0.8717 0.00 0.00 0.64 0.00 0.36
#> TCGA.B6.A0WW.01 3 0.5558 0.7276 0.00 0.08 0.56 0.00 0.36
#> TCGA.E9.A5UO.01 2 0.0609 0.9480 0.00 0.98 0.02 0.00 0.00
#> TCGA.A2.A0SV.01 4 0.0000 0.8991 0.00 0.00 0.00 1.00 0.00
#> TCGA.AR.A24R.01 5 0.0000 0.6755 0.00 0.00 0.00 0.00 1.00
#> TCGA.AO.A1KP.01 3 0.4126 0.8424 0.00 0.00 0.62 0.00 0.38
#> TCGA.D8.A1JP.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A0JM.01 3 0.4060 0.8717 0.00 0.00 0.64 0.00 0.36
#> TCGA.EW.A1PA.01 3 0.4458 0.5153 0.00 0.00 0.76 0.12 0.12
#> TCGA.AC.A3TM.01 1 0.2873 0.8903 0.86 0.00 0.12 0.02 0.00
#> TCGA.GM.A3NY.01 1 0.1410 0.9298 0.94 0.00 0.06 0.00 0.00
#> TCGA.S3.A6ZF.01 4 0.2280 0.8892 0.00 0.00 0.12 0.88 0.00
#> TCGA.AN.A0XO.01 4 0.0000 0.8991 0.00 0.00 0.00 1.00 0.00
#> TCGA.AR.A0U3.01 2 0.0609 0.9480 0.00 0.98 0.02 0.00 0.00
#> TCGA.EW.A1OX.01 2 0.4540 0.5581 0.00 0.64 0.02 0.00 0.34
#> TCGA.A2.A1FW.01 2 0.0000 0.9536 0.00 1.00 0.00 0.00 0.00
#> TCGA.GM.A3NW.01 3 0.4456 0.8260 0.00 0.00 0.66 0.02 0.32
#> TCGA.D8.A27W.01 4 0.2280 0.8892 0.00 0.00 0.12 0.88 0.00
#> TCGA.D8.A1XU.01 4 0.2516 0.8834 0.00 0.00 0.14 0.86 0.00
#> TCGA.BH.A1ES.06 4 0.1043 0.8882 0.00 0.00 0.04 0.96 0.00
#> TCGA.E9.A54Y.01 2 0.0000 0.9536 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A3TN.01 1 0.4263 0.8026 0.76 0.00 0.18 0.06 0.00
#> TCGA.AQ.A04L.01 3 0.4060 0.8717 0.00 0.00 0.64 0.00 0.36
#> TCGA.A7.A13F.01 5 0.0000 0.6755 0.00 0.00 0.00 0.00 1.00
#> TCGA.E2.A2P5.01 3 0.4060 0.8717 0.00 0.00 0.64 0.00 0.36
#> TCGA.AO.A1KS.01 4 0.3037 0.8313 0.04 0.00 0.10 0.86 0.00
#> TCGA.BH.A0DD.01 2 0.0000 0.9536 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A1X9.01 2 0.0000 0.9536 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A24X.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0GZ.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DH.01 2 0.0000 0.9536 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A8FY.01 2 0.0000 0.9536 0.00 1.00 0.00 0.00 0.00
#> TCGA.AO.A1KT.01 2 0.0000 0.9536 0.00 1.00 0.00 0.00 0.00
#> TCGA.A7.A26E.01 1 0.1043 0.9398 0.96 0.00 0.04 0.00 0.00
#> TCGA.LL.A7T0.01 1 0.1043 0.9398 0.96 0.00 0.04 0.00 0.00
#> TCGA.OL.A66O.01 2 0.0609 0.9480 0.00 0.98 0.02 0.00 0.00
#> TCGA.EW.A1PC.01 2 0.0000 0.9536 0.00 1.00 0.00 0.00 0.00
#> TCGA.3C.AALJ.01 2 0.4540 0.5581 0.00 0.64 0.02 0.00 0.34
#> TCGA.C8.A26V.01 1 0.2516 0.8758 0.86 0.00 0.14 0.00 0.00
#> TCGA.D8.A1JA.01 3 0.4060 0.8717 0.00 0.00 0.64 0.00 0.36
#> TCGA.B6.A1KN.01 3 0.4060 0.8717 0.00 0.00 0.64 0.00 0.36
#> TCGA.AR.A24K.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00
#> TCGA.LQ.A4E4.01 3 0.4060 0.8717 0.00 0.00 0.64 0.00 0.36
#> TCGA.E2.A105.01 2 0.0609 0.9480 0.00 0.98 0.02 0.00 0.00
#> TCGA.E9.A1R7.01 4 0.1732 0.8742 0.00 0.00 0.08 0.92 0.00
#> TCGA.E2.A10E.01 1 0.1043 0.9398 0.96 0.00 0.04 0.00 0.00
#> TCGA.E2.A1BD.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A1HE.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A12C.01 5 0.3319 0.5391 0.00 0.00 0.02 0.16 0.82
#> TCGA.B6.A40B.01 4 0.3109 0.8592 0.00 0.00 0.20 0.80 0.00
#> TCGA.WT.AB44.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A28Q.01 1 0.0000 0.9520 1.00 0.00 0.00 0.00 0.00
#> TCGA.AQ.A0Y5.01 4 0.3424 0.8376 0.00 0.00 0.24 0.76 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.GM.A2D9.01 4 0.4078 0.02788 0.00 0.00 0.02 0.64 0.00 0.34
#> TCGA.EW.A1PD.01 1 0.0000 0.89468 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A2DC.01 6 0.4265 0.73093 0.00 0.00 0.00 0.30 0.04 0.66
#> TCGA.A1.A0SJ.01 1 0.0000 0.89468 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A3IZ.01 3 0.4646 -0.15060 0.00 0.00 0.50 0.00 0.46 0.04
#> TCGA.AR.A24H.01 2 0.0937 0.90784 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.D8.A1XV.01 4 0.0937 0.29167 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.E9.A1R6.01 5 0.1556 0.86056 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.D8.A1XZ.01 3 0.2094 0.78256 0.00 0.00 0.90 0.02 0.00 0.08
#> TCGA.LL.A9Q3.01 6 0.3578 0.78128 0.00 0.00 0.00 0.34 0.00 0.66
#> TCGA.B6.A40C.01 4 0.1092 0.30946 0.00 0.00 0.02 0.96 0.02 0.00
#> TCGA.A7.A26H.01 4 0.4328 -0.45289 0.00 0.00 0.02 0.52 0.00 0.46
#> TCGA.OL.A5DA.01 1 0.0000 0.89468 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LL.A50Y.01 1 0.0000 0.89468 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FJ.01 5 0.2725 0.79676 0.00 0.06 0.02 0.00 0.88 0.04
#> TCGA.E9.A3HO.01 1 0.4348 0.63218 0.64 0.00 0.00 0.32 0.04 0.00
#> TCGA.B6.A0RN.01 5 0.4360 0.66036 0.00 0.00 0.26 0.00 0.68 0.06
#> TCGA.E2.A109.01 2 0.0000 0.91104 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FL.01 6 0.3869 0.51242 0.00 0.00 0.00 0.50 0.00 0.50
#> TCGA.AO.A12G.01 4 0.5381 -0.25498 0.40 0.00 0.00 0.52 0.04 0.04
#> TCGA.AN.A0XR.01 5 0.4873 0.28330 0.00 0.00 0.42 0.00 0.52 0.06
#> TCGA.AO.A125.01 3 0.4609 -0.00226 0.00 0.00 0.54 0.00 0.42 0.04
#> TCGA.UL.AAZ6.01 2 0.1814 0.87623 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.PE.A5DC.01 2 0.1267 0.90108 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.D8.A1JJ.01 1 0.4348 0.63218 0.64 0.00 0.00 0.32 0.04 0.00
#> TCGA.B6.A1KC.01 5 0.1556 0.86056 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.E9.A5UP.01 1 0.4348 0.63218 0.64 0.00 0.00 0.32 0.04 0.00
#> TCGA.A2.A1G4.01 1 0.0000 0.89468 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A15J.01 1 0.0000 0.89468 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A2LL.01 1 0.1480 0.87487 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.D8.A73X.01 1 0.0000 0.89468 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A0TV.01 3 0.3846 0.71648 0.00 0.00 0.80 0.10 0.02 0.08
#> TCGA.AC.A5XU.01 3 0.2512 0.73230 0.00 0.00 0.88 0.00 0.06 0.06
#> TCGA.B6.A0WW.01 3 0.3420 0.70376 0.00 0.04 0.84 0.00 0.06 0.06
#> TCGA.E9.A5UO.01 2 0.0937 0.90341 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.A2.A0SV.01 6 0.4337 0.47483 0.00 0.00 0.02 0.48 0.00 0.50
#> TCGA.AR.A24R.01 5 0.2094 0.85286 0.00 0.00 0.08 0.00 0.90 0.02
#> TCGA.AO.A1KP.01 3 0.3163 0.66331 0.00 0.00 0.82 0.00 0.14 0.04
#> TCGA.D8.A1JP.01 1 0.0000 0.89468 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A0JM.01 3 0.1556 0.78566 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.EW.A1PA.01 3 0.5195 0.37550 0.00 0.00 0.54 0.36 0.00 0.10
#> TCGA.AC.A3TM.01 1 0.5788 0.51983 0.54 0.00 0.00 0.34 0.06 0.06
#> TCGA.GM.A3NY.01 1 0.2190 0.85055 0.90 0.00 0.00 0.00 0.04 0.06
#> TCGA.S3.A6ZF.01 4 0.4552 0.13023 0.00 0.00 0.06 0.64 0.00 0.30
#> TCGA.AN.A0XO.01 4 0.3869 -0.62007 0.00 0.00 0.00 0.50 0.00 0.50
#> TCGA.AR.A0U3.01 2 0.0937 0.90341 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.EW.A1OX.01 2 0.5555 0.28046 0.00 0.48 0.00 0.00 0.38 0.14
#> TCGA.A2.A1FW.01 2 0.2048 0.87468 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.GM.A3NW.01 3 0.1865 0.76101 0.00 0.00 0.92 0.04 0.00 0.04
#> TCGA.D8.A27W.01 4 0.3578 -0.02473 0.00 0.00 0.00 0.66 0.00 0.34
#> TCGA.D8.A1XU.01 4 0.4265 0.12594 0.00 0.00 0.04 0.66 0.00 0.30
#> TCGA.BH.A1ES.06 6 0.4144 0.75669 0.00 0.00 0.00 0.36 0.02 0.62
#> TCGA.E9.A54Y.01 2 0.0000 0.91104 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A3TN.01 1 0.6057 0.45175 0.50 0.00 0.00 0.36 0.08 0.06
#> TCGA.AQ.A04L.01 3 0.2094 0.78256 0.00 0.00 0.90 0.02 0.00 0.08
#> TCGA.A7.A13F.01 5 0.1556 0.86056 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.E2.A2P5.01 3 0.0000 0.78277 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AO.A1KS.01 6 0.4765 0.68513 0.02 0.00 0.00 0.30 0.04 0.64
#> TCGA.BH.A0DD.01 2 0.0937 0.90784 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.D8.A1X9.01 2 0.0937 0.90784 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.AR.A24X.01 1 0.0000 0.89468 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0GZ.01 1 0.0000 0.89468 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DH.01 2 0.0937 0.90784 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.BH.A8FY.01 2 0.0000 0.91104 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A1KT.01 2 0.0937 0.90784 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.A7.A26E.01 1 0.1480 0.87487 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.LL.A7T0.01 1 0.1480 0.87487 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.OL.A66O.01 2 0.0937 0.90341 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.EW.A1PC.01 2 0.0000 0.91104 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.3C.AALJ.01 2 0.5555 0.28046 0.00 0.48 0.00 0.00 0.38 0.14
#> TCGA.C8.A26V.01 1 0.4348 0.63218 0.64 0.00 0.00 0.32 0.04 0.00
#> TCGA.D8.A1JA.01 3 0.1267 0.78773 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.B6.A1KN.01 3 0.2094 0.78256 0.00 0.00 0.90 0.02 0.00 0.08
#> TCGA.AR.A24K.01 1 0.0000 0.89468 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LQ.A4E4.01 3 0.0000 0.78277 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E2.A105.01 2 0.0937 0.90341 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.E9.A1R7.01 6 0.3578 0.78128 0.00 0.00 0.00 0.34 0.00 0.66
#> TCGA.E2.A10E.01 1 0.1480 0.87487 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.E2.A1BD.01 1 0.0000 0.89468 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A1HE.01 1 0.0000 0.89468 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A12C.01 5 0.2190 0.83164 0.00 0.00 0.04 0.00 0.90 0.06
#> TCGA.B6.A40B.01 4 0.4067 0.17942 0.00 0.00 0.04 0.70 0.00 0.26
#> TCGA.WT.AB44.01 1 0.0000 0.89468 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A28Q.01 1 0.0000 0.89468 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AQ.A0Y5.01 4 0.0000 0.30752 0.00 0.00 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.GM.A2D9.01 4 0.0504 0.540688 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.EW.A1PD.01 1 0.0000 0.893786 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A2DC.01 6 0.4264 0.692753 0.00 0.00 0.00 0.32 0.06 0.62 0.00
#> TCGA.A1.A0SJ.01 1 0.0000 0.893786 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A3IZ.01 3 0.4990 -0.141044 0.00 0.00 0.48 0.00 0.44 0.04 0.04
#> TCGA.AR.A24H.01 2 0.0504 0.898998 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.D8.A1XV.01 7 0.3047 0.363303 0.00 0.00 0.00 0.28 0.00 0.00 0.72
#> TCGA.E9.A1R6.01 5 0.1166 0.811184 0.00 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.D8.A1XZ.01 3 0.2829 0.728773 0.00 0.00 0.84 0.00 0.00 0.08 0.08
#> TCGA.LL.A9Q3.01 4 0.4070 0.168716 0.00 0.00 0.00 0.62 0.04 0.34 0.00
#> TCGA.B6.A40C.01 7 0.3496 0.113584 0.00 0.00 0.00 0.42 0.00 0.00 0.58
#> TCGA.A7.A26H.01 4 0.2912 0.511403 0.00 0.00 0.00 0.82 0.04 0.14 0.00
#> TCGA.OL.A5DA.01 1 0.0000 0.893786 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LL.A50Y.01 1 0.0000 0.893786 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FJ.01 5 0.2509 0.750600 0.00 0.06 0.00 0.00 0.88 0.04 0.02
#> TCGA.E9.A3HO.01 7 0.3139 0.712254 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.B6.A0RN.01 5 0.4832 0.371588 0.00 0.00 0.34 0.00 0.58 0.04 0.04
#> TCGA.E2.A109.01 2 0.0000 0.901247 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FL.01 4 0.3244 0.485322 0.00 0.00 0.00 0.78 0.04 0.18 0.00
#> TCGA.AO.A12G.01 7 0.4748 0.635025 0.14 0.00 0.00 0.06 0.00 0.10 0.70
#> TCGA.AN.A0XR.01 5 0.5394 0.187242 0.00 0.00 0.40 0.00 0.48 0.04 0.08
#> TCGA.AO.A125.01 3 0.5194 -0.023979 0.00 0.00 0.50 0.00 0.40 0.06 0.04
#> TCGA.UL.AAZ6.01 2 0.1363 0.887558 0.00 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.PE.A5DC.01 2 0.2213 0.863392 0.00 0.90 0.04 0.00 0.00 0.02 0.04
#> TCGA.D8.A1JJ.01 7 0.3294 0.684060 0.34 0.00 0.00 0.00 0.00 0.00 0.66
#> TCGA.B6.A1KC.01 5 0.1166 0.811184 0.00 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.E9.A5UP.01 7 0.3294 0.684060 0.34 0.00 0.00 0.00 0.00 0.00 0.66
#> TCGA.A2.A1G4.01 1 0.0000 0.893786 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A15J.01 1 0.0000 0.893786 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A2LL.01 1 0.3517 0.637367 0.70 0.00 0.00 0.00 0.00 0.28 0.02
#> TCGA.D8.A73X.01 1 0.0000 0.893786 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A0TV.01 3 0.4821 0.625975 0.00 0.00 0.66 0.04 0.00 0.08 0.22
#> TCGA.AC.A5XU.01 3 0.2563 0.698904 0.00 0.00 0.88 0.00 0.04 0.04 0.04
#> TCGA.B6.A0WW.01 3 0.3600 0.659286 0.00 0.08 0.82 0.00 0.04 0.02 0.04
#> TCGA.E9.A5UO.01 2 0.0863 0.894557 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.A2.A0SV.01 4 0.3086 0.498751 0.00 0.00 0.00 0.80 0.04 0.16 0.00
#> TCGA.AR.A24R.01 5 0.1664 0.804975 0.00 0.00 0.06 0.00 0.92 0.00 0.02
#> TCGA.AO.A1KP.01 3 0.5966 0.489541 0.00 0.00 0.62 0.04 0.14 0.10 0.10
#> TCGA.D8.A1JP.01 1 0.0000 0.893786 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A0JM.01 3 0.2829 0.728773 0.00 0.00 0.84 0.00 0.00 0.08 0.08
#> TCGA.EW.A1PA.01 4 0.6357 0.186695 0.00 0.00 0.20 0.50 0.00 0.16 0.14
#> TCGA.AC.A3TM.01 7 0.5490 0.496482 0.24 0.00 0.00 0.00 0.00 0.32 0.44
#> TCGA.GM.A3NY.01 1 0.3685 0.585373 0.66 0.00 0.00 0.00 0.00 0.32 0.02
#> TCGA.S3.A6ZF.01 4 0.3058 0.479649 0.00 0.00 0.00 0.82 0.00 0.10 0.08
#> TCGA.AN.A0XO.01 4 0.3244 0.485322 0.00 0.00 0.00 0.78 0.04 0.18 0.00
#> TCGA.AR.A0U3.01 2 0.0863 0.894557 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.EW.A1OX.01 2 0.5221 0.158483 0.00 0.46 0.00 0.00 0.44 0.06 0.04
#> TCGA.A2.A1FW.01 2 0.2509 0.856508 0.00 0.88 0.04 0.00 0.00 0.02 0.06
#> TCGA.GM.A3NW.01 3 0.4491 0.615482 0.00 0.00 0.74 0.14 0.02 0.04 0.06
#> TCGA.D8.A27W.01 4 0.2864 0.479453 0.00 0.00 0.00 0.84 0.02 0.12 0.02
#> TCGA.D8.A1XU.01 4 0.2829 0.487223 0.00 0.00 0.00 0.84 0.00 0.08 0.08
#> TCGA.BH.A1ES.06 4 0.4638 -0.000139 0.00 0.00 0.00 0.54 0.08 0.38 0.00
#> TCGA.E9.A54Y.01 2 0.0000 0.901247 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A3TN.01 7 0.5853 0.504147 0.16 0.00 0.00 0.04 0.00 0.32 0.48
#> TCGA.AQ.A04L.01 3 0.3487 0.723043 0.00 0.00 0.78 0.00 0.00 0.12 0.10
#> TCGA.A7.A13F.01 5 0.1166 0.811184 0.00 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.E2.A2P5.01 3 0.1006 0.725935 0.00 0.00 0.96 0.02 0.00 0.02 0.00
#> TCGA.AO.A1KS.01 6 0.3887 0.730626 0.02 0.00 0.00 0.26 0.00 0.70 0.02
#> TCGA.BH.A0DD.01 2 0.1505 0.885183 0.00 0.94 0.02 0.00 0.00 0.02 0.02
#> TCGA.D8.A1X9.01 2 0.0504 0.898998 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.AR.A24X.01 1 0.0000 0.893786 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0GZ.01 1 0.0000 0.893786 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DH.01 2 0.0504 0.898998 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.BH.A8FY.01 2 0.0000 0.901247 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A1KT.01 2 0.2213 0.863392 0.00 0.90 0.04 0.00 0.00 0.02 0.04
#> TCGA.A7.A26E.01 1 0.3517 0.637367 0.70 0.00 0.00 0.00 0.00 0.28 0.02
#> TCGA.LL.A7T0.01 1 0.3139 0.641660 0.70 0.00 0.00 0.00 0.00 0.30 0.00
#> TCGA.OL.A66O.01 2 0.0863 0.894557 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.EW.A1PC.01 2 0.0000 0.901247 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.3C.AALJ.01 2 0.5221 0.158483 0.00 0.46 0.00 0.00 0.44 0.06 0.04
#> TCGA.C8.A26V.01 7 0.3139 0.712254 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.D8.A1JA.01 3 0.2159 0.737816 0.00 0.00 0.90 0.02 0.00 0.06 0.02
#> TCGA.B6.A1KN.01 3 0.2829 0.728773 0.00 0.00 0.84 0.00 0.00 0.08 0.08
#> TCGA.AR.A24K.01 1 0.0000 0.893786 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LQ.A4E4.01 3 0.3061 0.703541 0.00 0.00 0.84 0.02 0.00 0.06 0.08
#> TCGA.E2.A105.01 2 0.0863 0.894557 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.E9.A1R7.01 4 0.4244 -0.094925 0.00 0.00 0.00 0.54 0.04 0.42 0.00
#> TCGA.E2.A10E.01 1 0.3517 0.637367 0.70 0.00 0.00 0.00 0.00 0.28 0.02
#> TCGA.E2.A1BD.01 1 0.0000 0.893786 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A1HE.01 1 0.0000 0.893786 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A12C.01 5 0.1505 0.755863 0.00 0.00 0.00 0.02 0.94 0.02 0.02
#> TCGA.B6.A40B.01 4 0.2569 0.489553 0.00 0.00 0.00 0.84 0.00 0.02 0.14
#> TCGA.WT.AB44.01 1 0.1166 0.853994 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.BH.A28Q.01 1 0.0000 0.893786 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AQ.A0Y5.01 4 0.3459 0.129485 0.00 0.00 0.00 0.60 0.00 0.00 0.40
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.GM.A2D9.01 4 0.4556 0.0276 0.00 0.00 0.02 0.54 0.00 0.38 0.06 0.00
#> TCGA.EW.A1PD.01 1 0.0000 0.9041 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A2DC.01 6 0.1563 0.4539 0.00 0.00 0.00 0.00 0.10 0.90 0.00 0.00
#> TCGA.A1.A0SJ.01 1 0.0000 0.9041 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A3IZ.01 8 0.2725 0.6317 0.00 0.00 0.14 0.00 0.04 0.00 0.00 0.82
#> TCGA.AR.A24H.01 2 0.0471 0.9095 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.D8.A1XV.01 7 0.4336 0.4225 0.00 0.00 0.02 0.14 0.02 0.06 0.74 0.02
#> TCGA.E9.A1R6.01 5 0.4105 0.5548 0.00 0.00 0.02 0.00 0.54 0.02 0.00 0.42
#> TCGA.D8.A1XZ.01 3 0.0471 0.7647 0.00 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.LL.A9Q3.01 6 0.2994 0.5144 0.00 0.00 0.00 0.14 0.00 0.80 0.06 0.00
#> TCGA.B6.A40C.01 7 0.5181 -0.2222 0.00 0.00 0.02 0.40 0.02 0.08 0.48 0.00
#> TCGA.A7.A26H.01 6 0.4619 0.1525 0.00 0.00 0.02 0.44 0.00 0.48 0.06 0.00
#> TCGA.OL.A5DA.01 1 0.0000 0.9041 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LL.A50Y.01 1 0.0000 0.9041 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FJ.01 8 0.4670 -0.5070 0.00 0.04 0.00 0.04 0.44 0.00 0.00 0.48
#> TCGA.E9.A3HO.01 7 0.2650 0.7515 0.24 0.00 0.00 0.00 0.00 0.00 0.76 0.00
#> TCGA.B6.A0RN.01 8 0.2807 0.6015 0.00 0.00 0.10 0.02 0.04 0.00 0.00 0.84
#> TCGA.E2.A109.01 2 0.0000 0.9123 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FL.01 6 0.4199 0.2534 0.00 0.00 0.00 0.42 0.00 0.52 0.06 0.00
#> TCGA.AO.A12G.01 7 0.3454 0.6843 0.12 0.00 0.00 0.04 0.00 0.02 0.80 0.02
#> TCGA.AN.A0XR.01 8 0.3503 0.6277 0.00 0.00 0.12 0.08 0.00 0.00 0.02 0.78
#> TCGA.AO.A125.01 8 0.2888 0.6292 0.00 0.00 0.16 0.04 0.00 0.00 0.00 0.80
#> TCGA.UL.AAZ6.01 2 0.3002 0.7929 0.00 0.82 0.00 0.02 0.12 0.00 0.04 0.00
#> TCGA.PE.A5DC.01 2 0.4110 0.7621 0.00 0.76 0.06 0.02 0.10 0.00 0.06 0.00
#> TCGA.D8.A1JJ.01 7 0.2650 0.7515 0.24 0.00 0.00 0.00 0.00 0.00 0.76 0.00
#> TCGA.B6.A1KC.01 5 0.4105 0.5548 0.00 0.00 0.02 0.00 0.54 0.02 0.00 0.42
#> TCGA.E9.A5UP.01 7 0.2650 0.7515 0.24 0.00 0.00 0.00 0.00 0.00 0.76 0.00
#> TCGA.A2.A1G4.01 1 0.0000 0.9041 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A15J.01 1 0.0000 0.9041 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A2LL.01 1 0.4787 0.6939 0.72 0.00 0.00 0.02 0.12 0.04 0.04 0.06
#> TCGA.D8.A73X.01 1 0.0000 0.9041 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A0TV.01 3 0.2859 0.6764 0.00 0.00 0.82 0.14 0.02 0.00 0.02 0.00
#> TCGA.AC.A5XU.01 3 0.4880 0.6258 0.00 0.00 0.68 0.02 0.10 0.00 0.06 0.14
#> TCGA.B6.A0WW.01 3 0.5533 0.5925 0.00 0.06 0.66 0.02 0.10 0.00 0.06 0.10
#> TCGA.E9.A5UO.01 2 0.0471 0.9078 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.A2.A0SV.01 6 0.4607 0.2122 0.00 0.00 0.02 0.42 0.00 0.50 0.06 0.00
#> TCGA.AR.A24R.01 5 0.3690 0.5263 0.00 0.00 0.02 0.00 0.56 0.00 0.00 0.42
#> TCGA.AO.A1KP.01 8 0.4849 0.2969 0.00 0.00 0.24 0.22 0.00 0.00 0.00 0.54
#> TCGA.D8.A1JP.01 1 0.0000 0.9041 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A0JM.01 3 0.0941 0.7629 0.00 0.00 0.96 0.00 0.02 0.00 0.00 0.02
#> TCGA.EW.A1PA.01 4 0.3504 0.2876 0.00 0.00 0.26 0.70 0.00 0.00 0.00 0.04
#> TCGA.AC.A3TM.01 7 0.6551 0.6167 0.18 0.00 0.00 0.04 0.12 0.06 0.54 0.06
#> TCGA.GM.A3NY.01 1 0.5514 0.6205 0.66 0.00 0.00 0.02 0.12 0.06 0.08 0.06
#> TCGA.S3.A6ZF.01 4 0.2569 0.5012 0.00 0.00 0.02 0.82 0.00 0.16 0.00 0.00
#> TCGA.AN.A0XO.01 6 0.4383 0.2471 0.00 0.00 0.02 0.42 0.00 0.52 0.04 0.00
#> TCGA.AR.A0U3.01 2 0.0471 0.9078 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.EW.A1OX.01 5 0.4401 0.3422 0.00 0.30 0.00 0.04 0.62 0.00 0.04 0.00
#> TCGA.A2.A1FW.01 2 0.5560 0.5997 0.00 0.60 0.06 0.04 0.20 0.00 0.10 0.00
#> TCGA.GM.A3NW.01 3 0.5945 0.3604 0.00 0.00 0.52 0.12 0.02 0.02 0.04 0.28
#> TCGA.D8.A27W.01 4 0.3658 0.1580 0.00 0.00 0.00 0.58 0.00 0.40 0.02 0.00
#> TCGA.D8.A1XU.01 4 0.2569 0.5012 0.00 0.00 0.02 0.82 0.00 0.16 0.00 0.00
#> TCGA.BH.A1ES.06 6 0.1804 0.5060 0.00 0.00 0.00 0.08 0.02 0.90 0.00 0.00
#> TCGA.E9.A54Y.01 2 0.0000 0.9123 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A3TN.01 7 0.6369 0.6210 0.12 0.00 0.00 0.04 0.12 0.08 0.58 0.06
#> TCGA.AQ.A04L.01 3 0.2407 0.7292 0.00 0.00 0.86 0.08 0.00 0.00 0.00 0.06
#> TCGA.A7.A13F.01 5 0.3714 0.5366 0.00 0.00 0.02 0.00 0.54 0.00 0.00 0.44
#> TCGA.E2.A2P5.01 3 0.3483 0.6879 0.00 0.00 0.76 0.04 0.00 0.00 0.02 0.18
#> TCGA.AO.A1KS.01 6 0.4604 0.4008 0.00 0.00 0.00 0.04 0.12 0.72 0.06 0.06
#> TCGA.BH.A0DD.01 2 0.3080 0.8328 0.00 0.84 0.02 0.02 0.06 0.00 0.06 0.00
#> TCGA.D8.A1X9.01 2 0.0471 0.9095 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.AR.A24X.01 1 0.0000 0.9041 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0GZ.01 1 0.0000 0.9041 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DH.01 2 0.0471 0.9095 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.BH.A8FY.01 2 0.0000 0.9123 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A1KT.01 2 0.3670 0.8019 0.00 0.80 0.06 0.02 0.06 0.00 0.06 0.00
#> TCGA.A7.A26E.01 1 0.4787 0.6939 0.72 0.00 0.00 0.02 0.12 0.04 0.04 0.06
#> TCGA.LL.A7T0.01 1 0.4787 0.6939 0.72 0.00 0.00 0.02 0.12 0.04 0.04 0.06
#> TCGA.OL.A66O.01 2 0.0471 0.9078 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.EW.A1PC.01 2 0.0000 0.9123 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.3C.AALJ.01 5 0.4294 0.3605 0.00 0.22 0.00 0.04 0.68 0.00 0.06 0.00
#> TCGA.C8.A26V.01 7 0.2650 0.7515 0.24 0.00 0.00 0.00 0.00 0.00 0.76 0.00
#> TCGA.D8.A1JA.01 3 0.2071 0.7501 0.00 0.00 0.90 0.02 0.00 0.00 0.04 0.04
#> TCGA.B6.A1KN.01 3 0.0471 0.7647 0.00 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.AR.A24K.01 1 0.0000 0.9041 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LQ.A4E4.01 3 0.4458 0.5910 0.00 0.00 0.62 0.18 0.00 0.00 0.00 0.20
#> TCGA.E2.A105.01 2 0.0941 0.9001 0.00 0.96 0.00 0.00 0.02 0.00 0.02 0.00
#> TCGA.E9.A1R7.01 6 0.3454 0.5169 0.00 0.00 0.00 0.08 0.06 0.80 0.06 0.00
#> TCGA.E2.A10E.01 1 0.5043 0.6692 0.70 0.00 0.00 0.02 0.12 0.06 0.04 0.06
#> TCGA.E2.A1BD.01 1 0.0000 0.9041 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A1HE.01 1 0.0000 0.9041 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A12C.01 5 0.5025 0.4981 0.00 0.00 0.00 0.04 0.56 0.10 0.00 0.30
#> TCGA.B6.A40B.01 4 0.5103 0.4442 0.00 0.00 0.04 0.64 0.02 0.16 0.14 0.00
#> TCGA.WT.AB44.01 1 0.2071 0.8424 0.90 0.00 0.00 0.00 0.04 0.00 0.02 0.04
#> TCGA.BH.A28Q.01 1 0.0000 0.9041 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AQ.A0Y5.01 4 0.4403 0.2111 0.00 0.00 0.00 0.48 0.00 0.08 0.44 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node024. Child nodes: Node02121-leaf , Node02122-leaf , Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02214-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02321-leaf , Node02322-leaf , Node02421-leaf , Node02422-leaf , Node02423-leaf , Node04111-leaf , Node04112-leaf , Node04113 , Node04131-leaf , Node04132-leaf , Node04133-leaf , Node04221-leaf , Node04222-leaf , Node04331-leaf , Node04332-leaf , Node04333-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0242"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 41 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4761 0.524 0.524
#> 3 3 0.997 0.958 0.982 0.3898 0.702 0.490
#> 4 4 0.726 0.740 0.874 0.0663 0.941 0.833
#> 5 5 0.669 0.652 0.808 0.0648 0.907 0.720
#> 6 6 0.680 0.620 0.797 0.0035 0.906 0.712
#> 7 7 0.671 0.537 0.774 0.0471 0.902 0.668
#> 8 8 0.665 0.468 0.765 0.0132 0.920 0.687
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.A7.A3IZ.01 1 0 1 1 0
#> TCGA.AR.A24H.01 2 0 1 0 1
#> TCGA.E9.A1R6.01 1 0 1 1 0
#> TCGA.D8.A1XZ.01 2 0 1 0 1
#> TCGA.BH.A1FJ.01 1 0 1 1 0
#> TCGA.B6.A0RN.01 1 0 1 1 0
#> TCGA.E2.A109.01 2 0 1 0 1
#> TCGA.AN.A0XR.01 1 0 1 1 0
#> TCGA.AO.A125.01 1 0 1 1 0
#> TCGA.UL.AAZ6.01 2 0 1 0 1
#> TCGA.PE.A5DC.01 2 0 1 0 1
#> TCGA.B6.A1KC.01 2 0 1 0 1
#> TCGA.AC.A5XU.01 2 0 1 0 1
#> TCGA.B6.A0WW.01 2 0 1 0 1
#> TCGA.E9.A5UO.01 1 0 1 1 0
#> TCGA.A2.A0SV.01 2 0 1 0 1
#> TCGA.AR.A24R.01 2 0 1 0 1
#> TCGA.AO.A1KP.01 2 0 1 0 1
#> TCGA.AO.A0JM.01 2 0 1 0 1
#> TCGA.EW.A1PA.01 2 0 1 0 1
#> TCGA.AR.A0U3.01 2 0 1 0 1
#> TCGA.EW.A1OX.01 2 0 1 0 1
#> TCGA.A2.A1FW.01 2 0 1 0 1
#> TCGA.GM.A3NW.01 1 0 1 1 0
#> TCGA.E9.A54Y.01 1 0 1 1 0
#> TCGA.AQ.A04L.01 2 0 1 0 1
#> TCGA.A7.A13F.01 1 0 1 1 0
#> TCGA.E2.A2P5.01 2 0 1 0 1
#> TCGA.BH.A0DD.01 1 0 1 1 0
#> TCGA.D8.A1X9.01 1 0 1 1 0
#> TCGA.BH.A0DH.01 1 0 1 1 0
#> TCGA.BH.A8FY.01 1 0 1 1 0
#> TCGA.AO.A1KT.01 2 0 1 0 1
#> TCGA.OL.A66O.01 1 0 1 1 0
#> TCGA.EW.A1PC.01 2 0 1 0 1
#> TCGA.3C.AALJ.01 2 0 1 0 1
#> TCGA.D8.A1JA.01 2 0 1 0 1
#> TCGA.B6.A1KN.01 2 0 1 0 1
#> TCGA.LQ.A4E4.01 2 0 1 0 1
#> TCGA.E2.A105.01 2 0 1 0 1
#> TCGA.AO.A12C.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.A7.A3IZ.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.AR.A24H.01 3 0.0000 0.995 0.00 0.00 1.00
#> TCGA.E9.A1R6.01 2 0.0000 0.962 0.00 1.00 0.00
#> TCGA.D8.A1XZ.01 3 0.0000 0.995 0.00 0.00 1.00
#> TCGA.BH.A1FJ.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.B6.A0RN.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.E2.A109.01 2 0.0000 0.962 0.00 1.00 0.00
#> TCGA.AN.A0XR.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.AO.A125.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.UL.AAZ6.01 2 0.0000 0.962 0.00 1.00 0.00
#> TCGA.PE.A5DC.01 3 0.0000 0.995 0.00 0.00 1.00
#> TCGA.B6.A1KC.01 2 0.0000 0.962 0.00 1.00 0.00
#> TCGA.AC.A5XU.01 2 0.2066 0.921 0.00 0.94 0.06
#> TCGA.B6.A0WW.01 2 0.0000 0.962 0.00 1.00 0.00
#> TCGA.E9.A5UO.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.A2.A0SV.01 3 0.0000 0.995 0.00 0.00 1.00
#> TCGA.AR.A24R.01 2 0.0000 0.962 0.00 1.00 0.00
#> TCGA.AO.A1KP.01 2 0.0000 0.962 0.00 1.00 0.00
#> TCGA.AO.A0JM.01 2 0.6244 0.242 0.00 0.56 0.44
#> TCGA.EW.A1PA.01 2 0.2959 0.882 0.00 0.90 0.10
#> TCGA.AR.A0U3.01 2 0.0000 0.962 0.00 1.00 0.00
#> TCGA.EW.A1OX.01 2 0.0000 0.962 0.00 1.00 0.00
#> TCGA.A2.A1FW.01 2 0.0000 0.962 0.00 1.00 0.00
#> TCGA.GM.A3NW.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.E9.A54Y.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.AQ.A04L.01 3 0.0000 0.995 0.00 0.00 1.00
#> TCGA.A7.A13F.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.E2.A2P5.01 3 0.1529 0.954 0.00 0.04 0.96
#> TCGA.BH.A0DD.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.D8.A1X9.01 2 0.0892 0.947 0.02 0.98 0.00
#> TCGA.BH.A0DH.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.BH.A8FY.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.AO.A1KT.01 3 0.0000 0.995 0.00 0.00 1.00
#> TCGA.OL.A66O.01 2 0.0000 0.962 0.00 1.00 0.00
#> TCGA.EW.A1PC.01 3 0.0000 0.995 0.00 0.00 1.00
#> TCGA.3C.AALJ.01 2 0.0000 0.962 0.00 1.00 0.00
#> TCGA.D8.A1JA.01 3 0.0000 0.995 0.00 0.00 1.00
#> TCGA.B6.A1KN.01 3 0.0000 0.995 0.00 0.00 1.00
#> TCGA.LQ.A4E4.01 2 0.2066 0.921 0.00 0.94 0.06
#> TCGA.E2.A105.01 2 0.0000 0.962 0.00 1.00 0.00
#> TCGA.AO.A12C.01 2 0.0000 0.962 0.00 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.A7.A3IZ.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.AR.A24H.01 4 0.5594 -0.166 0.00 0.02 0.46 0.52
#> TCGA.E9.A1R6.01 2 0.0000 0.873 0.00 1.00 0.00 0.00
#> TCGA.D8.A1XZ.01 4 0.0000 0.729 0.00 0.00 0.00 1.00
#> TCGA.BH.A1FJ.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.B6.A0RN.01 1 0.1211 0.940 0.96 0.00 0.04 0.00
#> TCGA.E2.A109.01 2 0.0707 0.862 0.00 0.98 0.02 0.00
#> TCGA.AN.A0XR.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.AO.A125.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.UL.AAZ6.01 2 0.0000 0.873 0.00 1.00 0.00 0.00
#> TCGA.PE.A5DC.01 4 0.3172 0.658 0.00 0.00 0.16 0.84
#> TCGA.B6.A1KC.01 2 0.0000 0.873 0.00 1.00 0.00 0.00
#> TCGA.AC.A5XU.01 2 0.5619 0.473 0.00 0.64 0.32 0.04
#> TCGA.B6.A0WW.01 2 0.6074 0.387 0.00 0.60 0.34 0.06
#> TCGA.E9.A5UO.01 1 0.2345 0.862 0.90 0.10 0.00 0.00
#> TCGA.A2.A0SV.01 3 0.3801 0.557 0.00 0.00 0.78 0.22
#> TCGA.AR.A24R.01 2 0.0000 0.873 0.00 1.00 0.00 0.00
#> TCGA.AO.A1KP.01 2 0.3400 0.722 0.00 0.82 0.18 0.00
#> TCGA.AO.A0JM.01 3 0.7198 0.464 0.00 0.28 0.54 0.18
#> TCGA.EW.A1PA.01 2 0.5986 0.373 0.00 0.62 0.32 0.06
#> TCGA.AR.A0U3.01 2 0.0000 0.873 0.00 1.00 0.00 0.00
#> TCGA.EW.A1OX.01 2 0.0000 0.873 0.00 1.00 0.00 0.00
#> TCGA.A2.A1FW.01 2 0.0707 0.862 0.00 0.98 0.02 0.00
#> TCGA.GM.A3NW.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.E9.A54Y.01 1 0.0707 0.956 0.98 0.00 0.02 0.00
#> TCGA.AQ.A04L.01 4 0.2921 0.690 0.00 0.00 0.14 0.86
#> TCGA.A7.A13F.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.E2.A2P5.01 3 0.7004 0.521 0.00 0.20 0.58 0.22
#> TCGA.BH.A0DD.01 1 0.5151 0.758 0.76 0.00 0.14 0.10
#> TCGA.D8.A1X9.01 2 0.0707 0.859 0.02 0.98 0.00 0.00
#> TCGA.BH.A0DH.01 1 0.0707 0.956 0.98 0.00 0.02 0.00
#> TCGA.BH.A8FY.01 1 0.0000 0.963 1.00 0.00 0.00 0.00
#> TCGA.AO.A1KT.01 4 0.0000 0.729 0.00 0.00 0.00 1.00
#> TCGA.OL.A66O.01 2 0.0000 0.873 0.00 1.00 0.00 0.00
#> TCGA.EW.A1PC.01 3 0.3801 0.499 0.00 0.00 0.78 0.22
#> TCGA.3C.AALJ.01 2 0.0000 0.873 0.00 1.00 0.00 0.00
#> TCGA.D8.A1JA.01 3 0.4406 0.461 0.00 0.00 0.70 0.30
#> TCGA.B6.A1KN.01 3 0.6570 0.531 0.00 0.10 0.58 0.32
#> TCGA.LQ.A4E4.01 2 0.6262 0.171 0.00 0.54 0.40 0.06
#> TCGA.E2.A105.01 2 0.0000 0.873 0.00 1.00 0.00 0.00
#> TCGA.AO.A12C.01 2 0.0000 0.873 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.A7.A3IZ.01 1 0.0609 0.8908 0.98 0.00 0.00 0.00 0.02
#> TCGA.AR.A24H.01 3 0.6912 0.1012 0.00 0.06 0.50 0.34 0.10
#> TCGA.E9.A1R6.01 2 0.2012 0.8049 0.02 0.92 0.00 0.00 0.06
#> TCGA.D8.A1XZ.01 4 0.0000 0.8538 0.00 0.00 0.00 1.00 0.00
#> TCGA.BH.A1FJ.01 1 0.0609 0.8915 0.98 0.00 0.00 0.00 0.02
#> TCGA.B6.A0RN.01 1 0.2516 0.8214 0.86 0.00 0.00 0.00 0.14
#> TCGA.E2.A109.01 2 0.3106 0.7215 0.00 0.84 0.14 0.00 0.02
#> TCGA.AN.A0XR.01 1 0.0609 0.8915 0.98 0.00 0.00 0.00 0.02
#> TCGA.AO.A125.01 1 0.0609 0.8908 0.98 0.00 0.00 0.00 0.02
#> TCGA.UL.AAZ6.01 2 0.0000 0.8473 0.00 1.00 0.00 0.00 0.00
#> TCGA.PE.A5DC.01 4 0.4132 0.6548 0.00 0.00 0.26 0.72 0.02
#> TCGA.B6.A1KC.01 2 0.0000 0.8473 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A5XU.01 3 0.7099 0.3375 0.00 0.34 0.42 0.02 0.22
#> TCGA.B6.A0WW.01 3 0.6766 0.3760 0.00 0.30 0.40 0.00 0.30
#> TCGA.E9.A5UO.01 1 0.3421 0.8135 0.84 0.08 0.00 0.00 0.08
#> TCGA.A2.A0SV.01 3 0.5012 0.3784 0.00 0.02 0.74 0.10 0.14
#> TCGA.AR.A24R.01 2 0.0000 0.8473 0.00 1.00 0.00 0.00 0.00
#> TCGA.AO.A1KP.01 2 0.5382 0.3571 0.00 0.64 0.26 0.00 0.10
#> TCGA.AO.A0JM.01 3 0.4825 0.5169 0.00 0.22 0.72 0.02 0.04
#> TCGA.EW.A1PA.01 3 0.5178 0.0409 0.00 0.48 0.48 0.00 0.04
#> TCGA.AR.A0U3.01 2 0.0000 0.8473 0.00 1.00 0.00 0.00 0.00
#> TCGA.EW.A1OX.01 2 0.0000 0.8473 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A1FW.01 2 0.3513 0.6742 0.00 0.80 0.18 0.00 0.02
#> TCGA.GM.A3NW.01 1 0.0000 0.8927 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A54Y.01 1 0.2516 0.8575 0.86 0.00 0.00 0.00 0.14
#> TCGA.AQ.A04L.01 4 0.3037 0.8035 0.00 0.00 0.10 0.86 0.04
#> TCGA.A7.A13F.01 1 0.1732 0.8755 0.92 0.00 0.00 0.00 0.08
#> TCGA.E2.A2P5.01 3 0.7258 0.4404 0.00 0.14 0.46 0.06 0.34
#> TCGA.BH.A0DD.01 1 0.6704 0.3347 0.48 0.00 0.04 0.10 0.38
#> TCGA.D8.A1X9.01 2 0.5440 0.5374 0.12 0.70 0.02 0.00 0.16
#> TCGA.BH.A0DH.01 1 0.2732 0.8410 0.84 0.00 0.00 0.00 0.16
#> TCGA.BH.A8FY.01 1 0.0609 0.8908 0.98 0.00 0.00 0.00 0.02
#> TCGA.AO.A1KT.01 4 0.0000 0.8538 0.00 0.00 0.00 1.00 0.00
#> TCGA.OL.A66O.01 2 0.2012 0.8049 0.02 0.92 0.00 0.00 0.06
#> TCGA.EW.A1PC.01 3 0.4854 0.2957 0.00 0.00 0.68 0.06 0.26
#> TCGA.3C.AALJ.01 2 0.0000 0.8473 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A1JA.01 3 0.5700 0.1850 0.00 0.00 0.60 0.12 0.28
#> TCGA.B6.A1KN.01 3 0.3971 0.4847 0.00 0.10 0.80 0.10 0.00
#> TCGA.LQ.A4E4.01 2 0.5457 -0.1490 0.00 0.48 0.46 0.00 0.06
#> TCGA.E2.A105.01 2 0.0000 0.8473 0.00 1.00 0.00 0.00 0.00
#> TCGA.AO.A12C.01 2 0.0000 0.8473 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.A7.A3IZ.01 1 0.0547 0.8964 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.AR.A24H.01 3 0.7385 0.0552 0.00 0.06 0.42 0.12 0.34 0.06
#> TCGA.E9.A1R6.01 2 0.1267 0.7891 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.D8.A1XZ.01 5 0.0000 0.8175 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BH.A1FJ.01 1 0.0000 0.9016 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0RN.01 1 0.3270 0.7320 0.82 0.00 0.06 0.00 0.00 0.12
#> TCGA.E2.A109.01 2 0.3321 0.7109 0.00 0.82 0.10 0.08 0.00 0.00
#> TCGA.AN.A0XR.01 1 0.0000 0.9016 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A125.01 1 0.1865 0.8768 0.92 0.00 0.00 0.04 0.00 0.04
#> TCGA.UL.AAZ6.01 2 0.0547 0.8002 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.PE.A5DC.01 5 0.2790 0.7105 0.00 0.00 0.14 0.02 0.84 0.00
#> TCGA.B6.A1KC.01 2 0.0000 0.8016 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A5XU.01 2 0.6659 0.0536 0.00 0.44 0.34 0.02 0.02 0.18
#> TCGA.B6.A0WW.01 2 0.6771 0.0753 0.00 0.44 0.20 0.06 0.00 0.30
#> TCGA.E9.A5UO.01 1 0.3660 0.5973 0.78 0.16 0.00 0.06 0.00 0.00
#> TCGA.A2.A0SV.01 3 0.5742 0.3685 0.00 0.04 0.66 0.12 0.16 0.02
#> TCGA.AR.A24R.01 2 0.0000 0.8016 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A1KP.01 2 0.3942 0.6980 0.00 0.80 0.10 0.06 0.00 0.04
#> TCGA.AO.A0JM.01 3 0.6429 0.0172 0.00 0.42 0.44 0.04 0.06 0.04
#> TCGA.EW.A1PA.01 2 0.4765 0.4697 0.00 0.64 0.30 0.02 0.04 0.00
#> TCGA.AR.A0U3.01 2 0.0547 0.8013 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.EW.A1OX.01 2 0.0547 0.8013 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.A2.A1FW.01 2 0.3928 0.6538 0.00 0.76 0.16 0.08 0.00 0.00
#> TCGA.GM.A3NW.01 1 0.0000 0.9016 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A54Y.01 1 0.1556 0.8747 0.92 0.00 0.00 0.08 0.00 0.00
#> TCGA.AQ.A04L.01 5 0.4066 0.6834 0.00 0.00 0.12 0.08 0.78 0.02
#> TCGA.A7.A13F.01 1 0.0937 0.8959 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.E2.A2P5.01 3 0.8625 0.2299 0.00 0.18 0.32 0.14 0.12 0.24
#> TCGA.BH.A0DD.01 6 0.2631 0.0000 0.18 0.00 0.00 0.00 0.00 0.82
#> TCGA.D8.A1X9.01 2 0.4162 0.6728 0.06 0.78 0.00 0.12 0.00 0.04
#> TCGA.BH.A0DH.01 1 0.2048 0.8481 0.88 0.00 0.00 0.12 0.00 0.00
#> TCGA.BH.A8FY.01 1 0.1092 0.8956 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.AO.A1KT.01 5 0.1267 0.8048 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.OL.A66O.01 2 0.1807 0.7792 0.02 0.92 0.00 0.06 0.00 0.00
#> TCGA.EW.A1PC.01 3 0.4646 0.2181 0.00 0.00 0.50 0.46 0.04 0.00
#> TCGA.3C.AALJ.01 2 0.0547 0.8002 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.D8.A1JA.01 3 0.6319 0.1468 0.00 0.00 0.42 0.36 0.20 0.02
#> TCGA.B6.A1KN.01 3 0.5507 0.3529 0.00 0.08 0.64 0.02 0.24 0.02
#> TCGA.LQ.A4E4.01 2 0.5124 0.3896 0.00 0.60 0.32 0.02 0.00 0.06
#> TCGA.E2.A105.01 2 0.0937 0.7944 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.AO.A12C.01 2 0.0547 0.8013 0.00 0.98 0.00 0.02 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.A7.A3IZ.01 1 0.2278 0.8120 0.88 0.00 0.00 0.04 0.00 0.08 0.00
#> TCGA.AR.A24H.01 3 0.4892 0.1263 0.00 0.04 0.70 0.02 0.16 0.00 0.08
#> TCGA.E9.A1R6.01 2 0.1006 0.7432 0.00 0.96 0.02 0.00 0.00 0.02 0.00
#> TCGA.D8.A1XZ.01 5 0.0504 0.7977 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.BH.A1FJ.01 1 0.0863 0.8387 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.B6.A0RN.01 1 0.4121 0.5654 0.70 0.00 0.00 0.20 0.00 0.10 0.00
#> TCGA.E2.A109.01 3 0.4278 -0.0622 0.00 0.46 0.50 0.04 0.00 0.00 0.00
#> TCGA.AN.A0XR.01 1 0.0000 0.8416 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A125.01 1 0.1166 0.8350 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.UL.AAZ6.01 2 0.1671 0.7309 0.00 0.90 0.10 0.00 0.00 0.00 0.00
#> TCGA.PE.A5DC.01 5 0.4015 0.5935 0.00 0.00 0.26 0.00 0.68 0.00 0.06
#> TCGA.B6.A1KC.01 2 0.0863 0.7586 0.00 0.96 0.04 0.00 0.00 0.00 0.00
#> TCGA.AC.A5XU.01 4 0.5077 0.5177 0.00 0.38 0.08 0.52 0.00 0.02 0.00
#> TCGA.B6.A0WW.01 4 0.6425 0.4667 0.00 0.34 0.14 0.44 0.00 0.06 0.02
#> TCGA.E9.A5UO.01 1 0.4675 0.4412 0.66 0.26 0.02 0.04 0.00 0.02 0.00
#> TCGA.A2.A0SV.01 7 0.6609 0.1980 0.00 0.04 0.30 0.26 0.00 0.02 0.38
#> TCGA.AR.A24R.01 2 0.0000 0.7669 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A1KP.01 2 0.3139 0.2840 0.00 0.70 0.00 0.30 0.00 0.00 0.00
#> TCGA.AO.A0JM.01 3 0.6787 0.2787 0.00 0.16 0.50 0.20 0.04 0.00 0.10
#> TCGA.EW.A1PA.01 2 0.6489 -0.4327 0.00 0.44 0.12 0.34 0.02 0.00 0.08
#> TCGA.AR.A0U3.01 2 0.0000 0.7669 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1OX.01 2 0.0000 0.7669 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A1FW.01 2 0.4278 -0.0755 0.00 0.50 0.46 0.04 0.00 0.00 0.00
#> TCGA.GM.A3NW.01 1 0.1505 0.8382 0.94 0.00 0.02 0.02 0.00 0.02 0.00
#> TCGA.E9.A54Y.01 1 0.3061 0.7934 0.84 0.00 0.02 0.06 0.00 0.08 0.00
#> TCGA.AQ.A04L.01 5 0.3887 0.7112 0.00 0.00 0.04 0.08 0.80 0.02 0.06
#> TCGA.A7.A13F.01 1 0.2355 0.8206 0.90 0.00 0.02 0.04 0.00 0.02 0.02
#> TCGA.E2.A2P5.01 4 0.5354 0.1352 0.00 0.08 0.12 0.70 0.04 0.02 0.04
#> TCGA.BH.A0DD.01 6 0.5937 0.0000 0.14 0.00 0.02 0.16 0.08 0.60 0.00
#> TCGA.D8.A1X9.01 2 0.4368 0.5282 0.06 0.78 0.02 0.08 0.00 0.04 0.02
#> TCGA.BH.A0DH.01 1 0.3404 0.7805 0.82 0.00 0.04 0.08 0.00 0.06 0.00
#> TCGA.BH.A8FY.01 1 0.1664 0.8381 0.92 0.00 0.00 0.02 0.00 0.06 0.00
#> TCGA.AO.A1KT.01 5 0.0000 0.7933 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.OL.A66O.01 2 0.1006 0.7432 0.00 0.96 0.02 0.00 0.00 0.02 0.00
#> TCGA.EW.A1PC.01 7 0.2159 0.3173 0.00 0.00 0.06 0.02 0.00 0.02 0.90
#> TCGA.3C.AALJ.01 2 0.1671 0.7309 0.00 0.90 0.10 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JA.01 7 0.6755 0.3950 0.00 0.00 0.18 0.08 0.02 0.30 0.42
#> TCGA.B6.A1KN.01 3 0.6980 0.1081 0.00 0.04 0.46 0.24 0.14 0.00 0.12
#> TCGA.LQ.A4E4.01 4 0.5429 0.4408 0.00 0.40 0.12 0.46 0.00 0.00 0.02
#> TCGA.E2.A105.01 2 0.1886 0.7135 0.00 0.88 0.12 0.00 0.00 0.00 0.00
#> TCGA.AO.A12C.01 2 0.0000 0.7669 0.00 1.00 0.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.A7.A3IZ.01 1 0.0941 0.82749 0.96 0.00 0.00 0.02 0.00 0.00 0.00 0.02
#> TCGA.AR.A24H.01 3 0.4077 0.02021 0.00 0.00 0.76 0.08 0.02 0.00 0.04 0.10
#> TCGA.E9.A1R6.01 2 0.3048 0.64745 0.02 0.84 0.02 0.08 0.00 0.00 0.00 0.04
#> TCGA.D8.A1XZ.01 5 0.0000 0.63332 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A1FJ.01 1 0.0471 0.82628 0.98 0.00 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0RN.01 1 0.4912 0.46845 0.60 0.02 0.00 0.28 0.00 0.08 0.02 0.00
#> TCGA.E2.A109.01 2 0.4358 0.00852 0.00 0.54 0.40 0.00 0.00 0.00 0.02 0.04
#> TCGA.AN.A0XR.01 1 0.2204 0.80599 0.90 0.02 0.02 0.04 0.00 0.00 0.00 0.02
#> TCGA.AO.A125.01 1 0.2532 0.79967 0.88 0.00 0.02 0.02 0.00 0.04 0.00 0.04
#> TCGA.UL.AAZ6.01 2 0.0808 0.70790 0.00 0.96 0.04 0.00 0.00 0.00 0.00 0.00
#> TCGA.PE.A5DC.01 5 0.6919 0.26354 0.00 0.02 0.12 0.06 0.50 0.04 0.22 0.04
#> TCGA.B6.A1KC.01 2 0.0000 0.71827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A5XU.01 2 0.7096 -0.21798 0.00 0.42 0.06 0.32 0.02 0.06 0.08 0.04
#> TCGA.B6.A0WW.01 4 0.5857 0.30896 0.00 0.34 0.04 0.50 0.02 0.06 0.04 0.00
#> TCGA.E9.A5UO.01 1 0.4626 0.59495 0.70 0.18 0.02 0.06 0.00 0.02 0.00 0.02
#> TCGA.A2.A0SV.01 7 0.6748 0.10957 0.00 0.06 0.16 0.14 0.00 0.00 0.46 0.18
#> TCGA.AR.A24R.01 2 0.0000 0.71827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A1KP.01 2 0.5636 0.40826 0.00 0.64 0.08 0.14 0.00 0.02 0.08 0.04
#> TCGA.AO.A0JM.01 3 0.6900 0.18960 0.00 0.16 0.42 0.14 0.00 0.00 0.22 0.06
#> TCGA.EW.A1PA.01 2 0.5815 0.17087 0.00 0.54 0.18 0.02 0.02 0.00 0.22 0.02
#> TCGA.AR.A0U3.01 2 0.2071 0.68398 0.00 0.90 0.02 0.04 0.00 0.00 0.00 0.04
#> TCGA.EW.A1OX.01 2 0.0000 0.71827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A1FW.01 3 0.4586 0.15106 0.00 0.40 0.52 0.00 0.00 0.00 0.06 0.02
#> TCGA.GM.A3NW.01 1 0.1607 0.82597 0.92 0.00 0.00 0.04 0.00 0.00 0.00 0.04
#> TCGA.E9.A54Y.01 1 0.3434 0.72245 0.76 0.00 0.00 0.00 0.00 0.10 0.00 0.14
#> TCGA.AQ.A04L.01 5 0.6262 0.40381 0.00 0.00 0.02 0.14 0.56 0.08 0.16 0.04
#> TCGA.A7.A13F.01 1 0.1557 0.82305 0.92 0.00 0.00 0.00 0.00 0.02 0.00 0.06
#> TCGA.E2.A2P5.01 4 0.5307 0.13246 0.00 0.08 0.08 0.68 0.02 0.04 0.10 0.00
#> TCGA.BH.A0DD.01 6 0.1741 0.00000 0.02 0.00 0.00 0.02 0.04 0.92 0.00 0.00
#> TCGA.D8.A1X9.01 2 0.5729 0.40445 0.12 0.64 0.06 0.08 0.00 0.02 0.00 0.08
#> TCGA.BH.A0DH.01 1 0.3601 0.73806 0.76 0.00 0.00 0.02 0.00 0.06 0.00 0.16
#> TCGA.BH.A8FY.01 1 0.1741 0.81431 0.92 0.00 0.02 0.00 0.00 0.02 0.00 0.04
#> TCGA.AO.A1KT.01 5 0.0941 0.63561 0.00 0.00 0.00 0.02 0.96 0.00 0.02 0.00
#> TCGA.OL.A66O.01 2 0.3048 0.64745 0.02 0.84 0.02 0.08 0.00 0.00 0.00 0.04
#> TCGA.EW.A1PC.01 8 0.5156 0.00000 0.00 0.02 0.10 0.06 0.00 0.02 0.12 0.68
#> TCGA.3C.AALJ.01 2 0.0808 0.70790 0.00 0.96 0.04 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JA.01 7 0.0941 0.23645 0.00 0.00 0.02 0.00 0.02 0.00 0.96 0.00
#> TCGA.B6.A1KN.01 3 0.6786 0.00441 0.00 0.04 0.48 0.12 0.02 0.02 0.26 0.06
#> TCGA.LQ.A4E4.01 2 0.6129 0.12514 0.00 0.56 0.12 0.18 0.00 0.02 0.10 0.02
#> TCGA.E2.A105.01 2 0.1341 0.68888 0.00 0.92 0.08 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A12C.01 2 0.0000 0.71827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node014-leaf , Node015 , Node021 , Node022 , Node023 , Node024 , Node031 , Node032 , Node033 , Node034 , Node041 , Node042 , Node043 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["03"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 134 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.985 0.955 0.982 0.5012 0.499 0.499
#> 3 3 1.000 0.984 0.994 0.3404 0.716 0.489
#> 4 4 1.000 0.967 0.987 0.0861 0.933 0.798
#> 5 5 0.844 0.802 0.903 0.0831 0.880 0.595
#> 6 6 0.833 0.777 0.880 0.0446 0.907 0.593
#> 7 7 0.847 0.787 0.887 0.0197 0.962 0.790
#> 8 8 0.810 0.697 0.831 0.0184 0.992 0.955
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.AR.A1AJ.01 1 0.000 0.978 1.00 0.00
#> TCGA.E9.A1ND.01 1 0.000 0.978 1.00 0.00
#> TCGA.AR.A1AQ.01 1 0.000 0.978 1.00 0.00
#> TCGA.E9.A3QA.01 1 0.000 0.978 1.00 0.00
#> TCGA.S3.AA15.01 1 0.000 0.978 1.00 0.00
#> TCGA.A2.A3XX.01 2 0.000 0.985 0.00 1.00
#> TCGA.A2.A3XT.01 1 0.000 0.978 1.00 0.00
#> TCGA.EW.A1P7.01 1 0.000 0.978 1.00 0.00
#> TCGA.E9.A5FL.01 1 0.000 0.978 1.00 0.00
#> TCGA.A2.A0T2.01 2 0.000 0.985 0.00 1.00
#> TCGA.AR.A0TP.01 2 0.000 0.985 0.00 1.00
#> TCGA.AR.A0TU.01 2 0.855 0.598 0.28 0.72
#> TCGA.A7.A26I.01 2 0.000 0.985 0.00 1.00
#> TCGA.A2.A0ST.01 1 0.000 0.978 1.00 0.00
#> TCGA.BH.A0WA.01 2 0.000 0.985 0.00 1.00
#> TCGA.AR.A1AY.01 2 0.000 0.985 0.00 1.00
#> TCGA.S3.AA10.01 1 0.000 0.978 1.00 0.00
#> TCGA.EW.A6SB.01 1 0.000 0.978 1.00 0.00
#> TCGA.A7.A5ZV.01 2 0.000 0.985 0.00 1.00
#> TCGA.B6.A0WX.01 2 0.141 0.966 0.02 0.98
#> TCGA.BH.A0E0.01 2 0.000 0.985 0.00 1.00
#> TCGA.B6.A0RU.01 2 0.000 0.985 0.00 1.00
#> TCGA.EW.A1PH.01 2 0.000 0.985 0.00 1.00
#> TCGA.A2.A3XS.01 2 0.000 0.985 0.00 1.00
#> TCGA.B6.A1KF.01 2 0.000 0.985 0.00 1.00
#> TCGA.E2.A1AZ.01 1 0.000 0.978 1.00 0.00
#> TCGA.AC.A62X.01 2 0.000 0.985 0.00 1.00
#> TCGA.E9.A22G.01 2 0.000 0.985 0.00 1.00
#> TCGA.D8.A27M.01 1 0.000 0.978 1.00 0.00
#> TCGA.BH.A0RX.01 1 0.000 0.978 1.00 0.00
#> TCGA.A2.A4S1.01 1 0.000 0.978 1.00 0.00
#> TCGA.D8.A1JM.01 2 0.000 0.985 0.00 1.00
#> TCGA.AC.A2QJ.01 1 0.000 0.978 1.00 0.00
#> TCGA.E2.A1II.01 1 0.000 0.978 1.00 0.00
#> TCGA.B6.A3ZX.01 1 0.000 0.978 1.00 0.00
#> TCGA.HN.A2NL.01 2 0.000 0.985 0.00 1.00
#> TCGA.A1.A0SK.01 2 0.000 0.985 0.00 1.00
#> TCGA.LL.A441.01 1 0.000 0.978 1.00 0.00
#> TCGA.A2.A0YM.01 2 0.000 0.985 0.00 1.00
#> TCGA.LL.A5YP.01 2 0.995 0.116 0.46 0.54
#> TCGA.LL.A6FR.01 2 0.000 0.985 0.00 1.00
#> TCGA.PL.A8LV.01 1 0.000 0.978 1.00 0.00
#> TCGA.AO.A1KR.01 1 0.000 0.978 1.00 0.00
#> TCGA.E9.A244.01 2 0.529 0.853 0.12 0.88
#> TCGA.B6.A400.01 1 0.242 0.943 0.96 0.04
#> TCGA.BH.A1FC.01 1 0.000 0.978 1.00 0.00
#> TCGA.BH.A0B9.01 1 0.000 0.978 1.00 0.00
#> TCGA.BH.A18V.06 1 0.000 0.978 1.00 0.00
#> TCGA.C8.A27B.01 2 0.000 0.985 0.00 1.00
#> TCGA.A7.A13E.01 2 0.000 0.985 0.00 1.00
#> TCGA.B6.A402.01 2 0.000 0.985 0.00 1.00
#> TCGA.AR.A1AI.01 1 0.000 0.978 1.00 0.00
#> TCGA.E2.A1LS.01 2 0.000 0.985 0.00 1.00
#> TCGA.D8.A1JL.01 1 0.000 0.978 1.00 0.00
#> TCGA.E2.A1LH.01 1 0.000 0.978 1.00 0.00
#> TCGA.A2.A3Y0.01 1 0.000 0.978 1.00 0.00
#> TCGA.AO.A129.01 1 0.000 0.978 1.00 0.00
#> TCGA.A2.A4RX.01 1 0.000 0.978 1.00 0.00
#> TCGA.E2.A1IP.01 1 0.000 0.978 1.00 0.00
#> TCGA.D8.A27H.01 2 0.000 0.985 0.00 1.00
#> TCGA.E9.A1NC.01 1 0.000 0.978 1.00 0.00
#> TCGA.AO.A124.01 2 0.000 0.985 0.00 1.00
#> TCGA.AR.A256.01 2 0.000 0.985 0.00 1.00
#> TCGA.EW.A1OW.01 2 0.000 0.985 0.00 1.00
#> TCGA.A2.A0YE.01 2 0.000 0.985 0.00 1.00
#> TCGA.A2.A0T0.01 1 0.242 0.943 0.96 0.04
#> TCGA.AC.A2QH.01 2 0.000 0.985 0.00 1.00
#> TCGA.E2.A573.01 1 0.000 0.978 1.00 0.00
#> TCGA.OL.A6VO.01 2 0.000 0.985 0.00 1.00
#> TCGA.A2.A3XU.01 2 0.000 0.985 0.00 1.00
#> TCGA.GM.A3XL.01 1 0.000 0.978 1.00 0.00
#> TCGA.AN.A0XU.01 2 0.000 0.985 0.00 1.00
#> TCGA.A7.A6VV.01 2 0.000 0.985 0.00 1.00
#> TCGA.EW.A3U0.01 1 0.000 0.978 1.00 0.00
#> TCGA.E9.A243.01 1 0.000 0.978 1.00 0.00
#> TCGA.OL.A5S0.01 1 0.000 0.978 1.00 0.00
#> TCGA.D8.A27F.01 2 0.000 0.985 0.00 1.00
#> TCGA.E2.A1LI.01 1 0.000 0.978 1.00 0.00
#> TCGA.A7.A26F.01 1 0.000 0.978 1.00 0.00
#> TCGA.B6.A0RE.01 2 0.000 0.985 0.00 1.00
#> TCGA.BH.A1F6.01 1 0.000 0.978 1.00 0.00
#> TCGA.E2.A14N.01 1 0.000 0.978 1.00 0.00
#> TCGA.OL.A5RW.01 2 0.000 0.985 0.00 1.00
#> TCGA.A1.A0SB.01 2 0.000 0.985 0.00 1.00
#> TCGA.AR.A2LR.01 2 0.000 0.985 0.00 1.00
#> TCGA.AR.A251.01 2 0.000 0.985 0.00 1.00
#> TCGA.AR.A1AR.01 1 0.000 0.978 1.00 0.00
#> TCGA.AO.A0JL.01 2 0.000 0.985 0.00 1.00
#> TCGA.EW.A1P8.01 1 0.402 0.903 0.92 0.08
#> TCGA.AR.A0U4.01 1 0.000 0.978 1.00 0.00
#> TCGA.B6.A409.01 1 0.943 0.450 0.64 0.36
#> TCGA.B6.A0X1.01 1 0.981 0.289 0.58 0.42
#> TCGA.A2.A0SX.01 1 0.000 0.978 1.00 0.00
#> TCGA.EW.A1P4.01 1 0.000 0.978 1.00 0.00
#> TCGA.AO.A128.01 1 0.000 0.978 1.00 0.00
#> TCGA.GM.A2DF.01 1 0.000 0.978 1.00 0.00
#> TCGA.A1.A0SP.01 1 0.000 0.978 1.00 0.00
#> TCGA.E2.A1LG.01 2 0.000 0.985 0.00 1.00
#> TCGA.A7.A6VY.01 1 0.000 0.978 1.00 0.00
#> TCGA.A7.A26G.01 1 0.000 0.978 1.00 0.00
#> TCGA.A2.A0YJ.01 2 0.000 0.985 0.00 1.00
#> TCGA.AC.A7VC.01 1 0.584 0.832 0.86 0.14
#> TCGA.OL.A66I.01 1 0.000 0.978 1.00 0.00
#> TCGA.A7.A6VW.01 2 0.000 0.985 0.00 1.00
#> TCGA.B6.A0I1.01 2 0.000 0.985 0.00 1.00
#> TCGA.LL.A73Y.01 1 0.000 0.978 1.00 0.00
#> TCGA.C8.A1HJ.01 2 0.000 0.985 0.00 1.00
#> TCGA.A2.A1G1.01 1 0.000 0.978 1.00 0.00
#> TCGA.A7.A13D.01 2 0.000 0.985 0.00 1.00
#> TCGA.A2.A3XY.01 1 0.000 0.978 1.00 0.00
#> TCGA.A7.A4SD.01 1 0.000 0.978 1.00 0.00
#> TCGA.D8.A1XQ.01 1 0.943 0.450 0.64 0.36
#> TCGA.AC.A6IW.01 1 0.000 0.978 1.00 0.00
#> TCGA.BH.A5IZ.01 2 0.000 0.985 0.00 1.00
#> TCGA.LL.A8F5.01 2 0.000 0.985 0.00 1.00
#> TCGA.D8.A1XW.01 1 0.469 0.881 0.90 0.10
#> TCGA.PL.A8LZ.01 1 0.000 0.978 1.00 0.00
#> TCGA.AC.A2BK.01 2 0.000 0.985 0.00 1.00
#> TCGA.GI.A2C9.01 2 0.000 0.985 0.00 1.00
#> TCGA.E2.A1LK.01 2 0.000 0.985 0.00 1.00
#> TCGA.OL.A5D7.01 1 0.000 0.978 1.00 0.00
#> TCGA.A7.A4SE.01 2 0.000 0.985 0.00 1.00
#> TCGA.S3.AA0Z.01 2 0.000 0.985 0.00 1.00
#> TCGA.BH.A0B3.01 1 0.000 0.978 1.00 0.00
#> TCGA.AQ.A54N.01 2 0.000 0.985 0.00 1.00
#> TCGA.D8.A1XK.01 1 0.000 0.978 1.00 0.00
#> TCGA.AC.A8OQ.01 1 0.000 0.978 1.00 0.00
#> TCGA.EW.A1PB.01 1 0.000 0.978 1.00 0.00
#> TCGA.E9.A1N8.01 2 0.000 0.985 0.00 1.00
#> TCGA.E2.A574.01 2 0.000 0.985 0.00 1.00
#> TCGA.A1.A0SO.01 2 0.000 0.985 0.00 1.00
#> TCGA.AR.A24Q.01 2 0.000 0.985 0.00 1.00
#> TCGA.BH.A1F0.01 1 0.000 0.978 1.00 0.00
#> TCGA.AR.A0U0.01 1 0.000 0.978 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.AR.A1AJ.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.E9.A1ND.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.AR.A1AQ.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.E9.A3QA.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.S3.AA15.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.A2.A3XX.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.A2.A3XT.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.EW.A1P7.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.E9.A5FL.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.A2.A0T2.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.AR.A0TP.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.AR.A0TU.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.A7.A26I.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.A2.A0ST.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.BH.A0WA.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.AR.A1AY.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.S3.AA10.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.EW.A6SB.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.A7.A5ZV.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.B6.A0WX.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.BH.A0E0.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.B6.A0RU.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.EW.A1PH.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.A2.A3XS.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.B6.A1KF.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.E2.A1AZ.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.AC.A62X.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.E9.A22G.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.D8.A27M.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.BH.A0RX.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.A2.A4S1.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.D8.A1JM.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.AC.A2QJ.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.E2.A1II.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.B6.A3ZX.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.HN.A2NL.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.A1.A0SK.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.LL.A441.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.A2.A0YM.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.LL.A5YP.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.LL.A6FR.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.PL.A8LV.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.AO.A1KR.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.E9.A244.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.B6.A400.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.BH.A1FC.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.BH.A0B9.01 3 0.6302 0.0766 0.48 0.00 0.52
#> TCGA.BH.A18V.06 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.C8.A27B.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.A7.A13E.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.B6.A402.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.AR.A1AI.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.E2.A1LS.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.D8.A1JL.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.E2.A1LH.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.A2.A3Y0.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.AO.A129.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.A2.A4RX.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.E2.A1IP.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.D8.A27H.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.E9.A1NC.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.AO.A124.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.AR.A256.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.EW.A1OW.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.A2.A0YE.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.A2.A0T0.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.AC.A2QH.01 2 0.5216 0.6475 0.00 0.74 0.26
#> TCGA.E2.A573.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.OL.A6VO.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.A2.A3XU.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.GM.A3XL.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.AN.A0XU.01 3 0.1529 0.9479 0.00 0.04 0.96
#> TCGA.A7.A6VV.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.EW.A3U0.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.E9.A243.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.OL.A5S0.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.D8.A27F.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.E2.A1LI.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.A7.A26F.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.B6.A0RE.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.BH.A1F6.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.E2.A14N.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.OL.A5RW.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.A1.A0SB.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.AR.A2LR.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.AR.A251.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.AR.A1AR.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.AO.A0JL.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.EW.A1P8.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.AR.A0U4.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.B6.A409.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.B6.A0X1.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.A2.A0SX.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.EW.A1P4.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.AO.A128.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.GM.A2DF.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.A1.A0SP.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.E2.A1LG.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.A7.A6VY.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.A7.A26G.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.A2.A0YJ.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.AC.A7VC.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.OL.A66I.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.A7.A6VW.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.B6.A0I1.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.LL.A73Y.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.C8.A1HJ.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.A2.A1G1.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.A7.A13D.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.A2.A3XY.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.A7.A4SD.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.D8.A1XQ.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.AC.A6IW.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.BH.A5IZ.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.LL.A8F5.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.D8.A1XW.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.PL.A8LZ.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.AC.A2BK.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.GI.A2C9.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.E2.A1LK.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.OL.A5D7.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.A7.A4SE.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.S3.AA0Z.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.BH.A0B3.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.AQ.A54N.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.D8.A1XK.01 3 0.0892 0.9689 0.02 0.00 0.98
#> TCGA.AC.A8OQ.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.EW.A1PB.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.E9.A1N8.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.E2.A574.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.A1.A0SO.01 2 0.0000 0.9939 0.00 1.00 0.00
#> TCGA.AR.A24Q.01 3 0.0000 0.9878 0.00 0.00 1.00
#> TCGA.BH.A1F0.01 1 0.0000 1.0000 1.00 0.00 0.00
#> TCGA.AR.A0U0.01 1 0.0000 1.0000 1.00 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.AR.A1AJ.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E9.A1ND.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AR.A1AQ.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E9.A3QA.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.S3.AA15.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A2.A3XX.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.A2.A3XT.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.EW.A1P7.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E9.A5FL.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A2.A0T2.01 4 0.0000 0.975 0.00 0.00 0.00 1.00
#> TCGA.AR.A0TP.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.AR.A0TU.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.A7.A26I.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.A2.A0ST.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BH.A0WA.01 4 0.0000 0.975 0.00 0.00 0.00 1.00
#> TCGA.AR.A1AY.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.S3.AA10.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EW.A6SB.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A7.A5ZV.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.B6.A0WX.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.BH.A0E0.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.B6.A0RU.01 3 0.3172 0.810 0.00 0.16 0.84 0.00
#> TCGA.EW.A1PH.01 4 0.0000 0.975 0.00 0.00 0.00 1.00
#> TCGA.A2.A3XS.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.B6.A1KF.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.E2.A1AZ.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.AC.A62X.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.E9.A22G.01 4 0.0000 0.975 0.00 0.00 0.00 1.00
#> TCGA.D8.A27M.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BH.A0RX.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A2.A4S1.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.D8.A1JM.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.AC.A2QJ.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E2.A1II.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B6.A3ZX.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HN.A2NL.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.A1.A0SK.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.LL.A441.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A2.A0YM.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.LL.A5YP.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.LL.A6FR.01 4 0.0000 0.975 0.00 0.00 0.00 1.00
#> TCGA.PL.A8LV.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.AO.A1KR.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.E9.A244.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.B6.A400.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.BH.A1FC.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.BH.A0B9.01 3 0.4277 0.601 0.28 0.00 0.72 0.00
#> TCGA.BH.A18V.06 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.C8.A27B.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.A7.A13E.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.B6.A402.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.AR.A1AI.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E2.A1LS.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.D8.A1JL.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E2.A1LH.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A2.A3Y0.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AO.A129.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A2.A4RX.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.E2.A1IP.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.D8.A27H.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.E9.A1NC.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AO.A124.01 4 0.0000 0.975 0.00 0.00 0.00 1.00
#> TCGA.AR.A256.01 4 0.0000 0.975 0.00 0.00 0.00 1.00
#> TCGA.EW.A1OW.01 4 0.0000 0.975 0.00 0.00 0.00 1.00
#> TCGA.A2.A0YE.01 4 0.0000 0.975 0.00 0.00 0.00 1.00
#> TCGA.A2.A0T0.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.AC.A2QH.01 4 0.0000 0.975 0.00 0.00 0.00 1.00
#> TCGA.E2.A573.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.OL.A6VO.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.A2.A3XU.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.GM.A3XL.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.AN.A0XU.01 3 0.4134 0.660 0.00 0.26 0.74 0.00
#> TCGA.A7.A6VV.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.EW.A3U0.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E9.A243.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.OL.A5S0.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.D8.A27F.01 4 0.0000 0.975 0.00 0.00 0.00 1.00
#> TCGA.E2.A1LI.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A7.A26F.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.B6.A0RE.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.BH.A1F6.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.E2.A14N.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.OL.A5RW.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.A1.A0SB.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.AR.A2LR.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.AR.A251.01 4 0.0000 0.975 0.00 0.00 0.00 1.00
#> TCGA.AR.A1AR.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.AO.A0JL.01 2 0.4977 0.155 0.00 0.54 0.00 0.46
#> TCGA.EW.A1P8.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.AR.A0U4.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.B6.A409.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.B6.A0X1.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.A2.A0SX.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.EW.A1P4.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AO.A128.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.GM.A2DF.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A1.A0SP.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.E2.A1LG.01 4 0.0000 0.975 0.00 0.00 0.00 1.00
#> TCGA.A7.A6VY.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.A7.A26G.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A2.A0YJ.01 4 0.0000 0.975 0.00 0.00 0.00 1.00
#> TCGA.AC.A7VC.01 4 0.4790 0.381 0.00 0.00 0.38 0.62
#> TCGA.OL.A66I.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A7.A6VW.01 3 0.3172 0.810 0.00 0.16 0.84 0.00
#> TCGA.B6.A0I1.01 4 0.0000 0.975 0.00 0.00 0.00 1.00
#> TCGA.LL.A73Y.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.C8.A1HJ.01 4 0.0000 0.975 0.00 0.00 0.00 1.00
#> TCGA.A2.A1G1.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.A7.A13D.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.A2.A3XY.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A7.A4SD.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.D8.A1XQ.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.AC.A6IW.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BH.A5IZ.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.LL.A8F5.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.D8.A1XW.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.PL.A8LZ.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AC.A2BK.01 4 0.0000 0.975 0.00 0.00 0.00 1.00
#> TCGA.GI.A2C9.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.E2.A1LK.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.OL.A5D7.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.A7.A4SE.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.S3.AA0Z.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.BH.A0B3.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.AQ.A54N.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.D8.A1XK.01 3 0.0707 0.956 0.02 0.00 0.98 0.00
#> TCGA.AC.A8OQ.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EW.A1PB.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E9.A1N8.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.E2.A574.01 4 0.0000 0.975 0.00 0.00 0.00 1.00
#> TCGA.A1.A0SO.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.AR.A24Q.01 3 0.0000 0.977 0.00 0.00 1.00 0.00
#> TCGA.BH.A1F0.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AR.A0U0.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.AR.A1AJ.01 1 0.0000 0.9435 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1ND.01 5 0.4262 0.2994 0.44 0.00 0.00 0.00 0.56
#> TCGA.AR.A1AQ.01 5 0.4262 0.2994 0.44 0.00 0.00 0.00 0.56
#> TCGA.E9.A3QA.01 1 0.0000 0.9435 1.00 0.00 0.00 0.00 0.00
#> TCGA.S3.AA15.01 1 0.0000 0.9435 1.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A3XX.01 3 0.0000 0.8885 0.00 0.00 1.00 0.00 0.00
#> TCGA.A2.A3XT.01 5 0.4182 0.3702 0.00 0.00 0.40 0.00 0.60
#> TCGA.EW.A1P7.01 1 0.0000 0.9435 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A5FL.01 5 0.4798 0.2565 0.44 0.00 0.02 0.00 0.54
#> TCGA.A2.A0T2.01 4 0.0000 0.9718 0.00 0.00 0.00 1.00 0.00
#> TCGA.AR.A0TP.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A0TU.01 5 0.2020 0.6374 0.00 0.00 0.10 0.00 0.90
#> TCGA.A7.A26I.01 3 0.0000 0.8885 0.00 0.00 1.00 0.00 0.00
#> TCGA.A2.A0ST.01 1 0.0000 0.9435 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0WA.01 4 0.0000 0.9718 0.00 0.00 0.00 1.00 0.00
#> TCGA.AR.A1AY.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00
#> TCGA.S3.AA10.01 1 0.2020 0.9115 0.90 0.00 0.00 0.00 0.10
#> TCGA.EW.A6SB.01 1 0.0000 0.9435 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A5ZV.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00
#> TCGA.B6.A0WX.01 3 0.4182 0.4682 0.00 0.00 0.60 0.00 0.40
#> TCGA.BH.A0E0.01 3 0.0000 0.8885 0.00 0.00 1.00 0.00 0.00
#> TCGA.B6.A0RU.01 3 0.4096 0.6780 0.00 0.20 0.76 0.00 0.04
#> TCGA.EW.A1PH.01 4 0.0000 0.9718 0.00 0.00 0.00 1.00 0.00
#> TCGA.A2.A3XS.01 3 0.4675 0.4783 0.00 0.02 0.60 0.00 0.38
#> TCGA.B6.A1KF.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00
#> TCGA.E2.A1AZ.01 5 0.4227 0.3413 0.00 0.00 0.42 0.00 0.58
#> TCGA.AC.A62X.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00
#> TCGA.E9.A22G.01 4 0.0000 0.9718 0.00 0.00 0.00 1.00 0.00
#> TCGA.D8.A27M.01 1 0.0000 0.9435 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0RX.01 1 0.0000 0.9435 1.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A4S1.01 1 0.1732 0.9292 0.92 0.00 0.00 0.00 0.08
#> TCGA.D8.A1JM.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A2QJ.01 1 0.1732 0.9292 0.92 0.00 0.00 0.00 0.08
#> TCGA.E2.A1II.01 1 0.1043 0.9417 0.96 0.00 0.00 0.00 0.04
#> TCGA.B6.A3ZX.01 1 0.0000 0.9435 1.00 0.00 0.00 0.00 0.00
#> TCGA.HN.A2NL.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00
#> TCGA.A1.A0SK.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00
#> TCGA.LL.A441.01 1 0.0000 0.9435 1.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0YM.01 2 0.3796 0.6075 0.00 0.70 0.00 0.00 0.30
#> TCGA.LL.A5YP.01 3 0.0000 0.8885 0.00 0.00 1.00 0.00 0.00
#> TCGA.LL.A6FR.01 4 0.0000 0.9718 0.00 0.00 0.00 1.00 0.00
#> TCGA.PL.A8LV.01 5 0.2732 0.6162 0.00 0.00 0.16 0.00 0.84
#> TCGA.AO.A1KR.01 5 0.2020 0.6374 0.00 0.00 0.10 0.00 0.90
#> TCGA.E9.A244.01 3 0.0000 0.8885 0.00 0.00 1.00 0.00 0.00
#> TCGA.B6.A400.01 3 0.0000 0.8885 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A1FC.01 5 0.2020 0.6374 0.00 0.00 0.10 0.00 0.90
#> TCGA.BH.A0B9.01 5 0.4726 0.3576 0.02 0.00 0.40 0.00 0.58
#> TCGA.BH.A18V.06 1 0.1410 0.9387 0.94 0.00 0.00 0.00 0.06
#> TCGA.C8.A27B.01 3 0.0000 0.8885 0.00 0.00 1.00 0.00 0.00
#> TCGA.A7.A13E.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00
#> TCGA.B6.A402.01 2 0.1410 0.9211 0.00 0.94 0.00 0.06 0.00
#> TCGA.AR.A1AI.01 1 0.1410 0.9387 0.94 0.00 0.00 0.00 0.06
#> TCGA.E2.A1LS.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A1JL.01 5 0.4262 0.2994 0.44 0.00 0.00 0.00 0.56
#> TCGA.E2.A1LH.01 1 0.1410 0.9387 0.94 0.00 0.00 0.00 0.06
#> TCGA.A2.A3Y0.01 1 0.1732 0.9292 0.92 0.00 0.00 0.00 0.08
#> TCGA.AO.A129.01 1 0.1410 0.9387 0.94 0.00 0.00 0.00 0.06
#> TCGA.A2.A4RX.01 5 0.3274 0.5756 0.00 0.00 0.22 0.00 0.78
#> TCGA.E2.A1IP.01 1 0.0000 0.9435 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A27H.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00
#> TCGA.E9.A1NC.01 1 0.1410 0.9387 0.94 0.00 0.00 0.00 0.06
#> TCGA.AO.A124.01 4 0.0000 0.9718 0.00 0.00 0.00 1.00 0.00
#> TCGA.AR.A256.01 4 0.0000 0.9718 0.00 0.00 0.00 1.00 0.00
#> TCGA.EW.A1OW.01 4 0.0000 0.9718 0.00 0.00 0.00 1.00 0.00
#> TCGA.A2.A0YE.01 4 0.0000 0.9718 0.00 0.00 0.00 1.00 0.00
#> TCGA.A2.A0T0.01 3 0.0609 0.8726 0.00 0.00 0.98 0.00 0.02
#> TCGA.AC.A2QH.01 4 0.3999 0.6436 0.00 0.00 0.24 0.74 0.02
#> TCGA.E2.A573.01 1 0.1410 0.9387 0.94 0.00 0.00 0.00 0.06
#> TCGA.OL.A6VO.01 2 0.3109 0.7311 0.00 0.80 0.20 0.00 0.00
#> TCGA.A2.A3XU.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00
#> TCGA.GM.A3XL.01 5 0.2020 0.6374 0.00 0.00 0.10 0.00 0.90
#> TCGA.AN.A0XU.01 3 0.2516 0.7682 0.00 0.14 0.86 0.00 0.00
#> TCGA.A7.A6VV.01 3 0.0000 0.8885 0.00 0.00 1.00 0.00 0.00
#> TCGA.EW.A3U0.01 1 0.0000 0.9435 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A243.01 1 0.0000 0.9435 1.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5S0.01 5 0.2732 0.6162 0.00 0.00 0.16 0.00 0.84
#> TCGA.D8.A27F.01 4 0.0000 0.9718 0.00 0.00 0.00 1.00 0.00
#> TCGA.E2.A1LI.01 5 0.4262 0.2994 0.44 0.00 0.00 0.00 0.56
#> TCGA.A7.A26F.01 5 0.1043 0.6461 0.00 0.00 0.04 0.00 0.96
#> TCGA.B6.A0RE.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A1F6.01 5 0.2020 0.6374 0.00 0.00 0.10 0.00 0.90
#> TCGA.E2.A14N.01 1 0.1410 0.9387 0.94 0.00 0.00 0.00 0.06
#> TCGA.OL.A5RW.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00
#> TCGA.A1.A0SB.01 2 0.0609 0.9592 0.00 0.98 0.00 0.02 0.00
#> TCGA.AR.A2LR.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A251.01 4 0.0000 0.9718 0.00 0.00 0.00 1.00 0.00
#> TCGA.AR.A1AR.01 5 0.1043 0.6473 0.00 0.00 0.04 0.00 0.96
#> TCGA.AO.A0JL.01 4 0.3274 0.7094 0.00 0.22 0.00 0.78 0.00
#> TCGA.EW.A1P8.01 3 0.0000 0.8885 0.00 0.00 1.00 0.00 0.00
#> TCGA.AR.A0U4.01 1 0.2929 0.7857 0.82 0.00 0.00 0.00 0.18
#> TCGA.B6.A409.01 3 0.0000 0.8885 0.00 0.00 1.00 0.00 0.00
#> TCGA.B6.A0X1.01 3 0.0000 0.8885 0.00 0.00 1.00 0.00 0.00
#> TCGA.A2.A0SX.01 5 0.4126 0.4107 0.00 0.00 0.38 0.00 0.62
#> TCGA.EW.A1P4.01 5 0.4227 0.3197 0.42 0.00 0.00 0.00 0.58
#> TCGA.AO.A128.01 1 0.0000 0.9435 1.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A2DF.01 1 0.1410 0.9387 0.94 0.00 0.00 0.00 0.06
#> TCGA.A1.A0SP.01 5 0.2020 0.6374 0.00 0.00 0.10 0.00 0.90
#> TCGA.E2.A1LG.01 4 0.0000 0.9718 0.00 0.00 0.00 1.00 0.00
#> TCGA.A7.A6VY.01 5 0.2020 0.6374 0.00 0.00 0.10 0.00 0.90
#> TCGA.A7.A26G.01 1 0.1410 0.9387 0.94 0.00 0.00 0.00 0.06
#> TCGA.A2.A0YJ.01 4 0.0000 0.9718 0.00 0.00 0.00 1.00 0.00
#> TCGA.AC.A7VC.01 3 0.2754 0.7841 0.00 0.00 0.88 0.08 0.04
#> TCGA.OL.A66I.01 5 0.4262 0.2994 0.44 0.00 0.00 0.00 0.56
#> TCGA.A7.A6VW.01 5 0.6778 -0.0888 0.00 0.34 0.28 0.00 0.38
#> TCGA.B6.A0I1.01 4 0.0000 0.9718 0.00 0.00 0.00 1.00 0.00
#> TCGA.LL.A73Y.01 3 0.0000 0.8885 0.00 0.00 1.00 0.00 0.00
#> TCGA.C8.A1HJ.01 4 0.0000 0.9718 0.00 0.00 0.00 1.00 0.00
#> TCGA.A2.A1G1.01 5 0.1732 0.6389 0.00 0.00 0.08 0.00 0.92
#> TCGA.A7.A13D.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A3XY.01 1 0.4287 0.0400 0.54 0.00 0.00 0.00 0.46
#> TCGA.A7.A4SD.01 1 0.1732 0.9292 0.92 0.00 0.00 0.00 0.08
#> TCGA.D8.A1XQ.01 3 0.0609 0.8726 0.00 0.00 0.98 0.00 0.02
#> TCGA.AC.A6IW.01 5 0.4262 0.2994 0.44 0.00 0.00 0.00 0.56
#> TCGA.BH.A5IZ.01 3 0.4182 0.4682 0.00 0.00 0.60 0.00 0.40
#> TCGA.LL.A8F5.01 3 0.4182 0.4682 0.00 0.00 0.60 0.00 0.40
#> TCGA.D8.A1XW.01 3 0.0000 0.8885 0.00 0.00 1.00 0.00 0.00
#> TCGA.PL.A8LZ.01 1 0.0000 0.9435 1.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A2BK.01 4 0.0000 0.9718 0.00 0.00 0.00 1.00 0.00
#> TCGA.GI.A2C9.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00
#> TCGA.E2.A1LK.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00
#> TCGA.OL.A5D7.01 5 0.2020 0.6374 0.00 0.00 0.10 0.00 0.90
#> TCGA.A7.A4SE.01 3 0.0000 0.8885 0.00 0.00 1.00 0.00 0.00
#> TCGA.S3.AA0Z.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0B3.01 5 0.4262 0.3013 0.00 0.00 0.44 0.00 0.56
#> TCGA.AQ.A54N.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A1XK.01 5 0.1043 0.6473 0.00 0.00 0.04 0.00 0.96
#> TCGA.AC.A8OQ.01 1 0.0000 0.9435 1.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1PB.01 1 0.1410 0.9387 0.94 0.00 0.00 0.00 0.06
#> TCGA.E9.A1N8.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00
#> TCGA.E2.A574.01 4 0.0000 0.9718 0.00 0.00 0.00 1.00 0.00
#> TCGA.A1.A0SO.01 2 0.0000 0.9755 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A24Q.01 3 0.0000 0.8885 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A1F0.01 1 0.0000 0.9435 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A0U0.01 5 0.4227 0.3197 0.42 0.00 0.00 0.00 0.58
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.AR.A1AJ.01 1 0.0000 0.8132 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1ND.01 6 0.2094 0.7623 0.08 0.00 0.00 0.00 0.02 0.90
#> TCGA.AR.A1AQ.01 6 0.2094 0.7623 0.08 0.00 0.00 0.00 0.02 0.90
#> TCGA.E9.A3QA.01 1 0.0000 0.8132 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S3.AA15.01 1 0.0000 0.8132 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A3XX.01 3 0.0547 0.9683 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.A2.A3XT.01 6 0.1814 0.7047 0.00 0.00 0.10 0.00 0.00 0.90
#> TCGA.EW.A1P7.01 1 0.0000 0.8132 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A5FL.01 6 0.2094 0.7654 0.08 0.00 0.02 0.00 0.00 0.90
#> TCGA.A2.A0T2.01 4 0.0000 0.9504 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AR.A0TP.01 2 0.0000 0.9535 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A0TU.01 5 0.2260 0.8164 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.A7.A26I.01 3 0.0547 0.9683 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.A2.A0ST.01 1 0.0000 0.8132 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0WA.01 4 0.0000 0.9504 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AR.A1AY.01 2 0.0937 0.9438 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.S3.AA10.01 6 0.3076 0.6805 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.EW.A6SB.01 1 0.0000 0.8132 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A5ZV.01 2 0.1556 0.9174 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.B6.A0WX.01 5 0.2048 0.7270 0.00 0.00 0.12 0.00 0.88 0.00
#> TCGA.BH.A0E0.01 3 0.0547 0.9683 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.B6.A0RU.01 3 0.2190 0.9090 0.00 0.04 0.90 0.00 0.06 0.00
#> TCGA.EW.A1PH.01 4 0.0000 0.9504 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A2.A3XS.01 5 0.2260 0.7117 0.00 0.00 0.14 0.00 0.86 0.00
#> TCGA.B6.A1KF.01 2 0.0000 0.9535 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1AZ.01 6 0.2631 0.6504 0.00 0.00 0.18 0.00 0.00 0.82
#> TCGA.AC.A62X.01 2 0.0000 0.9535 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A22G.01 4 0.0937 0.9262 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.D8.A27M.01 1 0.0547 0.7973 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.BH.A0RX.01 1 0.0000 0.8132 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A4S1.01 6 0.3828 0.3248 0.44 0.00 0.00 0.00 0.00 0.56
#> TCGA.D8.A1JM.01 2 0.0937 0.9438 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.AC.A2QJ.01 1 0.3864 -0.0675 0.52 0.00 0.00 0.00 0.00 0.48
#> TCGA.E2.A1II.01 1 0.3499 0.3714 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.B6.A3ZX.01 1 0.0000 0.8132 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HN.A2NL.01 2 0.0000 0.9535 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A1.A0SK.01 2 0.1556 0.8965 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.LL.A441.01 1 0.0000 0.8132 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0YM.01 5 0.3706 0.2824 0.00 0.38 0.00 0.00 0.62 0.00
#> TCGA.LL.A5YP.01 3 0.0000 0.9714 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.LL.A6FR.01 4 0.0000 0.9504 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.PL.A8LV.01 5 0.4282 0.6305 0.00 0.00 0.02 0.00 0.56 0.42
#> TCGA.AO.A1KR.01 5 0.2454 0.8218 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.E9.A244.01 3 0.0000 0.9714 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B6.A400.01 3 0.0000 0.9714 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A1FC.01 5 0.2454 0.8218 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.BH.A0B9.01 6 0.2581 0.7191 0.02 0.00 0.12 0.00 0.00 0.86
#> TCGA.BH.A18V.06 6 0.3828 0.3628 0.44 0.00 0.00 0.00 0.00 0.56
#> TCGA.C8.A27B.01 3 0.0547 0.9683 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.A7.A13E.01 2 0.0000 0.9535 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A402.01 2 0.2793 0.7533 0.00 0.80 0.00 0.20 0.00 0.00
#> TCGA.AR.A1AI.01 1 0.3851 0.0146 0.54 0.00 0.00 0.00 0.00 0.46
#> TCGA.E2.A1LS.01 2 0.0000 0.9535 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JL.01 6 0.2094 0.7623 0.08 0.00 0.00 0.00 0.02 0.90
#> TCGA.E2.A1LH.01 6 0.3756 0.4315 0.40 0.00 0.00 0.00 0.00 0.60
#> TCGA.A2.A3Y0.01 6 0.3916 0.6019 0.30 0.00 0.02 0.00 0.00 0.68
#> TCGA.AO.A129.01 1 0.3864 -0.0675 0.52 0.00 0.00 0.00 0.00 0.48
#> TCGA.A2.A4RX.01 5 0.4632 0.5809 0.00 0.00 0.04 0.00 0.52 0.44
#> TCGA.E2.A1IP.01 1 0.0000 0.8132 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A27H.01 2 0.0547 0.9465 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.E9.A1NC.01 1 0.3797 0.1254 0.58 0.00 0.00 0.00 0.00 0.42
#> TCGA.AO.A124.01 4 0.0000 0.9504 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AR.A256.01 4 0.0937 0.9262 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.EW.A1OW.01 4 0.0000 0.9504 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A2.A0YE.01 4 0.0000 0.9504 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A2.A0T0.01 3 0.0000 0.9714 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A2QH.01 4 0.6435 0.3387 0.00 0.00 0.28 0.52 0.12 0.08
#> TCGA.E2.A573.01 6 0.3828 0.3245 0.44 0.00 0.00 0.00 0.00 0.56
#> TCGA.OL.A6VO.01 2 0.4121 0.6774 0.00 0.72 0.22 0.00 0.06 0.00
#> TCGA.A2.A3XU.01 2 0.0000 0.9535 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A3XL.01 5 0.2454 0.8218 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.AN.A0XU.01 3 0.1807 0.9278 0.00 0.02 0.92 0.00 0.06 0.00
#> TCGA.A7.A6VV.01 3 0.0937 0.9575 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.EW.A3U0.01 1 0.0000 0.8132 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A243.01 1 0.0000 0.8132 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5S0.01 5 0.3819 0.7639 0.00 0.00 0.02 0.00 0.70 0.28
#> TCGA.D8.A27F.01 4 0.0000 0.9504 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E2.A1LI.01 6 0.1814 0.7654 0.10 0.00 0.00 0.00 0.00 0.90
#> TCGA.A7.A26F.01 5 0.3828 0.6177 0.00 0.00 0.00 0.00 0.56 0.44
#> TCGA.B6.A0RE.01 2 0.0937 0.9438 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.BH.A1F6.01 5 0.2454 0.8218 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.E2.A14N.01 6 0.3198 0.6703 0.26 0.00 0.00 0.00 0.00 0.74
#> TCGA.OL.A5RW.01 2 0.0937 0.9438 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.A1.A0SB.01 2 0.2260 0.8346 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.AR.A2LR.01 2 0.0000 0.9535 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A251.01 4 0.0000 0.9504 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AR.A1AR.01 5 0.3828 0.6177 0.00 0.00 0.00 0.00 0.56 0.44
#> TCGA.AO.A0JL.01 4 0.3409 0.5735 0.00 0.30 0.00 0.70 0.00 0.00
#> TCGA.EW.A1P8.01 3 0.0000 0.9714 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A0U4.01 6 0.3499 0.6123 0.32 0.00 0.00 0.00 0.00 0.68
#> TCGA.B6.A409.01 3 0.0000 0.9714 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B6.A0X1.01 3 0.0000 0.9714 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A0SX.01 6 0.2190 0.6757 0.00 0.00 0.04 0.00 0.06 0.90
#> TCGA.EW.A1P4.01 6 0.1556 0.7658 0.08 0.00 0.00 0.00 0.00 0.92
#> TCGA.AO.A128.01 1 0.0000 0.8132 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A2DF.01 6 0.3864 0.2679 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.A1.A0SP.01 5 0.2454 0.8218 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.E2.A1LG.01 4 0.0000 0.9504 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A7.A6VY.01 5 0.2454 0.8218 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.A7.A26G.01 1 0.3756 0.1789 0.60 0.00 0.00 0.00 0.00 0.40
#> TCGA.A2.A0YJ.01 4 0.0000 0.9504 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AC.A7VC.01 3 0.3567 0.8118 0.00 0.00 0.80 0.00 0.10 0.10
#> TCGA.OL.A66I.01 6 0.2790 0.7338 0.14 0.00 0.00 0.00 0.02 0.84
#> TCGA.A7.A6VW.01 5 0.2794 0.7270 0.00 0.08 0.06 0.00 0.86 0.00
#> TCGA.B6.A0I1.01 4 0.0000 0.9504 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.LL.A73Y.01 3 0.0000 0.9714 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.C8.A1HJ.01 4 0.0000 0.9504 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A2.A1G1.01 5 0.3076 0.7900 0.00 0.00 0.00 0.00 0.76 0.24
#> TCGA.A7.A13D.01 2 0.1267 0.9342 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.A2.A3XY.01 6 0.2260 0.7523 0.14 0.00 0.00 0.00 0.00 0.86
#> TCGA.A7.A4SD.01 1 0.3851 0.0146 0.54 0.00 0.00 0.00 0.00 0.46
#> TCGA.D8.A1XQ.01 3 0.0000 0.9714 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A6IW.01 6 0.2094 0.7623 0.08 0.00 0.00 0.00 0.02 0.90
#> TCGA.BH.A5IZ.01 5 0.2454 0.6913 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.LL.A8F5.01 5 0.2260 0.7117 0.00 0.00 0.14 0.00 0.86 0.00
#> TCGA.D8.A1XW.01 3 0.0000 0.9714 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.PL.A8LZ.01 1 0.0000 0.8132 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A2BK.01 4 0.0937 0.9262 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.GI.A2C9.01 2 0.0000 0.9535 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1LK.01 2 0.0000 0.9535 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5D7.01 5 0.2454 0.8218 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.A7.A4SE.01 3 0.1267 0.9427 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.S3.AA0Z.01 2 0.0937 0.9438 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.BH.A0B3.01 6 0.2260 0.6942 0.00 0.00 0.14 0.00 0.00 0.86
#> TCGA.AQ.A54N.01 2 0.0000 0.9535 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1XK.01 5 0.3828 0.6177 0.00 0.00 0.00 0.00 0.56 0.44
#> TCGA.AC.A8OQ.01 1 0.0000 0.8132 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1PB.01 6 0.3864 0.2679 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.E9.A1N8.01 2 0.0000 0.9535 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A574.01 4 0.0000 0.9504 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A1.A0SO.01 2 0.0937 0.9438 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.AR.A24Q.01 3 0.0547 0.9683 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.BH.A1F0.01 1 0.0000 0.8132 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A0U0.01 6 0.1556 0.7658 0.08 0.00 0.00 0.00 0.00 0.92
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.AR.A1AJ.01 1 0.0000 0.9583 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1ND.01 6 0.1006 0.7791 0.00 0.00 0.00 0.00 0.02 0.96 0.02
#> TCGA.AR.A1AQ.01 6 0.1363 0.7670 0.00 0.00 0.00 0.00 0.04 0.94 0.02
#> TCGA.E9.A3QA.01 1 0.0000 0.9583 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S3.AA15.01 1 0.0000 0.9583 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A3XX.01 3 0.0000 0.9031 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A3XT.01 6 0.1363 0.7759 0.00 0.00 0.04 0.00 0.00 0.94 0.02
#> TCGA.EW.A1P7.01 1 0.0000 0.9583 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A5FL.01 6 0.0863 0.7882 0.00 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.A2.A0T2.01 4 0.0863 0.8983 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.AR.A0TP.01 2 0.0504 0.8809 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.AR.A0TU.01 5 0.0504 0.7518 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.A7.A26I.01 3 0.0504 0.8924 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.A2.A0ST.01 1 0.0000 0.9583 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0WA.01 4 0.0000 0.9183 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A1AY.01 2 0.2163 0.8505 0.00 0.88 0.00 0.00 0.02 0.00 0.10
#> TCGA.S3.AA10.01 6 0.0863 0.7983 0.04 0.00 0.00 0.00 0.00 0.96 0.00
#> TCGA.EW.A6SB.01 1 0.0000 0.9583 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A5ZV.01 2 0.2512 0.8411 0.00 0.86 0.00 0.00 0.04 0.00 0.10
#> TCGA.B6.A0WX.01 5 0.1433 0.7023 0.00 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.BH.A0E0.01 3 0.0504 0.8859 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.B6.A0RU.01 3 0.3780 0.5711 0.00 0.02 0.72 0.00 0.02 0.00 0.24
#> TCGA.EW.A1PH.01 4 0.0000 0.9183 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A3XS.01 5 0.4092 0.5318 0.00 0.02 0.16 0.00 0.74 0.00 0.08
#> TCGA.B6.A1KF.01 2 0.1671 0.8509 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.E2.A1AZ.01 6 0.2163 0.7206 0.00 0.00 0.10 0.00 0.00 0.88 0.02
#> TCGA.AC.A62X.01 2 0.0000 0.8833 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A22G.01 4 0.3284 0.7609 0.00 0.10 0.00 0.80 0.00 0.00 0.10
#> TCGA.D8.A27M.01 1 0.1166 0.8833 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.BH.A0RX.01 1 0.0000 0.9583 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A4S1.01 6 0.3417 0.7128 0.26 0.00 0.00 0.00 0.00 0.72 0.02
#> TCGA.D8.A1JM.01 2 0.2512 0.8411 0.00 0.86 0.00 0.00 0.04 0.00 0.10
#> TCGA.AC.A2QJ.01 6 0.3685 0.6460 0.32 0.00 0.00 0.00 0.00 0.66 0.02
#> TCGA.E2.A1II.01 1 0.3496 -0.0529 0.58 0.00 0.00 0.00 0.00 0.42 0.00
#> TCGA.B6.A3ZX.01 1 0.0000 0.9583 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HN.A2NL.01 2 0.0000 0.8833 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A1.A0SK.01 2 0.3086 0.7873 0.00 0.80 0.00 0.04 0.00 0.00 0.16
#> TCGA.LL.A441.01 1 0.0000 0.9583 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0YM.01 5 0.4848 0.0445 0.00 0.40 0.00 0.00 0.50 0.00 0.10
#> TCGA.LL.A5YP.01 3 0.0000 0.9031 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.LL.A6FR.01 4 0.0000 0.9183 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.PL.A8LV.01 5 0.3927 0.6237 0.00 0.00 0.00 0.00 0.66 0.30 0.04
#> TCGA.AO.A1KR.01 5 0.0863 0.7619 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.E9.A244.01 3 0.0000 0.9031 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A400.01 3 0.0000 0.9031 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FC.01 5 0.0863 0.7619 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.BH.A0B9.01 6 0.1363 0.7759 0.00 0.00 0.04 0.00 0.00 0.94 0.02
#> TCGA.BH.A18V.06 6 0.2945 0.7194 0.26 0.00 0.00 0.00 0.00 0.74 0.00
#> TCGA.C8.A27B.01 3 0.0000 0.9031 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A13E.01 2 0.0863 0.8768 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.B6.A402.01 2 0.4873 0.4894 0.00 0.60 0.00 0.22 0.00 0.00 0.18
#> TCGA.AR.A1AI.01 6 0.3221 0.6579 0.32 0.00 0.00 0.00 0.00 0.68 0.00
#> TCGA.E2.A1LS.01 2 0.1671 0.8509 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.D8.A1JL.01 6 0.0504 0.7877 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.E2.A1LH.01 6 0.2945 0.7194 0.26 0.00 0.00 0.00 0.00 0.74 0.00
#> TCGA.A2.A3Y0.01 6 0.2376 0.7829 0.12 0.00 0.00 0.00 0.00 0.86 0.02
#> TCGA.AO.A129.01 6 0.3139 0.6814 0.30 0.00 0.00 0.00 0.00 0.70 0.00
#> TCGA.A2.A4RX.01 5 0.4703 0.5968 0.00 0.00 0.04 0.00 0.62 0.30 0.04
#> TCGA.E2.A1IP.01 1 0.0000 0.9583 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A27H.01 2 0.2081 0.8481 0.00 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.E9.A1NC.01 6 0.3294 0.6309 0.34 0.00 0.00 0.00 0.00 0.66 0.00
#> TCGA.AO.A124.01 4 0.0000 0.9183 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A256.01 4 0.2803 0.8083 0.00 0.06 0.00 0.84 0.00 0.00 0.10
#> TCGA.EW.A1OW.01 4 0.0000 0.9183 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A0YE.01 4 0.0000 0.9183 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A0T0.01 3 0.0504 0.8880 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AC.A2QH.01 7 0.4908 0.5836 0.00 0.00 0.10 0.26 0.02 0.00 0.62
#> TCGA.E2.A573.01 6 0.2945 0.7194 0.26 0.00 0.00 0.00 0.00 0.74 0.00
#> TCGA.OL.A6VO.01 3 0.5875 0.0105 0.00 0.30 0.44 0.00 0.02 0.00 0.24
#> TCGA.A2.A3XU.01 2 0.1166 0.8697 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.GM.A3XL.01 5 0.0863 0.7619 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.AN.A0XU.01 3 0.3661 0.6033 0.00 0.02 0.74 0.00 0.02 0.00 0.22
#> TCGA.A7.A6VV.01 3 0.1006 0.8765 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.EW.A3U0.01 1 0.0000 0.9583 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A243.01 1 0.0000 0.9583 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5S0.01 5 0.4533 0.6307 0.00 0.00 0.04 0.00 0.66 0.26 0.04
#> TCGA.D8.A27F.01 4 0.0000 0.9183 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E2.A1LI.01 6 0.0000 0.7923 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A7.A26F.01 5 0.4070 0.5859 0.00 0.00 0.00 0.00 0.62 0.34 0.04
#> TCGA.B6.A0RE.01 2 0.2163 0.8505 0.00 0.88 0.00 0.00 0.02 0.00 0.10
#> TCGA.BH.A1F6.01 5 0.0863 0.7619 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.E2.A14N.01 6 0.0863 0.7983 0.04 0.00 0.00 0.00 0.00 0.96 0.00
#> TCGA.OL.A5RW.01 2 0.2422 0.8339 0.00 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.A1.A0SB.01 2 0.4348 0.6364 0.00 0.68 0.00 0.14 0.00 0.00 0.18
#> TCGA.AR.A2LR.01 2 0.0504 0.8809 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.AR.A251.01 4 0.0000 0.9183 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A1AR.01 5 0.4070 0.5854 0.00 0.00 0.00 0.00 0.62 0.34 0.04
#> TCGA.AO.A0JL.01 4 0.4451 0.4937 0.00 0.26 0.00 0.64 0.00 0.00 0.10
#> TCGA.EW.A1P8.01 3 0.0000 0.9031 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A0U4.01 6 0.2376 0.7533 0.12 0.00 0.00 0.00 0.00 0.86 0.02
#> TCGA.B6.A409.01 3 0.0000 0.9031 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0X1.01 3 0.0000 0.9031 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0SX.01 6 0.2213 0.7391 0.00 0.00 0.02 0.00 0.04 0.90 0.04
#> TCGA.EW.A1P4.01 6 0.0000 0.7923 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AO.A128.01 1 0.0000 0.9583 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A2DF.01 6 0.3413 0.5789 0.38 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.A1.A0SP.01 5 0.0863 0.7619 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.E2.A1LG.01 4 0.0863 0.8872 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.A7.A6VY.01 5 0.0863 0.7619 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.A7.A26G.01 6 0.3358 0.6025 0.36 0.00 0.00 0.00 0.00 0.64 0.00
#> TCGA.A2.A0YJ.01 4 0.0000 0.9183 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A7VC.01 7 0.4146 0.5501 0.00 0.00 0.32 0.02 0.02 0.00 0.64
#> TCGA.OL.A66I.01 6 0.2421 0.7484 0.08 0.00 0.00 0.00 0.02 0.88 0.02
#> TCGA.A7.A6VW.01 5 0.3404 0.6318 0.00 0.06 0.04 0.00 0.82 0.00 0.08
#> TCGA.B6.A0I1.01 4 0.1928 0.8610 0.00 0.02 0.00 0.90 0.00 0.00 0.08
#> TCGA.LL.A73Y.01 3 0.0000 0.9031 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A1HJ.01 4 0.0000 0.9183 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A1G1.01 5 0.3086 0.7070 0.00 0.00 0.00 0.00 0.80 0.16 0.04
#> TCGA.A7.A13D.01 2 0.2569 0.8447 0.00 0.84 0.00 0.00 0.02 0.00 0.14
#> TCGA.A2.A3XY.01 6 0.0000 0.7923 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A7.A4SD.01 6 0.3606 0.6708 0.30 0.00 0.00 0.00 0.00 0.68 0.02
#> TCGA.D8.A1XQ.01 3 0.0504 0.8908 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AC.A6IW.01 6 0.0504 0.7877 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.BH.A5IZ.01 5 0.3908 0.4890 0.00 0.00 0.20 0.00 0.72 0.00 0.08
#> TCGA.LL.A8F5.01 5 0.1166 0.7172 0.00 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.D8.A1XW.01 3 0.0000 0.9031 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.PL.A8LZ.01 1 0.0000 0.9583 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A2BK.01 4 0.3058 0.7866 0.00 0.08 0.00 0.82 0.00 0.00 0.10
#> TCGA.GI.A2C9.01 2 0.0863 0.8841 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.E2.A1LK.01 2 0.0000 0.8833 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5D7.01 5 0.0863 0.7619 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.A7.A4SE.01 3 0.1363 0.8619 0.00 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.S3.AA0Z.01 2 0.2163 0.8505 0.00 0.88 0.00 0.00 0.02 0.00 0.10
#> TCGA.BH.A0B3.01 6 0.1718 0.7750 0.00 0.00 0.04 0.00 0.00 0.92 0.04
#> TCGA.AQ.A54N.01 2 0.0863 0.8764 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.D8.A1XK.01 5 0.4003 0.6071 0.00 0.00 0.00 0.00 0.64 0.32 0.04
#> TCGA.AC.A8OQ.01 1 0.0000 0.9583 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1PB.01 6 0.3413 0.5789 0.38 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.E9.A1N8.01 2 0.1166 0.8745 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.E2.A574.01 4 0.0000 0.9183 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A1.A0SO.01 2 0.2745 0.8317 0.00 0.82 0.00 0.00 0.02 0.00 0.16
#> TCGA.AR.A24Q.01 3 0.0504 0.8924 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BH.A1F0.01 1 0.0000 0.9583 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A0U0.01 6 0.0000 0.7923 0.00 0.00 0.00 0.00 0.00 1.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.AR.A1AJ.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1ND.01 6 0.1804 0.682 0.00 0.00 0.00 0.00 0.02 0.90 0.00 0.08
#> TCGA.AR.A1AQ.01 6 0.3054 0.588 0.00 0.00 0.00 0.00 0.12 0.80 0.00 0.08
#> TCGA.E9.A3QA.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S3.AA15.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A3XX.01 3 0.0808 0.795 0.00 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.A2.A3XT.01 6 0.2994 0.687 0.00 0.00 0.06 0.00 0.00 0.80 0.00 0.14
#> TCGA.EW.A1P7.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A5FL.01 6 0.2856 0.714 0.00 0.00 0.02 0.00 0.00 0.78 0.00 0.20
#> TCGA.A2.A0T2.01 4 0.1275 0.876 0.00 0.00 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.AR.A0TP.01 2 0.1091 0.765 0.00 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.AR.A0TU.01 5 0.0000 0.700 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A7.A26I.01 3 0.0471 0.804 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.A2.A0ST.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0WA.01 4 0.0000 0.889 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AY.01 2 0.2719 0.711 0.00 0.80 0.00 0.00 0.00 0.00 0.02 0.18
#> TCGA.S3.AA10.01 6 0.1563 0.731 0.00 0.00 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.EW.A6SB.01 1 0.0471 0.955 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.A7.A5ZV.01 2 0.3615 0.664 0.00 0.74 0.00 0.00 0.04 0.00 0.02 0.20
#> TCGA.B6.A0WX.01 5 0.1275 0.673 0.00 0.00 0.02 0.00 0.94 0.00 0.00 0.04
#> TCGA.BH.A0E0.01 3 0.1563 0.765 0.00 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.B6.A0RU.01 3 0.3729 -0.539 0.00 0.02 0.52 0.00 0.00 0.00 0.00 0.46
#> TCGA.EW.A1PH.01 4 0.0471 0.889 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.A2.A3XS.01 5 0.5201 0.331 0.00 0.04 0.08 0.00 0.58 0.00 0.02 0.28
#> TCGA.B6.A1KF.01 2 0.2132 0.740 0.00 0.88 0.00 0.00 0.00 0.00 0.08 0.04
#> TCGA.E2.A1AZ.01 6 0.4849 0.393 0.00 0.00 0.24 0.00 0.00 0.54 0.00 0.22
#> TCGA.AC.A62X.01 2 0.0808 0.773 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.E9.A22G.01 4 0.4079 0.712 0.00 0.12 0.00 0.74 0.00 0.00 0.08 0.06
#> TCGA.D8.A27M.01 1 0.2994 0.712 0.80 0.00 0.00 0.00 0.00 0.14 0.00 0.06
#> TCGA.BH.A0RX.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A4S1.01 6 0.5051 0.661 0.20 0.00 0.00 0.00 0.00 0.60 0.04 0.16
#> TCGA.D8.A1JM.01 2 0.2856 0.698 0.00 0.78 0.00 0.00 0.00 0.00 0.02 0.20
#> TCGA.AC.A2QJ.01 6 0.5151 0.643 0.22 0.00 0.00 0.00 0.00 0.58 0.04 0.16
#> TCGA.E2.A1II.01 6 0.3729 0.373 0.46 0.00 0.00 0.00 0.00 0.52 0.00 0.02
#> TCGA.B6.A3ZX.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HN.A2NL.01 2 0.0808 0.773 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.A1.A0SK.01 2 0.4650 0.556 0.00 0.66 0.00 0.08 0.00 0.00 0.06 0.20
#> TCGA.LL.A441.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0YM.01 5 0.5244 0.200 0.00 0.26 0.00 0.00 0.52 0.00 0.02 0.20
#> TCGA.LL.A5YP.01 3 0.0471 0.811 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.LL.A6FR.01 4 0.0000 0.889 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.PL.A8LV.01 5 0.5118 0.445 0.00 0.00 0.04 0.00 0.56 0.28 0.00 0.12
#> TCGA.AO.A1KR.01 5 0.0000 0.700 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E9.A244.01 3 0.0000 0.813 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A400.01 3 0.1091 0.799 0.00 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.BH.A1FC.01 5 0.0000 0.700 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0B9.01 6 0.3774 0.638 0.00 0.00 0.08 0.00 0.00 0.70 0.00 0.22
#> TCGA.BH.A18V.06 6 0.3856 0.704 0.20 0.00 0.00 0.00 0.00 0.70 0.00 0.10
#> TCGA.C8.A27B.01 3 0.0000 0.813 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A13E.01 2 0.0808 0.770 0.00 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.B6.A402.01 2 0.5244 0.275 0.00 0.48 0.00 0.16 0.00 0.00 0.02 0.34
#> TCGA.AR.A1AI.01 6 0.4482 0.646 0.26 0.00 0.00 0.00 0.00 0.60 0.00 0.14
#> TCGA.E2.A1LS.01 2 0.1887 0.751 0.00 0.90 0.00 0.00 0.00 0.00 0.06 0.04
#> TCGA.D8.A1JL.01 6 0.1341 0.694 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.E2.A1LH.01 6 0.3729 0.712 0.18 0.00 0.00 0.00 0.00 0.72 0.00 0.10
#> TCGA.A2.A3Y0.01 6 0.4169 0.709 0.10 0.00 0.02 0.00 0.00 0.70 0.00 0.18
#> TCGA.AO.A129.01 6 0.4396 0.665 0.24 0.00 0.00 0.00 0.00 0.62 0.00 0.14
#> TCGA.A2.A4RX.01 5 0.5363 0.387 0.00 0.00 0.04 0.00 0.50 0.32 0.00 0.14
#> TCGA.E2.A1IP.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A27H.01 2 0.3449 0.596 0.00 0.66 0.00 0.02 0.00 0.00 0.00 0.32
#> TCGA.E9.A1NC.01 6 0.4318 0.617 0.30 0.00 0.00 0.00 0.00 0.60 0.00 0.10
#> TCGA.AO.A124.01 4 0.0471 0.883 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AR.A256.01 4 0.3687 0.756 0.00 0.08 0.00 0.78 0.00 0.00 0.08 0.06
#> TCGA.EW.A1OW.01 4 0.0471 0.889 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.A2.A0YE.01 4 0.0471 0.883 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.A2.A0T0.01 3 0.1091 0.797 0.00 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.AC.A2QH.01 7 0.2719 0.738 0.00 0.00 0.02 0.18 0.00 0.00 0.80 0.00
#> TCGA.E2.A573.01 6 0.4033 0.701 0.20 0.00 0.00 0.00 0.00 0.68 0.00 0.12
#> TCGA.OL.A6VO.01 8 0.5301 0.000 0.00 0.16 0.40 0.00 0.00 0.00 0.02 0.42
#> TCGA.A2.A3XU.01 2 0.1887 0.751 0.00 0.90 0.00 0.00 0.00 0.00 0.06 0.04
#> TCGA.GM.A3XL.01 5 0.0000 0.700 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AN.A0XU.01 3 0.4105 -0.497 0.00 0.02 0.54 0.00 0.00 0.00 0.02 0.42
#> TCGA.A7.A6VV.01 3 0.2114 0.646 0.00 0.00 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.EW.A3U0.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A243.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5S0.01 5 0.4722 0.523 0.00 0.00 0.06 0.00 0.66 0.18 0.00 0.10
#> TCGA.D8.A27F.01 4 0.0000 0.889 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1LI.01 6 0.0471 0.725 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.A7.A26F.01 5 0.4255 0.459 0.00 0.00 0.00 0.00 0.58 0.34 0.00 0.08
#> TCGA.B6.A0RE.01 2 0.2856 0.698 0.00 0.78 0.00 0.00 0.00 0.00 0.02 0.20
#> TCGA.BH.A1F6.01 5 0.0471 0.696 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.E2.A14N.01 6 0.1275 0.731 0.02 0.00 0.00 0.00 0.00 0.94 0.00 0.04
#> TCGA.OL.A5RW.01 2 0.3449 0.640 0.00 0.66 0.00 0.00 0.00 0.00 0.02 0.32
#> TCGA.A1.A0SB.01 2 0.5037 0.346 0.00 0.54 0.00 0.14 0.00 0.00 0.02 0.30
#> TCGA.AR.A2LR.01 2 0.1275 0.767 0.00 0.94 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.AR.A251.01 4 0.0808 0.879 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.AR.A1AR.01 5 0.4340 0.416 0.00 0.00 0.00 0.00 0.54 0.38 0.00 0.08
#> TCGA.AO.A0JL.01 4 0.5137 0.377 0.00 0.32 0.00 0.54 0.00 0.00 0.08 0.06
#> TCGA.EW.A1P8.01 3 0.1341 0.777 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.AR.A0U4.01 6 0.2407 0.672 0.06 0.00 0.00 0.00 0.00 0.86 0.00 0.08
#> TCGA.B6.A409.01 3 0.0000 0.813 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0X1.01 3 0.1091 0.799 0.00 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.A2.A0SX.01 6 0.4188 0.547 0.00 0.00 0.04 0.00 0.10 0.72 0.00 0.14
#> TCGA.EW.A1P4.01 6 0.1091 0.701 0.00 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.AO.A128.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A2DF.01 6 0.3170 0.686 0.20 0.00 0.00 0.00 0.00 0.76 0.00 0.04
#> TCGA.A1.A0SP.01 5 0.0000 0.700 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E2.A1LG.01 4 0.1275 0.861 0.00 0.00 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.A7.A6VY.01 5 0.0000 0.700 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A7.A26G.01 6 0.4380 0.594 0.32 0.00 0.00 0.00 0.00 0.58 0.00 0.10
#> TCGA.A2.A0YJ.01 4 0.0471 0.883 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AC.A7VC.01 7 0.2025 0.718 0.00 0.00 0.10 0.00 0.00 0.00 0.88 0.02
#> TCGA.OL.A66I.01 6 0.2591 0.669 0.04 0.00 0.00 0.00 0.02 0.86 0.00 0.08
#> TCGA.A7.A6VW.01 5 0.4672 0.362 0.00 0.10 0.00 0.00 0.60 0.00 0.02 0.28
#> TCGA.B6.A0I1.01 4 0.2348 0.841 0.00 0.02 0.00 0.88 0.00 0.00 0.04 0.06
#> TCGA.LL.A73Y.01 3 0.1341 0.777 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.C8.A1HJ.01 4 0.0000 0.889 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A1G1.01 5 0.2350 0.648 0.00 0.00 0.00 0.00 0.86 0.10 0.00 0.04
#> TCGA.A7.A13D.01 2 0.3570 0.559 0.00 0.62 0.00 0.00 0.00 0.00 0.02 0.36
#> TCGA.A2.A3XY.01 6 0.1765 0.729 0.00 0.00 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.A7.A4SD.01 6 0.4531 0.655 0.24 0.00 0.00 0.00 0.00 0.60 0.00 0.16
#> TCGA.D8.A1XQ.01 3 0.2547 0.672 0.00 0.00 0.84 0.00 0.00 0.00 0.12 0.04
#> TCGA.AC.A6IW.01 6 0.1341 0.694 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.BH.A5IZ.01 5 0.3909 0.477 0.00 0.00 0.12 0.00 0.70 0.00 0.00 0.18
#> TCGA.LL.A8F5.01 5 0.2547 0.610 0.00 0.00 0.04 0.00 0.84 0.00 0.00 0.12
#> TCGA.D8.A1XW.01 3 0.0808 0.806 0.00 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.PL.A8LZ.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A2BK.01 4 0.4079 0.712 0.00 0.12 0.00 0.74 0.00 0.00 0.08 0.06
#> TCGA.GI.A2C9.01 2 0.1341 0.773 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.E2.A1LK.01 2 0.0808 0.773 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.OL.A5D7.01 5 0.0000 0.700 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A7.A4SE.01 3 0.2267 0.598 0.00 0.00 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.S3.AA0Z.01 2 0.2981 0.696 0.00 0.76 0.00 0.00 0.00 0.00 0.02 0.22
#> TCGA.BH.A0B3.01 6 0.3551 0.675 0.00 0.00 0.06 0.00 0.00 0.72 0.00 0.22
#> TCGA.AQ.A54N.01 2 0.1557 0.761 0.00 0.92 0.00 0.00 0.00 0.00 0.06 0.02
#> TCGA.D8.A1XK.01 5 0.4511 0.400 0.00 0.00 0.00 0.00 0.52 0.38 0.00 0.10
#> TCGA.AC.A8OQ.01 1 0.1887 0.871 0.90 0.00 0.00 0.00 0.00 0.04 0.00 0.06
#> TCGA.EW.A1PB.01 6 0.3170 0.686 0.20 0.00 0.00 0.00 0.00 0.76 0.00 0.04
#> TCGA.E9.A1N8.01 2 0.1887 0.756 0.00 0.90 0.00 0.00 0.00 0.00 0.04 0.06
#> TCGA.E2.A574.01 4 0.0471 0.889 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.A1.A0SO.01 2 0.3374 0.652 0.00 0.68 0.00 0.00 0.00 0.00 0.02 0.30
#> TCGA.AR.A24Q.01 3 0.1091 0.780 0.00 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.BH.A1F0.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A0U0.01 6 0.0000 0.722 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node03. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0115-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0151-leaf , Node0152-leaf , Node0153-leaf , Node0154-leaf , Node0211-leaf , Node0212 , Node0213 , Node0221 , Node0222 , Node0231-leaf , Node0232 , Node0233-leaf , Node0241-leaf , Node0242 , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0331-leaf , Node0332-leaf , Node0341-leaf , Node0342-leaf , Node0343-leaf , Node0411 , Node0412-leaf , Node0413 , Node0421-leaf , Node0422 , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["031"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 44 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.904 0.946 0.969 0.4150 0.556 0.556
#> 3 3 0.822 0.957 0.978 0.4939 0.608 0.409
#> 4 4 0.906 0.967 0.968 0.1668 0.836 0.601
#> 5 5 0.796 0.710 0.870 0.0721 0.966 0.878
#> 6 6 0.751 0.670 0.838 0.0482 0.939 0.755
#> 7 7 0.773 0.561 0.792 0.0337 0.964 0.827
#> 8 8 0.778 0.626 0.796 0.0214 0.934 0.661
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.AR.A1AJ.01 1 0.000 1.000 1.00 0.00
#> TCGA.E9.A1ND.01 1 0.000 1.000 1.00 0.00
#> TCGA.AR.A1AQ.01 1 0.000 1.000 1.00 0.00
#> TCGA.E9.A3QA.01 1 0.000 1.000 1.00 0.00
#> TCGA.S3.AA15.01 1 0.000 1.000 1.00 0.00
#> TCGA.EW.A1P7.01 1 0.000 1.000 1.00 0.00
#> TCGA.E9.A5FL.01 2 0.000 0.892 0.00 1.00
#> TCGA.A2.A0ST.01 1 0.000 1.000 1.00 0.00
#> TCGA.S3.AA10.01 2 0.680 0.801 0.18 0.82
#> TCGA.EW.A6SB.01 1 0.000 1.000 1.00 0.00
#> TCGA.D8.A27M.01 2 0.855 0.715 0.28 0.72
#> TCGA.BH.A0RX.01 1 0.000 1.000 1.00 0.00
#> TCGA.A2.A4S1.01 2 0.000 0.892 0.00 1.00
#> TCGA.AC.A2QJ.01 2 0.000 0.892 0.00 1.00
#> TCGA.E2.A1II.01 1 0.000 1.000 1.00 0.00
#> TCGA.B6.A3ZX.01 1 0.000 1.000 1.00 0.00
#> TCGA.LL.A441.01 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A18V.06 1 0.000 1.000 1.00 0.00
#> TCGA.AR.A1AI.01 2 0.000 0.892 0.00 1.00
#> TCGA.D8.A1JL.01 1 0.000 1.000 1.00 0.00
#> TCGA.E2.A1LH.01 1 0.000 1.000 1.00 0.00
#> TCGA.A2.A3Y0.01 2 0.000 0.892 0.00 1.00
#> TCGA.AO.A129.01 1 0.000 1.000 1.00 0.00
#> TCGA.E2.A1IP.01 2 0.000 0.892 0.00 1.00
#> TCGA.E9.A1NC.01 2 0.881 0.692 0.30 0.70
#> TCGA.E2.A573.01 1 0.000 1.000 1.00 0.00
#> TCGA.EW.A3U0.01 2 0.000 0.892 0.00 1.00
#> TCGA.E9.A243.01 2 0.881 0.692 0.30 0.70
#> TCGA.E2.A1LI.01 1 0.000 1.000 1.00 0.00
#> TCGA.E2.A14N.01 1 0.000 1.000 1.00 0.00
#> TCGA.AR.A0U4.01 1 0.000 1.000 1.00 0.00
#> TCGA.EW.A1P4.01 1 0.000 1.000 1.00 0.00
#> TCGA.AO.A128.01 1 0.000 1.000 1.00 0.00
#> TCGA.GM.A2DF.01 1 0.000 1.000 1.00 0.00
#> TCGA.A7.A26G.01 2 0.881 0.692 0.30 0.70
#> TCGA.OL.A66I.01 1 0.000 1.000 1.00 0.00
#> TCGA.A2.A3XY.01 1 0.000 1.000 1.00 0.00
#> TCGA.A7.A4SD.01 2 0.000 0.892 0.00 1.00
#> TCGA.AC.A6IW.01 1 0.000 1.000 1.00 0.00
#> TCGA.PL.A8LZ.01 1 0.000 1.000 1.00 0.00
#> TCGA.AC.A8OQ.01 2 0.000 0.892 0.00 1.00
#> TCGA.EW.A1PB.01 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A1F0.01 1 0.000 1.000 1.00 0.00
#> TCGA.AR.A0U0.01 1 0.000 1.000 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.AR.A1AJ.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.E9.A1ND.01 1 0.0000 0.965 1.00 0.00 0.00
#> TCGA.AR.A1AQ.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.E9.A3QA.01 1 0.3686 0.860 0.86 0.00 0.14
#> TCGA.S3.AA15.01 1 0.0000 0.965 1.00 0.00 0.00
#> TCGA.EW.A1P7.01 1 0.2959 0.897 0.90 0.00 0.10
#> TCGA.E9.A5FL.01 2 0.4002 0.843 0.16 0.84 0.00
#> TCGA.A2.A0ST.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.S3.AA10.01 1 0.0000 0.965 1.00 0.00 0.00
#> TCGA.EW.A6SB.01 1 0.0892 0.955 0.98 0.00 0.02
#> TCGA.D8.A27M.01 1 0.0000 0.965 1.00 0.00 0.00
#> TCGA.BH.A0RX.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.A2.A4S1.01 2 0.0000 0.949 0.00 1.00 0.00
#> TCGA.AC.A2QJ.01 2 0.0000 0.949 0.00 1.00 0.00
#> TCGA.E2.A1II.01 1 0.0000 0.965 1.00 0.00 0.00
#> TCGA.B6.A3ZX.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.LL.A441.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.BH.A18V.06 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.AR.A1AI.01 2 0.0000 0.949 0.00 1.00 0.00
#> TCGA.D8.A1JL.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.E2.A1LH.01 1 0.3686 0.860 0.86 0.00 0.14
#> TCGA.A2.A3Y0.01 2 0.0000 0.949 0.00 1.00 0.00
#> TCGA.AO.A129.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.E2.A1IP.01 1 0.0000 0.965 1.00 0.00 0.00
#> TCGA.E9.A1NC.01 1 0.0000 0.965 1.00 0.00 0.00
#> TCGA.E2.A573.01 1 0.3340 0.880 0.88 0.00 0.12
#> TCGA.EW.A3U0.01 2 0.4002 0.843 0.16 0.84 0.00
#> TCGA.E9.A243.01 1 0.0000 0.965 1.00 0.00 0.00
#> TCGA.E2.A1LI.01 1 0.0000 0.965 1.00 0.00 0.00
#> TCGA.E2.A14N.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.AR.A0U4.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.EW.A1P4.01 1 0.0892 0.955 0.98 0.00 0.02
#> TCGA.AO.A128.01 1 0.0000 0.965 1.00 0.00 0.00
#> TCGA.GM.A2DF.01 1 0.0000 0.965 1.00 0.00 0.00
#> TCGA.A7.A26G.01 1 0.0000 0.965 1.00 0.00 0.00
#> TCGA.OL.A66I.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.A2.A3XY.01 1 0.0000 0.965 1.00 0.00 0.00
#> TCGA.A7.A4SD.01 2 0.0000 0.949 0.00 1.00 0.00
#> TCGA.AC.A6IW.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.PL.A8LZ.01 1 0.0000 0.965 1.00 0.00 0.00
#> TCGA.AC.A8OQ.01 2 0.0000 0.949 0.00 1.00 0.00
#> TCGA.EW.A1PB.01 1 0.3340 0.880 0.88 0.00 0.12
#> TCGA.BH.A1F0.01 1 0.0000 0.965 1.00 0.00 0.00
#> TCGA.AR.A0U0.01 1 0.0000 0.965 1.00 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.AR.A1AJ.01 3 0.0000 1.000 0.00 0.0 1.0 0.00
#> TCGA.E9.A1ND.01 1 0.2345 0.963 0.90 0.0 0.0 0.10
#> TCGA.AR.A1AQ.01 3 0.0000 1.000 0.00 0.0 1.0 0.00
#> TCGA.E9.A3QA.01 1 0.2345 0.963 0.90 0.0 0.0 0.10
#> TCGA.S3.AA15.01 1 0.2345 0.963 0.90 0.0 0.0 0.10
#> TCGA.EW.A1P7.01 1 0.2345 0.963 0.90 0.0 0.0 0.10
#> TCGA.E9.A5FL.01 4 0.2345 0.878 0.00 0.1 0.0 0.90
#> TCGA.A2.A0ST.01 3 0.0000 1.000 0.00 0.0 1.0 0.00
#> TCGA.S3.AA10.01 4 0.0000 0.954 0.00 0.0 0.0 1.00
#> TCGA.EW.A6SB.01 1 0.2345 0.963 0.90 0.0 0.0 0.10
#> TCGA.D8.A27M.01 4 0.0707 0.949 0.02 0.0 0.0 0.98
#> TCGA.BH.A0RX.01 1 0.2345 0.891 0.90 0.0 0.1 0.00
#> TCGA.A2.A4S1.01 2 0.0000 1.000 0.00 1.0 0.0 0.00
#> TCGA.AC.A2QJ.01 2 0.0000 1.000 0.00 1.0 0.0 0.00
#> TCGA.E2.A1II.01 1 0.2345 0.963 0.90 0.0 0.0 0.10
#> TCGA.B6.A3ZX.01 3 0.0000 1.000 0.00 0.0 1.0 0.00
#> TCGA.LL.A441.01 3 0.0000 1.000 0.00 0.0 1.0 0.00
#> TCGA.BH.A18V.06 3 0.0000 1.000 0.00 0.0 1.0 0.00
#> TCGA.AR.A1AI.01 2 0.0000 1.000 0.00 1.0 0.0 0.00
#> TCGA.D8.A1JL.01 3 0.0000 1.000 0.00 0.0 1.0 0.00
#> TCGA.E2.A1LH.01 1 0.0000 0.930 1.00 0.0 0.0 0.00
#> TCGA.A2.A3Y0.01 2 0.0000 1.000 0.00 1.0 0.0 0.00
#> TCGA.AO.A129.01 3 0.0000 1.000 0.00 0.0 1.0 0.00
#> TCGA.E2.A1IP.01 4 0.0000 0.954 0.00 0.0 0.0 1.00
#> TCGA.E9.A1NC.01 4 0.0707 0.949 0.02 0.0 0.0 0.98
#> TCGA.E2.A573.01 1 0.0000 0.930 1.00 0.0 0.0 0.00
#> TCGA.EW.A3U0.01 4 0.2345 0.878 0.00 0.1 0.0 0.90
#> TCGA.E9.A243.01 4 0.0000 0.954 0.00 0.0 0.0 1.00
#> TCGA.E2.A1LI.01 1 0.2011 0.959 0.92 0.0 0.0 0.08
#> TCGA.E2.A14N.01 3 0.0000 1.000 0.00 0.0 1.0 0.00
#> TCGA.AR.A0U4.01 3 0.0000 1.000 0.00 0.0 1.0 0.00
#> TCGA.EW.A1P4.01 1 0.1211 0.944 0.96 0.0 0.0 0.04
#> TCGA.AO.A128.01 1 0.1637 0.954 0.94 0.0 0.0 0.06
#> TCGA.GM.A2DF.01 1 0.2011 0.959 0.92 0.0 0.0 0.08
#> TCGA.A7.A26G.01 4 0.0000 0.954 0.00 0.0 0.0 1.00
#> TCGA.OL.A66I.01 3 0.0000 1.000 0.00 0.0 1.0 0.00
#> TCGA.A2.A3XY.01 1 0.2345 0.963 0.90 0.0 0.0 0.10
#> TCGA.A7.A4SD.01 2 0.0000 1.000 0.00 1.0 0.0 0.00
#> TCGA.AC.A6IW.01 3 0.0000 1.000 0.00 0.0 1.0 0.00
#> TCGA.PL.A8LZ.01 1 0.2345 0.963 0.90 0.0 0.0 0.10
#> TCGA.AC.A8OQ.01 2 0.0000 1.000 0.00 1.0 0.0 0.00
#> TCGA.EW.A1PB.01 1 0.0000 0.930 1.00 0.0 0.0 0.00
#> TCGA.BH.A1F0.01 1 0.2345 0.963 0.90 0.0 0.0 0.10
#> TCGA.AR.A0U0.01 1 0.0000 0.930 1.00 0.0 0.0 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.AR.A1AJ.01 3 0.0000 0.914 0.00 0.00 1.00 0.00 0.00
#> TCGA.E9.A1ND.01 1 0.2280 0.547 0.88 0.00 0.00 0.00 0.12
#> TCGA.AR.A1AQ.01 3 0.0000 0.914 0.00 0.00 1.00 0.00 0.00
#> TCGA.E9.A3QA.01 1 0.1732 0.572 0.92 0.00 0.00 0.00 0.08
#> TCGA.S3.AA15.01 1 0.0609 0.635 0.98 0.00 0.00 0.00 0.02
#> TCGA.EW.A1P7.01 1 0.1732 0.572 0.92 0.00 0.00 0.00 0.08
#> TCGA.E9.A5FL.01 4 0.4060 0.647 0.00 0.00 0.00 0.64 0.36
#> TCGA.A2.A0ST.01 3 0.3037 0.873 0.04 0.00 0.86 0.00 0.10
#> TCGA.S3.AA10.01 4 0.0609 0.940 0.00 0.00 0.00 0.98 0.02
#> TCGA.EW.A6SB.01 1 0.0000 0.640 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A27M.01 4 0.0000 0.947 0.00 0.00 0.00 1.00 0.00
#> TCGA.BH.A0RX.01 1 0.2020 0.548 0.90 0.00 0.00 0.00 0.10
#> TCGA.A2.A4S1.01 2 0.0000 0.948 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A2QJ.01 2 0.0000 0.948 0.00 1.00 0.00 0.00 0.00
#> TCGA.E2.A1II.01 1 0.0000 0.640 1.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A3ZX.01 3 0.0000 0.914 0.00 0.00 1.00 0.00 0.00
#> TCGA.LL.A441.01 3 0.3037 0.873 0.04 0.00 0.86 0.00 0.10
#> TCGA.BH.A18V.06 3 0.2020 0.887 0.00 0.00 0.90 0.00 0.10
#> TCGA.AR.A1AI.01 2 0.0000 0.948 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A1JL.01 3 0.4254 0.816 0.04 0.00 0.74 0.00 0.22
#> TCGA.E2.A1LH.01 5 0.4227 1.000 0.42 0.00 0.00 0.00 0.58
#> TCGA.A2.A3Y0.01 2 0.3983 0.707 0.00 0.66 0.00 0.00 0.34
#> TCGA.AO.A129.01 3 0.4398 0.803 0.04 0.00 0.72 0.00 0.24
#> TCGA.E2.A1IP.01 4 0.0609 0.945 0.00 0.00 0.00 0.98 0.02
#> TCGA.E9.A1NC.01 4 0.0000 0.947 0.00 0.00 0.00 1.00 0.00
#> TCGA.E2.A573.01 5 0.4227 1.000 0.42 0.00 0.00 0.00 0.58
#> TCGA.EW.A3U0.01 4 0.0609 0.945 0.00 0.00 0.00 0.98 0.02
#> TCGA.E9.A243.01 4 0.0000 0.947 0.00 0.00 0.00 1.00 0.00
#> TCGA.E2.A1LI.01 1 0.4060 -0.105 0.64 0.00 0.00 0.00 0.36
#> TCGA.E2.A14N.01 3 0.0000 0.914 0.00 0.00 1.00 0.00 0.00
#> TCGA.AR.A0U4.01 3 0.0000 0.914 0.00 0.00 1.00 0.00 0.00
#> TCGA.EW.A1P4.01 1 0.3561 0.138 0.74 0.00 0.00 0.00 0.26
#> TCGA.AO.A128.01 1 0.3796 0.130 0.70 0.00 0.00 0.00 0.30
#> TCGA.GM.A2DF.01 1 0.3796 0.130 0.70 0.00 0.00 0.00 0.30
#> TCGA.A7.A26G.01 4 0.1043 0.940 0.00 0.00 0.00 0.96 0.04
#> TCGA.OL.A66I.01 3 0.0000 0.914 0.00 0.00 1.00 0.00 0.00
#> TCGA.A2.A3XY.01 1 0.1410 0.626 0.94 0.00 0.00 0.00 0.06
#> TCGA.A7.A4SD.01 2 0.0000 0.948 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A6IW.01 3 0.2280 0.886 0.00 0.00 0.88 0.00 0.12
#> TCGA.PL.A8LZ.01 1 0.0609 0.635 0.98 0.00 0.00 0.00 0.02
#> TCGA.AC.A8OQ.01 2 0.0000 0.948 0.00 1.00 0.00 0.00 0.00
#> TCGA.EW.A1PB.01 1 0.4126 -0.215 0.62 0.00 0.00 0.00 0.38
#> TCGA.BH.A1F0.01 1 0.1043 0.627 0.96 0.00 0.00 0.00 0.04
#> TCGA.AR.A0U0.01 1 0.4126 -0.215 0.62 0.00 0.00 0.00 0.38
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.AR.A1AJ.01 3 0.0000 0.8556 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E9.A1ND.01 1 0.5039 0.3102 0.64 0.00 0.00 0.00 0.18 0.18
#> TCGA.AR.A1AQ.01 3 0.0000 0.8556 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E9.A3QA.01 1 0.1807 0.6895 0.92 0.00 0.00 0.00 0.06 0.02
#> TCGA.S3.AA15.01 1 0.1092 0.6966 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.EW.A1P7.01 1 0.1480 0.7002 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.E9.A5FL.01 6 0.4902 -0.1414 0.00 0.00 0.00 0.46 0.06 0.48
#> TCGA.A2.A0ST.01 3 0.3631 0.7861 0.10 0.00 0.82 0.00 0.04 0.04
#> TCGA.S3.AA10.01 4 0.1865 0.9049 0.00 0.00 0.00 0.92 0.04 0.04
#> TCGA.EW.A6SB.01 1 0.0547 0.7051 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.D8.A27M.01 4 0.0547 0.9456 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.BH.A0RX.01 1 0.2190 0.6749 0.90 0.00 0.00 0.00 0.06 0.04
#> TCGA.A2.A4S1.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A2QJ.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1II.01 1 0.2094 0.6614 0.90 0.00 0.00 0.00 0.08 0.02
#> TCGA.B6.A3ZX.01 3 0.0000 0.8556 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.LL.A441.01 3 0.3631 0.7861 0.10 0.00 0.82 0.00 0.04 0.04
#> TCGA.BH.A18V.06 3 0.2512 0.8230 0.00 0.00 0.88 0.00 0.06 0.06
#> TCGA.AR.A1AI.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JL.01 3 0.6558 0.5340 0.12 0.00 0.52 0.00 0.26 0.10
#> TCGA.E2.A1LH.01 5 0.2260 0.6743 0.14 0.00 0.00 0.00 0.86 0.00
#> TCGA.A2.A3Y0.01 6 0.3864 -0.2293 0.00 0.48 0.00 0.00 0.00 0.52
#> TCGA.AO.A129.01 3 0.6939 0.4581 0.12 0.00 0.46 0.00 0.28 0.14
#> TCGA.E2.A1IP.01 4 0.0547 0.9389 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.E9.A1NC.01 4 0.0547 0.9456 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.E2.A573.01 5 0.2260 0.6743 0.14 0.00 0.00 0.00 0.86 0.00
#> TCGA.EW.A3U0.01 4 0.0937 0.9313 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.E9.A243.01 4 0.0547 0.9456 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.E2.A1LI.01 5 0.5708 0.3263 0.38 0.00 0.00 0.02 0.50 0.10
#> TCGA.E2.A14N.01 3 0.0000 0.8556 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A0U4.01 3 0.0000 0.8556 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EW.A1P4.01 1 0.4993 0.0766 0.56 0.00 0.00 0.00 0.36 0.08
#> TCGA.AO.A128.01 1 0.6086 -0.2021 0.48 0.00 0.00 0.02 0.34 0.16
#> TCGA.GM.A2DF.01 1 0.5736 -0.1991 0.48 0.00 0.00 0.00 0.34 0.18
#> TCGA.A7.A26G.01 4 0.1635 0.9163 0.02 0.00 0.00 0.94 0.02 0.02
#> TCGA.OL.A66I.01 3 0.0000 0.8556 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A3XY.01 1 0.3746 0.5817 0.78 0.00 0.00 0.00 0.14 0.08
#> TCGA.A7.A4SD.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A6IW.01 3 0.2512 0.8281 0.00 0.00 0.88 0.00 0.06 0.06
#> TCGA.PL.A8LZ.01 1 0.1480 0.6948 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.AC.A8OQ.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1PB.01 5 0.5419 0.6114 0.22 0.00 0.00 0.00 0.58 0.20
#> TCGA.BH.A1F0.01 1 0.2020 0.6905 0.92 0.00 0.00 0.02 0.04 0.02
#> TCGA.AR.A0U0.01 5 0.5628 0.6034 0.24 0.00 0.00 0.00 0.54 0.22
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.AR.A1AJ.01 3 0.0000 0.717 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1ND.01 1 0.4146 0.430 0.64 0.00 0.00 0.00 0.02 0.02 0.32
#> TCGA.AR.A1AQ.01 3 0.0000 0.717 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A3QA.01 1 0.2745 0.676 0.82 0.00 0.00 0.00 0.02 0.00 0.16
#> TCGA.S3.AA15.01 1 0.1006 0.712 0.96 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.EW.A1P7.01 1 0.2376 0.700 0.86 0.00 0.00 0.00 0.02 0.00 0.12
#> TCGA.E9.A5FL.01 6 0.3294 0.000 0.00 0.00 0.00 0.34 0.00 0.66 0.00
#> TCGA.A2.A0ST.01 3 0.4698 0.149 0.14 0.00 0.62 0.00 0.00 0.00 0.24
#> TCGA.S3.AA10.01 4 0.2769 0.729 0.00 0.00 0.00 0.86 0.02 0.04 0.08
#> TCGA.EW.A6SB.01 1 0.1433 0.717 0.92 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.D8.A27M.01 4 0.1363 0.807 0.00 0.00 0.00 0.94 0.02 0.00 0.04
#> TCGA.BH.A0RX.01 1 0.3417 0.599 0.72 0.00 0.00 0.00 0.02 0.00 0.26
#> TCGA.A2.A4S1.01 2 0.0000 0.895 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A2QJ.01 2 0.0000 0.895 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1II.01 1 0.2163 0.676 0.88 0.00 0.00 0.00 0.02 0.00 0.10
#> TCGA.B6.A3ZX.01 3 0.0000 0.717 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.LL.A441.01 3 0.4610 0.256 0.08 0.00 0.66 0.00 0.00 0.02 0.24
#> TCGA.BH.A18V.06 3 0.4100 0.509 0.00 0.00 0.76 0.00 0.04 0.10 0.10
#> TCGA.AR.A1AI.01 2 0.0000 0.895 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JL.01 3 0.7279 -0.788 0.04 0.00 0.36 0.00 0.22 0.10 0.28
#> TCGA.E2.A1LH.01 5 0.1363 0.551 0.04 0.00 0.00 0.00 0.94 0.02 0.00
#> TCGA.A2.A3Y0.01 2 0.5132 0.134 0.00 0.46 0.00 0.02 0.00 0.44 0.08
#> TCGA.AO.A129.01 7 0.7590 0.000 0.04 0.00 0.28 0.00 0.18 0.20 0.30
#> TCGA.E2.A1IP.01 4 0.1886 0.774 0.00 0.00 0.00 0.88 0.00 0.12 0.00
#> TCGA.E9.A1NC.01 4 0.1363 0.807 0.00 0.00 0.00 0.94 0.02 0.00 0.04
#> TCGA.E2.A573.01 5 0.0863 0.561 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.EW.A3U0.01 4 0.2259 0.732 0.00 0.00 0.00 0.84 0.00 0.16 0.00
#> TCGA.E9.A243.01 4 0.1006 0.811 0.00 0.00 0.00 0.96 0.02 0.00 0.02
#> TCGA.E2.A1LI.01 5 0.6663 0.444 0.24 0.00 0.00 0.02 0.48 0.10 0.16
#> TCGA.E2.A14N.01 3 0.0000 0.717 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A0U4.01 3 0.0000 0.717 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1P4.01 5 0.5378 0.348 0.30 0.00 0.00 0.00 0.48 0.00 0.22
#> TCGA.AO.A128.01 1 0.5083 0.297 0.56 0.00 0.00 0.00 0.24 0.00 0.20
#> TCGA.GM.A2DF.01 1 0.5128 0.247 0.52 0.00 0.00 0.00 0.16 0.00 0.32
#> TCGA.A7.A26G.01 4 0.2569 0.759 0.00 0.00 0.00 0.84 0.02 0.14 0.00
#> TCGA.OL.A66I.01 3 0.0000 0.717 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A3XY.01 1 0.4204 0.448 0.70 0.00 0.00 0.00 0.14 0.00 0.16
#> TCGA.A7.A4SD.01 2 0.0000 0.895 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A6IW.01 3 0.4298 0.481 0.00 0.00 0.74 0.00 0.04 0.10 0.12
#> TCGA.PL.A8LZ.01 1 0.1928 0.712 0.90 0.00 0.00 0.00 0.02 0.00 0.08
#> TCGA.AC.A8OQ.01 2 0.0000 0.895 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1PB.01 5 0.5946 0.456 0.10 0.00 0.00 0.00 0.52 0.10 0.28
#> TCGA.BH.A1F0.01 1 0.0504 0.716 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.AR.A0U0.01 5 0.5819 0.475 0.20 0.00 0.00 0.00 0.42 0.02 0.36
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.AR.A1AJ.01 3 0.0000 0.7612 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1ND.01 5 0.2938 0.3961 0.30 0.00 0.00 0.00 0.70 0.00 0.00 0.00
#> TCGA.AR.A1AQ.01 3 0.0000 0.7612 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A3QA.01 1 0.1765 0.6931 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.S3.AA15.01 1 0.2623 0.6644 0.84 0.00 0.00 0.00 0.10 0.06 0.00 0.00
#> TCGA.EW.A1P7.01 1 0.1765 0.6931 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.E9.A5FL.01 6 0.2756 0.3907 0.00 0.00 0.00 0.26 0.00 0.74 0.00 0.00
#> TCGA.A2.A0ST.01 3 0.4756 -0.0196 0.34 0.00 0.56 0.00 0.00 0.00 0.04 0.06
#> TCGA.S3.AA10.01 4 0.2994 0.7505 0.00 0.00 0.00 0.80 0.00 0.06 0.14 0.00
#> TCGA.EW.A6SB.01 1 0.0471 0.7132 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.D8.A27M.01 4 0.1091 0.8742 0.00 0.00 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.BH.A0RX.01 1 0.2350 0.6672 0.86 0.00 0.00 0.00 0.00 0.00 0.04 0.10
#> TCGA.A2.A4S1.01 2 0.0000 0.9949 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A2QJ.01 2 0.0000 0.9949 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1II.01 1 0.3374 0.4895 0.68 0.00 0.00 0.00 0.30 0.00 0.00 0.02
#> TCGA.B6.A3ZX.01 3 0.0000 0.7612 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LL.A441.01 3 0.5019 0.1140 0.22 0.00 0.60 0.00 0.00 0.00 0.14 0.04
#> TCGA.BH.A18V.06 3 0.3845 0.3556 0.00 0.00 0.66 0.00 0.00 0.00 0.28 0.06
#> TCGA.AR.A1AI.01 2 0.0471 0.9792 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.D8.A1JL.01 7 0.6597 0.8118 0.18 0.00 0.26 0.00 0.00 0.00 0.28 0.28
#> TCGA.E2.A1LH.01 8 0.1341 0.6993 0.00 0.00 0.00 0.00 0.08 0.00 0.00 0.92
#> TCGA.A2.A3Y0.01 6 0.5298 0.3658 0.00 0.30 0.00 0.00 0.02 0.56 0.06 0.06
#> TCGA.AO.A129.01 7 0.6271 0.8106 0.14 0.00 0.20 0.00 0.00 0.00 0.42 0.24
#> TCGA.E2.A1IP.01 4 0.1275 0.8616 0.00 0.00 0.00 0.94 0.02 0.04 0.00 0.00
#> TCGA.E9.A1NC.01 4 0.1091 0.8742 0.00 0.00 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.E2.A573.01 8 0.1341 0.6993 0.00 0.00 0.00 0.00 0.08 0.00 0.00 0.92
#> TCGA.EW.A3U0.01 4 0.2020 0.8477 0.00 0.00 0.00 0.90 0.02 0.06 0.00 0.02
#> TCGA.E9.A243.01 4 0.1091 0.8742 0.00 0.00 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.E2.A1LI.01 5 0.6669 0.1066 0.10 0.00 0.00 0.04 0.36 0.00 0.16 0.34
#> TCGA.E2.A14N.01 3 0.0000 0.7612 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A0U4.01 3 0.0000 0.7612 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1P4.01 8 0.6404 0.4107 0.16 0.00 0.00 0.00 0.14 0.06 0.12 0.52
#> TCGA.AO.A128.01 5 0.5647 0.3899 0.26 0.00 0.00 0.00 0.50 0.06 0.00 0.18
#> TCGA.GM.A2DF.01 5 0.3431 0.5272 0.20 0.00 0.00 0.00 0.74 0.00 0.00 0.06
#> TCGA.A7.A26G.01 4 0.3078 0.7903 0.06 0.00 0.00 0.82 0.02 0.10 0.00 0.00
#> TCGA.OL.A66I.01 3 0.0000 0.7612 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A3XY.01 1 0.6162 0.1607 0.48 0.00 0.00 0.00 0.30 0.10 0.06 0.06
#> TCGA.A7.A4SD.01 2 0.0000 0.9949 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A6IW.01 3 0.3291 0.4417 0.02 0.00 0.70 0.00 0.00 0.00 0.28 0.00
#> TCGA.PL.A8LZ.01 1 0.1607 0.7070 0.92 0.00 0.00 0.00 0.04 0.04 0.00 0.00
#> TCGA.AC.A8OQ.01 2 0.0000 0.9949 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1PB.01 5 0.5674 0.1072 0.00 0.00 0.00 0.00 0.50 0.06 0.20 0.24
#> TCGA.BH.A1F0.01 1 0.4865 0.5192 0.64 0.00 0.00 0.00 0.20 0.08 0.00 0.08
#> TCGA.AR.A0U0.01 5 0.4394 0.2299 0.00 0.00 0.00 0.00 0.70 0.06 0.08 0.16
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node03. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0115-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0151-leaf , Node0152-leaf , Node0153-leaf , Node0154-leaf , Node0211-leaf , Node0212 , Node0213 , Node0221 , Node0222 , Node0231-leaf , Node0232 , Node0233-leaf , Node0241-leaf , Node0242 , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0331-leaf , Node0332-leaf , Node0341-leaf , Node0342-leaf , Node0343-leaf , Node0411 , Node0412-leaf , Node0413 , Node0421-leaf , Node0422 , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["032"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 27 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.5133 0.487 0.487
#> 3 3 0.910 0.925 0.947 0.2416 0.840 0.684
#> 4 4 0.735 0.883 0.913 0.1889 0.823 0.541
#> 5 5 0.737 0.837 0.874 0.0519 1.000 1.000
#> 6 6 0.753 0.688 0.839 0.0319 0.977 0.901
#> 7 7 0.732 0.594 0.814 0.0234 0.949 0.757
#> 8 8 0.782 0.518 0.764 0.0202 0.963 0.800
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.AR.A0TP.01 1 0 1 1 0
#> TCGA.AR.A1AY.01 2 0 1 0 1
#> TCGA.A7.A5ZV.01 2 0 1 0 1
#> TCGA.B6.A1KF.01 2 0 1 0 1
#> TCGA.AC.A62X.01 2 0 1 0 1
#> TCGA.D8.A1JM.01 2 0 1 0 1
#> TCGA.HN.A2NL.01 2 0 1 0 1
#> TCGA.A1.A0SK.01 1 0 1 1 0
#> TCGA.A2.A0YM.01 2 0 1 0 1
#> TCGA.A7.A13E.01 2 0 1 0 1
#> TCGA.B6.A402.01 1 0 1 1 0
#> TCGA.E2.A1LS.01 2 0 1 0 1
#> TCGA.D8.A27H.01 1 0 1 1 0
#> TCGA.OL.A6VO.01 1 0 1 1 0
#> TCGA.A2.A3XU.01 1 0 1 1 0
#> TCGA.B6.A0RE.01 2 0 1 0 1
#> TCGA.OL.A5RW.01 1 0 1 1 0
#> TCGA.A1.A0SB.01 1 0 1 1 0
#> TCGA.AR.A2LR.01 1 0 1 1 0
#> TCGA.AO.A0JL.01 2 0 1 0 1
#> TCGA.A7.A13D.01 2 0 1 0 1
#> TCGA.GI.A2C9.01 2 0 1 0 1
#> TCGA.E2.A1LK.01 2 0 1 0 1
#> TCGA.S3.AA0Z.01 1 0 1 1 0
#> TCGA.AQ.A54N.01 2 0 1 0 1
#> TCGA.E9.A1N8.01 1 0 1 1 0
#> TCGA.A1.A0SO.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.AR.A0TP.01 3 0.0892 0.897 0.02 0.00 0.98
#> TCGA.AR.A1AY.01 2 0.0892 0.953 0.00 0.98 0.02
#> TCGA.A7.A5ZV.01 2 0.1529 0.953 0.04 0.96 0.00
#> TCGA.B6.A1KF.01 2 0.1529 0.953 0.04 0.96 0.00
#> TCGA.AC.A62X.01 2 0.1529 0.953 0.04 0.96 0.00
#> TCGA.D8.A1JM.01 2 0.0892 0.953 0.00 0.98 0.02
#> TCGA.HN.A2NL.01 3 0.5706 0.474 0.00 0.32 0.68
#> TCGA.A1.A0SK.01 1 0.1529 1.000 0.96 0.00 0.04
#> TCGA.A2.A0YM.01 2 0.0892 0.953 0.00 0.98 0.02
#> TCGA.A7.A13E.01 2 0.1529 0.953 0.04 0.96 0.00
#> TCGA.B6.A402.01 1 0.1529 1.000 0.96 0.00 0.04
#> TCGA.E2.A1LS.01 2 0.0000 0.955 0.00 1.00 0.00
#> TCGA.D8.A27H.01 3 0.0892 0.897 0.02 0.00 0.98
#> TCGA.OL.A6VO.01 3 0.2537 0.864 0.08 0.00 0.92
#> TCGA.A2.A3XU.01 1 0.1529 1.000 0.96 0.00 0.04
#> TCGA.B6.A0RE.01 2 0.0892 0.953 0.00 0.98 0.02
#> TCGA.OL.A5RW.01 1 0.1529 1.000 0.96 0.00 0.04
#> TCGA.A1.A0SB.01 1 0.1529 1.000 0.96 0.00 0.04
#> TCGA.AR.A2LR.01 3 0.2959 0.844 0.10 0.00 0.90
#> TCGA.AO.A0JL.01 2 0.1529 0.953 0.04 0.96 0.00
#> TCGA.A7.A13D.01 2 0.2959 0.906 0.00 0.90 0.10
#> TCGA.GI.A2C9.01 2 0.2959 0.906 0.00 0.90 0.10
#> TCGA.E2.A1LK.01 2 0.1529 0.953 0.04 0.96 0.00
#> TCGA.S3.AA0Z.01 3 0.0892 0.897 0.02 0.00 0.98
#> TCGA.AQ.A54N.01 2 0.2959 0.906 0.00 0.90 0.10
#> TCGA.E9.A1N8.01 1 0.1529 1.000 0.96 0.00 0.04
#> TCGA.A1.A0SO.01 3 0.0892 0.897 0.02 0.00 0.98
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.AR.A0TP.01 3 0.0000 0.940 0.00 0.00 1.00 0.00
#> TCGA.AR.A1AY.01 2 0.3801 0.783 0.00 0.78 0.00 0.22
#> TCGA.A7.A5ZV.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.B6.A1KF.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.AC.A62X.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.D8.A1JM.01 2 0.4907 0.602 0.00 0.58 0.00 0.42
#> TCGA.HN.A2NL.01 2 0.6089 0.598 0.00 0.64 0.28 0.08
#> TCGA.A1.A0SK.01 1 0.0000 0.992 1.00 0.00 0.00 0.00
#> TCGA.A2.A0YM.01 2 0.4907 0.602 0.00 0.58 0.00 0.42
#> TCGA.A7.A13E.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.B6.A402.01 1 0.0000 0.992 1.00 0.00 0.00 0.00
#> TCGA.E2.A1LS.01 2 0.4406 0.722 0.00 0.70 0.00 0.30
#> TCGA.D8.A27H.01 3 0.0707 0.945 0.02 0.00 0.98 0.00
#> TCGA.OL.A6VO.01 3 0.2921 0.863 0.14 0.00 0.86 0.00
#> TCGA.A2.A3XU.01 1 0.0707 0.977 0.98 0.00 0.02 0.00
#> TCGA.B6.A0RE.01 2 0.2345 0.803 0.00 0.90 0.00 0.10
#> TCGA.OL.A5RW.01 1 0.0000 0.992 1.00 0.00 0.00 0.00
#> TCGA.A1.A0SB.01 1 0.0000 0.992 1.00 0.00 0.00 0.00
#> TCGA.AR.A2LR.01 3 0.2647 0.885 0.12 0.00 0.88 0.00
#> TCGA.AO.A0JL.01 4 0.0707 0.971 0.00 0.02 0.00 0.98
#> TCGA.A7.A13D.01 2 0.2345 0.803 0.00 0.90 0.00 0.10
#> TCGA.GI.A2C9.01 2 0.2921 0.805 0.00 0.86 0.00 0.14
#> TCGA.E2.A1LK.01 4 0.0000 0.994 0.00 0.00 0.00 1.00
#> TCGA.S3.AA0Z.01 3 0.0707 0.945 0.02 0.00 0.98 0.00
#> TCGA.AQ.A54N.01 2 0.0000 0.744 0.00 1.00 0.00 0.00
#> TCGA.E9.A1N8.01 1 0.0707 0.982 0.98 0.02 0.00 0.00
#> TCGA.A1.A0SO.01 3 0.0000 0.940 0.00 0.00 1.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.AR.A0TP.01 3 0.2280 0.867 0.12 0.00 0.88 0.00 0.00
#> TCGA.AR.A1AY.01 2 0.2873 0.781 0.02 0.86 0.00 0.12 0.00
#> TCGA.A7.A5ZV.01 4 0.0609 0.936 0.00 0.02 0.00 0.98 0.00
#> TCGA.B6.A1KF.01 4 0.2616 0.874 0.10 0.02 0.00 0.88 0.00
#> TCGA.AC.A62X.01 4 0.0609 0.936 0.00 0.02 0.00 0.98 0.00
#> TCGA.D8.A1JM.01 2 0.3274 0.734 0.00 0.78 0.00 0.22 0.00
#> TCGA.HN.A2NL.01 2 0.5599 0.459 0.26 0.62 0.12 0.00 0.00
#> TCGA.A1.A0SK.01 5 0.0000 0.972 0.00 0.00 0.00 0.00 1.00
#> TCGA.A2.A0YM.01 2 0.3274 0.734 0.00 0.78 0.00 0.22 0.00
#> TCGA.A7.A13E.01 4 0.0609 0.936 0.00 0.02 0.00 0.98 0.00
#> TCGA.B6.A402.01 5 0.0000 0.972 0.00 0.00 0.00 0.00 1.00
#> TCGA.E2.A1LS.01 2 0.4818 0.706 0.10 0.72 0.00 0.18 0.00
#> TCGA.D8.A27H.01 3 0.0609 0.882 0.00 0.02 0.98 0.00 0.00
#> TCGA.OL.A6VO.01 3 0.3390 0.840 0.06 0.00 0.84 0.00 0.10
#> TCGA.A2.A3XU.01 5 0.2438 0.904 0.06 0.00 0.04 0.00 0.90
#> TCGA.B6.A0RE.01 2 0.2616 0.783 0.10 0.88 0.00 0.02 0.00
#> TCGA.OL.A5RW.01 5 0.0000 0.972 0.00 0.00 0.00 0.00 1.00
#> TCGA.A1.A0SB.01 5 0.0000 0.972 0.00 0.00 0.00 0.00 1.00
#> TCGA.AR.A2LR.01 3 0.3731 0.835 0.16 0.00 0.80 0.00 0.04
#> TCGA.AO.A0JL.01 4 0.3946 0.824 0.12 0.08 0.00 0.80 0.00
#> TCGA.A7.A13D.01 2 0.3209 0.779 0.10 0.86 0.02 0.02 0.00
#> TCGA.GI.A2C9.01 2 0.1216 0.787 0.00 0.96 0.02 0.02 0.00
#> TCGA.E2.A1LK.01 4 0.0609 0.936 0.00 0.02 0.00 0.98 0.00
#> TCGA.S3.AA0Z.01 3 0.1732 0.883 0.08 0.00 0.92 0.00 0.00
#> TCGA.AQ.A54N.01 2 0.4302 0.541 0.48 0.52 0.00 0.00 0.00
#> TCGA.E9.A1N8.01 5 0.1410 0.947 0.06 0.00 0.00 0.00 0.94
#> TCGA.A1.A0SO.01 3 0.3852 0.811 0.22 0.02 0.76 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.AR.A0TP.01 3 0.3834 0.772 0.20 0.02 0.76 0.00 0.00 0.02
#> TCGA.AR.A1AY.01 2 0.2260 0.631 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.A7.A5ZV.01 4 0.0547 0.877 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.B6.A1KF.01 4 0.2790 0.779 0.14 0.02 0.00 0.84 0.00 0.00
#> TCGA.AC.A62X.01 4 0.0547 0.877 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.D8.A1JM.01 2 0.3076 0.581 0.00 0.76 0.00 0.24 0.00 0.00
#> TCGA.HN.A2NL.01 2 0.7294 -0.118 0.28 0.40 0.18 0.00 0.00 0.14
#> TCGA.A1.A0SK.01 5 0.0000 0.939 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A2.A0YM.01 2 0.2631 0.625 0.00 0.82 0.00 0.18 0.00 0.00
#> TCGA.A7.A13E.01 4 0.0547 0.877 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.B6.A402.01 5 0.0000 0.939 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.E2.A1LS.01 2 0.5778 0.441 0.16 0.64 0.00 0.12 0.00 0.08
#> TCGA.D8.A27H.01 3 0.1480 0.816 0.04 0.02 0.94 0.00 0.00 0.00
#> TCGA.OL.A6VO.01 3 0.2725 0.793 0.04 0.00 0.88 0.00 0.06 0.02
#> TCGA.A2.A3XU.01 5 0.3258 0.848 0.10 0.00 0.02 0.00 0.84 0.04
#> TCGA.B6.A0RE.01 2 0.2790 0.503 0.02 0.84 0.00 0.00 0.00 0.14
#> TCGA.OL.A5RW.01 5 0.0000 0.939 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A1.A0SB.01 5 0.0000 0.939 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AR.A2LR.01 3 0.4403 0.726 0.18 0.00 0.74 0.00 0.04 0.04
#> TCGA.AO.A0JL.01 4 0.4806 0.500 0.38 0.06 0.00 0.56 0.00 0.00
#> TCGA.A7.A13D.01 2 0.3688 0.467 0.04 0.80 0.00 0.02 0.00 0.14
#> TCGA.GI.A2C9.01 2 0.1865 0.609 0.04 0.92 0.00 0.04 0.00 0.00
#> TCGA.E2.A1LK.01 4 0.0547 0.877 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.S3.AA0Z.01 3 0.2474 0.810 0.08 0.00 0.88 0.00 0.00 0.04
#> TCGA.AQ.A54N.01 6 0.3198 0.000 0.00 0.26 0.00 0.00 0.00 0.74
#> TCGA.E9.A1N8.01 5 0.3321 0.829 0.08 0.00 0.00 0.00 0.82 0.10
#> TCGA.A1.A0SO.01 3 0.4377 0.713 0.16 0.00 0.72 0.00 0.00 0.12
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.AR.A0TP.01 3 0.4844 0.5182 0.20 0.02 0.68 0.00 0.00 0.02 0.08
#> TCGA.AR.A1AY.01 2 0.2569 0.6517 0.00 0.84 0.00 0.14 0.00 0.02 0.00
#> TCGA.A7.A5ZV.01 4 0.0000 0.9291 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B6.A1KF.01 4 0.2081 0.6440 0.00 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.AC.A62X.01 4 0.0000 0.9291 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A1JM.01 2 0.3139 0.5902 0.00 0.70 0.00 0.30 0.00 0.00 0.00
#> TCGA.HN.A2NL.01 1 0.5225 0.0599 0.56 0.34 0.02 0.00 0.00 0.02 0.06
#> TCGA.A1.A0SK.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A2.A0YM.01 2 0.2945 0.6179 0.00 0.74 0.00 0.26 0.00 0.00 0.00
#> TCGA.A7.A13E.01 4 0.0000 0.9291 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B6.A402.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E2.A1LS.01 2 0.6899 0.0746 0.02 0.38 0.00 0.14 0.00 0.12 0.34
#> TCGA.D8.A27H.01 3 0.1166 0.7025 0.06 0.00 0.94 0.00 0.00 0.00 0.00
#> TCGA.OL.A6VO.01 3 0.0504 0.7079 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.A2.A3XU.01 5 0.3826 0.7873 0.04 0.00 0.10 0.00 0.80 0.02 0.04
#> TCGA.B6.A0RE.01 2 0.4527 0.4876 0.02 0.72 0.00 0.04 0.00 0.18 0.04
#> TCGA.OL.A5RW.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A1.A0SB.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AR.A2LR.01 3 0.5369 0.4640 0.20 0.00 0.64 0.00 0.02 0.04 0.10
#> TCGA.AO.A0JL.01 7 0.4266 0.0000 0.00 0.04 0.00 0.44 0.00 0.00 0.52
#> TCGA.A7.A13D.01 2 0.5232 0.4052 0.06 0.68 0.00 0.02 0.00 0.12 0.12
#> TCGA.GI.A2C9.01 2 0.3485 0.6401 0.02 0.82 0.00 0.10 0.00 0.02 0.04
#> TCGA.E2.A1LK.01 4 0.0000 0.9291 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S3.AA0Z.01 3 0.3734 0.6463 0.14 0.04 0.78 0.00 0.00 0.00 0.04
#> TCGA.AQ.A54N.01 6 0.1886 0.0000 0.00 0.12 0.00 0.00 0.00 0.88 0.00
#> TCGA.E9.A1N8.01 5 0.3396 0.7950 0.00 0.00 0.02 0.00 0.80 0.14 0.04
#> TCGA.A1.A0SO.01 1 0.3943 -0.1739 0.56 0.00 0.42 0.00 0.00 0.02 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.AR.A0TP.01 1 0.265 0.0883 0.76 0.00 0.24 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AY.01 2 0.272 0.6554 0.00 0.86 0.00 0.02 0.00 0.02 0.02 0.08
#> TCGA.A7.A5ZV.01 8 0.000 0.8948 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.B6.A1KF.01 8 0.301 0.3769 0.00 0.00 0.00 0.00 0.00 0.00 0.32 0.68
#> TCGA.AC.A62X.01 8 0.000 0.8948 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D8.A1JM.01 2 0.330 0.6351 0.00 0.76 0.00 0.02 0.00 0.00 0.02 0.20
#> TCGA.HN.A2NL.01 2 0.691 -0.0816 0.20 0.36 0.02 0.30 0.00 0.02 0.10 0.00
#> TCGA.A1.A0SK.01 5 0.000 0.8638 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A0YM.01 2 0.343 0.6199 0.00 0.74 0.00 0.02 0.00 0.00 0.02 0.22
#> TCGA.A7.A13E.01 8 0.000 0.8948 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.B6.A402.01 5 0.000 0.8638 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E2.A1LS.01 2 0.608 0.4997 0.02 0.58 0.00 0.04 0.00 0.08 0.18 0.10
#> TCGA.D8.A27H.01 3 0.381 0.1959 0.34 0.00 0.62 0.04 0.00 0.00 0.00 0.00
#> TCGA.OL.A6VO.01 3 0.318 0.4162 0.14 0.00 0.80 0.04 0.02 0.00 0.00 0.00
#> TCGA.A2.A3XU.01 5 0.432 0.5559 0.00 0.00 0.10 0.30 0.60 0.00 0.00 0.00
#> TCGA.B6.A0RE.01 2 0.435 0.5083 0.00 0.72 0.00 0.06 0.00 0.16 0.04 0.02
#> TCGA.OL.A5RW.01 5 0.000 0.8638 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A1.A0SB.01 5 0.000 0.8638 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A2LR.01 3 0.416 0.3085 0.04 0.02 0.78 0.10 0.02 0.02 0.02 0.00
#> TCGA.AO.A0JL.01 7 0.334 0.0000 0.02 0.04 0.00 0.00 0.00 0.00 0.78 0.16
#> TCGA.A7.A13D.01 2 0.470 0.4297 0.00 0.68 0.00 0.10 0.00 0.12 0.10 0.00
#> TCGA.GI.A2C9.01 2 0.180 0.6592 0.00 0.90 0.00 0.02 0.00 0.00 0.00 0.08
#> TCGA.E2.A1LK.01 8 0.000 0.8948 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.S3.AA0Z.01 3 0.462 0.2559 0.32 0.00 0.58 0.08 0.00 0.00 0.02 0.00
#> TCGA.AQ.A54N.01 6 0.109 0.0000 0.00 0.06 0.00 0.00 0.00 0.94 0.00 0.00
#> TCGA.E9.A1N8.01 5 0.447 0.6426 0.00 0.00 0.04 0.18 0.68 0.10 0.00 0.00
#> TCGA.A1.A0SO.01 1 0.511 0.1961 0.58 0.00 0.24 0.14 0.00 0.00 0.04 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node03. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0115-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0151-leaf , Node0152-leaf , Node0153-leaf , Node0154-leaf , Node0211-leaf , Node0212 , Node0213 , Node0221 , Node0222 , Node0231-leaf , Node0232 , Node0233-leaf , Node0241-leaf , Node0242 , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0331-leaf , Node0332-leaf , Node0341-leaf , Node0342-leaf , Node0343-leaf , Node0411 , Node0412-leaf , Node0413 , Node0421-leaf , Node0422 , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["033"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 44 columns.
#> Top rows (1000) are extracted by 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.977 0.991 0.4810 0.515 0.515
#> 3 3 0.573 0.596 0.731 0.3471 0.748 0.536
#> 4 4 0.757 0.794 0.876 0.1488 0.858 0.599
#> 5 5 0.741 0.646 0.772 0.0700 0.876 0.563
#> 6 6 0.751 0.635 0.779 0.0393 0.902 0.569
#> 7 7 0.718 0.542 0.696 0.0269 0.949 0.702
#> 8 8 0.778 0.599 0.760 0.0294 0.956 0.708
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.A2.A3XX.01 2 0.000 1.000 0.00 1.00
#> TCGA.A2.A3XT.01 2 0.000 1.000 0.00 1.00
#> TCGA.AR.A0TU.01 1 0.000 0.975 1.00 0.00
#> TCGA.A7.A26I.01 2 0.000 1.000 0.00 1.00
#> TCGA.B6.A0WX.01 1 0.000 0.975 1.00 0.00
#> TCGA.BH.A0E0.01 2 0.000 1.000 0.00 1.00
#> TCGA.B6.A0RU.01 2 0.000 1.000 0.00 1.00
#> TCGA.A2.A3XS.01 1 0.000 0.975 1.00 0.00
#> TCGA.E2.A1AZ.01 2 0.000 1.000 0.00 1.00
#> TCGA.LL.A5YP.01 2 0.000 1.000 0.00 1.00
#> TCGA.PL.A8LV.01 2 0.000 1.000 0.00 1.00
#> TCGA.AO.A1KR.01 1 0.000 0.975 1.00 0.00
#> TCGA.E9.A244.01 2 0.000 1.000 0.00 1.00
#> TCGA.B6.A400.01 2 0.000 1.000 0.00 1.00
#> TCGA.BH.A1FC.01 1 0.000 0.975 1.00 0.00
#> TCGA.BH.A0B9.01 2 0.000 1.000 0.00 1.00
#> TCGA.C8.A27B.01 2 0.000 1.000 0.00 1.00
#> TCGA.A2.A4RX.01 2 0.000 1.000 0.00 1.00
#> TCGA.A2.A0T0.01 2 0.000 1.000 0.00 1.00
#> TCGA.GM.A3XL.01 1 0.000 0.975 1.00 0.00
#> TCGA.AN.A0XU.01 2 0.000 1.000 0.00 1.00
#> TCGA.A7.A6VV.01 2 0.000 1.000 0.00 1.00
#> TCGA.OL.A5S0.01 2 0.000 1.000 0.00 1.00
#> TCGA.A7.A26F.01 1 0.000 0.975 1.00 0.00
#> TCGA.BH.A1F6.01 1 0.000 0.975 1.00 0.00
#> TCGA.AR.A1AR.01 1 0.000 0.975 1.00 0.00
#> TCGA.EW.A1P8.01 2 0.000 1.000 0.00 1.00
#> TCGA.B6.A409.01 2 0.000 1.000 0.00 1.00
#> TCGA.B6.A0X1.01 2 0.000 1.000 0.00 1.00
#> TCGA.A2.A0SX.01 2 0.000 1.000 0.00 1.00
#> TCGA.A1.A0SP.01 1 0.000 0.975 1.00 0.00
#> TCGA.A7.A6VY.01 1 0.000 0.975 1.00 0.00
#> TCGA.A7.A6VW.01 1 0.000 0.975 1.00 0.00
#> TCGA.LL.A73Y.01 2 0.000 1.000 0.00 1.00
#> TCGA.A2.A1G1.01 1 0.000 0.975 1.00 0.00
#> TCGA.D8.A1XQ.01 2 0.000 1.000 0.00 1.00
#> TCGA.BH.A5IZ.01 1 0.000 0.975 1.00 0.00
#> TCGA.LL.A8F5.01 1 0.958 0.390 0.62 0.38
#> TCGA.D8.A1XW.01 2 0.000 1.000 0.00 1.00
#> TCGA.OL.A5D7.01 1 0.000 0.975 1.00 0.00
#> TCGA.A7.A4SE.01 2 0.000 1.000 0.00 1.00
#> TCGA.BH.A0B3.01 2 0.000 1.000 0.00 1.00
#> TCGA.D8.A1XK.01 1 0.141 0.957 0.98 0.02
#> TCGA.AR.A24Q.01 2 0.000 1.000 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.A2.A3XX.01 3 0.6244 0.5021 0.00 0.44 0.56
#> TCGA.A2.A3XT.01 3 0.5016 0.4801 0.00 0.24 0.76
#> TCGA.AR.A0TU.01 1 0.0000 0.9179 1.00 0.00 0.00
#> TCGA.A7.A26I.01 2 0.1529 0.6705 0.00 0.96 0.04
#> TCGA.B6.A0WX.01 1 0.3686 0.9112 0.86 0.00 0.14
#> TCGA.BH.A0E0.01 3 0.6309 0.3983 0.00 0.50 0.50
#> TCGA.B6.A0RU.01 3 0.4796 0.4781 0.00 0.22 0.78
#> TCGA.A2.A3XS.01 1 0.4002 0.9057 0.84 0.00 0.16
#> TCGA.E2.A1AZ.01 2 0.5835 0.1189 0.00 0.66 0.34
#> TCGA.LL.A5YP.01 2 0.1529 0.6767 0.00 0.96 0.04
#> TCGA.PL.A8LV.01 3 0.5560 0.3927 0.00 0.30 0.70
#> TCGA.AO.A1KR.01 1 0.0000 0.9179 1.00 0.00 0.00
#> TCGA.E9.A244.01 3 0.6280 0.4746 0.00 0.46 0.54
#> TCGA.B6.A400.01 3 0.6280 0.4746 0.00 0.46 0.54
#> TCGA.BH.A1FC.01 1 0.0000 0.9179 1.00 0.00 0.00
#> TCGA.BH.A0B9.01 2 0.0000 0.6991 0.00 1.00 0.00
#> TCGA.C8.A27B.01 2 0.6126 -0.1490 0.00 0.60 0.40
#> TCGA.A2.A4RX.01 3 0.6302 0.0389 0.00 0.48 0.52
#> TCGA.A2.A0T0.01 2 0.5706 0.2160 0.00 0.68 0.32
#> TCGA.GM.A3XL.01 1 0.0892 0.9132 0.98 0.00 0.02
#> TCGA.AN.A0XU.01 2 0.4002 0.5605 0.00 0.84 0.16
#> TCGA.A7.A6VV.01 2 0.5216 0.3045 0.00 0.74 0.26
#> TCGA.OL.A5S0.01 2 0.5560 0.3510 0.00 0.70 0.30
#> TCGA.A7.A26F.01 1 0.3686 0.9126 0.86 0.00 0.14
#> TCGA.BH.A1F6.01 1 0.3340 0.9152 0.88 0.00 0.12
#> TCGA.AR.A1AR.01 1 0.0892 0.9132 0.98 0.00 0.02
#> TCGA.EW.A1P8.01 2 0.0000 0.6991 0.00 1.00 0.00
#> TCGA.B6.A409.01 3 0.6280 0.4746 0.00 0.46 0.54
#> TCGA.B6.A0X1.01 2 0.0000 0.6991 0.00 1.00 0.00
#> TCGA.A2.A0SX.01 2 0.0000 0.6991 0.00 1.00 0.00
#> TCGA.A1.A0SP.01 1 0.3686 0.9126 0.86 0.00 0.14
#> TCGA.A7.A6VY.01 1 0.0892 0.9132 0.98 0.00 0.02
#> TCGA.A7.A6VW.01 1 0.4002 0.9057 0.84 0.00 0.16
#> TCGA.LL.A73Y.01 2 0.5560 0.3510 0.00 0.70 0.30
#> TCGA.A2.A1G1.01 1 0.3686 0.9126 0.86 0.00 0.14
#> TCGA.D8.A1XQ.01 3 0.6244 0.5021 0.00 0.44 0.56
#> TCGA.BH.A5IZ.01 3 0.6803 0.1346 0.28 0.04 0.68
#> TCGA.LL.A8F5.01 3 0.4449 0.4179 0.04 0.10 0.86
#> TCGA.D8.A1XW.01 2 0.0000 0.6991 0.00 1.00 0.00
#> TCGA.OL.A5D7.01 1 0.0000 0.9179 1.00 0.00 0.00
#> TCGA.A7.A4SE.01 3 0.4555 0.4978 0.00 0.20 0.80
#> TCGA.BH.A0B3.01 3 0.6244 0.5021 0.00 0.44 0.56
#> TCGA.D8.A1XK.01 1 0.7277 0.5652 0.66 0.06 0.28
#> TCGA.AR.A24Q.01 3 0.6244 0.5021 0.00 0.44 0.56
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.A2.A3XX.01 3 0.0000 0.883 0.00 0.00 1.00 0.00
#> TCGA.A2.A3XT.01 4 0.3821 0.836 0.00 0.04 0.12 0.84
#> TCGA.AR.A0TU.01 1 0.2011 0.885 0.92 0.00 0.00 0.08
#> TCGA.A7.A26I.01 2 0.2011 0.881 0.00 0.92 0.08 0.00
#> TCGA.B6.A0WX.01 1 0.3247 0.906 0.88 0.06 0.00 0.06
#> TCGA.BH.A0E0.01 3 0.0000 0.883 0.00 0.00 1.00 0.00
#> TCGA.B6.A0RU.01 4 0.3821 0.836 0.00 0.04 0.12 0.84
#> TCGA.A2.A3XS.01 1 0.3247 0.906 0.88 0.06 0.00 0.06
#> TCGA.E2.A1AZ.01 3 0.0707 0.867 0.00 0.02 0.98 0.00
#> TCGA.LL.A5YP.01 2 0.4292 0.846 0.00 0.82 0.10 0.08
#> TCGA.PL.A8LV.01 4 0.3972 0.827 0.00 0.08 0.08 0.84
#> TCGA.AO.A1KR.01 1 0.1913 0.900 0.94 0.02 0.00 0.04
#> TCGA.E9.A244.01 3 0.0000 0.883 0.00 0.00 1.00 0.00
#> TCGA.B6.A400.01 3 0.0000 0.883 0.00 0.00 1.00 0.00
#> TCGA.BH.A1FC.01 1 0.1637 0.892 0.94 0.00 0.00 0.06
#> TCGA.BH.A0B9.01 2 0.2011 0.881 0.00 0.92 0.08 0.00
#> TCGA.C8.A27B.01 3 0.4994 -0.158 0.00 0.48 0.52 0.00
#> TCGA.A2.A4RX.01 4 0.3935 0.808 0.00 0.10 0.06 0.84
#> TCGA.A2.A0T0.01 3 0.3172 0.717 0.00 0.16 0.84 0.00
#> TCGA.GM.A3XL.01 1 0.2345 0.874 0.90 0.00 0.00 0.10
#> TCGA.AN.A0XU.01 2 0.6011 0.128 0.00 0.48 0.48 0.04
#> TCGA.A7.A6VV.01 2 0.5428 0.764 0.00 0.74 0.12 0.14
#> TCGA.OL.A5S0.01 2 0.4079 0.767 0.00 0.80 0.02 0.18
#> TCGA.A7.A26F.01 1 0.3247 0.906 0.88 0.06 0.00 0.06
#> TCGA.BH.A1F6.01 1 0.3247 0.906 0.88 0.06 0.00 0.06
#> TCGA.AR.A1AR.01 1 0.2706 0.876 0.90 0.02 0.00 0.08
#> TCGA.EW.A1P8.01 2 0.2011 0.881 0.00 0.92 0.08 0.00
#> TCGA.B6.A409.01 3 0.0000 0.883 0.00 0.00 1.00 0.00
#> TCGA.B6.A0X1.01 2 0.2011 0.881 0.00 0.92 0.08 0.00
#> TCGA.A2.A0SX.01 2 0.2011 0.881 0.00 0.92 0.08 0.00
#> TCGA.A1.A0SP.01 1 0.3247 0.906 0.88 0.06 0.00 0.06
#> TCGA.A7.A6VY.01 1 0.2335 0.886 0.92 0.02 0.00 0.06
#> TCGA.A7.A6VW.01 1 0.3247 0.906 0.88 0.06 0.00 0.06
#> TCGA.LL.A73Y.01 2 0.3606 0.803 0.00 0.84 0.02 0.14
#> TCGA.A2.A1G1.01 1 0.3247 0.906 0.88 0.06 0.00 0.06
#> TCGA.D8.A1XQ.01 3 0.0000 0.883 0.00 0.00 1.00 0.00
#> TCGA.BH.A5IZ.01 4 0.2335 0.826 0.02 0.00 0.06 0.92
#> TCGA.LL.A8F5.01 4 0.2706 0.831 0.02 0.00 0.08 0.90
#> TCGA.D8.A1XW.01 2 0.2011 0.881 0.00 0.92 0.08 0.00
#> TCGA.OL.A5D7.01 1 0.1913 0.893 0.94 0.02 0.00 0.04
#> TCGA.A7.A4SE.01 3 0.4855 0.199 0.00 0.00 0.60 0.40
#> TCGA.BH.A0B3.01 3 0.0000 0.883 0.00 0.00 1.00 0.00
#> TCGA.D8.A1XK.01 4 0.4907 0.167 0.42 0.00 0.00 0.58
#> TCGA.AR.A24Q.01 3 0.0000 0.883 0.00 0.00 1.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.A2.A3XX.01 3 0.1043 0.8297 0.00 0.00 0.96 0.00 0.04
#> TCGA.A2.A3XT.01 4 0.1820 0.8804 0.00 0.02 0.02 0.94 0.02
#> TCGA.AR.A0TU.01 1 0.2616 0.6208 0.88 0.00 0.00 0.02 0.10
#> TCGA.A7.A26I.01 2 0.1410 0.8025 0.00 0.94 0.00 0.00 0.06
#> TCGA.B6.A0WX.01 1 0.4302 -0.9110 0.52 0.00 0.00 0.00 0.48
#> TCGA.BH.A0E0.01 3 0.1410 0.8225 0.00 0.00 0.94 0.00 0.06
#> TCGA.B6.A0RU.01 4 0.1216 0.8801 0.00 0.02 0.02 0.96 0.00
#> TCGA.A2.A3XS.01 5 0.4287 0.9655 0.46 0.00 0.00 0.00 0.54
#> TCGA.E2.A1AZ.01 3 0.1410 0.8225 0.00 0.00 0.94 0.00 0.06
#> TCGA.LL.A5YP.01 2 0.6379 0.6723 0.00 0.64 0.08 0.10 0.18
#> TCGA.PL.A8LV.01 4 0.1043 0.8757 0.00 0.04 0.00 0.96 0.00
#> TCGA.AO.A1KR.01 1 0.1410 0.5360 0.94 0.00 0.00 0.00 0.06
#> TCGA.E9.A244.01 3 0.3109 0.7934 0.00 0.00 0.80 0.00 0.20
#> TCGA.B6.A400.01 3 0.2280 0.8167 0.00 0.00 0.88 0.00 0.12
#> TCGA.BH.A1FC.01 1 0.0000 0.6107 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0B9.01 2 0.0000 0.8155 0.00 1.00 0.00 0.00 0.00
#> TCGA.C8.A27B.01 2 0.6447 -0.0334 0.00 0.44 0.38 0.00 0.18
#> TCGA.A2.A4RX.01 4 0.1043 0.8757 0.00 0.04 0.00 0.96 0.00
#> TCGA.A2.A0T0.01 3 0.5210 0.5790 0.00 0.20 0.68 0.00 0.12
#> TCGA.GM.A3XL.01 1 0.3037 0.6216 0.86 0.00 0.00 0.04 0.10
#> TCGA.AN.A0XU.01 3 0.7051 -0.0396 0.00 0.40 0.42 0.04 0.14
#> TCGA.A7.A6VV.01 2 0.6540 0.6035 0.00 0.60 0.04 0.18 0.18
#> TCGA.OL.A5S0.01 2 0.5263 0.6391 0.00 0.66 0.00 0.24 0.10
#> TCGA.A7.A26F.01 5 0.4302 0.9767 0.48 0.00 0.00 0.00 0.52
#> TCGA.BH.A1F6.01 1 0.4307 -0.9486 0.50 0.00 0.00 0.00 0.50
#> TCGA.AR.A1AR.01 1 0.3037 0.6216 0.86 0.00 0.00 0.04 0.10
#> TCGA.EW.A1P8.01 2 0.0000 0.8155 0.00 1.00 0.00 0.00 0.00
#> TCGA.B6.A409.01 3 0.1043 0.8353 0.00 0.00 0.96 0.00 0.04
#> TCGA.B6.A0X1.01 2 0.0000 0.8155 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A0SX.01 2 0.0000 0.8155 0.00 1.00 0.00 0.00 0.00
#> TCGA.A1.A0SP.01 5 0.4302 0.9767 0.48 0.00 0.00 0.00 0.52
#> TCGA.A7.A6VY.01 1 0.0609 0.6111 0.98 0.00 0.00 0.02 0.00
#> TCGA.A7.A6VW.01 5 0.4287 0.9655 0.46 0.00 0.00 0.00 0.54
#> TCGA.LL.A73Y.01 2 0.4170 0.7375 0.00 0.78 0.00 0.14 0.08
#> TCGA.A2.A1G1.01 5 0.4302 0.9767 0.48 0.00 0.00 0.00 0.52
#> TCGA.D8.A1XQ.01 3 0.1410 0.8303 0.00 0.00 0.94 0.00 0.06
#> TCGA.BH.A5IZ.01 4 0.1043 0.8734 0.00 0.00 0.00 0.96 0.04
#> TCGA.LL.A8F5.01 4 0.1043 0.8734 0.00 0.00 0.00 0.96 0.04
#> TCGA.D8.A1XW.01 2 0.0000 0.8155 0.00 1.00 0.00 0.00 0.00
#> TCGA.OL.A5D7.01 1 0.0000 0.6107 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A4SE.01 4 0.6629 0.1591 0.00 0.02 0.34 0.50 0.14
#> TCGA.BH.A0B3.01 3 0.1043 0.8267 0.00 0.00 0.96 0.04 0.00
#> TCGA.D8.A1XK.01 1 0.5579 0.3792 0.60 0.00 0.00 0.30 0.10
#> TCGA.AR.A24Q.01 3 0.3690 0.7836 0.00 0.00 0.78 0.02 0.20
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.A2.A3XX.01 3 0.2190 0.680 0.04 0.00 0.90 0.00 0.00 0.06
#> TCGA.A2.A3XT.01 4 0.0937 0.904 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.AR.A0TU.01 1 0.4105 0.759 0.72 0.02 0.00 0.00 0.24 0.02
#> TCGA.A7.A26I.01 2 0.1092 0.804 0.00 0.96 0.02 0.00 0.00 0.02
#> TCGA.B6.A0WX.01 5 0.1480 0.810 0.02 0.00 0.00 0.00 0.94 0.04
#> TCGA.BH.A0E0.01 3 0.3270 0.680 0.12 0.00 0.82 0.00 0.00 0.06
#> TCGA.B6.A0RU.01 4 0.2345 0.882 0.02 0.00 0.02 0.90 0.00 0.06
#> TCGA.A2.A3XS.01 5 0.0937 0.840 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.E2.A1AZ.01 3 0.3321 0.683 0.10 0.00 0.82 0.00 0.00 0.08
#> TCGA.LL.A5YP.01 6 0.4913 0.310 0.00 0.34 0.02 0.04 0.00 0.60
#> TCGA.PL.A8LV.01 4 0.1267 0.903 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.AO.A1KR.01 5 0.4632 -0.527 0.44 0.00 0.00 0.00 0.52 0.04
#> TCGA.E9.A244.01 3 0.5474 0.559 0.08 0.00 0.54 0.02 0.00 0.36
#> TCGA.B6.A400.01 3 0.4711 0.632 0.08 0.00 0.64 0.00 0.00 0.28
#> TCGA.BH.A1FC.01 1 0.4806 0.708 0.56 0.00 0.00 0.00 0.38 0.06
#> TCGA.BH.A0B9.01 2 0.0547 0.802 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.C8.A27B.01 3 0.6973 0.108 0.06 0.28 0.38 0.00 0.00 0.28
#> TCGA.A2.A4RX.01 4 0.3460 0.720 0.02 0.00 0.00 0.76 0.00 0.22
#> TCGA.A2.A0T0.01 3 0.4042 0.616 0.02 0.04 0.76 0.00 0.00 0.18
#> TCGA.GM.A3XL.01 1 0.4105 0.759 0.72 0.02 0.00 0.00 0.24 0.02
#> TCGA.AN.A0XU.01 6 0.6158 0.195 0.04 0.12 0.36 0.00 0.00 0.48
#> TCGA.A7.A6VV.01 6 0.5626 0.326 0.02 0.34 0.00 0.10 0.00 0.54
#> TCGA.OL.A5S0.01 2 0.5574 -0.209 0.02 0.46 0.00 0.08 0.00 0.44
#> TCGA.A7.A26F.01 5 0.0000 0.851 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BH.A1F6.01 5 0.0547 0.843 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.AR.A1AR.01 1 0.4613 0.764 0.66 0.00 0.00 0.00 0.26 0.08
#> TCGA.EW.A1P8.01 2 0.0547 0.802 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.B6.A409.01 3 0.2474 0.714 0.04 0.00 0.88 0.00 0.00 0.08
#> TCGA.B6.A0X1.01 2 0.1092 0.804 0.00 0.96 0.02 0.00 0.00 0.02
#> TCGA.A2.A0SX.01 2 0.1092 0.804 0.00 0.96 0.02 0.00 0.00 0.02
#> TCGA.A1.A0SP.01 5 0.0547 0.845 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.A7.A6VY.01 1 0.5235 0.699 0.52 0.00 0.00 0.00 0.38 0.10
#> TCGA.A7.A6VW.01 5 0.2020 0.808 0.02 0.00 0.00 0.02 0.92 0.04
#> TCGA.LL.A73Y.01 2 0.4971 0.165 0.02 0.58 0.00 0.04 0.00 0.36
#> TCGA.A2.A1G1.01 5 0.0000 0.851 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D8.A1XQ.01 3 0.3045 0.707 0.06 0.00 0.84 0.00 0.00 0.10
#> TCGA.BH.A5IZ.01 4 0.0547 0.892 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.LL.A8F5.01 4 0.0547 0.892 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.D8.A1XW.01 2 0.0547 0.802 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.OL.A5D7.01 1 0.5235 0.699 0.52 0.00 0.00 0.00 0.38 0.10
#> TCGA.A7.A4SE.01 6 0.6646 0.163 0.04 0.00 0.22 0.32 0.00 0.42
#> TCGA.BH.A0B3.01 3 0.2020 0.717 0.02 0.00 0.92 0.02 0.00 0.04
#> TCGA.D8.A1XK.01 1 0.5916 0.605 0.66 0.02 0.00 0.08 0.14 0.10
#> TCGA.AR.A24Q.01 3 0.4613 0.590 0.08 0.00 0.66 0.00 0.00 0.26
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.A2.A3XX.01 7 0.6113 0.2489 0.08 0.00 0.40 0.00 0.00 0.12 0.40
#> TCGA.A2.A3XT.01 4 0.0863 0.8183 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.AR.A0TU.01 1 0.4107 0.6560 0.70 0.00 0.00 0.00 0.24 0.04 0.02
#> TCGA.A7.A26I.01 2 0.1664 0.9117 0.06 0.92 0.00 0.00 0.00 0.00 0.02
#> TCGA.B6.A0WX.01 5 0.2722 0.6846 0.00 0.00 0.00 0.00 0.84 0.04 0.12
#> TCGA.BH.A0E0.01 7 0.3294 0.3539 0.00 0.00 0.34 0.00 0.00 0.00 0.66
#> TCGA.B6.A0RU.01 4 0.3396 0.7451 0.02 0.00 0.04 0.80 0.00 0.14 0.00
#> TCGA.A2.A3XS.01 5 0.1664 0.7858 0.00 0.00 0.00 0.00 0.92 0.06 0.02
#> TCGA.E2.A1AZ.01 7 0.3815 0.3245 0.00 0.02 0.36 0.00 0.00 0.00 0.62
#> TCGA.LL.A5YP.01 6 0.6032 0.4812 0.00 0.16 0.34 0.02 0.00 0.46 0.02
#> TCGA.PL.A8LV.01 4 0.0863 0.8163 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.AO.A1KR.01 5 0.6116 -0.5767 0.34 0.00 0.00 0.00 0.44 0.06 0.16
#> TCGA.E9.A244.01 3 0.3199 0.3382 0.00 0.00 0.80 0.00 0.00 0.06 0.14
#> TCGA.B6.A400.01 3 0.4538 0.2307 0.00 0.00 0.62 0.00 0.00 0.10 0.28
#> TCGA.BH.A1FC.01 1 0.6403 0.6634 0.44 0.00 0.00 0.00 0.30 0.10 0.16
#> TCGA.BH.A0B9.01 2 0.0000 0.9831 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A27B.01 3 0.2864 0.2878 0.02 0.12 0.84 0.00 0.00 0.02 0.00
#> TCGA.A2.A4RX.01 4 0.3755 0.4809 0.02 0.00 0.00 0.64 0.00 0.34 0.00
#> TCGA.A2.A0T0.01 7 0.7706 0.1356 0.14 0.06 0.28 0.00 0.00 0.24 0.28
#> TCGA.GM.A3XL.01 1 0.3186 0.6439 0.76 0.00 0.00 0.02 0.22 0.00 0.00
#> TCGA.AN.A0XU.01 6 0.6065 0.3394 0.06 0.10 0.10 0.00 0.00 0.62 0.12
#> TCGA.A7.A6VV.01 6 0.6612 0.4792 0.00 0.14 0.34 0.08 0.00 0.42 0.02
#> TCGA.OL.A5S0.01 6 0.5437 0.4559 0.00 0.20 0.02 0.22 0.00 0.56 0.00
#> TCGA.A7.A26F.01 5 0.0000 0.8204 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A1F6.01 5 0.0000 0.8204 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AR.A1AR.01 1 0.5961 0.6905 0.52 0.00 0.00 0.00 0.24 0.06 0.18
#> TCGA.EW.A1P8.01 2 0.0000 0.9831 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A409.01 3 0.4902 0.0989 0.00 0.00 0.54 0.00 0.00 0.12 0.34
#> TCGA.B6.A0X1.01 2 0.0000 0.9831 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0SX.01 2 0.0000 0.9831 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A1.A0SP.01 5 0.0000 0.8204 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A7.A6VY.01 1 0.6513 0.6333 0.38 0.00 0.00 0.00 0.32 0.08 0.22
#> TCGA.A7.A6VW.01 5 0.2509 0.7501 0.00 0.00 0.00 0.04 0.88 0.06 0.02
#> TCGA.LL.A73Y.01 6 0.5542 0.3428 0.02 0.38 0.00 0.14 0.00 0.46 0.00
#> TCGA.A2.A1G1.01 5 0.0000 0.8204 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D8.A1XQ.01 3 0.4139 0.1016 0.06 0.00 0.72 0.00 0.00 0.02 0.20
#> TCGA.BH.A5IZ.01 4 0.1006 0.8115 0.02 0.00 0.00 0.96 0.00 0.00 0.02
#> TCGA.LL.A8F5.01 4 0.2804 0.7645 0.06 0.00 0.00 0.86 0.00 0.06 0.02
#> TCGA.D8.A1XW.01 2 0.0000 0.9831 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5D7.01 1 0.6544 0.6484 0.38 0.00 0.00 0.00 0.30 0.08 0.24
#> TCGA.A7.A4SE.01 6 0.6597 0.1866 0.00 0.00 0.26 0.32 0.00 0.34 0.08
#> TCGA.BH.A0B3.01 3 0.5862 -0.2761 0.06 0.00 0.50 0.04 0.00 0.04 0.36
#> TCGA.D8.A1XK.01 1 0.4455 0.3349 0.70 0.00 0.00 0.10 0.02 0.18 0.00
#> TCGA.AR.A24Q.01 3 0.3244 0.2727 0.04 0.00 0.78 0.00 0.00 0.18 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.A2.A3XX.01 7 0.3586 0.468 0.00 0.00 0.06 0.00 0.12 0.04 0.78 0.00
#> TCGA.A2.A3XT.01 4 0.0000 0.827 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A0TU.01 1 0.2532 0.673 0.88 0.00 0.02 0.00 0.04 0.04 0.00 0.02
#> TCGA.A7.A26I.01 2 0.3178 0.774 0.00 0.80 0.04 0.00 0.14 0.02 0.00 0.00
#> TCGA.B6.A0WX.01 8 0.4529 0.607 0.08 0.00 0.06 0.00 0.18 0.00 0.00 0.68
#> TCGA.BH.A0E0.01 7 0.1804 0.481 0.00 0.00 0.02 0.00 0.08 0.00 0.90 0.00
#> TCGA.B6.A0RU.01 4 0.2224 0.762 0.00 0.00 0.00 0.86 0.02 0.12 0.00 0.00
#> TCGA.A2.A3XS.01 8 0.2224 0.859 0.00 0.00 0.12 0.00 0.02 0.00 0.00 0.86
#> TCGA.E2.A1AZ.01 7 0.1804 0.481 0.00 0.00 0.02 0.00 0.08 0.00 0.90 0.00
#> TCGA.LL.A5YP.01 6 0.4804 0.497 0.00 0.12 0.14 0.02 0.04 0.68 0.00 0.00
#> TCGA.PL.A8LV.01 4 0.0000 0.827 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A1KR.01 1 0.5230 0.513 0.40 0.00 0.00 0.00 0.28 0.00 0.00 0.32
#> TCGA.E9.A244.01 3 0.4990 0.303 0.00 0.00 0.44 0.00 0.00 0.18 0.38 0.00
#> TCGA.B6.A400.01 7 0.4622 -0.239 0.00 0.00 0.30 0.00 0.00 0.14 0.56 0.00
#> TCGA.BH.A1FC.01 1 0.4981 0.715 0.58 0.00 0.02 0.00 0.30 0.02 0.00 0.08
#> TCGA.BH.A0B9.01 2 0.0000 0.954 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A27B.01 3 0.6034 0.402 0.02 0.18 0.58 0.00 0.04 0.06 0.12 0.00
#> TCGA.A2.A4RX.01 4 0.3618 0.343 0.00 0.00 0.00 0.60 0.02 0.38 0.00 0.00
#> TCGA.A2.A0T0.01 7 0.6245 0.194 0.00 0.00 0.14 0.00 0.26 0.18 0.42 0.00
#> TCGA.GM.A3XL.01 1 0.0471 0.674 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.AN.A0XU.01 6 0.5862 0.309 0.00 0.04 0.08 0.00 0.22 0.56 0.10 0.00
#> TCGA.A7.A6VV.01 6 0.5295 0.414 0.00 0.12 0.22 0.04 0.02 0.60 0.00 0.00
#> TCGA.OL.A5S0.01 6 0.4169 0.552 0.00 0.18 0.00 0.10 0.02 0.70 0.00 0.00
#> TCGA.A7.A26F.01 8 0.0000 0.894 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BH.A1F6.01 8 0.0808 0.870 0.04 0.00 0.00 0.00 0.00 0.00 0.00 0.96
#> TCGA.AR.A1AR.01 1 0.3995 0.711 0.60 0.00 0.00 0.00 0.36 0.02 0.00 0.02
#> TCGA.EW.A1P8.01 2 0.0000 0.954 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A409.01 7 0.3619 0.251 0.00 0.00 0.12 0.00 0.00 0.14 0.74 0.00
#> TCGA.B6.A0X1.01 2 0.0000 0.954 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0SX.01 2 0.0471 0.943 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.A1.A0SP.01 8 0.0000 0.894 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.A7.A6VY.01 1 0.4370 0.711 0.52 0.00 0.00 0.00 0.40 0.00 0.00 0.08
#> TCGA.A7.A6VW.01 8 0.2224 0.859 0.00 0.00 0.12 0.00 0.02 0.00 0.00 0.86
#> TCGA.LL.A73Y.01 6 0.5155 0.517 0.00 0.22 0.00 0.10 0.08 0.60 0.00 0.00
#> TCGA.A2.A1G1.01 8 0.0000 0.894 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D8.A1XQ.01 7 0.3193 0.156 0.00 0.00 0.38 0.00 0.00 0.00 0.62 0.00
#> TCGA.BH.A5IZ.01 4 0.2132 0.801 0.00 0.00 0.08 0.88 0.04 0.00 0.00 0.00
#> TCGA.LL.A8F5.01 4 0.2591 0.793 0.00 0.00 0.08 0.86 0.04 0.02 0.00 0.00
#> TCGA.D8.A1XW.01 2 0.0000 0.954 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5D7.01 1 0.4794 0.706 0.48 0.00 0.02 0.00 0.42 0.00 0.00 0.08
#> TCGA.A7.A4SE.01 6 0.6510 -0.197 0.00 0.00 0.28 0.18 0.00 0.34 0.20 0.00
#> TCGA.BH.A0B3.01 7 0.4471 0.410 0.00 0.00 0.16 0.10 0.02 0.02 0.70 0.00
#> TCGA.D8.A1XK.01 1 0.3687 0.523 0.78 0.00 0.00 0.06 0.08 0.08 0.00 0.00
#> TCGA.AR.A24Q.01 3 0.4677 0.362 0.00 0.00 0.54 0.00 0.00 0.14 0.32 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node03. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0115-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0151-leaf , Node0152-leaf , Node0153-leaf , Node0154-leaf , Node0211-leaf , Node0212 , Node0213 , Node0221 , Node0222 , Node0231-leaf , Node0232 , Node0233-leaf , Node0241-leaf , Node0242 , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0331-leaf , Node0332-leaf , Node0341-leaf , Node0342-leaf , Node0343-leaf , Node0411 , Node0412-leaf , Node0413 , Node0421-leaf , Node0422 , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["034"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 19 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.444 0.718 0.843 0.3622 0.509 0.509
#> 3 3 1.000 0.999 0.993 0.5957 0.848 0.717
#> 4 4 0.813 0.844 0.944 0.1372 0.942 0.859
#> 5 5 0.848 0.710 0.892 0.1065 0.836 0.569
#> 6 6 0.848 0.725 0.893 0.0583 0.947 0.795
#> 7 7 0.789 0.595 0.824 0.0378 0.942 0.762
#> 8 8 0.766 0.594 0.879 0.0447 0.959 0.806
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.A2.A0T2.01 2 0.999 0.6435 0.48 0.52
#> TCGA.BH.A0WA.01 1 0.795 0.4031 0.76 0.24
#> TCGA.EW.A1PH.01 1 0.000 0.9107 1.00 0.00
#> TCGA.E9.A22G.01 2 0.999 0.6435 0.48 0.52
#> TCGA.LL.A6FR.01 1 0.000 0.9107 1.00 0.00
#> TCGA.AO.A124.01 1 0.000 0.9107 1.00 0.00
#> TCGA.AR.A256.01 1 0.000 0.9107 1.00 0.00
#> TCGA.EW.A1OW.01 1 0.000 0.9107 1.00 0.00
#> TCGA.A2.A0YE.01 1 0.000 0.9107 1.00 0.00
#> TCGA.AC.A2QH.01 2 0.000 0.4844 0.00 1.00
#> TCGA.D8.A27F.01 2 0.999 0.6435 0.48 0.52
#> TCGA.AR.A251.01 2 0.999 0.6435 0.48 0.52
#> TCGA.E2.A1LG.01 1 0.000 0.9107 1.00 0.00
#> TCGA.A2.A0YJ.01 1 0.000 0.9107 1.00 0.00
#> TCGA.AC.A7VC.01 2 0.000 0.4844 0.00 1.00
#> TCGA.B6.A0I1.01 1 0.000 0.9107 1.00 0.00
#> TCGA.C8.A1HJ.01 2 0.999 0.6435 0.48 0.52
#> TCGA.AC.A2BK.01 1 0.925 -0.0483 0.66 0.34
#> TCGA.E2.A574.01 1 0.000 0.9107 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.A2.A0T2.01 2 0.0892 1.00 0.02 0.98 0.00
#> TCGA.BH.A0WA.01 2 0.0892 1.00 0.02 0.98 0.00
#> TCGA.EW.A1PH.01 1 0.0000 1.00 1.00 0.00 0.00
#> TCGA.E9.A22G.01 2 0.0892 1.00 0.02 0.98 0.00
#> TCGA.LL.A6FR.01 1 0.0000 1.00 1.00 0.00 0.00
#> TCGA.AO.A124.01 1 0.0000 1.00 1.00 0.00 0.00
#> TCGA.AR.A256.01 1 0.0000 1.00 1.00 0.00 0.00
#> TCGA.EW.A1OW.01 1 0.0000 1.00 1.00 0.00 0.00
#> TCGA.A2.A0YE.01 1 0.0000 1.00 1.00 0.00 0.00
#> TCGA.AC.A2QH.01 3 0.0000 0.99 0.00 0.00 1.00
#> TCGA.D8.A27F.01 2 0.0892 1.00 0.02 0.98 0.00
#> TCGA.AR.A251.01 2 0.0892 1.00 0.02 0.98 0.00
#> TCGA.E2.A1LG.01 1 0.0000 1.00 1.00 0.00 0.00
#> TCGA.A2.A0YJ.01 1 0.0000 1.00 1.00 0.00 0.00
#> TCGA.AC.A7VC.01 3 0.0892 0.99 0.00 0.02 0.98
#> TCGA.B6.A0I1.01 1 0.0000 1.00 1.00 0.00 0.00
#> TCGA.C8.A1HJ.01 2 0.0892 1.00 0.02 0.98 0.00
#> TCGA.AC.A2BK.01 1 0.0000 1.00 1.00 0.00 0.00
#> TCGA.E2.A574.01 1 0.0000 1.00 1.00 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.A2.A0T2.01 2 0.0000 0.959 0.00 1.00 0 0.00
#> TCGA.BH.A0WA.01 2 0.3400 0.804 0.00 0.82 0 0.18
#> TCGA.EW.A1PH.01 1 0.0000 0.910 1.00 0.00 0 0.00
#> TCGA.E9.A22G.01 2 0.0000 0.959 0.00 1.00 0 0.00
#> TCGA.LL.A6FR.01 1 0.5147 0.604 0.74 0.06 0 0.20
#> TCGA.AO.A124.01 1 0.0000 0.910 1.00 0.00 0 0.00
#> TCGA.AR.A256.01 1 0.0000 0.910 1.00 0.00 0 0.00
#> TCGA.EW.A1OW.01 1 0.0000 0.910 1.00 0.00 0 0.00
#> TCGA.A2.A0YE.01 1 0.0000 0.910 1.00 0.00 0 0.00
#> TCGA.AC.A2QH.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.D8.A27F.01 2 0.0707 0.950 0.00 0.98 0 0.02
#> TCGA.AR.A251.01 2 0.0000 0.959 0.00 1.00 0 0.00
#> TCGA.E2.A1LG.01 1 0.4406 0.555 0.70 0.00 0 0.30
#> TCGA.A2.A0YJ.01 1 0.0000 0.910 1.00 0.00 0 0.00
#> TCGA.AC.A7VC.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.B6.A0I1.01 1 0.0000 0.910 1.00 0.00 0 0.00
#> TCGA.C8.A1HJ.01 2 0.0000 0.959 0.00 1.00 0 0.00
#> TCGA.AC.A2BK.01 4 0.4406 0.000 0.30 0.00 0 0.70
#> TCGA.E2.A574.01 1 0.0000 0.910 1.00 0.00 0 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.A2.A0T2.01 2 0.426 0.977 0.00 0.56 0.00 0.00 0.44
#> TCGA.BH.A0WA.01 5 0.104 0.179 0.00 0.04 0.00 0.00 0.96
#> TCGA.EW.A1PH.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A22G.01 2 0.418 0.931 0.00 0.60 0.00 0.00 0.40
#> TCGA.LL.A6FR.01 5 0.342 0.318 0.24 0.00 0.00 0.00 0.76
#> TCGA.AO.A124.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A256.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1OW.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0YE.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A2QH.01 3 0.000 0.933 0.00 0.00 1.00 0.00 0.00
#> TCGA.D8.A27F.01 5 0.429 -0.836 0.00 0.46 0.00 0.00 0.54
#> TCGA.AR.A251.01 2 0.426 0.977 0.00 0.56 0.00 0.00 0.44
#> TCGA.E2.A1LG.01 5 0.556 0.106 0.08 0.00 0.00 0.36 0.56
#> TCGA.A2.A0YJ.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A7VC.01 3 0.208 0.933 0.00 0.04 0.92 0.04 0.00
#> TCGA.B6.A0I1.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A1HJ.01 2 0.426 0.977 0.00 0.56 0.00 0.00 0.44
#> TCGA.AC.A2BK.01 4 0.499 0.000 0.04 0.36 0.00 0.60 0.00
#> TCGA.E2.A574.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.A2.A0T2.01 2 0.3309 0.740 0.00 0.72 0.00 0 0.28 0.00
#> TCGA.BH.A0WA.01 5 0.1267 0.695 0.00 0.06 0.00 0 0.94 0.00
#> TCGA.EW.A1PH.01 1 0.0937 0.953 0.96 0.00 0.00 0 0.00 0.04
#> TCGA.E9.A22G.01 2 0.0547 0.589 0.00 0.98 0.00 0 0.02 0.00
#> TCGA.LL.A6FR.01 5 0.0547 0.647 0.02 0.00 0.00 0 0.98 0.00
#> TCGA.AO.A124.01 1 0.0000 0.955 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.AR.A256.01 1 0.0000 0.955 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.EW.A1OW.01 1 0.1480 0.947 0.94 0.00 0.00 0 0.02 0.04
#> TCGA.A2.A0YE.01 1 0.0547 0.951 0.98 0.00 0.00 0 0.02 0.00
#> TCGA.AC.A2QH.01 3 0.2882 0.880 0.00 0.02 0.86 0 0.02 0.10
#> TCGA.D8.A27F.01 5 0.3198 0.622 0.00 0.26 0.00 0 0.74 0.00
#> TCGA.AR.A251.01 5 0.3578 0.476 0.00 0.34 0.00 0 0.66 0.00
#> TCGA.E2.A1LG.01 6 0.3711 0.000 0.02 0.00 0.00 0 0.26 0.72
#> TCGA.A2.A0YJ.01 1 0.0000 0.955 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.AC.A7VC.01 3 0.0000 0.880 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.B6.A0I1.01 1 0.0937 0.953 0.96 0.00 0.00 0 0.00 0.04
#> TCGA.C8.A1HJ.01 2 0.3309 0.740 0.00 0.72 0.00 0 0.28 0.00
#> TCGA.AC.A2BK.01 4 0.0000 0.000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.E2.A574.01 1 0.3156 0.827 0.80 0.00 0.00 0 0.02 0.18
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.A2.A0T2.01 2 0.000 0.487 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.BH.A0WA.01 5 0.294 0.819 0.00 0.26 0.00 0 0.74 0.00 0.00
#> TCGA.EW.A1PH.01 1 0.101 0.899 0.96 0.00 0.00 0 0.00 0.02 0.02
#> TCGA.E9.A22G.01 7 0.355 0.000 0.00 0.46 0.00 0 0.00 0.00 0.54
#> TCGA.LL.A6FR.01 5 0.242 0.835 0.00 0.18 0.00 0 0.82 0.00 0.00
#> TCGA.AO.A124.01 1 0.000 0.903 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.AR.A256.01 1 0.000 0.903 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.EW.A1OW.01 1 0.242 0.872 0.88 0.00 0.00 0 0.08 0.02 0.02
#> TCGA.A2.A0YE.01 1 0.136 0.884 0.94 0.00 0.00 0 0.02 0.04 0.00
#> TCGA.AC.A2QH.01 3 0.000 0.712 0.00 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.D8.A27F.01 2 0.350 0.126 0.00 0.58 0.00 0 0.42 0.00 0.00
#> TCGA.AR.A251.01 2 0.322 0.386 0.00 0.68 0.00 0 0.32 0.00 0.00
#> TCGA.E2.A1LG.01 6 0.208 0.000 0.00 0.00 0.00 0 0.14 0.86 0.00
#> TCGA.A2.A0YJ.01 1 0.000 0.903 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.AC.A7VC.01 3 0.493 0.712 0.00 0.00 0.68 0 0.08 0.08 0.16
#> TCGA.B6.A0I1.01 1 0.216 0.877 0.90 0.00 0.00 0 0.06 0.02 0.02
#> TCGA.C8.A1HJ.01 2 0.000 0.487 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.AC.A2BK.01 4 0.000 0.000 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.E2.A574.01 1 0.479 0.494 0.58 0.00 0.00 0 0.12 0.00 0.30
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.A2.A0T2.01 2 0.1091 0.742 0.00 0.94 0.00 0 0.00 0.00 0.00 0.06
#> TCGA.BH.A0WA.01 5 0.2852 0.664 0.00 0.28 0.00 0 0.72 0.00 0.00 0.00
#> TCGA.EW.A1PH.01 1 0.1275 0.818 0.94 0.00 0.00 0 0.00 0.00 0.02 0.04
#> TCGA.E9.A22G.01 7 0.2406 0.000 0.00 0.20 0.00 0 0.00 0.00 0.80 0.00
#> TCGA.LL.A6FR.01 5 0.1765 0.721 0.00 0.12 0.00 0 0.88 0.00 0.00 0.00
#> TCGA.AO.A124.01 1 0.0000 0.832 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.AR.A256.01 1 0.0000 0.832 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.EW.A1OW.01 1 0.3785 0.723 0.76 0.00 0.00 0 0.16 0.02 0.02 0.04
#> TCGA.A2.A0YE.01 1 0.4079 0.589 0.74 0.00 0.00 0 0.08 0.00 0.12 0.06
#> TCGA.AC.A2QH.01 3 0.0000 0.844 0.00 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.D8.A27F.01 2 0.3095 0.619 0.00 0.74 0.00 0 0.24 0.00 0.00 0.02
#> TCGA.AR.A251.01 2 0.2114 0.736 0.00 0.84 0.00 0 0.16 0.00 0.00 0.00
#> TCGA.E2.A1LG.01 6 0.0471 0.000 0.00 0.00 0.00 0 0.02 0.98 0.00 0.00
#> TCGA.A2.A0YJ.01 1 0.0000 0.832 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.AC.A7VC.01 3 0.3185 0.844 0.00 0.00 0.82 0 0.04 0.00 0.06 0.08
#> TCGA.B6.A0I1.01 1 0.3785 0.723 0.76 0.00 0.00 0 0.16 0.02 0.02 0.04
#> TCGA.C8.A1HJ.01 2 0.0000 0.767 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.AC.A2BK.01 4 0.0000 0.000 0.00 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.E2.A574.01 8 0.2534 0.000 0.22 0.00 0.00 0 0.00 0.00 0.00 0.78
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node014-leaf , Node015 , Node021 , Node022 , Node023 , Node024 , Node031 , Node032 , Node033 , Node034 , Node041 , Node042 , Node043 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["04"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 288 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.985 0.994 0.4701 0.531 0.531
#> 3 3 1.000 0.964 0.985 0.3877 0.692 0.481
#> 4 4 0.918 0.879 0.953 0.1344 0.772 0.452
#> 5 5 0.767 0.560 0.724 0.0673 0.857 0.575
#> 6 6 0.763 0.650 0.814 0.0333 0.846 0.491
#> 7 7 0.765 0.573 0.763 0.0282 0.922 0.617
#> 8 8 0.831 0.755 0.851 0.0186 0.933 0.634
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.OL.A66H.01 1 0.000 0.993 1.00 0.00
#> TCGA.3C.AALK.01 2 0.000 0.995 0.00 1.00
#> TCGA.AC.A5EH.01 1 0.000 0.993 1.00 0.00
#> TCGA.E9.A1R0.01 1 0.000 0.993 1.00 0.00
#> TCGA.AC.A62Y.01 1 0.000 0.993 1.00 0.00
#> TCGA.E9.A1R2.01 1 0.000 0.993 1.00 0.00
#> TCGA.E9.A3X8.01 1 0.000 0.993 1.00 0.00
#> TCGA.AR.A255.01 2 0.000 0.995 0.00 1.00
#> TCGA.E2.A10B.01 1 0.000 0.993 1.00 0.00
#> TCGA.AO.A0JD.01 1 0.000 0.993 1.00 0.00
#> TCGA.A8.A0A6.01 2 0.000 0.995 0.00 1.00
#> TCGA.A7.A3IY.01 1 0.000 0.993 1.00 0.00
#> TCGA.D8.A3Z5.01 1 0.000 0.993 1.00 0.00
#> TCGA.E9.A1RD.01 2 0.995 0.131 0.46 0.54
#> TCGA.LD.A66U.01 1 0.000 0.993 1.00 0.00
#> TCGA.AC.A3QP.01 1 0.000 0.993 1.00 0.00
#> TCGA.GM.A2DK.01 1 0.000 0.993 1.00 0.00
#> TCGA.E2.A1B0.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A1EY.01 2 0.000 0.995 0.00 1.00
#> TCGA.AC.A8OS.01 1 0.971 0.343 0.60 0.40
#> TCGA.GM.A2DN.01 2 0.000 0.995 0.00 1.00
#> TCGA.AO.A03M.01 1 0.000 0.993 1.00 0.00
#> TCGA.A2.A4RW.01 2 0.000 0.995 0.00 1.00
#> TCGA.AC.A6IV.01 1 0.000 0.993 1.00 0.00
#> TCGA.LL.A7SZ.01 1 0.000 0.993 1.00 0.00
#> TCGA.AR.A2LJ.01 1 0.000 0.993 1.00 0.00
#> TCGA.AQ.A1H3.01 2 0.000 0.995 0.00 1.00
#> TCGA.D8.A1JB.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A0BC.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A1EW.01 2 0.000 0.995 0.00 1.00
#> TCGA.GM.A2DH.01 2 0.000 0.995 0.00 1.00
#> TCGA.D8.A27P.01 1 0.000 0.993 1.00 0.00
#> TCGA.EW.A2FS.01 2 0.000 0.995 0.00 1.00
#> TCGA.OL.A66J.01 1 0.000 0.993 1.00 0.00
#> TCGA.AR.A2LO.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A201.01 1 0.000 0.993 1.00 0.00
#> TCGA.S3.AA14.01 1 0.000 0.993 1.00 0.00
#> TCGA.B6.A0RS.01 1 0.000 0.993 1.00 0.00
#> TCGA.AR.A1AT.01 2 0.000 0.995 0.00 1.00
#> TCGA.A2.A1G0.01 1 0.000 0.993 1.00 0.00
#> TCGA.AC.A3OD.01 2 0.000 0.995 0.00 1.00
#> TCGA.UU.A93S.01 2 0.000 0.995 0.00 1.00
#> TCGA.XX.A89A.01 1 0.000 0.993 1.00 0.00
#> TCGA.AR.A5QM.01 2 0.000 0.995 0.00 1.00
#> TCGA.PE.A5DE.01 1 0.000 0.993 1.00 0.00
#> TCGA.AC.A23H.01 2 0.000 0.995 0.00 1.00
#> TCGA.D8.A27V.01 1 0.000 0.993 1.00 0.00
#> TCGA.A2.A1FZ.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A0BA.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.AB28.01 2 0.000 0.995 0.00 1.00
#> TCGA.D8.A27R.01 2 0.000 0.995 0.00 1.00
#> TCGA.OL.A5D6.01 2 0.000 0.995 0.00 1.00
#> TCGA.E2.A3DX.01 1 0.000 0.993 1.00 0.00
#> TCGA.A1.A0SE.01 1 0.000 0.993 1.00 0.00
#> TCGA.D8.A1XT.01 1 0.000 0.993 1.00 0.00
#> TCGA.C8.A1HI.01 1 0.000 0.993 1.00 0.00
#> TCGA.A2.A0T4.01 2 0.000 0.995 0.00 1.00
#> TCGA.MS.A51U.01 1 0.000 0.993 1.00 0.00
#> TCGA.D8.A1Y2.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A0DG.01 2 0.000 0.995 0.00 1.00
#> TCGA.C8.A3M7.01 2 0.000 0.995 0.00 1.00
#> TCGA.E2.A1L6.01 1 0.000 0.993 1.00 0.00
#> TCGA.D8.A1XY.01 1 0.000 0.993 1.00 0.00
#> TCGA.D8.A27G.01 2 0.000 0.995 0.00 1.00
#> TCGA.AR.A1AM.01 1 0.000 0.993 1.00 0.00
#> TCGA.4H.AAAK.01 1 0.000 0.993 1.00 0.00
#> TCGA.AC.A5XS.01 1 0.000 0.993 1.00 0.00
#> TCGA.E2.A1IF.01 1 0.000 0.993 1.00 0.00
#> TCGA.AC.A2FO.01 1 0.000 0.993 1.00 0.00
#> TCGA.AR.A24S.01 1 0.000 0.993 1.00 0.00
#> TCGA.A2.A3KD.01 1 0.000 0.993 1.00 0.00
#> TCGA.E9.A226.01 1 0.000 0.993 1.00 0.00
#> TCGA.D8.A1X8.01 1 0.000 0.993 1.00 0.00
#> TCGA.A2.A0T5.01 1 0.402 0.916 0.92 0.08
#> TCGA.LD.A74U.01 2 0.000 0.995 0.00 1.00
#> TCGA.AR.A0TQ.01 2 0.000 0.995 0.00 1.00
#> TCGA.AO.A0JE.01 2 0.000 0.995 0.00 1.00
#> TCGA.E9.A228.01 2 0.000 0.995 0.00 1.00
#> TCGA.E9.A1RA.01 1 0.000 0.993 1.00 0.00
#> TCGA.LL.A740.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A0BZ.01 2 0.000 0.995 0.00 1.00
#> TCGA.EW.A2FV.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A0DV.01 1 0.000 0.993 1.00 0.00
#> TCGA.A2.A0YI.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A0BM.01 1 0.000 0.993 1.00 0.00
#> TCGA.D8.A27I.01 1 0.000 0.993 1.00 0.00
#> TCGA.A2.A0YD.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A0C0.01 2 0.000 0.995 0.00 1.00
#> TCGA.E9.A1NG.01 1 0.000 0.993 1.00 0.00
#> TCGA.EW.A1IW.01 2 0.000 0.995 0.00 1.00
#> TCGA.JL.A3YW.01 2 0.000 0.995 0.00 1.00
#> TCGA.AN.A0XN.01 2 0.000 0.995 0.00 1.00
#> TCGA.E9.A6HE.01 2 0.000 0.995 0.00 1.00
#> TCGA.C8.A26W.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A0DP.01 2 0.000 0.995 0.00 1.00
#> TCGA.AR.A2LN.01 1 0.000 0.993 1.00 0.00
#> TCGA.D8.A1JF.01 2 0.000 0.995 0.00 1.00
#> TCGA.OL.A6VQ.01 1 0.000 0.993 1.00 0.00
#> TCGA.E2.A1LL.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A0AU.01 1 0.000 0.993 1.00 0.00
#> TCGA.A2.A0T1.01 1 0.000 0.993 1.00 0.00
#> TCGA.AR.A24W.01 1 0.000 0.993 1.00 0.00
#> TCGA.AR.A0TT.01 2 0.000 0.995 0.00 1.00
#> TCGA.AC.A3W6.01 2 0.000 0.995 0.00 1.00
#> TCGA.OL.A66P.01 1 0.000 0.993 1.00 0.00
#> TCGA.AR.A24L.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A0H3.01 1 0.000 0.993 1.00 0.00
#> TCGA.EW.A1IZ.01 1 0.242 0.956 0.96 0.04
#> TCGA.AO.A0JA.01 2 0.000 0.995 0.00 1.00
#> TCGA.AR.A0TX.01 1 0.000 0.993 1.00 0.00
#> TCGA.AO.A0JG.01 2 0.000 0.995 0.00 1.00
#> TCGA.OL.A66N.01 2 0.000 0.995 0.00 1.00
#> TCGA.A7.A4SC.01 2 0.000 0.995 0.00 1.00
#> TCGA.GM.A2DB.01 1 0.000 0.993 1.00 0.00
#> TCGA.E9.A1N3.01 1 0.000 0.993 1.00 0.00
#> TCGA.AN.A0XL.01 1 0.000 0.993 1.00 0.00
#> TCGA.E9.A24A.01 1 0.000 0.993 1.00 0.00
#> TCGA.GM.A2DL.01 2 0.000 0.995 0.00 1.00
#> TCGA.E9.A22B.01 2 0.000 0.995 0.00 1.00
#> TCGA.A2.A3XV.01 2 0.000 0.995 0.00 1.00
#> TCGA.AC.A6IX.06 2 0.000 0.995 0.00 1.00
#> TCGA.AC.A6IX.01 2 0.000 0.995 0.00 1.00
#> TCGA.B6.A0WY.01 1 0.000 0.993 1.00 0.00
#> TCGA.E9.A1R4.01 1 0.000 0.993 1.00 0.00
#> TCGA.EW.A1J2.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A0GY.01 1 0.000 0.993 1.00 0.00
#> TCGA.W8.A86G.01 1 0.000 0.993 1.00 0.00
#> TCGA.A7.A5ZW.01 1 0.000 0.993 1.00 0.00
#> TCGA.C8.A1HF.01 2 0.000 0.995 0.00 1.00
#> TCGA.A2.A0T7.01 1 0.000 0.993 1.00 0.00
#> TCGA.AO.A0JJ.01 1 0.000 0.993 1.00 0.00
#> TCGA.B6.A0X7.01 1 0.327 0.937 0.94 0.06
#> TCGA.OL.A5RV.01 1 0.000 0.993 1.00 0.00
#> TCGA.E2.A1BC.01 1 0.000 0.993 1.00 0.00
#> TCGA.E9.A22D.01 2 0.000 0.995 0.00 1.00
#> TCGA.A1.A0SF.01 2 0.000 0.995 0.00 1.00
#> TCGA.EW.A6SD.01 1 0.000 0.993 1.00 0.00
#> TCGA.A7.A426.01 1 0.000 0.993 1.00 0.00
#> TCGA.AR.A1AU.01 1 0.327 0.937 0.94 0.06
#> TCGA.E9.A1N6.01 1 0.000 0.993 1.00 0.00
#> TCGA.D8.A27L.01 1 0.000 0.993 1.00 0.00
#> TCGA.E9.A1NF.01 2 0.000 0.995 0.00 1.00
#> TCGA.A1.A0SM.01 2 0.000 0.995 0.00 1.00
#> TCGA.LD.A7W5.01 2 0.000 0.995 0.00 1.00
#> TCGA.E2.A1LA.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A42V.01 1 0.000 0.993 1.00 0.00
#> TCGA.E9.A5FK.01 2 0.000 0.995 0.00 1.00
#> TCGA.D8.A1XB.01 2 0.000 0.995 0.00 1.00
#> TCGA.E9.A227.01 1 0.000 0.993 1.00 0.00
#> TCGA.A2.A0YL.01 1 0.000 0.993 1.00 0.00
#> TCGA.A7.A5ZX.01 1 0.402 0.916 0.92 0.08
#> TCGA.D8.A1JG.01 2 0.000 0.995 0.00 1.00
#> TCGA.AO.A0JF.01 1 0.000 0.993 1.00 0.00
#> TCGA.C8.A8HQ.01 2 0.000 0.995 0.00 1.00
#> TCGA.AC.A2B8.01 1 0.000 0.993 1.00 0.00
#> TCGA.A2.A4S3.01 1 0.000 0.993 1.00 0.00
#> TCGA.A2.A0CO.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A0AZ.01 1 0.000 0.993 1.00 0.00
#> TCGA.E2.A1LE.01 2 0.000 0.995 0.00 1.00
#> TCGA.A2.A0YH.01 1 0.000 0.993 1.00 0.00
#> TCGA.LL.A5YN.01 1 0.000 0.993 1.00 0.00
#> TCGA.AC.A23G.01 1 0.000 0.993 1.00 0.00
#> TCGA.GM.A3XN.01 1 0.000 0.993 1.00 0.00
#> TCGA.C8.A275.01 2 0.000 0.995 0.00 1.00
#> TCGA.E2.A1IK.01 1 0.000 0.993 1.00 0.00
#> TCGA.AQ.A7U7.01 2 0.000 0.995 0.00 1.00
#> TCGA.A1.A0SI.01 1 0.000 0.993 1.00 0.00
#> TCGA.A2.A25A.01 1 0.000 0.993 1.00 0.00
#> TCGA.E9.A1RH.01 1 0.000 0.993 1.00 0.00
#> TCGA.AO.A12E.01 2 0.000 0.995 0.00 1.00
#> TCGA.A7.A13H.01 1 0.000 0.993 1.00 0.00
#> TCGA.E2.A1IO.01 1 0.000 0.993 1.00 0.00
#> TCGA.C8.A26Y.01 1 0.000 0.993 1.00 0.00
#> TCGA.A2.A25D.01 2 0.000 0.995 0.00 1.00
#> TCGA.AN.A0XW.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A0AW.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A0B6.01 1 0.000 0.993 1.00 0.00
#> TCGA.E9.A229.01 1 0.000 0.993 1.00 0.00
#> TCGA.D8.A1JK.01 1 0.000 0.993 1.00 0.00
#> TCGA.GM.A5PX.01 1 0.000 0.993 1.00 0.00
#> TCGA.AR.A5QN.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A208.01 1 0.000 0.993 1.00 0.00
#> TCGA.EW.A1IX.01 1 0.000 0.993 1.00 0.00
#> TCGA.A2.A259.01 1 0.000 0.993 1.00 0.00
#> TCGA.GM.A2DD.01 1 0.000 0.993 1.00 0.00
#> TCGA.E2.A1B1.01 1 0.000 0.993 1.00 0.00
#> TCGA.D8.A73U.01 1 0.000 0.993 1.00 0.00
#> TCGA.D8.A27N.01 2 0.000 0.995 0.00 1.00
#> TCGA.E9.A22E.01 1 0.000 0.993 1.00 0.00
#> TCGA.OL.A5RX.01 1 0.402 0.916 0.92 0.08
#> TCGA.D8.A1XO.01 1 0.000 0.993 1.00 0.00
#> TCGA.AC.A23C.01 2 0.000 0.995 0.00 1.00
#> TCGA.A7.A56D.01 1 0.000 0.993 1.00 0.00
#> TCGA.A1.A0SH.01 1 0.000 0.993 1.00 0.00
#> TCGA.AR.A5QP.01 2 0.000 0.995 0.00 1.00
#> TCGA.D8.A1Y0.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A2L8.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A202.01 2 0.000 0.995 0.00 1.00
#> TCGA.EW.A1OV.01 2 0.000 0.995 0.00 1.00
#> TCGA.A1.A0SN.01 2 0.000 0.995 0.00 1.00
#> TCGA.E9.A295.01 2 0.000 0.995 0.00 1.00
#> TCGA.AC.A8OP.01 2 0.000 0.995 0.00 1.00
#> TCGA.GI.A2C8.01 2 0.000 0.995 0.00 1.00
#> TCGA.AR.A24P.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A0B2.01 2 0.469 0.885 0.10 0.90
#> TCGA.A2.A0SU.01 1 0.000 0.993 1.00 0.00
#> TCGA.AR.A24T.01 2 0.000 0.995 0.00 1.00
#> TCGA.AC.A2FE.01 2 0.000 0.995 0.00 1.00
#> TCGA.E9.A1N4.01 1 0.000 0.993 1.00 0.00
#> TCGA.XX.A899.01 2 0.000 0.995 0.00 1.00
#> TCGA.E9.A1N9.01 1 0.000 0.993 1.00 0.00
#> TCGA.S3.AA17.01 2 0.000 0.995 0.00 1.00
#> TCGA.EW.A1PF.01 1 0.000 0.993 1.00 0.00
#> TCGA.AO.A03L.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A0HF.01 1 0.000 0.993 1.00 0.00
#> TCGA.AC.A2QI.01 1 0.000 0.993 1.00 0.00
#> TCGA.A2.A4S2.01 2 0.000 0.995 0.00 1.00
#> TCGA.GM.A2DA.01 1 0.000 0.993 1.00 0.00
#> TCGA.A7.A4SA.01 1 0.000 0.993 1.00 0.00
#> TCGA.A2.A3KC.01 2 0.000 0.995 0.00 1.00
#> TCGA.OL.A66L.01 2 0.000 0.995 0.00 1.00
#> TCGA.AR.A2LM.01 1 0.000 0.993 1.00 0.00
#> TCGA.E2.A10C.01 1 0.000 0.993 1.00 0.00
#> TCGA.AR.A1AN.01 1 0.000 0.993 1.00 0.00
#> TCGA.5L.AAT1.01 2 0.000 0.995 0.00 1.00
#> TCGA.HN.A2OB.01 1 0.000 0.993 1.00 0.00
#> TCGA.GM.A5PV.01 1 0.000 0.993 1.00 0.00
#> TCGA.E2.A1IJ.01 1 0.000 0.993 1.00 0.00
#> TCGA.OK.A5Q2.01 2 0.000 0.995 0.00 1.00
#> TCGA.E9.A1R3.01 1 0.000 0.993 1.00 0.00
#> TCGA.AR.A254.01 2 0.000 0.995 0.00 1.00
#> TCGA.AR.A0TW.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A8G0.01 1 0.000 0.993 1.00 0.00
#> TCGA.B6.A401.01 1 0.000 0.993 1.00 0.00
#> TCGA.E2.A1LB.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A0W5.01 1 0.000 0.993 1.00 0.00
#> TCGA.AC.A3W7.01 2 0.000 0.995 0.00 1.00
#> TCGA.AC.A3W5.01 1 0.327 0.937 0.94 0.06
#> TCGA.B6.A1KI.01 1 0.000 0.993 1.00 0.00
#> TCGA.E9.A1RI.01 1 0.000 0.993 1.00 0.00
#> TCGA.A2.A0T6.01 2 0.000 0.995 0.00 1.00
#> TCGA.EW.A3E8.01 2 0.000 0.995 0.00 1.00
#> TCGA.OL.A5RU.01 1 0.000 0.993 1.00 0.00
#> TCGA.E2.A10F.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A0C3.01 1 0.000 0.993 1.00 0.00
#> TCGA.B6.A0RV.01 1 0.402 0.916 0.92 0.08
#> TCGA.E2.A1IH.01 1 0.000 0.993 1.00 0.00
#> TCGA.EW.A1IY.01 1 0.000 0.993 1.00 0.00
#> TCGA.AR.A24O.01 1 0.000 0.993 1.00 0.00
#> TCGA.C8.A278.01 2 0.000 0.995 0.00 1.00
#> TCGA.AC.A3HN.01 1 0.000 0.993 1.00 0.00
#> TCGA.AC.A3BB.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A1FE.01 1 0.000 0.993 1.00 0.00
#> TCGA.A2.A0EN.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A0BF.01 1 0.402 0.916 0.92 0.08
#> TCGA.WT.AB41.01 2 0.000 0.995 0.00 1.00
#> TCGA.LL.A5YL.01 2 0.000 0.995 0.00 1.00
#> TCGA.AR.A1AK.01 1 0.402 0.916 0.92 0.08
#> TCGA.C8.A26X.01 2 0.000 0.995 0.00 1.00
#> TCGA.A7.A3J1.01 1 0.000 0.993 1.00 0.00
#> TCGA.D8.A1Y3.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A0DK.01 2 0.000 0.995 0.00 1.00
#> TCGA.D8.A1JE.01 1 0.000 0.993 1.00 0.00
#> TCGA.EW.A2FR.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A0W4.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A0BJ.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A203.01 2 0.000 0.995 0.00 1.00
#> TCGA.E2.A14U.01 1 0.000 0.993 1.00 0.00
#> TCGA.D8.A1XM.01 1 0.000 0.993 1.00 0.00
#> TCGA.D8.A1JH.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A1EU.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A1FR.01 1 0.000 0.993 1.00 0.00
#> TCGA.A7.A425.01 1 0.000 0.993 1.00 0.00
#> TCGA.B6.A0IK.01 2 0.000 0.995 0.00 1.00
#> TCGA.E9.A1RF.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A0HP.01 2 0.000 0.995 0.00 1.00
#> TCGA.BH.A8FZ.01 1 0.000 0.993 1.00 0.00
#> TCGA.AC.A2FG.01 1 0.000 0.993 1.00 0.00
#> TCGA.AR.A1AL.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A1EO.01 2 0.000 0.995 0.00 1.00
#> TCGA.D8.A27K.01 2 0.000 0.995 0.00 1.00
#> TCGA.C8.A1HG.01 1 0.000 0.993 1.00 0.00
#> TCGA.D8.A1JU.01 1 0.000 0.993 1.00 0.00
#> TCGA.A2.A0YK.01 1 0.402 0.916 0.92 0.08
#> TCGA.BH.A0DI.01 2 0.000 0.995 0.00 1.00
#> TCGA.E2.A107.01 1 0.402 0.916 0.92 0.08
#> TCGA.5L.AAT0.01 1 0.000 0.993 1.00 0.00
#> TCGA.D8.A27E.01 1 0.000 0.993 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.OL.A66H.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.3C.AALK.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.AC.A5EH.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.E9.A1R0.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AC.A62Y.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.E9.A1R2.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.E9.A3X8.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.AR.A255.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.E2.A10B.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.AO.A0JD.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A8.A0A6.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.A7.A3IY.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D8.A3Z5.01 1 0.0892 0.968 0.98 0.00 0.02
#> TCGA.E9.A1RD.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.LD.A66U.01 3 0.6126 0.335 0.40 0.00 0.60
#> TCGA.AC.A3QP.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.GM.A2DK.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.E2.A1B0.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BH.A1EY.01 2 0.6045 0.400 0.00 0.62 0.38
#> TCGA.AC.A8OS.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.GM.A2DN.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.AO.A03M.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A2.A4RW.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.AC.A6IV.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.LL.A7SZ.01 3 0.0892 0.959 0.02 0.00 0.98
#> TCGA.AR.A2LJ.01 1 0.5948 0.440 0.64 0.00 0.36
#> TCGA.AQ.A1H3.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.D8.A1JB.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BH.A0BC.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BH.A1EW.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.GM.A2DH.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.D8.A27P.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.EW.A2FS.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.OL.A66J.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AR.A2LO.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.BH.A201.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.S3.AA14.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.B6.A0RS.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AR.A1AT.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.A2.A1G0.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AC.A3OD.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.UU.A93S.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.XX.A89A.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AR.A5QM.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.PE.A5DE.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AC.A23H.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.D8.A27V.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A2.A1FZ.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.BH.A0BA.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BH.AB28.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.D8.A27R.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.OL.A5D6.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.E2.A3DX.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A1.A0SE.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D8.A1XT.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.C8.A1HI.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.A2.A0T4.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.MS.A51U.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D8.A1Y2.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BH.A0DG.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.C8.A3M7.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.E2.A1L6.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D8.A1XY.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D8.A27G.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.AR.A1AM.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.4H.AAAK.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.AC.A5XS.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.E2.A1IF.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AC.A2FO.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.AR.A24S.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A2.A3KD.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.E9.A226.01 1 0.5216 0.652 0.74 0.00 0.26
#> TCGA.D8.A1X8.01 3 0.0892 0.959 0.02 0.00 0.98
#> TCGA.A2.A0T5.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.LD.A74U.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.AR.A0TQ.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.AO.A0JE.01 2 0.4555 0.750 0.00 0.80 0.20
#> TCGA.E9.A228.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.E9.A1RA.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.LL.A740.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.BH.A0BZ.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.EW.A2FV.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BH.A0DV.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A2.A0YI.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BH.A0BM.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D8.A27I.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A2.A0YD.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.BH.A0C0.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.E9.A1NG.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.EW.A1IW.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.JL.A3YW.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.AN.A0XN.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.E9.A6HE.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.C8.A26W.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BH.A0DP.01 3 0.5016 0.671 0.00 0.24 0.76
#> TCGA.AR.A2LN.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.D8.A1JF.01 2 0.5948 0.449 0.00 0.64 0.36
#> TCGA.OL.A6VQ.01 1 0.0892 0.968 0.98 0.00 0.02
#> TCGA.E2.A1LL.01 1 0.0892 0.968 0.98 0.00 0.02
#> TCGA.BH.A0AU.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A2.A0T1.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AR.A24W.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AR.A0TT.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.AC.A3W6.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.OL.A66P.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.AR.A24L.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BH.A0H3.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.EW.A1IZ.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.AO.A0JA.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.AR.A0TX.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AO.A0JG.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.OL.A66N.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.A7.A4SC.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.GM.A2DB.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.E9.A1N3.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AN.A0XL.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.E9.A24A.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.GM.A2DL.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.E9.A22B.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.A2.A3XV.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.AC.A6IX.06 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.AC.A6IX.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.B6.A0WY.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.E9.A1R4.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.EW.A1J2.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.BH.A0GY.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.W8.A86G.01 3 0.3340 0.846 0.12 0.00 0.88
#> TCGA.A7.A5ZW.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.C8.A1HF.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.A2.A0T7.01 3 0.3686 0.822 0.14 0.00 0.86
#> TCGA.AO.A0JJ.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.B6.A0X7.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.OL.A5RV.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.E2.A1BC.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.E9.A22D.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.A1.A0SF.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.EW.A6SD.01 3 0.5706 0.531 0.32 0.00 0.68
#> TCGA.A7.A426.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AR.A1AU.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.E9.A1N6.01 1 0.1529 0.947 0.96 0.00 0.04
#> TCGA.D8.A27L.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.E9.A1NF.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.A1.A0SM.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.LD.A7W5.01 3 0.4796 0.706 0.00 0.22 0.78
#> TCGA.E2.A1LA.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BH.A42V.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.E9.A5FK.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.D8.A1XB.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.E9.A227.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A2.A0YL.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A7.A5ZX.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.D8.A1JG.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.AO.A0JF.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.C8.A8HQ.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.AC.A2B8.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.A2.A4S3.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A2.A0CO.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.BH.A0AZ.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.E2.A1LE.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.A2.A0YH.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.LL.A5YN.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AC.A23G.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.GM.A3XN.01 3 0.6126 0.334 0.40 0.00 0.60
#> TCGA.C8.A275.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.E2.A1IK.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AQ.A7U7.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.A1.A0SI.01 1 0.3686 0.835 0.86 0.00 0.14
#> TCGA.A2.A25A.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.E9.A1RH.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AO.A12E.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.A7.A13H.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.E2.A1IO.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.C8.A26Y.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A2.A25D.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.AN.A0XW.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BH.A0AW.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.BH.A0B6.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.E9.A229.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D8.A1JK.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.GM.A5PX.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.AR.A5QN.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.BH.A208.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.EW.A1IX.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A2.A259.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.GM.A2DD.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.E2.A1B1.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D8.A73U.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.D8.A27N.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.E9.A22E.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.OL.A5RX.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.D8.A1XO.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AC.A23C.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.A7.A56D.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.A1.A0SH.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AR.A5QP.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.D8.A1Y0.01 1 0.5560 0.575 0.70 0.00 0.30
#> TCGA.BH.A2L8.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.BH.A202.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.EW.A1OV.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.A1.A0SN.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.E9.A295.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.AC.A8OP.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.GI.A2C8.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.AR.A24P.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.BH.A0B2.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.A2.A0SU.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AR.A24T.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.AC.A2FE.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.E9.A1N4.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.XX.A899.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.E9.A1N9.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.S3.AA17.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.EW.A1PF.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AO.A03L.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.BH.A0HF.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AC.A2QI.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A2.A4S2.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.GM.A2DA.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A7.A4SA.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A2.A3KC.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.OL.A66L.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.AR.A2LM.01 1 0.4291 0.780 0.82 0.00 0.18
#> TCGA.E2.A10C.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.AR.A1AN.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.5L.AAT1.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.HN.A2OB.01 3 0.1529 0.937 0.04 0.00 0.96
#> TCGA.GM.A5PV.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.E2.A1IJ.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.OK.A5Q2.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.E9.A1R3.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AR.A254.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.AR.A0TW.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.BH.A8G0.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.B6.A401.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.E2.A1LB.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.BH.A0W5.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AC.A3W7.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.AC.A3W5.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.B6.A1KI.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.E9.A1RI.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.A2.A0T6.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.EW.A3E8.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.OL.A5RU.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.E2.A10F.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.BH.A0C3.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.B6.A0RV.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.E2.A1IH.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.EW.A1IY.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.AR.A24O.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.C8.A278.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.AC.A3HN.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AC.A3BB.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.BH.A1FE.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.A2.A0EN.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.BH.A0BF.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.WT.AB41.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.LL.A5YL.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.AR.A1AK.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.C8.A26X.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.A7.A3J1.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.D8.A1Y3.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.BH.A0DK.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.D8.A1JE.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.EW.A2FR.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BH.A0W4.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BH.A0BJ.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BH.A203.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.E2.A14U.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D8.A1XM.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.D8.A1JH.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BH.A1EU.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BH.A1FR.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A7.A425.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.B6.A0IK.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.E9.A1RF.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.BH.A0HP.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.BH.A8FZ.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AC.A2FG.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AR.A1AL.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BH.A1EO.01 2 0.0892 0.967 0.00 0.98 0.02
#> TCGA.D8.A27K.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.C8.A1HG.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D8.A1JU.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A2.A0YK.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.BH.A0DI.01 2 0.0000 0.985 0.00 1.00 0.00
#> TCGA.E2.A107.01 3 0.0000 0.979 0.00 0.00 1.00
#> TCGA.5L.AAT0.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D8.A27E.01 1 0.0000 0.987 1.00 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.OL.A66H.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.3C.AALK.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.AC.A5EH.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.E9.A1R0.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.AC.A62Y.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.E9.A1R2.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.E9.A3X8.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.AR.A255.01 4 0.3610 0.6889 0.00 0.20 0.00 0.80
#> TCGA.E2.A10B.01 3 0.2011 0.8808 0.00 0.00 0.92 0.08
#> TCGA.AO.A0JD.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.A8.A0A6.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.A7.A3IY.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.D8.A3Z5.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.E9.A1RD.01 4 0.4522 0.5259 0.00 0.00 0.32 0.68
#> TCGA.LD.A66U.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.AC.A3QP.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.GM.A2DK.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.E2.A1B0.01 3 0.0707 0.9296 0.02 0.00 0.98 0.00
#> TCGA.BH.A1EY.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.AC.A8OS.01 4 0.2011 0.8271 0.00 0.00 0.08 0.92
#> TCGA.GM.A2DN.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.AO.A03M.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.A2.A4RW.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.AC.A6IV.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.LL.A7SZ.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.AR.A2LJ.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.AQ.A1H3.01 4 0.2011 0.8232 0.00 0.08 0.00 0.92
#> TCGA.D8.A1JB.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.BH.A0BC.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.BH.A1EW.01 2 0.3400 0.7686 0.00 0.82 0.00 0.18
#> TCGA.GM.A2DH.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.D8.A27P.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.EW.A2FS.01 4 0.2345 0.8048 0.00 0.10 0.00 0.90
#> TCGA.OL.A66J.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.AR.A2LO.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.BH.A201.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.S3.AA14.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.B6.A0RS.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.AR.A1AT.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.A2.A1G0.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.AC.A3OD.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.UU.A93S.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.XX.A89A.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.AR.A5QM.01 4 0.3801 0.6597 0.00 0.22 0.00 0.78
#> TCGA.PE.A5DE.01 1 0.4907 0.3045 0.58 0.00 0.42 0.00
#> TCGA.AC.A23H.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.D8.A27V.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.A2.A1FZ.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.BH.A0BA.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.BH.AB28.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.D8.A27R.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.OL.A5D6.01 4 0.1637 0.8411 0.00 0.06 0.00 0.94
#> TCGA.E2.A3DX.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.A1.A0SE.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.D8.A1XT.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.C8.A1HI.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.A2.A0T4.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.MS.A51U.01 1 0.4948 0.2470 0.56 0.00 0.44 0.00
#> TCGA.D8.A1Y2.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.BH.A0DG.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.C8.A3M7.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.E2.A1L6.01 3 0.2345 0.8488 0.10 0.00 0.90 0.00
#> TCGA.D8.A1XY.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.D8.A27G.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.AR.A1AM.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.4H.AAAK.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.AC.A5XS.01 3 0.1211 0.9118 0.04 0.00 0.96 0.00
#> TCGA.E2.A1IF.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.AC.A2FO.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.AR.A24S.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.A2.A3KD.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.E9.A226.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.D8.A1X8.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.A2.A0T5.01 4 0.4994 0.1204 0.00 0.00 0.48 0.52
#> TCGA.LD.A74U.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.AR.A0TQ.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.AO.A0JE.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.E9.A228.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.E9.A1RA.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.LL.A740.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.BH.A0BZ.01 4 0.3975 0.6281 0.00 0.24 0.00 0.76
#> TCGA.EW.A2FV.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.BH.A0DV.01 3 0.2011 0.8707 0.08 0.00 0.92 0.00
#> TCGA.A2.A0YI.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.BH.A0BM.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.D8.A27I.01 3 0.3610 0.7241 0.20 0.00 0.80 0.00
#> TCGA.A2.A0YD.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.BH.A0C0.01 4 0.4790 0.3344 0.00 0.38 0.00 0.62
#> TCGA.E9.A1NG.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.EW.A1IW.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.JL.A3YW.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.AN.A0XN.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.E9.A6HE.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.C8.A26W.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.BH.A0DP.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.AR.A2LN.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.D8.A1JF.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.OL.A6VQ.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.E2.A1LL.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.BH.A0AU.01 3 0.3400 0.7519 0.18 0.00 0.82 0.00
#> TCGA.A2.A0T1.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.AR.A24W.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.AR.A0TT.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.AC.A3W6.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.OL.A66P.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.AR.A24L.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.BH.A0H3.01 3 0.1211 0.9174 0.00 0.00 0.96 0.04
#> TCGA.EW.A1IZ.01 4 0.4790 0.4058 0.00 0.00 0.38 0.62
#> TCGA.AO.A0JA.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.AR.A0TX.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.AO.A0JG.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.OL.A66N.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.A7.A4SC.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.GM.A2DB.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.E9.A1N3.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.AN.A0XL.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.E9.A24A.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.GM.A2DL.01 4 0.2647 0.7846 0.00 0.12 0.00 0.88
#> TCGA.E9.A22B.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.A2.A3XV.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.AC.A6IX.06 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.AC.A6IX.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.B6.A0WY.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.E9.A1R4.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.EW.A1J2.01 3 0.4855 0.2929 0.00 0.00 0.60 0.40
#> TCGA.BH.A0GY.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.W8.A86G.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.A7.A5ZW.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.C8.A1HF.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.A2.A0T7.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.AO.A0JJ.01 3 0.0707 0.9330 0.00 0.00 0.98 0.02
#> TCGA.B6.A0X7.01 4 0.4994 0.1196 0.00 0.00 0.48 0.52
#> TCGA.OL.A5RV.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.E2.A1BC.01 3 0.2011 0.8808 0.00 0.00 0.92 0.08
#> TCGA.E9.A22D.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.A1.A0SF.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.EW.A6SD.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.A7.A426.01 3 0.1637 0.8916 0.06 0.00 0.94 0.00
#> TCGA.AR.A1AU.01 3 0.4948 0.1634 0.00 0.00 0.56 0.44
#> TCGA.E9.A1N6.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.D8.A27L.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.E9.A1NF.01 4 0.3400 0.7154 0.00 0.18 0.00 0.82
#> TCGA.A1.A0SM.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.LD.A7W5.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.E2.A1LA.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.BH.A42V.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.E9.A5FK.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.D8.A1XB.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.E9.A227.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.A2.A0YL.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.A7.A5ZX.01 4 0.4907 0.3081 0.00 0.00 0.42 0.58
#> TCGA.D8.A1JG.01 4 0.3610 0.6893 0.00 0.20 0.00 0.80
#> TCGA.AO.A0JF.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.C8.A8HQ.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.AC.A2B8.01 3 0.4994 0.0132 0.00 0.00 0.52 0.48
#> TCGA.A2.A4S3.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.A2.A0CO.01 3 0.2345 0.8597 0.00 0.00 0.90 0.10
#> TCGA.BH.A0AZ.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.E2.A1LE.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.A2.A0YH.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.LL.A5YN.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.AC.A23G.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.GM.A3XN.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.C8.A275.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.E2.A1IK.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.AQ.A7U7.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.A1.A0SI.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.A2.A25A.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.E9.A1RH.01 1 0.4907 0.3045 0.58 0.00 0.42 0.00
#> TCGA.AO.A12E.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.A7.A13H.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.E2.A1IO.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.C8.A26Y.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.A2.A25D.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.AN.A0XW.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.BH.A0AW.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.BH.A0B6.01 3 0.1211 0.9174 0.00 0.00 0.96 0.04
#> TCGA.E9.A229.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.D8.A1JK.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.GM.A5PX.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.AR.A5QN.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.BH.A208.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.EW.A1IX.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.A2.A259.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.GM.A2DD.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.E2.A1B1.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.D8.A73U.01 3 0.2011 0.8808 0.00 0.00 0.92 0.08
#> TCGA.D8.A27N.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.E9.A22E.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.OL.A5RX.01 3 0.5000 -0.0681 0.00 0.00 0.50 0.50
#> TCGA.D8.A1XO.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.AC.A23C.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.A7.A56D.01 3 0.4855 0.2933 0.00 0.00 0.60 0.40
#> TCGA.A1.A0SH.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.AR.A5QP.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.D8.A1Y0.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.BH.A2L8.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.BH.A202.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.EW.A1OV.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.A1.A0SN.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.E9.A295.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.AC.A8OP.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.GI.A2C8.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.AR.A24P.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.BH.A0B2.01 4 0.0707 0.8712 0.00 0.00 0.02 0.98
#> TCGA.A2.A0SU.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.AR.A24T.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.AC.A2FE.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.E9.A1N4.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.XX.A899.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.E9.A1N9.01 3 0.3400 0.7586 0.00 0.00 0.82 0.18
#> TCGA.S3.AA17.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.EW.A1PF.01 3 0.4624 0.4480 0.34 0.00 0.66 0.00
#> TCGA.AO.A03L.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.BH.A0HF.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.AC.A2QI.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.A2.A4S2.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.GM.A2DA.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.A7.A4SA.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.A2.A3KC.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.OL.A66L.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.AR.A2LM.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.E2.A10C.01 3 0.0707 0.9330 0.00 0.00 0.98 0.02
#> TCGA.AR.A1AN.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.5L.AAT1.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.HN.A2OB.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.GM.A5PV.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.E2.A1IJ.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.OK.A5Q2.01 4 0.0707 0.8701 0.00 0.02 0.00 0.98
#> TCGA.E9.A1R3.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.AR.A254.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.AR.A0TW.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.BH.A8G0.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.B6.A401.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.E2.A1LB.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.BH.A0W5.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.AC.A3W7.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.AC.A3W5.01 4 0.4948 0.2516 0.00 0.00 0.44 0.56
#> TCGA.B6.A1KI.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.E9.A1RI.01 3 0.0707 0.9330 0.00 0.00 0.98 0.02
#> TCGA.A2.A0T6.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.EW.A3E8.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.OL.A5RU.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.E2.A10F.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.BH.A0C3.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.B6.A0RV.01 4 0.4907 0.3084 0.00 0.00 0.42 0.58
#> TCGA.E2.A1IH.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.EW.A1IY.01 3 0.3400 0.7586 0.00 0.00 0.82 0.18
#> TCGA.AR.A24O.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.C8.A278.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.AC.A3HN.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.AC.A3BB.01 3 0.0707 0.9330 0.00 0.00 0.98 0.02
#> TCGA.BH.A1FE.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.A2.A0EN.01 3 0.2921 0.8129 0.00 0.00 0.86 0.14
#> TCGA.BH.A0BF.01 4 0.4907 0.3084 0.00 0.00 0.42 0.58
#> TCGA.WT.AB41.01 4 0.2011 0.8232 0.00 0.08 0.00 0.92
#> TCGA.LL.A5YL.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.AR.A1AK.01 4 0.4977 0.1891 0.00 0.00 0.46 0.54
#> TCGA.C8.A26X.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.A7.A3J1.01 3 0.0707 0.9330 0.00 0.00 0.98 0.02
#> TCGA.D8.A1Y3.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.BH.A0DK.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.D8.A1JE.01 1 0.4948 0.2471 0.56 0.00 0.44 0.00
#> TCGA.EW.A2FR.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.BH.A0W4.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.BH.A0BJ.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.BH.A203.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.E2.A14U.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.D8.A1XM.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.D8.A1JH.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.BH.A1EU.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.BH.A1FR.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.A7.A425.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.B6.A0IK.01 2 0.0000 0.9774 0.00 1.00 0.00 0.00
#> TCGA.E9.A1RF.01 2 0.4977 0.1700 0.00 0.54 0.00 0.46
#> TCGA.BH.A0HP.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.BH.A8FZ.01 1 0.0707 0.9544 0.98 0.00 0.02 0.00
#> TCGA.AC.A2FG.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.AR.A1AL.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.BH.A1EO.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.D8.A27K.01 4 0.0000 0.8838 0.00 0.00 0.00 1.00
#> TCGA.C8.A1HG.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.D8.A1JU.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
#> TCGA.A2.A0YK.01 4 0.4277 0.5956 0.00 0.00 0.28 0.72
#> TCGA.BH.A0DI.01 2 0.4907 0.2971 0.00 0.58 0.00 0.42
#> TCGA.E2.A107.01 4 0.4855 0.3588 0.00 0.00 0.40 0.60
#> TCGA.5L.AAT0.01 3 0.0000 0.9458 0.00 0.00 1.00 0.00
#> TCGA.D8.A27E.01 1 0.0000 0.9747 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.OL.A66H.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.3C.AALK.01 2 0.2929 0.89324 0.18 0.82 0.00 0.00 0.00
#> TCGA.AC.A5EH.01 5 0.6723 -0.13138 0.30 0.00 0.28 0.00 0.42
#> TCGA.E9.A1R0.01 3 0.5673 0.36145 0.08 0.00 0.50 0.00 0.42
#> TCGA.AC.A62Y.01 3 0.5131 0.39982 0.04 0.00 0.54 0.00 0.42
#> TCGA.E9.A1R2.01 3 0.3390 0.58028 0.06 0.00 0.84 0.00 0.10
#> TCGA.E9.A3X8.01 3 0.3106 0.59029 0.02 0.00 0.84 0.14 0.00
#> TCGA.AR.A255.01 4 0.4854 0.74033 0.26 0.06 0.00 0.68 0.00
#> TCGA.E2.A10B.01 3 0.3424 0.55246 0.00 0.00 0.76 0.24 0.00
#> TCGA.AO.A0JD.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.A8.A0A6.01 2 0.2280 0.90446 0.12 0.88 0.00 0.00 0.00
#> TCGA.A7.A3IY.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.D8.A3Z5.01 3 0.5131 0.39982 0.04 0.00 0.54 0.00 0.42
#> TCGA.E9.A1RD.01 3 0.3895 0.49533 0.00 0.00 0.68 0.32 0.00
#> TCGA.LD.A66U.01 3 0.5095 0.41624 0.04 0.00 0.56 0.00 0.40
#> TCGA.AC.A3QP.01 5 0.4182 0.63083 0.40 0.00 0.00 0.00 0.60
#> TCGA.GM.A2DK.01 5 0.6671 -0.20622 0.24 0.00 0.34 0.00 0.42
#> TCGA.E2.A1B0.01 5 0.6705 -0.12837 0.32 0.00 0.26 0.00 0.42
#> TCGA.BH.A1EY.01 4 0.3561 0.79413 0.26 0.00 0.00 0.74 0.00
#> TCGA.AC.A8OS.01 3 0.4126 0.40314 0.00 0.00 0.62 0.38 0.00
#> TCGA.GM.A2DN.01 4 0.2280 0.68178 0.00 0.00 0.12 0.88 0.00
#> TCGA.AO.A03M.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.A2.A4RW.01 2 0.3109 0.88644 0.20 0.80 0.00 0.00 0.00
#> TCGA.AC.A6IV.01 3 0.3922 0.54165 0.04 0.00 0.78 0.00 0.18
#> TCGA.LL.A7SZ.01 3 0.4990 0.44168 0.04 0.00 0.60 0.00 0.36
#> TCGA.AR.A2LJ.01 3 0.5394 0.41420 0.06 0.00 0.54 0.00 0.40
#> TCGA.AQ.A1H3.01 4 0.3561 0.79413 0.26 0.00 0.00 0.74 0.00
#> TCGA.D8.A1JB.01 5 0.6548 -0.25365 0.20 0.00 0.38 0.00 0.42
#> TCGA.BH.A0BC.01 5 0.0000 0.43421 0.00 0.00 0.00 0.00 1.00
#> TCGA.BH.A1EW.01 4 0.6619 0.12441 0.22 0.36 0.00 0.42 0.00
#> TCGA.GM.A2DH.01 4 0.1732 0.82668 0.08 0.00 0.00 0.92 0.00
#> TCGA.D8.A27P.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.EW.A2FS.01 4 0.3561 0.79413 0.26 0.00 0.00 0.74 0.00
#> TCGA.OL.A66J.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.AR.A2LO.01 3 0.1732 0.60640 0.00 0.00 0.92 0.08 0.00
#> TCGA.BH.A201.01 3 0.1043 0.61337 0.00 0.00 0.96 0.04 0.00
#> TCGA.S3.AA14.01 3 0.5425 0.39702 0.06 0.00 0.52 0.00 0.42
#> TCGA.B6.A0RS.01 5 0.6619 -0.22935 0.22 0.00 0.36 0.00 0.42
#> TCGA.AR.A1AT.01 2 0.2280 0.90446 0.12 0.88 0.00 0.00 0.00
#> TCGA.A2.A1G0.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.AC.A3OD.01 2 0.2280 0.90446 0.12 0.88 0.00 0.00 0.00
#> TCGA.UU.A93S.01 4 0.1410 0.81653 0.06 0.00 0.00 0.94 0.00
#> TCGA.XX.A89A.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.AR.A5QM.01 4 0.4854 0.74033 0.26 0.06 0.00 0.68 0.00
#> TCGA.PE.A5DE.01 5 0.4748 0.03276 0.04 0.00 0.30 0.00 0.66
#> TCGA.AC.A23H.01 2 0.0000 0.89965 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A27V.01 5 0.4182 0.63083 0.40 0.00 0.00 0.00 0.60
#> TCGA.A2.A1FZ.01 4 0.1732 0.82668 0.08 0.00 0.00 0.92 0.00
#> TCGA.BH.A0BA.01 5 0.6723 -0.13138 0.30 0.00 0.28 0.00 0.42
#> TCGA.BH.AB28.01 2 0.0000 0.89965 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A27R.01 4 0.0000 0.80029 0.00 0.00 0.00 1.00 0.00
#> TCGA.OL.A5D6.01 4 0.3561 0.79413 0.26 0.00 0.00 0.74 0.00
#> TCGA.E2.A3DX.01 5 0.0609 0.41822 0.00 0.00 0.02 0.00 0.98
#> TCGA.A1.A0SE.01 5 0.0609 0.44680 0.02 0.00 0.00 0.00 0.98
#> TCGA.D8.A1XT.01 5 0.6757 -0.15190 0.32 0.00 0.28 0.00 0.40
#> TCGA.C8.A1HI.01 3 0.5394 0.41420 0.06 0.00 0.54 0.00 0.40
#> TCGA.A2.A0T4.01 2 0.3109 0.88644 0.20 0.80 0.00 0.00 0.00
#> TCGA.MS.A51U.01 5 0.4840 -0.00205 0.04 0.00 0.32 0.00 0.64
#> TCGA.D8.A1Y2.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.BH.A0DG.01 4 0.3561 0.79413 0.26 0.00 0.00 0.74 0.00
#> TCGA.C8.A3M7.01 4 0.1732 0.73082 0.00 0.00 0.08 0.92 0.00
#> TCGA.E2.A1L6.01 5 0.5095 -0.16977 0.04 0.00 0.40 0.00 0.56
#> TCGA.D8.A1XY.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.D8.A27G.01 2 0.2280 0.90446 0.12 0.88 0.00 0.00 0.00
#> TCGA.AR.A1AM.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.4H.AAAK.01 3 0.0609 0.61709 0.02 0.00 0.98 0.00 0.00
#> TCGA.AC.A5XS.01 5 0.6723 -0.13138 0.30 0.00 0.28 0.00 0.42
#> TCGA.E2.A1IF.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.AC.A2FO.01 3 0.0609 0.61827 0.02 0.00 0.98 0.00 0.00
#> TCGA.AR.A24S.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.A2.A3KD.01 5 0.0000 0.43421 0.00 0.00 0.00 0.00 1.00
#> TCGA.E9.A226.01 3 0.5884 0.35862 0.10 0.00 0.48 0.00 0.42
#> TCGA.D8.A1X8.01 3 0.5095 0.41624 0.04 0.00 0.56 0.00 0.40
#> TCGA.A2.A0T5.01 3 0.3895 0.49533 0.00 0.00 0.68 0.32 0.00
#> TCGA.LD.A74U.01 4 0.1043 0.81780 0.04 0.00 0.00 0.96 0.00
#> TCGA.AR.A0TQ.01 2 0.6359 0.44356 0.26 0.52 0.00 0.22 0.00
#> TCGA.AO.A0JE.01 4 0.3561 0.79413 0.26 0.00 0.00 0.74 0.00
#> TCGA.E9.A228.01 2 0.0000 0.89965 0.00 1.00 0.00 0.00 0.00
#> TCGA.E9.A1RA.01 3 0.1043 0.61696 0.04 0.00 0.96 0.00 0.00
#> TCGA.LL.A740.01 2 0.0000 0.89965 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0BZ.01 4 0.4854 0.74033 0.26 0.06 0.00 0.68 0.00
#> TCGA.EW.A2FV.01 5 0.6723 -0.13138 0.30 0.00 0.28 0.00 0.42
#> TCGA.BH.A0DV.01 5 0.5156 -0.02240 0.06 0.00 0.32 0.00 0.62
#> TCGA.A2.A0YI.01 5 0.6705 -0.16279 0.26 0.00 0.32 0.00 0.42
#> TCGA.BH.A0BM.01 5 0.3983 0.61151 0.34 0.00 0.00 0.00 0.66
#> TCGA.D8.A27I.01 5 0.5156 -0.02240 0.06 0.00 0.32 0.00 0.62
#> TCGA.A2.A0YD.01 4 0.4287 -0.03154 0.00 0.00 0.46 0.54 0.00
#> TCGA.BH.A0C0.01 4 0.4854 0.74033 0.26 0.06 0.00 0.68 0.00
#> TCGA.E9.A1NG.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.EW.A1IW.01 2 0.0000 0.89965 0.00 1.00 0.00 0.00 0.00
#> TCGA.JL.A3YW.01 2 0.3109 0.88644 0.20 0.80 0.00 0.00 0.00
#> TCGA.AN.A0XN.01 2 0.0000 0.89965 0.00 1.00 0.00 0.00 0.00
#> TCGA.E9.A6HE.01 4 0.0609 0.78969 0.00 0.00 0.02 0.98 0.00
#> TCGA.C8.A26W.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.BH.A0DP.01 4 0.2280 0.83043 0.12 0.00 0.00 0.88 0.00
#> TCGA.AR.A2LN.01 3 0.0609 0.61827 0.02 0.00 0.98 0.00 0.00
#> TCGA.D8.A1JF.01 4 0.3561 0.79413 0.26 0.00 0.00 0.74 0.00
#> TCGA.OL.A6VQ.01 3 0.5131 0.39982 0.04 0.00 0.54 0.00 0.42
#> TCGA.E2.A1LL.01 5 0.6723 -0.13138 0.30 0.00 0.28 0.00 0.42
#> TCGA.BH.A0AU.01 5 0.6705 -0.12837 0.32 0.00 0.26 0.00 0.42
#> TCGA.A2.A0T1.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.AR.A24W.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.AR.A0TT.01 4 0.0000 0.80029 0.00 0.00 0.00 1.00 0.00
#> TCGA.AC.A3W6.01 4 0.4227 0.08632 0.00 0.00 0.42 0.58 0.00
#> TCGA.OL.A66P.01 5 0.6766 -0.15536 0.30 0.00 0.30 0.00 0.40
#> TCGA.AR.A24L.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.BH.A0H3.01 3 0.4132 0.53922 0.02 0.00 0.72 0.26 0.00
#> TCGA.EW.A1IZ.01 3 0.3895 0.49533 0.00 0.00 0.68 0.32 0.00
#> TCGA.AO.A0JA.01 4 0.1410 0.81653 0.06 0.00 0.00 0.94 0.00
#> TCGA.AR.A0TX.01 5 0.0609 0.44676 0.02 0.00 0.00 0.00 0.98
#> TCGA.AO.A0JG.01 4 0.0000 0.80029 0.00 0.00 0.00 1.00 0.00
#> TCGA.OL.A66N.01 2 0.3109 0.88644 0.20 0.80 0.00 0.00 0.00
#> TCGA.A7.A4SC.01 2 0.2280 0.90446 0.12 0.88 0.00 0.00 0.00
#> TCGA.GM.A2DB.01 5 0.6766 -0.15536 0.30 0.00 0.30 0.00 0.40
#> TCGA.E9.A1N3.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.AN.A0XL.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.E9.A24A.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.GM.A2DL.01 4 0.3561 0.79413 0.26 0.00 0.00 0.74 0.00
#> TCGA.E9.A22B.01 2 0.0000 0.89965 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A3XV.01 2 0.0000 0.89965 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A6IX.06 4 0.1043 0.81764 0.04 0.00 0.00 0.96 0.00
#> TCGA.AC.A6IX.01 2 0.2929 0.89324 0.18 0.82 0.00 0.00 0.00
#> TCGA.B6.A0WY.01 5 0.6705 -0.12837 0.32 0.00 0.26 0.00 0.42
#> TCGA.E9.A1R4.01 3 0.5425 0.38161 0.06 0.00 0.52 0.00 0.42
#> TCGA.EW.A1J2.01 3 0.3895 0.49533 0.00 0.00 0.68 0.32 0.00
#> TCGA.BH.A0GY.01 5 0.6757 -0.15190 0.32 0.00 0.28 0.00 0.40
#> TCGA.W8.A86G.01 3 0.5351 0.42820 0.06 0.00 0.56 0.00 0.38
#> TCGA.A7.A5ZW.01 5 0.0000 0.43421 0.00 0.00 0.00 0.00 1.00
#> TCGA.C8.A1HF.01 4 0.1043 0.81764 0.04 0.00 0.00 0.96 0.00
#> TCGA.A2.A0T7.01 5 0.6705 -0.12837 0.32 0.00 0.26 0.00 0.42
#> TCGA.AO.A0JJ.01 3 0.3109 0.57011 0.00 0.00 0.80 0.20 0.00
#> TCGA.B6.A0X7.01 3 0.3895 0.49533 0.00 0.00 0.68 0.32 0.00
#> TCGA.OL.A5RV.01 3 0.5425 0.39702 0.06 0.00 0.52 0.00 0.42
#> TCGA.E2.A1BC.01 3 0.3561 0.54155 0.00 0.00 0.74 0.26 0.00
#> TCGA.E9.A22D.01 2 0.0000 0.89965 0.00 1.00 0.00 0.00 0.00
#> TCGA.A1.A0SF.01 4 0.0609 0.78969 0.00 0.00 0.02 0.98 0.00
#> TCGA.EW.A6SD.01 5 0.6632 -0.25400 0.22 0.00 0.38 0.00 0.40
#> TCGA.A7.A426.01 5 0.6705 -0.16279 0.26 0.00 0.32 0.00 0.42
#> TCGA.AR.A1AU.01 3 0.3895 0.49533 0.00 0.00 0.68 0.32 0.00
#> TCGA.E9.A1N6.01 5 0.6705 -0.12837 0.32 0.00 0.26 0.00 0.42
#> TCGA.D8.A27L.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.E9.A1NF.01 4 0.4854 0.74033 0.26 0.06 0.00 0.68 0.00
#> TCGA.A1.A0SM.01 2 0.0000 0.89965 0.00 1.00 0.00 0.00 0.00
#> TCGA.LD.A7W5.01 4 0.3561 0.79413 0.26 0.00 0.00 0.74 0.00
#> TCGA.E2.A1LA.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.BH.A42V.01 3 0.1732 0.60640 0.00 0.00 0.92 0.08 0.00
#> TCGA.E9.A5FK.01 4 0.0000 0.80029 0.00 0.00 0.00 1.00 0.00
#> TCGA.D8.A1XB.01 4 0.0609 0.78969 0.00 0.00 0.02 0.98 0.00
#> TCGA.E9.A227.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.A2.A0YL.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.A7.A5ZX.01 3 0.3895 0.49533 0.00 0.00 0.68 0.32 0.00
#> TCGA.D8.A1JG.01 4 0.4854 0.74033 0.26 0.06 0.00 0.68 0.00
#> TCGA.AO.A0JF.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.C8.A8HQ.01 2 0.3109 0.88644 0.20 0.80 0.00 0.00 0.00
#> TCGA.AC.A2B8.01 3 0.3796 0.51073 0.00 0.00 0.70 0.30 0.00
#> TCGA.A2.A4S3.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.A2.A0CO.01 3 0.3561 0.54155 0.00 0.00 0.74 0.26 0.00
#> TCGA.BH.A0AZ.01 5 0.4182 0.63083 0.40 0.00 0.00 0.00 0.60
#> TCGA.E2.A1LE.01 2 0.3109 0.88644 0.20 0.80 0.00 0.00 0.00
#> TCGA.A2.A0YH.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.LL.A5YN.01 5 0.6723 -0.13138 0.30 0.00 0.28 0.00 0.42
#> TCGA.AC.A23G.01 3 0.0609 0.61827 0.02 0.00 0.98 0.00 0.00
#> TCGA.GM.A3XN.01 3 0.5394 0.41420 0.06 0.00 0.54 0.00 0.40
#> TCGA.C8.A275.01 2 0.2516 0.90159 0.14 0.86 0.00 0.00 0.00
#> TCGA.E2.A1IK.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.AQ.A7U7.01 4 0.2280 0.83019 0.12 0.00 0.00 0.88 0.00
#> TCGA.A1.A0SI.01 3 0.5095 0.41624 0.04 0.00 0.56 0.00 0.40
#> TCGA.A2.A25A.01 3 0.0609 0.61827 0.02 0.00 0.98 0.00 0.00
#> TCGA.E9.A1RH.01 5 0.6723 -0.13138 0.30 0.00 0.28 0.00 0.42
#> TCGA.AO.A12E.01 2 0.0000 0.89965 0.00 1.00 0.00 0.00 0.00
#> TCGA.A7.A13H.01 3 0.5131 0.39982 0.04 0.00 0.54 0.00 0.42
#> TCGA.E2.A1IO.01 5 0.0000 0.43421 0.00 0.00 0.00 0.00 1.00
#> TCGA.C8.A26Y.01 5 0.4252 0.18053 0.28 0.00 0.02 0.00 0.70
#> TCGA.A2.A25D.01 4 0.1732 0.82668 0.08 0.00 0.00 0.92 0.00
#> TCGA.AN.A0XW.01 5 0.4182 0.63083 0.40 0.00 0.00 0.00 0.60
#> TCGA.BH.A0AW.01 4 0.3424 0.80170 0.24 0.00 0.00 0.76 0.00
#> TCGA.BH.A0B6.01 3 0.3424 0.55246 0.00 0.00 0.76 0.24 0.00
#> TCGA.E9.A229.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.D8.A1JK.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.GM.A5PX.01 3 0.2020 0.60169 0.00 0.00 0.90 0.10 0.00
#> TCGA.AR.A5QN.01 2 0.0000 0.89965 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A208.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.EW.A1IX.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.A2.A259.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.GM.A2DD.01 3 0.5068 0.45705 0.30 0.00 0.64 0.00 0.06
#> TCGA.E2.A1B1.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.D8.A73U.01 3 0.3561 0.54155 0.00 0.00 0.74 0.26 0.00
#> TCGA.D8.A27N.01 2 0.2280 0.90446 0.12 0.88 0.00 0.00 0.00
#> TCGA.E9.A22E.01 5 0.1043 0.45845 0.04 0.00 0.00 0.00 0.96
#> TCGA.OL.A5RX.01 3 0.3895 0.49533 0.00 0.00 0.68 0.32 0.00
#> TCGA.D8.A1XO.01 3 0.5131 0.39982 0.04 0.00 0.54 0.00 0.42
#> TCGA.AC.A23C.01 4 0.0609 0.78969 0.00 0.00 0.02 0.98 0.00
#> TCGA.A7.A56D.01 3 0.6458 0.38120 0.26 0.00 0.50 0.24 0.00
#> TCGA.A1.A0SH.01 5 0.0000 0.43421 0.00 0.00 0.00 0.00 1.00
#> TCGA.AR.A5QP.01 4 0.0609 0.78969 0.00 0.00 0.02 0.98 0.00
#> TCGA.D8.A1Y0.01 5 0.6723 -0.13138 0.30 0.00 0.28 0.00 0.42
#> TCGA.BH.A2L8.01 3 0.2077 0.61108 0.04 0.00 0.92 0.00 0.04
#> TCGA.BH.A202.01 2 0.3109 0.88644 0.20 0.80 0.00 0.00 0.00
#> TCGA.EW.A1OV.01 4 0.2280 0.82845 0.12 0.00 0.00 0.88 0.00
#> TCGA.A1.A0SN.01 2 0.0000 0.89965 0.00 1.00 0.00 0.00 0.00
#> TCGA.E9.A295.01 2 0.0000 0.89965 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A8OP.01 2 0.3561 0.83439 0.26 0.74 0.00 0.00 0.00
#> TCGA.GI.A2C8.01 2 0.3109 0.88644 0.20 0.80 0.00 0.00 0.00
#> TCGA.AR.A24P.01 4 0.0609 0.78969 0.00 0.00 0.02 0.98 0.00
#> TCGA.BH.A0B2.01 3 0.3895 0.49533 0.00 0.00 0.68 0.32 0.00
#> TCGA.A2.A0SU.01 5 0.4182 0.63083 0.40 0.00 0.00 0.00 0.60
#> TCGA.AR.A24T.01 2 0.0000 0.89965 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A2FE.01 2 0.3109 0.88644 0.20 0.80 0.00 0.00 0.00
#> TCGA.E9.A1N4.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.XX.A899.01 4 0.0000 0.80029 0.00 0.00 0.00 1.00 0.00
#> TCGA.E9.A1N9.01 3 0.4252 0.52500 0.02 0.00 0.70 0.28 0.00
#> TCGA.S3.AA17.01 2 0.0000 0.89965 0.00 1.00 0.00 0.00 0.00
#> TCGA.EW.A1PF.01 5 0.6705 -0.12837 0.32 0.00 0.26 0.00 0.42
#> TCGA.AO.A03L.01 4 0.3796 0.37473 0.00 0.00 0.30 0.70 0.00
#> TCGA.BH.A0HF.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.AC.A2QI.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.A2.A4S2.01 4 0.1410 0.82276 0.06 0.00 0.00 0.94 0.00
#> TCGA.GM.A2DA.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.A7.A4SA.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.A2.A3KC.01 2 0.2929 0.89324 0.18 0.82 0.00 0.00 0.00
#> TCGA.OL.A66L.01 2 0.3109 0.88644 0.20 0.80 0.00 0.00 0.00
#> TCGA.AR.A2LM.01 3 0.5425 0.39702 0.06 0.00 0.52 0.00 0.42
#> TCGA.E2.A10C.01 3 0.5788 0.47065 0.30 0.00 0.58 0.12 0.00
#> TCGA.AR.A1AN.01 5 0.4182 0.63083 0.40 0.00 0.00 0.00 0.60
#> TCGA.5L.AAT1.01 4 0.2732 0.82449 0.16 0.00 0.00 0.84 0.00
#> TCGA.HN.A2OB.01 3 0.4254 0.52017 0.04 0.00 0.74 0.00 0.22
#> TCGA.GM.A5PV.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.E2.A1IJ.01 3 0.0609 0.61827 0.02 0.00 0.98 0.00 0.00
#> TCGA.OK.A5Q2.01 4 0.3561 0.79413 0.26 0.00 0.00 0.74 0.00
#> TCGA.E9.A1R3.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.AR.A254.01 2 0.3109 0.88644 0.20 0.80 0.00 0.00 0.00
#> TCGA.AR.A0TW.01 4 0.3561 0.79413 0.26 0.00 0.00 0.74 0.00
#> TCGA.BH.A8G0.01 3 0.5131 0.39982 0.04 0.00 0.54 0.00 0.42
#> TCGA.B6.A401.01 3 0.5607 0.40326 0.08 0.00 0.54 0.00 0.38
#> TCGA.E2.A1LB.01 4 0.0609 0.78969 0.00 0.00 0.02 0.98 0.00
#> TCGA.BH.A0W5.01 5 0.0609 0.41822 0.00 0.00 0.02 0.00 0.98
#> TCGA.AC.A3W7.01 4 0.0609 0.78969 0.00 0.00 0.02 0.98 0.00
#> TCGA.AC.A3W5.01 3 0.6498 0.30420 0.20 0.00 0.46 0.34 0.00
#> TCGA.B6.A1KI.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.E9.A1RI.01 3 0.4132 0.53922 0.02 0.00 0.72 0.26 0.00
#> TCGA.A2.A0T6.01 2 0.0609 0.90130 0.02 0.98 0.00 0.00 0.00
#> TCGA.EW.A3E8.01 2 0.3109 0.88644 0.20 0.80 0.00 0.00 0.00
#> TCGA.OL.A5RU.01 3 0.5351 0.42813 0.06 0.00 0.56 0.00 0.38
#> TCGA.E2.A10F.01 4 0.2516 0.82800 0.14 0.00 0.00 0.86 0.00
#> TCGA.BH.A0C3.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.B6.A0RV.01 3 0.3895 0.49533 0.00 0.00 0.68 0.32 0.00
#> TCGA.E2.A1IH.01 5 0.6766 -0.16660 0.30 0.00 0.30 0.00 0.40
#> TCGA.EW.A1IY.01 3 0.4132 0.53922 0.02 0.00 0.72 0.26 0.00
#> TCGA.AR.A24O.01 5 0.4182 0.63083 0.40 0.00 0.00 0.00 0.60
#> TCGA.C8.A278.01 4 0.2516 0.82800 0.14 0.00 0.00 0.86 0.00
#> TCGA.AC.A3HN.01 3 0.5425 0.39702 0.06 0.00 0.52 0.00 0.42
#> TCGA.AC.A3BB.01 3 0.3274 0.56217 0.00 0.00 0.78 0.22 0.00
#> TCGA.BH.A1FE.01 3 0.0609 0.61827 0.02 0.00 0.98 0.00 0.00
#> TCGA.A2.A0EN.01 3 0.3561 0.54155 0.00 0.00 0.74 0.26 0.00
#> TCGA.BH.A0BF.01 3 0.3895 0.49533 0.00 0.00 0.68 0.32 0.00
#> TCGA.WT.AB41.01 4 0.3561 0.79413 0.26 0.00 0.00 0.74 0.00
#> TCGA.LL.A5YL.01 2 0.0000 0.89965 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A1AK.01 3 0.3895 0.49533 0.00 0.00 0.68 0.32 0.00
#> TCGA.C8.A26X.01 2 0.3109 0.88644 0.20 0.80 0.00 0.00 0.00
#> TCGA.A7.A3J1.01 3 0.3561 0.54155 0.00 0.00 0.74 0.26 0.00
#> TCGA.D8.A1Y3.01 2 0.0000 0.89965 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0DK.01 2 0.0000 0.89965 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A1JE.01 5 0.4840 -0.00205 0.04 0.00 0.32 0.00 0.64
#> TCGA.EW.A2FR.01 5 0.6723 -0.14289 0.30 0.00 0.28 0.00 0.42
#> TCGA.BH.A0W4.01 5 0.4182 0.63083 0.40 0.00 0.00 0.00 0.60
#> TCGA.BH.A0BJ.01 5 0.4182 0.63083 0.40 0.00 0.00 0.00 0.60
#> TCGA.BH.A203.01 2 0.0000 0.89965 0.00 1.00 0.00 0.00 0.00
#> TCGA.E2.A14U.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.D8.A1XM.01 3 0.0609 0.61709 0.02 0.00 0.98 0.00 0.00
#> TCGA.D8.A1JH.01 3 0.5425 0.39702 0.06 0.00 0.52 0.00 0.42
#> TCGA.BH.A1EU.01 5 0.2754 0.32231 0.04 0.00 0.08 0.00 0.88
#> TCGA.BH.A1FR.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.A7.A425.01 5 0.4182 0.63083 0.40 0.00 0.00 0.00 0.60
#> TCGA.B6.A0IK.01 2 0.3109 0.88644 0.20 0.80 0.00 0.00 0.00
#> TCGA.E9.A1RF.01 4 0.5136 0.71811 0.26 0.08 0.00 0.66 0.00
#> TCGA.BH.A0HP.01 4 0.0609 0.78969 0.00 0.00 0.02 0.98 0.00
#> TCGA.BH.A8FZ.01 5 0.2616 0.32293 0.02 0.00 0.10 0.00 0.88
#> TCGA.AC.A2FG.01 5 0.2616 0.32167 0.02 0.00 0.10 0.00 0.88
#> TCGA.AR.A1AL.01 5 0.3895 0.60271 0.32 0.00 0.00 0.00 0.68
#> TCGA.BH.A1EO.01 4 0.3561 0.79413 0.26 0.00 0.00 0.74 0.00
#> TCGA.D8.A27K.01 3 0.4307 0.12505 0.00 0.00 0.50 0.50 0.00
#> TCGA.C8.A1HG.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
#> TCGA.D8.A1JU.01 5 0.0609 0.41822 0.00 0.00 0.02 0.00 0.98
#> TCGA.A2.A0YK.01 3 0.3895 0.49533 0.00 0.00 0.68 0.32 0.00
#> TCGA.BH.A0DI.01 4 0.4854 0.74033 0.26 0.06 0.00 0.68 0.00
#> TCGA.E2.A107.01 3 0.3895 0.49533 0.00 0.00 0.68 0.32 0.00
#> TCGA.5L.AAT0.01 3 0.5131 0.39982 0.04 0.00 0.54 0.00 0.42
#> TCGA.D8.A27E.01 5 0.4227 0.63365 0.42 0.00 0.00 0.00 0.58
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.OL.A66H.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.3C.AALK.01 2 0.0937 0.8575 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.AC.A5EH.01 1 0.3797 0.8187 0.58 0.00 0.00 0.00 0.00 0.42
#> TCGA.E9.A1R0.01 6 0.0000 0.6043 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AC.A62Y.01 6 0.0547 0.6114 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.E9.A1R2.01 3 0.5095 0.2782 0.08 0.00 0.50 0.00 0.00 0.42
#> TCGA.E9.A3X8.01 3 0.3351 0.6847 0.04 0.00 0.80 0.00 0.00 0.16
#> TCGA.AR.A255.01 4 0.3163 0.6548 0.14 0.04 0.00 0.82 0.00 0.00
#> TCGA.E2.A10B.01 3 0.1865 0.7383 0.04 0.00 0.92 0.00 0.00 0.04
#> TCGA.AO.A0JD.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A8.A0A6.01 2 0.0937 0.8575 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.A7.A3IY.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D8.A3Z5.01 6 0.1807 0.5762 0.06 0.00 0.02 0.00 0.00 0.92
#> TCGA.E9.A1RD.01 3 0.0547 0.7122 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.LD.A66U.01 6 0.2794 0.5139 0.08 0.00 0.06 0.00 0.00 0.86
#> TCGA.AC.A3QP.01 5 0.3869 -0.0163 0.00 0.00 0.00 0.00 0.50 0.50
#> TCGA.GM.A2DK.01 6 0.0937 0.5847 0.04 0.00 0.00 0.00 0.00 0.96
#> TCGA.E2.A1B0.01 1 0.3797 0.8187 0.58 0.00 0.00 0.00 0.00 0.42
#> TCGA.BH.A1EY.01 4 0.0937 0.7126 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.AC.A8OS.01 3 0.0547 0.7122 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.GM.A2DN.01 3 0.3851 -0.3890 0.00 0.00 0.54 0.46 0.00 0.00
#> TCGA.AO.A03M.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A2.A4RW.01 2 0.1814 0.8422 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.AC.A6IV.01 3 0.5095 0.2775 0.08 0.00 0.50 0.00 0.00 0.42
#> TCGA.LL.A7SZ.01 6 0.4380 0.2594 0.08 0.00 0.22 0.00 0.00 0.70
#> TCGA.AR.A2LJ.01 6 0.2512 0.5404 0.06 0.00 0.06 0.00 0.00 0.88
#> TCGA.AQ.A1H3.01 4 0.3821 0.6272 0.00 0.22 0.04 0.74 0.00 0.00
#> TCGA.D8.A1JB.01 6 0.0937 0.5847 0.04 0.00 0.00 0.00 0.00 0.96
#> TCGA.BH.A0BC.01 6 0.3706 0.3606 0.00 0.00 0.00 0.00 0.38 0.62
#> TCGA.BH.A1EW.01 2 0.3864 0.0698 0.00 0.52 0.00 0.48 0.00 0.00
#> TCGA.GM.A2DH.01 4 0.4002 0.6695 0.02 0.00 0.32 0.66 0.00 0.00
#> TCGA.D8.A27P.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EW.A2FS.01 4 0.2350 0.6800 0.02 0.10 0.00 0.88 0.00 0.00
#> TCGA.OL.A66J.01 5 0.2454 0.7632 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.AR.A2LO.01 3 0.4172 0.5654 0.04 0.00 0.68 0.00 0.00 0.28
#> TCGA.BH.A201.01 3 0.4067 0.5894 0.04 0.00 0.70 0.00 0.00 0.26
#> TCGA.S3.AA14.01 6 0.0547 0.6114 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.B6.A0RS.01 6 0.0937 0.5847 0.04 0.00 0.00 0.00 0.00 0.96
#> TCGA.AR.A1AT.01 2 0.0937 0.8575 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.A2.A1G0.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AC.A3OD.01 2 0.0937 0.8575 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.UU.A93S.01 4 0.3985 0.6859 0.14 0.00 0.10 0.76 0.00 0.00
#> TCGA.XX.A89A.01 5 0.0547 0.9078 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.AR.A5QM.01 4 0.3163 0.6548 0.14 0.04 0.00 0.82 0.00 0.00
#> TCGA.PE.A5DE.01 6 0.1267 0.5935 0.00 0.00 0.00 0.00 0.06 0.94
#> TCGA.AC.A23H.01 2 0.2941 0.8038 0.22 0.78 0.00 0.00 0.00 0.00
#> TCGA.D8.A27V.01 5 0.3647 0.4139 0.00 0.00 0.00 0.00 0.64 0.36
#> TCGA.A2.A1FZ.01 4 0.3499 0.6741 0.00 0.00 0.32 0.68 0.00 0.00
#> TCGA.BH.A0BA.01 6 0.3756 -0.3989 0.40 0.00 0.00 0.00 0.00 0.60
#> TCGA.BH.AB28.01 2 0.2941 0.8038 0.22 0.78 0.00 0.00 0.00 0.00
#> TCGA.D8.A27R.01 4 0.4348 0.6616 0.04 0.00 0.32 0.64 0.00 0.00
#> TCGA.OL.A5D6.01 4 0.2956 0.6658 0.12 0.04 0.00 0.84 0.00 0.00
#> TCGA.E2.A3DX.01 6 0.3578 0.4420 0.00 0.00 0.00 0.00 0.34 0.66
#> TCGA.A1.A0SE.01 6 0.3706 0.3606 0.00 0.00 0.00 0.00 0.38 0.62
#> TCGA.D8.A1XT.01 1 0.4144 0.8407 0.62 0.00 0.02 0.00 0.00 0.36
#> TCGA.C8.A1HI.01 6 0.4004 0.3613 0.12 0.00 0.12 0.00 0.00 0.76
#> TCGA.A2.A0T4.01 2 0.1814 0.8422 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.MS.A51U.01 6 0.0547 0.6111 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.D8.A1Y2.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BH.A0DG.01 4 0.3315 0.6415 0.00 0.20 0.02 0.78 0.00 0.00
#> TCGA.C8.A3M7.01 4 0.3869 0.4636 0.00 0.00 0.50 0.50 0.00 0.00
#> TCGA.E2.A1L6.01 6 0.0547 0.6111 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.D8.A1XY.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D8.A27G.01 2 0.0937 0.8575 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.AR.A1AM.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.4H.AAAK.01 3 0.4873 0.4590 0.08 0.00 0.60 0.00 0.00 0.32
#> TCGA.AC.A5XS.01 1 0.3797 0.8187 0.58 0.00 0.00 0.00 0.00 0.42
#> TCGA.E2.A1IF.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AC.A2FO.01 3 0.5071 0.3221 0.08 0.00 0.52 0.00 0.00 0.40
#> TCGA.AR.A24S.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A2.A3KD.01 6 0.3706 0.3606 0.00 0.00 0.00 0.00 0.38 0.62
#> TCGA.E9.A226.01 6 0.0937 0.5847 0.04 0.00 0.00 0.00 0.00 0.96
#> TCGA.D8.A1X8.01 6 0.3746 0.3963 0.08 0.00 0.14 0.00 0.00 0.78
#> TCGA.A2.A0T5.01 3 0.0547 0.7122 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.LD.A74U.01 4 0.3578 0.6623 0.00 0.00 0.34 0.66 0.00 0.00
#> TCGA.AR.A0TQ.01 2 0.5295 0.0319 0.10 0.46 0.00 0.44 0.00 0.00
#> TCGA.AO.A0JE.01 4 0.2260 0.6764 0.14 0.00 0.00 0.86 0.00 0.00
#> TCGA.E9.A228.01 2 0.2941 0.8038 0.22 0.78 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RA.01 3 0.4806 0.3960 0.06 0.00 0.56 0.00 0.00 0.38
#> TCGA.LL.A740.01 2 0.2941 0.8038 0.22 0.78 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BZ.01 4 0.3163 0.6548 0.14 0.04 0.00 0.82 0.00 0.00
#> TCGA.EW.A2FV.01 6 0.3864 -0.6424 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.BH.A0DV.01 6 0.0000 0.6043 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.A2.A0YI.01 6 0.0937 0.5847 0.04 0.00 0.00 0.00 0.00 0.96
#> TCGA.BH.A0BM.01 6 0.3864 0.0614 0.00 0.00 0.00 0.00 0.48 0.52
#> TCGA.D8.A27I.01 6 0.0000 0.6043 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.A2.A0YD.01 3 0.2048 0.5868 0.00 0.00 0.88 0.12 0.00 0.00
#> TCGA.BH.A0C0.01 4 0.3076 0.5974 0.00 0.24 0.00 0.76 0.00 0.00
#> TCGA.E9.A1NG.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EW.A1IW.01 2 0.2941 0.8038 0.22 0.78 0.00 0.00 0.00 0.00
#> TCGA.JL.A3YW.01 2 0.1814 0.8422 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.AN.A0XN.01 2 0.2941 0.8038 0.22 0.78 0.00 0.00 0.00 0.00
#> TCGA.E9.A6HE.01 4 0.3869 0.4636 0.00 0.00 0.50 0.50 0.00 0.00
#> TCGA.C8.A26W.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BH.A0DP.01 4 0.3950 0.7025 0.00 0.04 0.24 0.72 0.00 0.00
#> TCGA.AR.A2LN.01 3 0.5037 0.3611 0.08 0.00 0.54 0.00 0.00 0.38
#> TCGA.D8.A1JF.01 4 0.2260 0.6764 0.14 0.00 0.00 0.86 0.00 0.00
#> TCGA.OL.A6VQ.01 6 0.1807 0.5762 0.06 0.00 0.02 0.00 0.00 0.92
#> TCGA.E2.A1LL.01 1 0.3706 0.8449 0.62 0.00 0.00 0.00 0.00 0.38
#> TCGA.BH.A0AU.01 6 0.2631 0.3524 0.18 0.00 0.00 0.00 0.00 0.82
#> TCGA.A2.A0T1.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AR.A24W.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AR.A0TT.01 4 0.3460 0.6995 0.02 0.00 0.22 0.76 0.00 0.00
#> TCGA.AC.A3W6.01 3 0.2631 0.4926 0.00 0.00 0.82 0.18 0.00 0.00
#> TCGA.OL.A66P.01 1 0.4420 0.8299 0.62 0.00 0.04 0.00 0.00 0.34
#> TCGA.AR.A24L.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BH.A0H3.01 3 0.1865 0.7383 0.04 0.00 0.92 0.00 0.00 0.04
#> TCGA.EW.A1IZ.01 3 0.1807 0.7191 0.06 0.00 0.92 0.02 0.00 0.00
#> TCGA.AO.A0JA.01 4 0.3985 0.6859 0.14 0.00 0.10 0.76 0.00 0.00
#> TCGA.AR.A0TX.01 6 0.3828 0.1994 0.00 0.00 0.00 0.00 0.44 0.56
#> TCGA.AO.A0JG.01 4 0.3592 0.6927 0.02 0.00 0.24 0.74 0.00 0.00
#> TCGA.OL.A66N.01 2 0.1814 0.8422 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.A7.A4SC.01 2 0.0937 0.8575 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.GM.A2DB.01 1 0.4420 0.8299 0.62 0.00 0.04 0.00 0.00 0.34
#> TCGA.E9.A1N3.01 5 0.0937 0.8909 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.AN.A0XL.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.E9.A24A.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.GM.A2DL.01 4 0.3460 0.6152 0.02 0.22 0.00 0.76 0.00 0.00
#> TCGA.E9.A22B.01 2 0.2941 0.8038 0.22 0.78 0.00 0.00 0.00 0.00
#> TCGA.A2.A3XV.01 2 0.2941 0.8038 0.22 0.78 0.00 0.00 0.00 0.00
#> TCGA.AC.A6IX.06 4 0.3499 0.6749 0.00 0.00 0.32 0.68 0.00 0.00
#> TCGA.AC.A6IX.01 2 0.1267 0.8541 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.B6.A0WY.01 1 0.3797 0.8187 0.58 0.00 0.00 0.00 0.00 0.42
#> TCGA.E9.A1R4.01 6 0.0937 0.5847 0.04 0.00 0.00 0.00 0.00 0.96
#> TCGA.EW.A1J2.01 3 0.0000 0.7223 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0GY.01 1 0.4420 0.8299 0.62 0.00 0.04 0.00 0.00 0.34
#> TCGA.W8.A86G.01 6 0.3746 0.4083 0.08 0.00 0.14 0.00 0.00 0.78
#> TCGA.A7.A5ZW.01 6 0.3647 0.4021 0.00 0.00 0.00 0.00 0.36 0.64
#> TCGA.C8.A1HF.01 4 0.4199 0.6213 0.02 0.00 0.38 0.60 0.00 0.00
#> TCGA.A2.A0T7.01 1 0.3706 0.8449 0.62 0.00 0.00 0.00 0.00 0.38
#> TCGA.AO.A0JJ.01 3 0.2474 0.7333 0.04 0.00 0.88 0.00 0.00 0.08
#> TCGA.B6.A0X7.01 3 0.0547 0.7122 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.OL.A5RV.01 6 0.0547 0.6114 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.E2.A1BC.01 3 0.0937 0.7344 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.E9.A22D.01 2 0.0937 0.8497 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.A1.A0SF.01 4 0.3851 0.5378 0.00 0.00 0.46 0.54 0.00 0.00
#> TCGA.EW.A6SD.01 6 0.4462 -0.0557 0.28 0.00 0.06 0.00 0.00 0.66
#> TCGA.A7.A426.01 6 0.0000 0.6043 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AR.A1AU.01 3 0.0547 0.7122 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.E9.A1N6.01 1 0.3756 0.8346 0.60 0.00 0.00 0.00 0.00 0.40
#> TCGA.D8.A27L.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.E9.A1NF.01 4 0.3460 0.6152 0.02 0.22 0.00 0.76 0.00 0.00
#> TCGA.A1.A0SM.01 2 0.0937 0.8497 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.LD.A7W5.01 4 0.0547 0.7153 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.E2.A1LA.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BH.A42V.01 3 0.3821 0.6249 0.04 0.00 0.74 0.00 0.00 0.22
#> TCGA.E9.A5FK.01 4 0.3797 0.5906 0.00 0.00 0.42 0.58 0.00 0.00
#> TCGA.D8.A1XB.01 4 0.3864 0.5045 0.00 0.00 0.48 0.52 0.00 0.00
#> TCGA.E9.A227.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A2.A0YL.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A7.A5ZX.01 3 0.0547 0.7122 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.D8.A1JG.01 4 0.3163 0.6548 0.14 0.04 0.00 0.82 0.00 0.00
#> TCGA.AO.A0JF.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.C8.A8HQ.01 2 0.1814 0.8422 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.AC.A2B8.01 3 0.0937 0.7344 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.A2.A4S3.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A2.A0CO.01 3 0.1480 0.7377 0.04 0.00 0.94 0.00 0.00 0.02
#> TCGA.BH.A0AZ.01 5 0.3869 -0.0163 0.00 0.00 0.00 0.00 0.50 0.50
#> TCGA.E2.A1LE.01 2 0.1814 0.8422 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.A2.A0YH.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.LL.A5YN.01 1 0.3756 0.8366 0.60 0.00 0.00 0.00 0.00 0.40
#> TCGA.AC.A23G.01 3 0.4758 0.4269 0.06 0.00 0.58 0.00 0.00 0.36
#> TCGA.GM.A3XN.01 6 0.3073 0.4879 0.08 0.00 0.08 0.00 0.00 0.84
#> TCGA.C8.A275.01 2 0.0937 0.8575 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.E2.A1IK.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AQ.A7U7.01 4 0.3309 0.6922 0.00 0.00 0.28 0.72 0.00 0.00
#> TCGA.A1.A0SI.01 6 0.2474 0.5374 0.08 0.00 0.04 0.00 0.00 0.88
#> TCGA.A2.A25A.01 3 0.4993 0.3911 0.08 0.00 0.56 0.00 0.00 0.36
#> TCGA.E9.A1RH.01 1 0.3797 0.8187 0.58 0.00 0.00 0.00 0.00 0.42
#> TCGA.AO.A12E.01 2 0.2454 0.8226 0.16 0.84 0.00 0.00 0.00 0.00
#> TCGA.A7.A13H.01 6 0.0547 0.6114 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.E2.A1IO.01 6 0.3578 0.4420 0.00 0.00 0.00 0.00 0.34 0.66
#> TCGA.C8.A26Y.01 1 0.5608 0.4137 0.54 0.00 0.00 0.00 0.20 0.26
#> TCGA.A2.A25D.01 4 0.4002 0.6695 0.02 0.00 0.32 0.66 0.00 0.00
#> TCGA.AN.A0XW.01 5 0.3578 0.4630 0.00 0.00 0.00 0.00 0.66 0.34
#> TCGA.BH.A0AW.01 4 0.3163 0.6910 0.14 0.00 0.04 0.82 0.00 0.00
#> TCGA.BH.A0B6.01 3 0.2474 0.7333 0.04 0.00 0.88 0.00 0.00 0.08
#> TCGA.E9.A229.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D8.A1JK.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.GM.A5PX.01 3 0.4172 0.5650 0.04 0.00 0.68 0.00 0.00 0.28
#> TCGA.AR.A5QN.01 2 0.2941 0.8038 0.22 0.78 0.00 0.00 0.00 0.00
#> TCGA.BH.A208.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EW.A1IX.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A2.A259.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.GM.A2DD.01 1 0.4834 0.7499 0.64 0.00 0.10 0.00 0.00 0.26
#> TCGA.E2.A1B1.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D8.A73U.01 3 0.0937 0.7344 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.D8.A27N.01 2 0.0937 0.8575 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.E9.A22E.01 6 0.3756 0.3124 0.00 0.00 0.00 0.00 0.40 0.60
#> TCGA.OL.A5RX.01 3 0.0547 0.7122 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.D8.A1XO.01 6 0.0547 0.6114 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.AC.A23C.01 4 0.3864 0.5045 0.00 0.00 0.48 0.52 0.00 0.00
#> TCGA.A7.A56D.01 1 0.5208 0.3301 0.62 0.00 0.28 0.08 0.00 0.02
#> TCGA.A1.A0SH.01 6 0.3706 0.3606 0.00 0.00 0.00 0.00 0.38 0.62
#> TCGA.AR.A5QP.01 4 0.3797 0.5906 0.00 0.00 0.42 0.58 0.00 0.00
#> TCGA.D8.A1Y0.01 1 0.3706 0.8449 0.62 0.00 0.00 0.00 0.00 0.38
#> TCGA.BH.A2L8.01 3 0.5095 0.2843 0.08 0.00 0.50 0.00 0.00 0.42
#> TCGA.BH.A202.01 2 0.1814 0.8422 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.EW.A1OV.01 4 0.1865 0.7238 0.04 0.00 0.04 0.92 0.00 0.00
#> TCGA.A1.A0SN.01 2 0.2941 0.8038 0.22 0.78 0.00 0.00 0.00 0.00
#> TCGA.E9.A295.01 2 0.2941 0.8038 0.22 0.78 0.00 0.00 0.00 0.00
#> TCGA.AC.A8OP.01 2 0.5199 0.5423 0.12 0.58 0.00 0.30 0.00 0.00
#> TCGA.GI.A2C8.01 2 0.1814 0.8422 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.AR.A24P.01 4 0.3864 0.5045 0.00 0.00 0.48 0.52 0.00 0.00
#> TCGA.BH.A0B2.01 3 0.0937 0.6898 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.A2.A0SU.01 6 0.3869 -0.0180 0.00 0.00 0.00 0.00 0.50 0.50
#> TCGA.AR.A24T.01 2 0.0937 0.8497 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.AC.A2FE.01 2 0.1814 0.8422 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.E9.A1N4.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.XX.A899.01 4 0.3797 0.5906 0.00 0.00 0.42 0.58 0.00 0.00
#> TCGA.E9.A1N9.01 3 0.0547 0.7218 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.S3.AA17.01 2 0.0937 0.8497 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.EW.A1PF.01 6 0.2048 0.4691 0.12 0.00 0.00 0.00 0.00 0.88
#> TCGA.AO.A03L.01 3 0.3309 0.2287 0.00 0.00 0.72 0.28 0.00 0.00
#> TCGA.BH.A0HF.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AC.A2QI.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A2.A4S2.01 4 0.3578 0.6623 0.00 0.00 0.34 0.66 0.00 0.00
#> TCGA.GM.A2DA.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A7.A4SA.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A2.A3KC.01 2 0.1267 0.8541 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.OL.A66L.01 2 0.1814 0.8422 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.AR.A2LM.01 6 0.2512 0.5404 0.06 0.00 0.06 0.00 0.00 0.88
#> TCGA.E2.A10C.01 1 0.5363 0.6926 0.64 0.00 0.14 0.02 0.00 0.20
#> TCGA.AR.A1AN.01 5 0.3309 0.5823 0.00 0.00 0.00 0.00 0.72 0.28
#> TCGA.5L.AAT1.01 4 0.1480 0.7269 0.02 0.00 0.04 0.94 0.00 0.00
#> TCGA.HN.A2OB.01 6 0.4503 0.2479 0.08 0.00 0.24 0.00 0.00 0.68
#> TCGA.GM.A5PV.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.E2.A1IJ.01 3 0.4938 0.4243 0.08 0.00 0.58 0.00 0.00 0.34
#> TCGA.OK.A5Q2.01 4 0.2941 0.6212 0.00 0.22 0.00 0.78 0.00 0.00
#> TCGA.E9.A1R3.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AR.A254.01 2 0.2454 0.7897 0.00 0.84 0.00 0.16 0.00 0.00
#> TCGA.AR.A0TW.01 4 0.3163 0.6910 0.14 0.00 0.04 0.82 0.00 0.00
#> TCGA.BH.A8G0.01 6 0.0547 0.6114 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.B6.A401.01 6 0.5144 -0.3724 0.34 0.00 0.10 0.00 0.00 0.56
#> TCGA.E2.A1LB.01 4 0.3797 0.5906 0.00 0.00 0.42 0.58 0.00 0.00
#> TCGA.BH.A0W5.01 6 0.3647 0.4048 0.00 0.00 0.00 0.00 0.36 0.64
#> TCGA.AC.A3W7.01 4 0.3851 0.5378 0.00 0.00 0.46 0.54 0.00 0.00
#> TCGA.AC.A3W5.01 3 0.5288 0.2638 0.38 0.00 0.54 0.06 0.00 0.02
#> TCGA.B6.A1KI.01 5 0.1814 0.8328 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.E9.A1RI.01 3 0.2190 0.7364 0.04 0.00 0.90 0.00 0.00 0.06
#> TCGA.A2.A0T6.01 2 0.0547 0.8567 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.EW.A3E8.01 2 0.1814 0.8422 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.OL.A5RU.01 6 0.4380 0.2624 0.08 0.00 0.22 0.00 0.00 0.70
#> TCGA.E2.A10F.01 4 0.1267 0.7294 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.BH.A0C3.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.B6.A0RV.01 3 0.0547 0.7122 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.E2.A1IH.01 1 0.4482 0.8154 0.60 0.00 0.04 0.00 0.00 0.36
#> TCGA.EW.A1IY.01 3 0.0000 0.7223 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A24O.01 5 0.3499 0.5039 0.00 0.00 0.00 0.00 0.68 0.32
#> TCGA.C8.A278.01 4 0.0937 0.7288 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.AC.A3HN.01 6 0.0547 0.6114 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.AC.A3BB.01 3 0.2474 0.7333 0.04 0.00 0.88 0.00 0.00 0.08
#> TCGA.BH.A1FE.01 3 0.4938 0.4243 0.08 0.00 0.58 0.00 0.00 0.34
#> TCGA.A2.A0EN.01 3 0.0937 0.7344 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.BH.A0BF.01 3 0.0937 0.7344 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.WT.AB41.01 4 0.2941 0.6212 0.00 0.22 0.00 0.78 0.00 0.00
#> TCGA.LL.A5YL.01 2 0.2941 0.8038 0.22 0.78 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AK.01 3 0.0547 0.7122 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.C8.A26X.01 2 0.1814 0.8422 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.A7.A3J1.01 3 0.2474 0.7333 0.04 0.00 0.88 0.00 0.00 0.08
#> TCGA.D8.A1Y3.01 2 0.2941 0.8038 0.22 0.78 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DK.01 2 0.2941 0.8038 0.22 0.78 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JE.01 6 0.0547 0.6111 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.EW.A2FR.01 6 0.3076 0.2080 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.BH.A0W4.01 5 0.3864 0.0593 0.00 0.00 0.00 0.00 0.52 0.48
#> TCGA.BH.A0BJ.01 5 0.3828 0.1931 0.00 0.00 0.00 0.00 0.56 0.44
#> TCGA.BH.A203.01 2 0.2941 0.8038 0.22 0.78 0.00 0.00 0.00 0.00
#> TCGA.E2.A14U.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D8.A1XM.01 3 0.4806 0.3960 0.06 0.00 0.56 0.00 0.00 0.38
#> TCGA.D8.A1JH.01 6 0.0547 0.6114 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.BH.A1EU.01 6 0.3076 0.5040 0.00 0.00 0.00 0.00 0.24 0.76
#> TCGA.BH.A1FR.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A7.A425.01 6 0.3869 -0.0180 0.00 0.00 0.00 0.00 0.50 0.50
#> TCGA.B6.A0IK.01 2 0.1814 0.8422 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.E9.A1RF.01 4 0.3163 0.6548 0.14 0.04 0.00 0.82 0.00 0.00
#> TCGA.BH.A0HP.01 4 0.3864 0.5045 0.00 0.00 0.48 0.52 0.00 0.00
#> TCGA.BH.A8FZ.01 6 0.3076 0.5036 0.00 0.00 0.00 0.00 0.24 0.76
#> TCGA.AC.A2FG.01 6 0.2631 0.5353 0.00 0.00 0.00 0.00 0.18 0.82
#> TCGA.AR.A1AL.01 6 0.3864 0.0621 0.00 0.00 0.00 0.00 0.48 0.52
#> TCGA.BH.A1EO.01 4 0.1092 0.7087 0.02 0.02 0.00 0.96 0.00 0.00
#> TCGA.D8.A27K.01 3 0.2048 0.5870 0.00 0.00 0.88 0.12 0.00 0.00
#> TCGA.C8.A1HG.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D8.A1JU.01 6 0.3499 0.4694 0.00 0.00 0.00 0.00 0.32 0.68
#> TCGA.A2.A0YK.01 3 0.0547 0.7122 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.BH.A0DI.01 4 0.3460 0.6152 0.02 0.22 0.00 0.76 0.00 0.00
#> TCGA.E2.A107.01 3 0.0547 0.7292 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.5L.AAT0.01 6 0.1807 0.5762 0.06 0.00 0.02 0.00 0.00 0.92
#> TCGA.D8.A27E.01 5 0.0000 0.9233 0.00 0.00 0.00 0.00 1.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.OL.A66H.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.3C.AALK.01 2 0.0504 0.76260 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.AC.A5EH.01 1 0.2722 0.88295 0.84 0.00 0.04 0.00 0.00 0.12 0.00
#> TCGA.E9.A1R0.01 6 0.2422 0.69061 0.00 0.00 0.18 0.00 0.00 0.82 0.00
#> TCGA.AC.A62Y.01 6 0.3496 0.49314 0.00 0.00 0.42 0.00 0.00 0.58 0.00
#> TCGA.E9.A1R2.01 3 0.1363 0.62249 0.00 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.E9.A3X8.01 3 0.0863 0.61946 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.AR.A255.01 4 0.5567 0.44773 0.00 0.18 0.00 0.52 0.00 0.02 0.28
#> TCGA.E2.A10B.01 3 0.4127 -0.06378 0.00 0.00 0.60 0.04 0.00 0.00 0.36
#> TCGA.AO.A0JD.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A8.A0A6.01 2 0.0000 0.76473 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A3IY.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D8.A3Z5.01 3 0.3562 -0.35874 0.00 0.00 0.50 0.00 0.00 0.50 0.00
#> TCGA.E9.A1RD.01 7 0.3985 0.41336 0.00 0.00 0.46 0.02 0.00 0.00 0.52
#> TCGA.LD.A66U.01 3 0.2832 0.40787 0.00 0.00 0.76 0.00 0.00 0.24 0.00
#> TCGA.AC.A3QP.01 6 0.3047 0.65500 0.00 0.00 0.00 0.00 0.28 0.72 0.00
#> TCGA.GM.A2DK.01 6 0.3496 0.48137 0.00 0.00 0.42 0.00 0.00 0.58 0.00
#> TCGA.E2.A1B0.01 1 0.3208 0.88203 0.82 0.00 0.04 0.00 0.00 0.12 0.02
#> TCGA.BH.A1EY.01 4 0.2016 0.56389 0.00 0.04 0.00 0.90 0.00 0.00 0.06
#> TCGA.AC.A8OS.01 7 0.5635 0.53148 0.02 0.00 0.36 0.16 0.00 0.00 0.46
#> TCGA.GM.A2DN.01 7 0.3562 0.34839 0.00 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.AO.A03M.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A2.A4RW.01 2 0.1433 0.70949 0.00 0.92 0.00 0.08 0.00 0.00 0.00
#> TCGA.AC.A6IV.01 3 0.0863 0.62376 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.LL.A7SZ.01 3 0.2081 0.57267 0.00 0.00 0.86 0.00 0.00 0.14 0.00
#> TCGA.AR.A2LJ.01 3 0.3685 0.19670 0.00 0.00 0.66 0.00 0.00 0.32 0.02
#> TCGA.AQ.A1H3.01 4 0.4505 0.35456 0.00 0.44 0.00 0.50 0.00 0.00 0.06
#> TCGA.D8.A1JB.01 6 0.3546 0.40775 0.00 0.00 0.46 0.00 0.00 0.54 0.00
#> TCGA.BH.A0BC.01 6 0.3052 0.71475 0.00 0.00 0.02 0.00 0.20 0.78 0.00
#> TCGA.BH.A1EW.01 2 0.3525 -0.10976 0.00 0.56 0.00 0.44 0.00 0.00 0.00
#> TCGA.GM.A2DH.01 4 0.2945 0.33812 0.00 0.00 0.00 0.74 0.00 0.00 0.26
#> TCGA.D8.A27P.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EW.A2FS.01 4 0.3047 0.51126 0.00 0.28 0.00 0.72 0.00 0.00 0.00
#> TCGA.OL.A66J.01 6 0.3562 0.13242 0.00 0.00 0.00 0.00 0.50 0.50 0.00
#> TCGA.AR.A2LO.01 3 0.0000 0.62871 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A201.01 3 0.0000 0.62871 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S3.AA14.01 6 0.3496 0.49314 0.00 0.00 0.42 0.00 0.00 0.58 0.00
#> TCGA.B6.A0RS.01 6 0.4408 0.40660 0.02 0.00 0.44 0.00 0.00 0.52 0.02
#> TCGA.AR.A1AT.01 2 0.0000 0.76473 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A1G0.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AC.A3OD.01 2 0.0000 0.76473 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UU.A93S.01 4 0.3841 0.50584 0.04 0.00 0.00 0.68 0.00 0.00 0.28
#> TCGA.XX.A89A.01 5 0.2259 0.78766 0.00 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.AR.A5QM.01 4 0.5567 0.44773 0.00 0.18 0.00 0.52 0.00 0.02 0.28
#> TCGA.PE.A5DE.01 6 0.2745 0.69720 0.00 0.00 0.16 0.00 0.02 0.82 0.00
#> TCGA.AC.A23H.01 2 0.6125 0.64727 0.14 0.54 0.00 0.00 0.00 0.14 0.18
#> TCGA.D8.A27V.01 6 0.3358 0.52096 0.00 0.00 0.00 0.00 0.36 0.64 0.00
#> TCGA.A2.A1FZ.01 4 0.3139 0.28183 0.00 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.BH.A0BA.01 1 0.4338 0.64708 0.64 0.00 0.08 0.00 0.00 0.28 0.00
#> TCGA.BH.AB28.01 2 0.6125 0.64727 0.14 0.54 0.00 0.00 0.00 0.14 0.18
#> TCGA.D8.A27R.01 4 0.3417 0.34998 0.00 0.00 0.00 0.72 0.00 0.02 0.26
#> TCGA.OL.A5D6.01 4 0.5055 0.47577 0.00 0.18 0.00 0.56 0.00 0.00 0.26
#> TCGA.E2.A3DX.01 6 0.3370 0.72115 0.00 0.00 0.06 0.00 0.16 0.78 0.00
#> TCGA.A1.A0SE.01 6 0.3052 0.71475 0.00 0.00 0.02 0.00 0.20 0.78 0.00
#> TCGA.D8.A1XT.01 1 0.3494 0.88284 0.80 0.00 0.06 0.00 0.00 0.12 0.02
#> TCGA.C8.A1HI.01 3 0.3991 0.39697 0.02 0.00 0.72 0.00 0.00 0.22 0.04
#> TCGA.A2.A0T4.01 2 0.0504 0.76260 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.MS.A51U.01 6 0.2422 0.69061 0.00 0.00 0.18 0.00 0.00 0.82 0.00
#> TCGA.D8.A1Y2.01 5 0.0863 0.93910 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.BH.A0DG.01 4 0.4264 0.50222 0.00 0.32 0.00 0.62 0.00 0.00 0.06
#> TCGA.C8.A3M7.01 7 0.3994 0.39912 0.00 0.00 0.02 0.48 0.00 0.00 0.50
#> TCGA.E2.A1L6.01 6 0.2422 0.69061 0.00 0.00 0.18 0.00 0.00 0.82 0.00
#> TCGA.D8.A1XY.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D8.A27G.01 2 0.0000 0.76473 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AM.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.4H.AAAK.01 3 0.0504 0.62695 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AC.A5XS.01 1 0.2722 0.88295 0.84 0.00 0.04 0.00 0.00 0.12 0.00
#> TCGA.E2.A1IF.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AC.A2FO.01 3 0.0000 0.62871 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A24S.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A2.A3KD.01 6 0.3052 0.71475 0.00 0.00 0.02 0.00 0.20 0.78 0.00
#> TCGA.E9.A226.01 3 0.4278 -0.29206 0.00 0.00 0.50 0.00 0.00 0.46 0.04
#> TCGA.D8.A1X8.01 3 0.2572 0.47588 0.00 0.00 0.80 0.00 0.00 0.20 0.00
#> TCGA.A2.A0T5.01 7 0.3985 0.41336 0.00 0.00 0.46 0.02 0.00 0.00 0.52
#> TCGA.LD.A74U.01 4 0.3139 0.28183 0.00 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.AR.A0TQ.01 2 0.5338 -0.13429 0.00 0.48 0.00 0.32 0.00 0.00 0.20
#> TCGA.AO.A0JE.01 4 0.4305 0.52657 0.00 0.04 0.00 0.66 0.00 0.02 0.28
#> TCGA.E9.A228.01 2 0.6125 0.64727 0.14 0.54 0.00 0.00 0.00 0.14 0.18
#> TCGA.E9.A1RA.01 3 0.0504 0.62695 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.LL.A740.01 2 0.6125 0.64727 0.14 0.54 0.00 0.00 0.00 0.14 0.18
#> TCGA.BH.A0BZ.01 4 0.5567 0.44773 0.00 0.18 0.00 0.52 0.00 0.02 0.28
#> TCGA.EW.A2FV.01 1 0.4033 0.74603 0.70 0.00 0.08 0.00 0.00 0.22 0.00
#> TCGA.BH.A0DV.01 6 0.2422 0.69061 0.00 0.00 0.18 0.00 0.00 0.82 0.00
#> TCGA.A2.A0YI.01 6 0.3413 0.53684 0.00 0.00 0.38 0.00 0.00 0.62 0.00
#> TCGA.BH.A0BM.01 6 0.3417 0.67867 0.00 0.00 0.02 0.00 0.26 0.72 0.00
#> TCGA.D8.A27I.01 6 0.2422 0.69061 0.00 0.00 0.18 0.00 0.00 0.82 0.00
#> TCGA.A2.A0YD.01 7 0.5291 0.57426 0.00 0.00 0.20 0.30 0.00 0.00 0.50
#> TCGA.BH.A0C0.01 4 0.3546 0.31858 0.00 0.46 0.00 0.54 0.00 0.00 0.00
#> TCGA.E9.A1NG.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EW.A1IW.01 2 0.6125 0.64727 0.14 0.54 0.00 0.00 0.00 0.14 0.18
#> TCGA.JL.A3YW.01 2 0.0504 0.76260 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.AN.A0XN.01 2 0.6125 0.64727 0.14 0.54 0.00 0.00 0.00 0.14 0.18
#> TCGA.E9.A6HE.01 7 0.3562 0.34839 0.00 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.C8.A26W.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A0DP.01 4 0.3047 0.31818 0.00 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.AR.A2LN.01 3 0.0000 0.62871 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JF.01 4 0.4675 0.52715 0.02 0.04 0.00 0.66 0.00 0.02 0.26
#> TCGA.OL.A6VQ.01 6 0.3558 0.38080 0.00 0.00 0.48 0.00 0.00 0.52 0.00
#> TCGA.E2.A1LL.01 1 0.2803 0.88842 0.84 0.00 0.06 0.00 0.00 0.10 0.00
#> TCGA.BH.A0AU.01 6 0.3927 0.58835 0.14 0.00 0.08 0.00 0.00 0.76 0.02
#> TCGA.A2.A0T1.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AR.A24W.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AR.A0TT.01 4 0.2906 0.44190 0.02 0.00 0.00 0.80 0.00 0.00 0.18
#> TCGA.AC.A3W6.01 7 0.4848 0.49629 0.00 0.00 0.10 0.40 0.00 0.00 0.50
#> TCGA.OL.A66P.01 1 0.2803 0.88842 0.84 0.00 0.06 0.00 0.00 0.10 0.00
#> TCGA.AR.A24L.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A0H3.01 3 0.3358 0.11755 0.00 0.00 0.64 0.00 0.00 0.00 0.36
#> TCGA.EW.A1IZ.01 3 0.5429 -0.40733 0.02 0.00 0.46 0.12 0.00 0.00 0.40
#> TCGA.AO.A0JA.01 4 0.3221 0.49835 0.00 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.AR.A0TX.01 6 0.2708 0.70247 0.00 0.00 0.00 0.00 0.22 0.78 0.00
#> TCGA.AO.A0JG.01 4 0.4146 0.10329 0.02 0.00 0.02 0.64 0.00 0.00 0.32
#> TCGA.OL.A66N.01 2 0.0863 0.74791 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.A7.A4SC.01 2 0.0504 0.76260 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.GM.A2DB.01 1 0.2803 0.88842 0.84 0.00 0.06 0.00 0.00 0.10 0.00
#> TCGA.E9.A1N3.01 5 0.3139 0.52986 0.00 0.00 0.00 0.00 0.70 0.30 0.00
#> TCGA.AN.A0XL.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E9.A24A.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.GM.A2DL.01 4 0.3546 0.31858 0.00 0.46 0.00 0.54 0.00 0.00 0.00
#> TCGA.E9.A22B.01 2 0.6125 0.64727 0.14 0.54 0.00 0.00 0.00 0.14 0.18
#> TCGA.A2.A3XV.01 2 0.6125 0.64727 0.14 0.54 0.00 0.00 0.00 0.14 0.18
#> TCGA.AC.A6IX.06 4 0.3139 0.28183 0.00 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.AC.A6IX.01 2 0.0504 0.76260 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.B6.A0WY.01 1 0.3494 0.87306 0.80 0.00 0.06 0.00 0.00 0.12 0.02
#> TCGA.E9.A1R4.01 6 0.3525 0.44793 0.00 0.00 0.44 0.00 0.00 0.56 0.00
#> TCGA.EW.A1J2.01 3 0.3968 -0.28017 0.00 0.00 0.54 0.02 0.00 0.00 0.44
#> TCGA.BH.A0GY.01 1 0.3289 0.88676 0.82 0.00 0.06 0.00 0.00 0.10 0.02
#> TCGA.W8.A86G.01 3 0.2906 0.50024 0.00 0.00 0.80 0.00 0.00 0.18 0.02
#> TCGA.A7.A5ZW.01 6 0.3052 0.71475 0.00 0.00 0.02 0.00 0.20 0.78 0.00
#> TCGA.C8.A1HF.01 4 0.3496 -0.16612 0.00 0.00 0.00 0.58 0.00 0.00 0.42
#> TCGA.A2.A0T7.01 1 0.3289 0.88676 0.82 0.00 0.06 0.00 0.00 0.10 0.02
#> TCGA.AO.A0JJ.01 3 0.2422 0.45652 0.00 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.B6.A0X7.01 3 0.3994 -0.33943 0.00 0.00 0.50 0.02 0.00 0.00 0.48
#> TCGA.OL.A5RV.01 6 0.2945 0.64637 0.00 0.00 0.26 0.00 0.00 0.74 0.00
#> TCGA.E2.A1BC.01 3 0.3413 -0.00957 0.00 0.00 0.62 0.00 0.00 0.00 0.38
#> TCGA.E9.A22D.01 2 0.2864 0.74025 0.02 0.84 0.00 0.00 0.00 0.02 0.12
#> TCGA.A1.A0SF.01 4 0.3562 -0.39057 0.00 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.EW.A6SD.01 3 0.5738 0.15955 0.20 0.00 0.54 0.00 0.00 0.22 0.04
#> TCGA.A7.A426.01 6 0.2422 0.69061 0.00 0.00 0.18 0.00 0.00 0.82 0.00
#> TCGA.AR.A1AU.01 7 0.3985 0.41336 0.00 0.00 0.46 0.02 0.00 0.00 0.52
#> TCGA.E9.A1N6.01 1 0.3289 0.88676 0.82 0.00 0.06 0.00 0.00 0.10 0.02
#> TCGA.D8.A27L.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E9.A1NF.01 4 0.3546 0.31858 0.00 0.46 0.00 0.54 0.00 0.00 0.00
#> TCGA.A1.A0SM.01 2 0.2654 0.74450 0.02 0.86 0.00 0.00 0.00 0.02 0.10
#> TCGA.LD.A7W5.01 4 0.0504 0.55131 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.E2.A1LA.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A42V.01 3 0.0504 0.61387 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.E9.A5FK.01 4 0.3358 0.10618 0.00 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.D8.A1XB.01 7 0.3994 0.39912 0.00 0.00 0.02 0.48 0.00 0.00 0.50
#> TCGA.E9.A227.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A2.A0YL.01 5 0.0504 0.95949 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.A7.A5ZX.01 7 0.4278 0.44914 0.00 0.00 0.46 0.04 0.00 0.00 0.50
#> TCGA.D8.A1JG.01 4 0.5567 0.44773 0.00 0.18 0.00 0.52 0.00 0.02 0.28
#> TCGA.AO.A0JF.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.C8.A8HQ.01 2 0.0504 0.76260 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.AC.A2B8.01 3 0.4901 -0.26871 0.02 0.00 0.52 0.06 0.00 0.00 0.40
#> TCGA.A2.A4S3.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A2.A0CO.01 3 0.3413 -0.00998 0.00 0.00 0.62 0.00 0.00 0.00 0.38
#> TCGA.BH.A0AZ.01 6 0.3047 0.65500 0.00 0.00 0.00 0.00 0.28 0.72 0.00
#> TCGA.E2.A1LE.01 2 0.0504 0.76260 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.A2.A0YH.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.LL.A5YN.01 1 0.2803 0.88842 0.84 0.00 0.06 0.00 0.00 0.10 0.00
#> TCGA.AC.A23G.01 3 0.0000 0.62871 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A3XN.01 3 0.3307 0.39900 0.00 0.00 0.74 0.00 0.00 0.24 0.02
#> TCGA.C8.A275.01 2 0.0504 0.76260 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.E2.A1IK.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AQ.A7U7.01 4 0.3047 0.31818 0.00 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.A1.A0SI.01 3 0.3546 -0.24020 0.00 0.00 0.54 0.00 0.00 0.46 0.00
#> TCGA.A2.A25A.01 3 0.0000 0.62871 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RH.01 1 0.2569 0.86709 0.84 0.00 0.02 0.00 0.00 0.14 0.00
#> TCGA.AO.A12E.01 2 0.4748 0.70289 0.10 0.70 0.00 0.00 0.00 0.06 0.14
#> TCGA.A7.A13H.01 6 0.3413 0.53673 0.00 0.00 0.38 0.00 0.00 0.62 0.00
#> TCGA.E2.A1IO.01 6 0.3052 0.71475 0.00 0.00 0.02 0.00 0.20 0.78 0.00
#> TCGA.C8.A26Y.01 1 0.2569 0.84911 0.84 0.00 0.00 0.00 0.02 0.14 0.00
#> TCGA.A2.A25D.01 4 0.2945 0.33812 0.00 0.00 0.00 0.74 0.00 0.00 0.26
#> TCGA.AN.A0XW.01 6 0.3139 0.62765 0.00 0.00 0.00 0.00 0.30 0.70 0.00
#> TCGA.BH.A0AW.01 4 0.3984 0.52096 0.00 0.02 0.00 0.68 0.00 0.02 0.28
#> TCGA.BH.A0B6.01 3 0.2945 0.33104 0.00 0.00 0.74 0.00 0.00 0.00 0.26
#> TCGA.E9.A229.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D8.A1JK.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.GM.A5PX.01 3 0.0000 0.62871 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A5QN.01 2 0.6125 0.64727 0.14 0.54 0.00 0.00 0.00 0.14 0.18
#> TCGA.BH.A208.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EW.A1IX.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A2.A259.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.GM.A2DD.01 1 0.3142 0.80143 0.84 0.00 0.10 0.02 0.00 0.02 0.02
#> TCGA.E2.A1B1.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D8.A73U.01 3 0.3413 -0.00998 0.00 0.00 0.62 0.00 0.00 0.00 0.38
#> TCGA.D8.A27N.01 2 0.0000 0.76473 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A22E.01 6 0.3052 0.71475 0.00 0.00 0.02 0.00 0.20 0.78 0.00
#> TCGA.OL.A5RX.01 7 0.3985 0.41336 0.00 0.00 0.46 0.02 0.00 0.00 0.52
#> TCGA.D8.A1XO.01 6 0.3496 0.49314 0.00 0.00 0.42 0.00 0.00 0.58 0.00
#> TCGA.AC.A23C.01 7 0.3994 0.39912 0.00 0.00 0.02 0.48 0.00 0.00 0.50
#> TCGA.A7.A56D.01 1 0.3061 0.77148 0.84 0.00 0.08 0.06 0.00 0.00 0.02
#> TCGA.A1.A0SH.01 6 0.3052 0.71475 0.00 0.00 0.02 0.00 0.20 0.78 0.00
#> TCGA.AR.A5QP.01 4 0.3562 -0.39057 0.00 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.D8.A1Y0.01 1 0.2803 0.88842 0.84 0.00 0.06 0.00 0.00 0.10 0.00
#> TCGA.BH.A2L8.01 3 0.0504 0.62695 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BH.A202.01 2 0.1166 0.73078 0.00 0.94 0.00 0.06 0.00 0.00 0.00
#> TCGA.EW.A1OV.01 4 0.1664 0.52985 0.02 0.00 0.00 0.92 0.00 0.00 0.06
#> TCGA.A1.A0SN.01 2 0.6125 0.64727 0.14 0.54 0.00 0.00 0.00 0.14 0.18
#> TCGA.E9.A295.01 2 0.6125 0.64727 0.14 0.54 0.00 0.00 0.00 0.14 0.18
#> TCGA.AC.A8OP.01 2 0.5695 0.22660 0.00 0.50 0.00 0.22 0.00 0.02 0.26
#> TCGA.GI.A2C8.01 2 0.0504 0.76260 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.AR.A24P.01 4 0.3562 -0.39057 0.00 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.BH.A0B2.01 7 0.4669 0.50276 0.00 0.00 0.40 0.08 0.00 0.00 0.52
#> TCGA.A2.A0SU.01 6 0.3047 0.65500 0.00 0.00 0.00 0.00 0.28 0.72 0.00
#> TCGA.AR.A24T.01 2 0.3055 0.73551 0.02 0.82 0.00 0.00 0.00 0.02 0.14
#> TCGA.AC.A2FE.01 2 0.0504 0.76260 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.E9.A1N4.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.XX.A899.01 4 0.3459 -0.04596 0.00 0.00 0.00 0.60 0.00 0.00 0.40
#> TCGA.E9.A1N9.01 7 0.4408 0.37319 0.00 0.00 0.44 0.02 0.00 0.02 0.52
#> TCGA.S3.AA17.01 2 0.3055 0.73551 0.02 0.82 0.00 0.00 0.00 0.02 0.14
#> TCGA.EW.A1PF.01 6 0.3058 0.65489 0.08 0.00 0.10 0.00 0.00 0.82 0.00
#> TCGA.AO.A03L.01 7 0.4505 0.44949 0.00 0.00 0.06 0.44 0.00 0.00 0.50
#> TCGA.BH.A0HF.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AC.A2QI.01 5 0.0863 0.93996 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.A2.A4S2.01 4 0.3139 0.28183 0.00 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.GM.A2DA.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A7.A4SA.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A2.A3KC.01 2 0.0504 0.76260 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.OL.A66L.01 2 0.0504 0.76260 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.AR.A2LM.01 3 0.3943 -0.14434 0.00 0.00 0.56 0.00 0.00 0.42 0.02
#> TCGA.E2.A10C.01 1 0.3142 0.80143 0.84 0.00 0.10 0.02 0.00 0.02 0.02
#> TCGA.AR.A1AN.01 6 0.3358 0.52381 0.00 0.00 0.00 0.00 0.36 0.64 0.00
#> TCGA.5L.AAT1.01 4 0.0504 0.55131 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.HN.A2OB.01 3 0.1664 0.61800 0.00 0.00 0.92 0.00 0.00 0.06 0.02
#> TCGA.GM.A5PV.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E2.A1IJ.01 3 0.0000 0.62871 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.OK.A5Q2.01 4 0.3413 0.43858 0.00 0.38 0.00 0.62 0.00 0.00 0.00
#> TCGA.E9.A1R3.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AR.A254.01 2 0.2422 0.57224 0.00 0.82 0.00 0.18 0.00 0.00 0.00
#> TCGA.AR.A0TW.01 4 0.4305 0.52657 0.00 0.04 0.00 0.66 0.00 0.02 0.28
#> TCGA.BH.A8G0.01 6 0.3139 0.61552 0.00 0.00 0.30 0.00 0.00 0.70 0.00
#> TCGA.B6.A401.01 3 0.3985 0.36815 0.18 0.00 0.72 0.00 0.00 0.10 0.00
#> TCGA.E2.A1LB.01 7 0.3994 0.39912 0.00 0.00 0.02 0.48 0.00 0.00 0.50
#> TCGA.BH.A0W5.01 6 0.3052 0.71475 0.00 0.00 0.02 0.00 0.20 0.78 0.00
#> TCGA.AC.A3W7.01 7 0.3562 0.34839 0.00 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.AC.A3W5.01 1 0.6759 -0.11255 0.38 0.00 0.16 0.16 0.00 0.00 0.30
#> TCGA.B6.A1KI.01 5 0.3047 0.57611 0.00 0.00 0.00 0.00 0.72 0.28 0.00
#> TCGA.E9.A1RI.01 3 0.3221 0.23650 0.00 0.00 0.68 0.00 0.00 0.00 0.32
#> TCGA.A2.A0T6.01 2 0.0504 0.76295 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EW.A3E8.01 2 0.0504 0.76260 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.OL.A5RU.01 3 0.2376 0.58223 0.00 0.00 0.86 0.00 0.00 0.12 0.02
#> TCGA.E2.A10F.01 4 0.0863 0.52723 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.BH.A0C3.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B6.A0RV.01 7 0.4278 0.44914 0.00 0.00 0.46 0.04 0.00 0.00 0.50
#> TCGA.E2.A1IH.01 1 0.5293 0.35503 0.46 0.00 0.42 0.00 0.00 0.10 0.02
#> TCGA.EW.A1IY.01 3 0.3985 -0.28486 0.00 0.00 0.52 0.02 0.00 0.00 0.46
#> TCGA.AR.A24O.01 6 0.3294 0.56097 0.00 0.00 0.00 0.00 0.34 0.66 0.00
#> TCGA.C8.A278.01 4 0.0863 0.52723 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.AC.A3HN.01 6 0.3496 0.49314 0.00 0.00 0.42 0.00 0.00 0.58 0.00
#> TCGA.AC.A3BB.01 3 0.2832 0.36511 0.00 0.00 0.76 0.00 0.00 0.00 0.24
#> TCGA.BH.A1FE.01 3 0.0000 0.62871 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0EN.01 3 0.3943 -0.21931 0.00 0.00 0.56 0.02 0.00 0.00 0.42
#> TCGA.BH.A0BF.01 3 0.4487 -0.31320 0.00 0.00 0.52 0.06 0.00 0.00 0.42
#> TCGA.WT.AB41.01 4 0.3413 0.43858 0.00 0.38 0.00 0.62 0.00 0.00 0.00
#> TCGA.LL.A5YL.01 2 0.6125 0.64727 0.14 0.54 0.00 0.00 0.00 0.14 0.18
#> TCGA.AR.A1AK.01 7 0.4278 0.44914 0.00 0.00 0.46 0.04 0.00 0.00 0.50
#> TCGA.C8.A26X.01 2 0.0504 0.76260 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.A7.A3J1.01 3 0.3139 0.24314 0.00 0.00 0.70 0.00 0.00 0.00 0.30
#> TCGA.D8.A1Y3.01 2 0.6125 0.64727 0.14 0.54 0.00 0.00 0.00 0.14 0.18
#> TCGA.BH.A0DK.01 2 0.6125 0.64727 0.14 0.54 0.00 0.00 0.00 0.14 0.18
#> TCGA.D8.A1JE.01 6 0.2422 0.69061 0.00 0.00 0.18 0.00 0.00 0.82 0.00
#> TCGA.EW.A2FR.01 6 0.5196 0.47983 0.16 0.00 0.22 0.00 0.00 0.60 0.02
#> TCGA.BH.A0W4.01 6 0.3139 0.62765 0.00 0.00 0.00 0.00 0.30 0.70 0.00
#> TCGA.BH.A0BJ.01 6 0.3139 0.62765 0.00 0.00 0.00 0.00 0.30 0.70 0.00
#> TCGA.BH.A203.01 2 0.6125 0.64727 0.14 0.54 0.00 0.00 0.00 0.14 0.18
#> TCGA.E2.A14U.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D8.A1XM.01 3 0.0504 0.62695 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.D8.A1JH.01 6 0.3413 0.53526 0.00 0.00 0.38 0.00 0.00 0.62 0.00
#> TCGA.BH.A1EU.01 6 0.3011 0.71502 0.00 0.00 0.06 0.00 0.12 0.82 0.00
#> TCGA.BH.A1FR.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A7.A425.01 6 0.3047 0.65500 0.00 0.00 0.00 0.00 0.28 0.72 0.00
#> TCGA.B6.A0IK.01 2 0.0504 0.76260 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.E9.A1RF.01 4 0.5567 0.44773 0.00 0.18 0.00 0.52 0.00 0.02 0.28
#> TCGA.BH.A0HP.01 7 0.3994 0.39912 0.00 0.00 0.02 0.48 0.00 0.00 0.50
#> TCGA.BH.A8FZ.01 6 0.3011 0.71502 0.00 0.00 0.06 0.00 0.12 0.82 0.00
#> TCGA.AC.A2FG.01 6 0.3058 0.71409 0.00 0.00 0.08 0.00 0.10 0.82 0.00
#> TCGA.AR.A1AL.01 6 0.2945 0.67766 0.00 0.00 0.00 0.00 0.26 0.74 0.00
#> TCGA.BH.A1EO.01 4 0.1166 0.56329 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.D8.A27K.01 7 0.5233 0.58414 0.00 0.00 0.20 0.28 0.00 0.00 0.52
#> TCGA.C8.A1HG.01 5 0.1166 0.91716 0.00 0.00 0.00 0.00 0.94 0.06 0.00
#> TCGA.D8.A1JU.01 6 0.3370 0.72115 0.00 0.00 0.06 0.00 0.16 0.78 0.00
#> TCGA.A2.A0YK.01 7 0.4866 0.50044 0.00 0.00 0.42 0.10 0.00 0.00 0.48
#> TCGA.BH.A0DI.01 4 0.3546 0.31858 0.00 0.46 0.00 0.54 0.00 0.00 0.00
#> TCGA.E2.A107.01 3 0.4487 -0.31320 0.00 0.00 0.52 0.06 0.00 0.00 0.42
#> TCGA.5L.AAT0.01 6 0.3525 0.44793 0.00 0.00 0.44 0.00 0.00 0.56 0.00
#> TCGA.D8.A27E.01 5 0.0000 0.97728 0.00 0.00 0.00 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.OL.A66H.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.3C.AALK.01 2 0.0471 0.7959 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.AC.A5EH.01 1 0.0471 0.8885 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.E9.A1R0.01 6 0.2020 0.8079 0.02 0.00 0.06 0.00 0.00 0.90 0.00 0.02
#> TCGA.AC.A62Y.01 6 0.4321 0.7272 0.02 0.00 0.14 0.00 0.00 0.72 0.02 0.10
#> TCGA.E9.A1R2.01 3 0.4835 0.5769 0.02 0.00 0.64 0.00 0.00 0.02 0.10 0.22
#> TCGA.E9.A3X8.01 3 0.0941 0.7473 0.00 0.00 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.AR.A255.01 7 0.2025 0.9031 0.00 0.10 0.00 0.02 0.00 0.00 0.88 0.00
#> TCGA.E2.A10B.01 3 0.2680 0.7364 0.02 0.00 0.84 0.12 0.00 0.00 0.02 0.00
#> TCGA.AO.A0JD.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A8.A0A6.01 2 0.0471 0.7959 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.A7.A3IY.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A3Z5.01 6 0.4471 0.7101 0.02 0.00 0.16 0.00 0.00 0.70 0.02 0.10
#> TCGA.E9.A1RD.01 3 0.4860 0.3730 0.00 0.00 0.50 0.40 0.00 0.00 0.04 0.06
#> TCGA.LD.A66U.01 3 0.4835 0.4661 0.02 0.00 0.64 0.00 0.00 0.22 0.02 0.10
#> TCGA.AC.A3QP.01 6 0.1341 0.8159 0.00 0.00 0.00 0.00 0.08 0.92 0.00 0.00
#> TCGA.GM.A2DK.01 6 0.4155 0.7420 0.02 0.00 0.12 0.00 0.00 0.74 0.02 0.10
#> TCGA.E2.A1B0.01 1 0.1275 0.8819 0.94 0.00 0.00 0.00 0.00 0.02 0.04 0.00
#> TCGA.BH.A1EY.01 4 0.3714 0.2169 0.00 0.02 0.00 0.54 0.00 0.00 0.44 0.00
#> TCGA.AC.A8OS.01 3 0.3729 0.3250 0.02 0.00 0.52 0.46 0.00 0.00 0.00 0.00
#> TCGA.GM.A2DN.01 4 0.0000 0.8228 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A03M.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A4RW.01 2 0.0471 0.7937 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.AC.A6IV.01 3 0.2724 0.7073 0.02 0.00 0.86 0.00 0.00 0.02 0.02 0.08
#> TCGA.LL.A7SZ.01 3 0.3970 0.6435 0.02 0.00 0.76 0.00 0.00 0.10 0.02 0.10
#> TCGA.AR.A2LJ.01 3 0.5295 0.0802 0.02 0.00 0.50 0.00 0.00 0.36 0.02 0.10
#> TCGA.AQ.A1H3.01 2 0.3757 0.5276 0.00 0.68 0.00 0.26 0.00 0.00 0.06 0.00
#> TCGA.D8.A1JB.01 6 0.4804 0.7014 0.04 0.00 0.14 0.00 0.00 0.68 0.02 0.12
#> TCGA.BH.A0BC.01 6 0.1091 0.8234 0.00 0.00 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.BH.A1EW.01 2 0.3551 0.5801 0.00 0.72 0.00 0.22 0.00 0.00 0.06 0.00
#> TCGA.GM.A2DH.01 4 0.1275 0.8167 0.00 0.02 0.00 0.94 0.00 0.00 0.04 0.00
#> TCGA.D8.A27P.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EW.A2FS.01 2 0.5230 -0.1128 0.00 0.40 0.00 0.28 0.00 0.00 0.32 0.00
#> TCGA.OL.A66J.01 6 0.2938 0.5523 0.00 0.00 0.00 0.00 0.30 0.70 0.00 0.00
#> TCGA.AR.A2LO.01 3 0.0471 0.7465 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.BH.A201.01 3 0.1275 0.7429 0.00 0.00 0.94 0.00 0.00 0.02 0.00 0.04
#> TCGA.S3.AA14.01 6 0.4155 0.7420 0.02 0.00 0.12 0.00 0.00 0.74 0.02 0.10
#> TCGA.B6.A0RS.01 6 0.5924 0.5635 0.04 0.00 0.12 0.00 0.00 0.56 0.08 0.20
#> TCGA.AR.A1AT.01 2 0.0471 0.7959 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.A2.A1G0.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A3OD.01 2 0.0471 0.7959 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.UU.A93S.01 7 0.2350 0.8734 0.04 0.00 0.00 0.10 0.00 0.00 0.86 0.00
#> TCGA.XX.A89A.01 5 0.2114 0.8040 0.00 0.00 0.00 0.00 0.84 0.16 0.00 0.00
#> TCGA.AR.A5QM.01 7 0.2025 0.9031 0.00 0.10 0.00 0.02 0.00 0.00 0.88 0.00
#> TCGA.PE.A5DE.01 6 0.1275 0.8246 0.02 0.00 0.00 0.00 0.04 0.94 0.00 0.00
#> TCGA.AC.A23H.01 8 0.2938 0.9268 0.00 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.D8.A27V.01 6 0.1947 0.7694 0.00 0.00 0.00 0.00 0.14 0.86 0.00 0.00
#> TCGA.A2.A1FZ.01 4 0.1275 0.8167 0.00 0.02 0.00 0.94 0.00 0.00 0.04 0.00
#> TCGA.BH.A0BA.01 1 0.3015 0.4921 0.68 0.00 0.00 0.00 0.00 0.32 0.00 0.00
#> TCGA.BH.AB28.01 8 0.2938 0.9268 0.00 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.D8.A27R.01 4 0.2265 0.7815 0.00 0.00 0.00 0.88 0.00 0.02 0.02 0.08
#> TCGA.OL.A5D6.01 7 0.2623 0.8853 0.00 0.10 0.00 0.06 0.00 0.00 0.84 0.00
#> TCGA.E2.A3DX.01 6 0.0808 0.8254 0.00 0.00 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.A1.A0SE.01 6 0.1091 0.8234 0.00 0.00 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.D8.A1XT.01 1 0.2914 0.8377 0.84 0.00 0.00 0.00 0.00 0.04 0.04 0.08
#> TCGA.C8.A1HI.01 3 0.6152 0.4256 0.04 0.00 0.52 0.00 0.00 0.14 0.08 0.22
#> TCGA.A2.A0T4.01 2 0.0000 0.8014 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MS.A51U.01 6 0.0808 0.8184 0.00 0.00 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.D8.A1Y2.01 5 0.0808 0.9391 0.00 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.BH.A0DG.01 4 0.4199 0.1212 0.00 0.42 0.00 0.52 0.00 0.00 0.06 0.00
#> TCGA.C8.A3M7.01 4 0.0000 0.8228 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1L6.01 6 0.1275 0.8167 0.02 0.00 0.04 0.00 0.00 0.94 0.00 0.00
#> TCGA.D8.A1XY.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A27G.01 2 0.0471 0.7959 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.AR.A1AM.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.4H.AAAK.01 3 0.2680 0.7196 0.00 0.00 0.84 0.00 0.00 0.02 0.02 0.12
#> TCGA.AC.A5XS.01 1 0.0471 0.8885 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.E2.A1IF.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A2FO.01 3 0.2724 0.7073 0.02 0.00 0.86 0.00 0.00 0.02 0.02 0.08
#> TCGA.AR.A24S.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A3KD.01 6 0.1091 0.8234 0.00 0.00 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.E9.A226.01 6 0.6326 0.5195 0.06 0.00 0.12 0.00 0.00 0.52 0.10 0.20
#> TCGA.D8.A1X8.01 3 0.4471 0.5716 0.02 0.00 0.70 0.00 0.00 0.16 0.02 0.10
#> TCGA.A2.A0T5.01 3 0.4040 0.4950 0.00 0.00 0.58 0.38 0.00 0.00 0.02 0.02
#> TCGA.LD.A74U.01 4 0.1275 0.8167 0.00 0.02 0.00 0.94 0.00 0.00 0.04 0.00
#> TCGA.AR.A0TQ.01 2 0.3198 0.5505 0.00 0.72 0.00 0.02 0.00 0.00 0.26 0.00
#> TCGA.AO.A0JE.01 7 0.2025 0.8908 0.00 0.02 0.00 0.10 0.00 0.00 0.88 0.00
#> TCGA.E9.A228.01 8 0.2938 0.9268 0.00 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.E9.A1RA.01 3 0.2680 0.7118 0.00 0.00 0.84 0.00 0.00 0.02 0.02 0.12
#> TCGA.LL.A740.01 8 0.2938 0.9268 0.00 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.BH.A0BZ.01 7 0.2025 0.9031 0.00 0.10 0.00 0.02 0.00 0.00 0.88 0.00
#> TCGA.EW.A2FV.01 1 0.2534 0.6722 0.78 0.00 0.00 0.00 0.00 0.22 0.00 0.00
#> TCGA.BH.A0DV.01 6 0.1275 0.8167 0.02 0.00 0.04 0.00 0.00 0.94 0.00 0.00
#> TCGA.A2.A0YI.01 6 0.4564 0.7281 0.08 0.00 0.08 0.00 0.00 0.72 0.02 0.10
#> TCGA.BH.A0BM.01 6 0.1341 0.8159 0.00 0.00 0.00 0.00 0.08 0.92 0.00 0.00
#> TCGA.D8.A27I.01 6 0.1275 0.8167 0.02 0.00 0.04 0.00 0.00 0.94 0.00 0.00
#> TCGA.A2.A0YD.01 4 0.3170 0.5602 0.00 0.00 0.20 0.76 0.00 0.00 0.04 0.00
#> TCGA.BH.A0C0.01 2 0.3660 0.5523 0.00 0.70 0.00 0.24 0.00 0.00 0.06 0.00
#> TCGA.E9.A1NG.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EW.A1IW.01 8 0.2938 0.9268 0.00 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.JL.A3YW.01 2 0.0471 0.7957 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.AN.A0XN.01 8 0.2938 0.9268 0.00 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.E9.A6HE.01 4 0.0000 0.8228 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A26W.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0DP.01 4 0.1557 0.8078 0.00 0.02 0.00 0.92 0.00 0.00 0.06 0.00
#> TCGA.AR.A2LN.01 3 0.2940 0.6994 0.02 0.00 0.84 0.00 0.00 0.02 0.02 0.10
#> TCGA.D8.A1JF.01 7 0.2025 0.8908 0.00 0.02 0.00 0.10 0.00 0.00 0.88 0.00
#> TCGA.OL.A6VQ.01 6 0.4835 0.6328 0.02 0.00 0.22 0.00 0.00 0.64 0.02 0.10
#> TCGA.E2.A1LL.01 1 0.0471 0.8885 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.BH.A0AU.01 6 0.4053 0.6120 0.18 0.00 0.00 0.00 0.00 0.72 0.06 0.04
#> TCGA.A2.A0T1.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A24W.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A0TT.01 4 0.2224 0.7724 0.02 0.00 0.00 0.86 0.00 0.00 0.12 0.00
#> TCGA.AC.A3W6.01 4 0.2025 0.7209 0.00 0.00 0.10 0.88 0.00 0.00 0.02 0.00
#> TCGA.OL.A66P.01 1 0.0471 0.8885 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.AR.A24L.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0H3.01 3 0.3048 0.7324 0.00 0.00 0.84 0.08 0.00 0.02 0.02 0.04
#> TCGA.EW.A1IZ.01 3 0.2569 0.7220 0.02 0.00 0.82 0.16 0.00 0.00 0.00 0.00
#> TCGA.AO.A0JA.01 7 0.2719 0.7970 0.02 0.00 0.00 0.18 0.00 0.00 0.80 0.00
#> TCGA.AR.A0TX.01 6 0.1091 0.8234 0.00 0.00 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.AO.A0JG.01 4 0.2569 0.7246 0.02 0.00 0.00 0.82 0.00 0.00 0.16 0.00
#> TCGA.OL.A66N.01 2 0.0471 0.7939 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.A7.A4SC.01 2 0.0471 0.7959 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.GM.A2DB.01 1 0.0471 0.8885 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.E9.A1N3.01 5 0.3142 0.4658 0.00 0.00 0.00 0.00 0.64 0.36 0.00 0.00
#> TCGA.AN.A0XL.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E9.A24A.01 5 0.0471 0.9553 0.00 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.GM.A2DL.01 2 0.3757 0.5276 0.00 0.68 0.00 0.26 0.00 0.00 0.06 0.00
#> TCGA.E9.A22B.01 8 0.2938 0.9268 0.00 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.A2.A3XV.01 8 0.2938 0.9268 0.00 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.AC.A6IX.06 4 0.1557 0.8078 0.00 0.02 0.00 0.92 0.00 0.00 0.06 0.00
#> TCGA.AC.A6IX.01 2 0.0471 0.7959 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.B6.A0WY.01 1 0.1741 0.8761 0.92 0.00 0.00 0.00 0.00 0.02 0.04 0.02
#> TCGA.E9.A1R4.01 6 0.4155 0.7420 0.02 0.00 0.12 0.00 0.00 0.74 0.02 0.10
#> TCGA.EW.A1J2.01 3 0.2404 0.7281 0.00 0.00 0.84 0.14 0.00 0.00 0.02 0.00
#> TCGA.BH.A0GY.01 1 0.2591 0.8447 0.86 0.00 0.00 0.00 0.00 0.04 0.02 0.08
#> TCGA.W8.A86G.01 3 0.4835 0.4650 0.02 0.00 0.64 0.00 0.00 0.22 0.02 0.10
#> TCGA.A7.A5ZW.01 6 0.1091 0.8234 0.00 0.00 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.C8.A1HF.01 4 0.1275 0.8196 0.00 0.02 0.00 0.94 0.00 0.00 0.04 0.00
#> TCGA.A2.A0T7.01 1 0.1741 0.8756 0.92 0.00 0.00 0.00 0.00 0.02 0.04 0.02
#> TCGA.AO.A0JJ.01 3 0.1557 0.7492 0.00 0.00 0.92 0.06 0.00 0.02 0.00 0.00
#> TCGA.B6.A0X7.01 3 0.3942 0.5533 0.00 0.00 0.62 0.34 0.00 0.00 0.02 0.02
#> TCGA.OL.A5RV.01 6 0.3554 0.7727 0.02 0.00 0.08 0.00 0.00 0.80 0.02 0.08
#> TCGA.E2.A1BC.01 3 0.1947 0.7341 0.00 0.00 0.86 0.14 0.00 0.00 0.00 0.00
#> TCGA.E9.A22D.01 2 0.1765 0.6751 0.00 0.88 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.A1.A0SF.01 4 0.0000 0.8228 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A6SD.01 8 0.7351 -0.2427 0.16 0.00 0.26 0.00 0.00 0.20 0.08 0.30
#> TCGA.A7.A426.01 6 0.1275 0.8167 0.02 0.00 0.04 0.00 0.00 0.94 0.00 0.00
#> TCGA.AR.A1AU.01 3 0.3880 0.5794 0.00 0.00 0.64 0.32 0.00 0.00 0.02 0.02
#> TCGA.E9.A1N6.01 1 0.1275 0.8819 0.94 0.00 0.00 0.00 0.00 0.02 0.04 0.00
#> TCGA.D8.A27L.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E9.A1NF.01 2 0.3660 0.5523 0.00 0.70 0.00 0.24 0.00 0.00 0.06 0.00
#> TCGA.A1.A0SM.01 2 0.1765 0.6751 0.00 0.88 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.LD.A7W5.01 4 0.3570 0.4133 0.00 0.02 0.00 0.62 0.00 0.00 0.36 0.00
#> TCGA.E2.A1LA.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A42V.01 3 0.0471 0.7465 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.E9.A5FK.01 4 0.0471 0.8237 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.D8.A1XB.01 4 0.0000 0.8228 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A227.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A0YL.01 5 0.0808 0.9392 0.00 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.A7.A5ZX.01 3 0.3449 0.5763 0.00 0.00 0.66 0.32 0.00 0.00 0.02 0.00
#> TCGA.D8.A1JG.01 7 0.2025 0.9031 0.00 0.10 0.00 0.02 0.00 0.00 0.88 0.00
#> TCGA.AO.A0JF.01 5 0.0471 0.9553 0.00 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.C8.A8HQ.01 2 0.0471 0.7957 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.AC.A2B8.01 3 0.2569 0.7220 0.02 0.00 0.82 0.16 0.00 0.00 0.00 0.00
#> TCGA.A2.A4S3.01 5 0.0808 0.9395 0.00 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.A2.A0CO.01 3 0.1563 0.7461 0.00 0.00 0.90 0.10 0.00 0.00 0.00 0.00
#> TCGA.BH.A0AZ.01 6 0.1563 0.8028 0.00 0.00 0.00 0.00 0.10 0.90 0.00 0.00
#> TCGA.E2.A1LE.01 2 0.0471 0.7957 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.A2.A0YH.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.LL.A5YN.01 1 0.0471 0.8885 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.AC.A23G.01 3 0.1557 0.7335 0.00 0.00 0.92 0.00 0.00 0.02 0.00 0.06
#> TCGA.GM.A3XN.01 3 0.5093 0.3302 0.02 0.00 0.58 0.00 0.00 0.28 0.02 0.10
#> TCGA.C8.A275.01 2 0.0471 0.7959 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.E2.A1IK.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AQ.A7U7.01 4 0.1557 0.8078 0.00 0.02 0.00 0.92 0.00 0.00 0.06 0.00
#> TCGA.A1.A0SI.01 6 0.5295 0.3615 0.02 0.00 0.36 0.00 0.00 0.50 0.02 0.10
#> TCGA.A2.A25A.01 3 0.0941 0.7444 0.00 0.00 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.E9.A1RH.01 1 0.0471 0.8885 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.AO.A12E.01 2 0.2852 0.2991 0.00 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.A7.A13H.01 6 0.3970 0.7534 0.02 0.00 0.10 0.00 0.00 0.76 0.02 0.10
#> TCGA.E2.A1IO.01 6 0.1091 0.8234 0.00 0.00 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.C8.A26Y.01 1 0.1607 0.8738 0.92 0.00 0.00 0.00 0.00 0.04 0.04 0.00
#> TCGA.A2.A25D.01 4 0.1275 0.8167 0.00 0.02 0.00 0.94 0.00 0.00 0.04 0.00
#> TCGA.AN.A0XW.01 6 0.2114 0.7494 0.00 0.00 0.00 0.00 0.16 0.84 0.00 0.00
#> TCGA.BH.A0AW.01 7 0.1765 0.8723 0.00 0.00 0.00 0.12 0.00 0.00 0.88 0.00
#> TCGA.BH.A0B6.01 3 0.1341 0.7491 0.00 0.00 0.92 0.08 0.00 0.00 0.00 0.00
#> TCGA.E9.A229.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A1JK.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.GM.A5PX.01 3 0.0471 0.7465 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.AR.A5QN.01 8 0.2938 0.9268 0.00 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.BH.A208.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EW.A1IX.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A259.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.GM.A2DD.01 1 0.0471 0.8693 0.98 0.00 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1B1.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A73U.01 3 0.1563 0.7461 0.00 0.00 0.90 0.10 0.00 0.00 0.00 0.00
#> TCGA.D8.A27N.01 2 0.0471 0.7959 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.E9.A22E.01 6 0.1091 0.8234 0.00 0.00 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.OL.A5RX.01 3 0.3942 0.5533 0.00 0.00 0.62 0.34 0.00 0.00 0.02 0.02
#> TCGA.D8.A1XO.01 6 0.4321 0.7272 0.02 0.00 0.14 0.00 0.00 0.72 0.02 0.10
#> TCGA.AC.A23C.01 4 0.0000 0.8228 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A56D.01 1 0.1275 0.8404 0.94 0.00 0.04 0.02 0.00 0.00 0.00 0.00
#> TCGA.A1.A0SH.01 6 0.1091 0.8234 0.00 0.00 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.AR.A5QP.01 4 0.0000 0.8228 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1Y0.01 1 0.0471 0.8885 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.BH.A2L8.01 3 0.3135 0.6990 0.02 0.00 0.82 0.00 0.00 0.02 0.02 0.12
#> TCGA.BH.A202.01 2 0.0471 0.7937 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.EW.A1OV.01 4 0.4105 0.2336 0.02 0.02 0.00 0.54 0.00 0.00 0.42 0.00
#> TCGA.A1.A0SN.01 8 0.2938 0.9268 0.00 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.E9.A295.01 8 0.2938 0.9268 0.00 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.AC.A8OP.01 7 0.2406 0.7644 0.00 0.20 0.00 0.00 0.00 0.00 0.80 0.00
#> TCGA.GI.A2C8.01 2 0.0000 0.8014 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A24P.01 4 0.0471 0.8134 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.BH.A0B2.01 3 0.4137 0.3311 0.00 0.00 0.50 0.46 0.00 0.00 0.02 0.02
#> TCGA.A2.A0SU.01 6 0.1341 0.8159 0.00 0.00 0.00 0.00 0.08 0.92 0.00 0.00
#> TCGA.AR.A24T.01 2 0.1765 0.6751 0.00 0.88 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.AC.A2FE.01 2 0.0000 0.8014 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1N4.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.XX.A899.01 4 0.0471 0.8237 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.E9.A1N9.01 3 0.6523 0.3758 0.00 0.00 0.44 0.24 0.00 0.04 0.08 0.20
#> TCGA.S3.AA17.01 2 0.1563 0.7028 0.00 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.EW.A1PF.01 6 0.1091 0.8012 0.06 0.00 0.00 0.00 0.00 0.94 0.00 0.00
#> TCGA.AO.A03L.01 4 0.1947 0.6859 0.00 0.00 0.14 0.86 0.00 0.00 0.00 0.00
#> TCGA.BH.A0HF.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A2QI.01 5 0.1091 0.9200 0.00 0.00 0.00 0.00 0.94 0.06 0.00 0.00
#> TCGA.A2.A4S2.01 4 0.1275 0.8167 0.00 0.02 0.00 0.94 0.00 0.00 0.04 0.00
#> TCGA.GM.A2DA.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A7.A4SA.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A3KC.01 2 0.0000 0.8014 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A66L.01 2 0.0000 0.8014 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A2LM.01 6 0.5340 0.2418 0.02 0.00 0.40 0.00 0.00 0.46 0.02 0.10
#> TCGA.E2.A10C.01 1 0.0808 0.8525 0.96 0.00 0.04 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AN.01 6 0.2114 0.7491 0.00 0.00 0.00 0.00 0.16 0.84 0.00 0.00
#> TCGA.5L.AAT1.01 4 0.3514 0.4526 0.00 0.02 0.00 0.64 0.00 0.00 0.34 0.00
#> TCGA.HN.A2OB.01 3 0.3763 0.6604 0.02 0.00 0.78 0.00 0.00 0.08 0.02 0.10
#> TCGA.GM.A5PV.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E2.A1IJ.01 3 0.0941 0.7444 0.00 0.00 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.OK.A5Q2.01 2 0.4174 0.2498 0.00 0.54 0.00 0.40 0.00 0.00 0.06 0.00
#> TCGA.E9.A1R3.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A254.01 2 0.1804 0.7387 0.00 0.90 0.00 0.08 0.00 0.00 0.02 0.00
#> TCGA.AR.A0TW.01 7 0.1765 0.8723 0.00 0.00 0.00 0.12 0.00 0.00 0.88 0.00
#> TCGA.BH.A8G0.01 6 0.3763 0.7636 0.02 0.00 0.10 0.00 0.00 0.78 0.02 0.08
#> TCGA.B6.A401.01 3 0.5426 0.5000 0.16 0.00 0.62 0.00 0.00 0.10 0.02 0.10
#> TCGA.E2.A1LB.01 4 0.0000 0.8228 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0W5.01 6 0.1091 0.8234 0.00 0.00 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.AC.A3W7.01 4 0.0471 0.8134 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.AC.A3W5.01 1 0.4686 0.3227 0.56 0.00 0.28 0.16 0.00 0.00 0.00 0.00
#> TCGA.B6.A1KI.01 5 0.3193 0.4171 0.00 0.00 0.00 0.00 0.62 0.38 0.00 0.00
#> TCGA.E9.A1RI.01 3 0.2265 0.7466 0.00 0.00 0.88 0.08 0.00 0.00 0.02 0.02
#> TCGA.A2.A0T6.01 2 0.0471 0.7959 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.EW.A3E8.01 2 0.0000 0.8014 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5RU.01 3 0.3763 0.6594 0.02 0.00 0.78 0.00 0.00 0.08 0.02 0.10
#> TCGA.E2.A10F.01 4 0.2981 0.6500 0.00 0.02 0.00 0.76 0.00 0.00 0.22 0.00
#> TCGA.BH.A0C3.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.B6.A0RV.01 3 0.4125 0.3726 0.00 0.00 0.52 0.44 0.00 0.00 0.02 0.02
#> TCGA.E2.A1IH.01 1 0.5639 0.5671 0.60 0.00 0.16 0.00 0.00 0.04 0.06 0.14
#> TCGA.EW.A1IY.01 3 0.3426 0.6794 0.00 0.00 0.74 0.22 0.00 0.00 0.02 0.02
#> TCGA.AR.A24O.01 6 0.2114 0.7491 0.00 0.00 0.00 0.00 0.16 0.84 0.00 0.00
#> TCGA.C8.A278.01 4 0.3514 0.4526 0.00 0.02 0.00 0.64 0.00 0.00 0.34 0.00
#> TCGA.AC.A3HN.01 6 0.4155 0.7420 0.02 0.00 0.12 0.00 0.00 0.74 0.02 0.10
#> TCGA.AC.A3BB.01 3 0.1341 0.7491 0.00 0.00 0.92 0.08 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FE.01 3 0.0941 0.7444 0.00 0.00 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.A2.A0EN.01 3 0.2404 0.7281 0.00 0.00 0.84 0.14 0.00 0.00 0.02 0.00
#> TCGA.BH.A0BF.01 3 0.2569 0.7220 0.02 0.00 0.82 0.16 0.00 0.00 0.00 0.00
#> TCGA.WT.AB41.01 2 0.4174 0.2554 0.00 0.54 0.00 0.40 0.00 0.00 0.06 0.00
#> TCGA.LL.A5YL.01 8 0.2938 0.9268 0.00 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.AR.A1AK.01 3 0.3942 0.5533 0.00 0.00 0.62 0.34 0.00 0.00 0.02 0.02
#> TCGA.C8.A26X.01 2 0.0000 0.8014 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A3J1.01 3 0.1341 0.7491 0.00 0.00 0.92 0.08 0.00 0.00 0.00 0.00
#> TCGA.D8.A1Y3.01 8 0.2938 0.9268 0.00 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.BH.A0DK.01 8 0.2938 0.9268 0.00 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.D8.A1JE.01 6 0.1275 0.8167 0.02 0.00 0.04 0.00 0.00 0.94 0.00 0.00
#> TCGA.EW.A2FR.01 6 0.5874 0.4365 0.22 0.00 0.02 0.00 0.00 0.54 0.08 0.14
#> TCGA.BH.A0W4.01 6 0.1765 0.7869 0.00 0.00 0.00 0.00 0.12 0.88 0.00 0.00
#> TCGA.BH.A0BJ.01 6 0.1765 0.7876 0.00 0.00 0.00 0.00 0.12 0.88 0.00 0.00
#> TCGA.BH.A203.01 8 0.2938 0.9268 0.00 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.E2.A14U.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A1XM.01 3 0.2680 0.7118 0.00 0.00 0.84 0.00 0.00 0.02 0.02 0.12
#> TCGA.D8.A1JH.01 6 0.4155 0.7420 0.02 0.00 0.12 0.00 0.00 0.74 0.02 0.10
#> TCGA.BH.A1EU.01 6 0.0808 0.8254 0.00 0.00 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.BH.A1FR.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A7.A425.01 6 0.1341 0.8159 0.00 0.00 0.00 0.00 0.08 0.92 0.00 0.00
#> TCGA.B6.A0IK.01 2 0.0000 0.8014 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RF.01 7 0.2025 0.9031 0.00 0.10 0.00 0.02 0.00 0.00 0.88 0.00
#> TCGA.BH.A0HP.01 4 0.0000 0.8228 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A8FZ.01 6 0.1091 0.8234 0.00 0.00 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.AC.A2FG.01 6 0.0808 0.8254 0.00 0.00 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.AR.A1AL.01 6 0.1341 0.8159 0.00 0.00 0.00 0.00 0.08 0.92 0.00 0.00
#> TCGA.BH.A1EO.01 4 0.3862 0.3753 0.00 0.04 0.00 0.60 0.00 0.00 0.36 0.00
#> TCGA.D8.A27K.01 4 0.3303 0.5536 0.00 0.00 0.20 0.76 0.00 0.00 0.02 0.02
#> TCGA.C8.A1HG.01 5 0.1341 0.8989 0.00 0.00 0.00 0.00 0.92 0.08 0.00 0.00
#> TCGA.D8.A1JU.01 6 0.0808 0.8254 0.00 0.00 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.A2.A0YK.01 3 0.3618 0.4886 0.00 0.00 0.60 0.38 0.00 0.00 0.02 0.00
#> TCGA.BH.A0DI.01 2 0.3660 0.5523 0.00 0.70 0.00 0.24 0.00 0.00 0.06 0.00
#> TCGA.E2.A107.01 3 0.3941 0.6246 0.02 0.00 0.68 0.26 0.00 0.00 0.04 0.00
#> TCGA.5L.AAT0.01 6 0.4321 0.7272 0.02 0.00 0.14 0.00 0.00 0.72 0.02 0.10
#> TCGA.D8.A27E.01 5 0.0000 0.9697 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node04. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0115-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0151-leaf , Node0152-leaf , Node0153-leaf , Node0154-leaf , Node0211-leaf , Node0212 , Node0213 , Node0221 , Node0222 , Node0231-leaf , Node0232 , Node0233-leaf , Node0241-leaf , Node0242 , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0331-leaf , Node0332-leaf , Node0341-leaf , Node0342-leaf , Node0343-leaf , Node0411 , Node0412-leaf , Node0413 , Node0421-leaf , Node0422 , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["041"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 117 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.987 0.995 0.4450 0.558 0.558
#> 3 3 1.000 0.992 0.997 0.3924 0.674 0.484
#> 4 4 0.995 0.937 0.977 0.1373 0.873 0.683
#> 5 5 0.788 0.718 0.852 0.0715 0.956 0.854
#> 6 6 0.797 0.747 0.841 0.0436 0.910 0.676
#> 7 7 0.773 0.734 0.789 0.0263 0.956 0.797
#> 8 8 0.764 0.662 0.806 0.0302 0.992 0.955
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2 3
There is also optional best \(k\) = 2 3 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.OL.A66H.01 1 0.000 0.994 1.00 0.00
#> TCGA.AC.A5EH.01 2 0.000 0.996 0.00 1.00
#> TCGA.E9.A1R0.01 2 0.000 0.996 0.00 1.00
#> TCGA.AC.A62Y.01 1 0.000 0.994 1.00 0.00
#> TCGA.AO.A0JD.01 2 0.000 0.996 0.00 1.00
#> TCGA.A7.A3IY.01 1 0.000 0.994 1.00 0.00
#> TCGA.D8.A3Z5.01 1 0.000 0.994 1.00 0.00
#> TCGA.AC.A3QP.01 1 0.000 0.994 1.00 0.00
#> TCGA.GM.A2DK.01 1 0.000 0.994 1.00 0.00
#> TCGA.E2.A1B0.01 2 0.000 0.996 0.00 1.00
#> TCGA.AO.A03M.01 1 0.000 0.994 1.00 0.00
#> TCGA.AR.A2LJ.01 1 0.000 0.994 1.00 0.00
#> TCGA.D8.A1JB.01 1 0.000 0.994 1.00 0.00
#> TCGA.BH.A0BC.01 1 0.000 0.994 1.00 0.00
#> TCGA.D8.A27P.01 1 0.000 0.994 1.00 0.00
#> TCGA.OL.A66J.01 2 0.000 0.996 0.00 1.00
#> TCGA.S3.AA14.01 1 0.000 0.994 1.00 0.00
#> TCGA.B6.A0RS.01 2 0.000 0.996 0.00 1.00
#> TCGA.A2.A1G0.01 1 0.000 0.994 1.00 0.00
#> TCGA.XX.A89A.01 2 0.000 0.996 0.00 1.00
#> TCGA.PE.A5DE.01 2 0.000 0.996 0.00 1.00
#> TCGA.D8.A27V.01 2 0.000 0.996 0.00 1.00
#> TCGA.BH.A0BA.01 2 0.000 0.996 0.00 1.00
#> TCGA.E2.A3DX.01 1 0.000 0.994 1.00 0.00
#> TCGA.A1.A0SE.01 1 0.242 0.954 0.96 0.04
#> TCGA.MS.A51U.01 1 0.000 0.994 1.00 0.00
#> TCGA.D8.A1Y2.01 1 0.000 0.994 1.00 0.00
#> TCGA.E2.A1L6.01 1 0.000 0.994 1.00 0.00
#> TCGA.D8.A1XY.01 2 0.000 0.996 0.00 1.00
#> TCGA.AR.A1AM.01 2 0.000 0.996 0.00 1.00
#> TCGA.AC.A5XS.01 2 0.000 0.996 0.00 1.00
#> TCGA.E2.A1IF.01 1 0.000 0.994 1.00 0.00
#> TCGA.AR.A24S.01 2 0.000 0.996 0.00 1.00
#> TCGA.A2.A3KD.01 1 0.000 0.994 1.00 0.00
#> TCGA.E9.A226.01 1 0.000 0.994 1.00 0.00
#> TCGA.EW.A2FV.01 2 0.000 0.996 0.00 1.00
#> TCGA.BH.A0DV.01 1 0.000 0.994 1.00 0.00
#> TCGA.A2.A0YI.01 1 0.000 0.994 1.00 0.00
#> TCGA.BH.A0BM.01 1 0.000 0.994 1.00 0.00
#> TCGA.D8.A27I.01 1 0.000 0.994 1.00 0.00
#> TCGA.E9.A1NG.01 1 0.971 0.332 0.60 0.40
#> TCGA.C8.A26W.01 2 0.000 0.996 0.00 1.00
#> TCGA.OL.A6VQ.01 1 0.000 0.994 1.00 0.00
#> TCGA.E2.A1LL.01 2 0.000 0.996 0.00 1.00
#> TCGA.BH.A0AU.01 1 0.000 0.994 1.00 0.00
#> TCGA.A2.A0T1.01 2 0.000 0.996 0.00 1.00
#> TCGA.AR.A24W.01 1 0.000 0.994 1.00 0.00
#> TCGA.AR.A24L.01 2 0.000 0.996 0.00 1.00
#> TCGA.AR.A0TX.01 1 0.000 0.994 1.00 0.00
#> TCGA.E9.A1N3.01 1 0.000 0.994 1.00 0.00
#> TCGA.AN.A0XL.01 2 0.000 0.996 0.00 1.00
#> TCGA.E9.A24A.01 1 0.000 0.994 1.00 0.00
#> TCGA.B6.A0WY.01 1 0.000 0.994 1.00 0.00
#> TCGA.E9.A1R4.01 1 0.000 0.994 1.00 0.00
#> TCGA.A7.A5ZW.01 1 0.000 0.994 1.00 0.00
#> TCGA.OL.A5RV.01 1 0.000 0.994 1.00 0.00
#> TCGA.A7.A426.01 2 0.141 0.977 0.02 0.98
#> TCGA.E9.A1N6.01 1 0.000 0.994 1.00 0.00
#> TCGA.D8.A27L.01 2 0.000 0.996 0.00 1.00
#> TCGA.E2.A1LA.01 2 0.000 0.996 0.00 1.00
#> TCGA.E9.A227.01 1 0.000 0.994 1.00 0.00
#> TCGA.A2.A0YL.01 1 0.000 0.994 1.00 0.00
#> TCGA.AO.A0JF.01 1 0.000 0.994 1.00 0.00
#> TCGA.A2.A4S3.01 2 0.529 0.863 0.12 0.88
#> TCGA.BH.A0AZ.01 1 0.000 0.994 1.00 0.00
#> TCGA.A2.A0YH.01 2 0.000 0.996 0.00 1.00
#> TCGA.LL.A5YN.01 2 0.000 0.996 0.00 1.00
#> TCGA.E2.A1IK.01 1 0.000 0.994 1.00 0.00
#> TCGA.A1.A0SI.01 2 0.000 0.996 0.00 1.00
#> TCGA.E9.A1RH.01 2 0.000 0.996 0.00 1.00
#> TCGA.A7.A13H.01 1 0.000 0.994 1.00 0.00
#> TCGA.E2.A1IO.01 1 0.000 0.994 1.00 0.00
#> TCGA.C8.A26Y.01 2 0.000 0.996 0.00 1.00
#> TCGA.AN.A0XW.01 1 0.000 0.994 1.00 0.00
#> TCGA.E9.A229.01 1 0.000 0.994 1.00 0.00
#> TCGA.D8.A1JK.01 2 0.000 0.996 0.00 1.00
#> TCGA.BH.A208.01 2 0.000 0.996 0.00 1.00
#> TCGA.EW.A1IX.01 1 0.000 0.994 1.00 0.00
#> TCGA.A2.A259.01 1 0.000 0.994 1.00 0.00
#> TCGA.E2.A1B1.01 1 0.000 0.994 1.00 0.00
#> TCGA.E9.A22E.01 1 0.000 0.994 1.00 0.00
#> TCGA.D8.A1XO.01 1 0.000 0.994 1.00 0.00
#> TCGA.A1.A0SH.01 1 0.000 0.994 1.00 0.00
#> TCGA.D8.A1Y0.01 1 0.000 0.994 1.00 0.00
#> TCGA.A2.A0SU.01 1 0.000 0.994 1.00 0.00
#> TCGA.E9.A1N4.01 2 0.000 0.996 0.00 1.00
#> TCGA.EW.A1PF.01 1 0.000 0.994 1.00 0.00
#> TCGA.BH.A0HF.01 1 0.000 0.994 1.00 0.00
#> TCGA.AC.A2QI.01 2 0.000 0.996 0.00 1.00
#> TCGA.GM.A2DA.01 2 0.000 0.996 0.00 1.00
#> TCGA.A7.A4SA.01 1 0.327 0.932 0.94 0.06
#> TCGA.AR.A2LM.01 1 0.000 0.994 1.00 0.00
#> TCGA.AR.A1AN.01 1 0.000 0.994 1.00 0.00
#> TCGA.GM.A5PV.01 2 0.000 0.996 0.00 1.00
#> TCGA.E9.A1R3.01 1 0.000 0.994 1.00 0.00
#> TCGA.BH.A8G0.01 1 0.000 0.994 1.00 0.00
#> TCGA.BH.A0W5.01 1 0.000 0.994 1.00 0.00
#> TCGA.B6.A1KI.01 1 0.000 0.994 1.00 0.00
#> TCGA.BH.A0C3.01 1 0.000 0.994 1.00 0.00
#> TCGA.AR.A24O.01 1 0.000 0.994 1.00 0.00
#> TCGA.AC.A3HN.01 1 0.000 0.994 1.00 0.00
#> TCGA.D8.A1JE.01 1 0.000 0.994 1.00 0.00
#> TCGA.EW.A2FR.01 1 0.000 0.994 1.00 0.00
#> TCGA.BH.A0W4.01 1 0.000 0.994 1.00 0.00
#> TCGA.BH.A0BJ.01 1 0.000 0.994 1.00 0.00
#> TCGA.E2.A14U.01 1 0.000 0.994 1.00 0.00
#> TCGA.D8.A1JH.01 1 0.000 0.994 1.00 0.00
#> TCGA.BH.A1EU.01 1 0.000 0.994 1.00 0.00
#> TCGA.BH.A1FR.01 1 0.000 0.994 1.00 0.00
#> TCGA.A7.A425.01 2 0.000 0.996 0.00 1.00
#> TCGA.BH.A8FZ.01 1 0.000 0.994 1.00 0.00
#> TCGA.AC.A2FG.01 2 0.000 0.996 0.00 1.00
#> TCGA.AR.A1AL.01 1 0.000 0.994 1.00 0.00
#> TCGA.C8.A1HG.01 2 0.000 0.996 0.00 1.00
#> TCGA.D8.A1JU.01 1 0.000 0.994 1.00 0.00
#> TCGA.5L.AAT0.01 1 0.000 0.994 1.00 0.00
#> TCGA.D8.A27E.01 1 0.000 0.994 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.OL.A66H.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.AC.A5EH.01 3 0.595 0.437 0 0.36 0.64
#> TCGA.E9.A1R0.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.AC.A62Y.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.AO.A0JD.01 3 0.000 0.979 0 0.00 1.00
#> TCGA.A7.A3IY.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.D8.A3Z5.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.AC.A3QP.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.GM.A2DK.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.E2.A1B0.01 3 0.000 0.979 0 0.00 1.00
#> TCGA.AO.A03M.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.AR.A2LJ.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.D8.A1JB.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.BH.A0BC.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.D8.A27P.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.OL.A66J.01 3 0.000 0.979 0 0.00 1.00
#> TCGA.S3.AA14.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.B6.A0RS.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.A2.A1G0.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.XX.A89A.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.PE.A5DE.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.D8.A27V.01 3 0.000 0.979 0 0.00 1.00
#> TCGA.BH.A0BA.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.E2.A3DX.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.A1.A0SE.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.MS.A51U.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.D8.A1Y2.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.E2.A1L6.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.D8.A1XY.01 3 0.000 0.979 0 0.00 1.00
#> TCGA.AR.A1AM.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.AC.A5XS.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.E2.A1IF.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.AR.A24S.01 3 0.000 0.979 0 0.00 1.00
#> TCGA.A2.A3KD.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.E9.A226.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.EW.A2FV.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.BH.A0DV.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.A2.A0YI.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.BH.A0BM.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.D8.A27I.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.E9.A1NG.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.C8.A26W.01 3 0.000 0.979 0 0.00 1.00
#> TCGA.OL.A6VQ.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.E2.A1LL.01 3 0.000 0.979 0 0.00 1.00
#> TCGA.BH.A0AU.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.A2.A0T1.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.AR.A24W.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.AR.A24L.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.AR.A0TX.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.E9.A1N3.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.AN.A0XL.01 3 0.000 0.979 0 0.00 1.00
#> TCGA.E9.A24A.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.B6.A0WY.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.E9.A1R4.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.A7.A5ZW.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.OL.A5RV.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.A7.A426.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.E9.A1N6.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.D8.A27L.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.E2.A1LA.01 3 0.000 0.979 0 0.00 1.00
#> TCGA.E9.A227.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.A2.A0YL.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.AO.A0JF.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.A2.A4S3.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.BH.A0AZ.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.A2.A0YH.01 3 0.000 0.979 0 0.00 1.00
#> TCGA.LL.A5YN.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.E2.A1IK.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.A1.A0SI.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.E9.A1RH.01 3 0.000 0.979 0 0.00 1.00
#> TCGA.A7.A13H.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.E2.A1IO.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.C8.A26Y.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.AN.A0XW.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.E9.A229.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.D8.A1JK.01 3 0.000 0.979 0 0.00 1.00
#> TCGA.BH.A208.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.EW.A1IX.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.A2.A259.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.E2.A1B1.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.E9.A22E.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.D8.A1XO.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.A1.A0SH.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.D8.A1Y0.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.A2.A0SU.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.E9.A1N4.01 3 0.000 0.979 0 0.00 1.00
#> TCGA.EW.A1PF.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.BH.A0HF.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.AC.A2QI.01 3 0.000 0.979 0 0.00 1.00
#> TCGA.GM.A2DA.01 3 0.000 0.979 0 0.00 1.00
#> TCGA.A7.A4SA.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.AR.A2LM.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.AR.A1AN.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.GM.A5PV.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.E9.A1R3.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.BH.A8G0.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.BH.A0W5.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.B6.A1KI.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.BH.A0C3.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.AR.A24O.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.AC.A3HN.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.D8.A1JE.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.EW.A2FR.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.BH.A0W4.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.BH.A0BJ.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.E2.A14U.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.D8.A1JH.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.BH.A1EU.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.BH.A1FR.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.A7.A425.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.BH.A8FZ.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.AC.A2FG.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.AR.A1AL.01 2 0.000 1.000 0 1.00 0.00
#> TCGA.C8.A1HG.01 3 0.000 0.979 0 0.00 1.00
#> TCGA.D8.A1JU.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.5L.AAT0.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.D8.A27E.01 1 0.000 1.000 1 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.OL.A66H.01 2 0.0000 0.943 0.00 1.00 0.00 0.00
#> TCGA.AC.A5EH.01 4 0.0707 0.946 0.00 0.02 0.00 0.98
#> TCGA.E9.A1R0.01 4 0.0000 0.959 0.00 0.00 0.00 1.00
#> TCGA.AC.A62Y.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.AO.A0JD.01 3 0.0000 0.990 0.00 0.00 1.00 0.00
#> TCGA.A7.A3IY.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.D8.A3Z5.01 2 0.4977 0.150 0.46 0.54 0.00 0.00
#> TCGA.AC.A3QP.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.GM.A2DK.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.E2.A1B0.01 3 0.2921 0.835 0.00 0.00 0.86 0.14
#> TCGA.AO.A03M.01 2 0.0000 0.943 0.00 1.00 0.00 0.00
#> TCGA.AR.A2LJ.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.D8.A1JB.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.BH.A0BC.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.D8.A27P.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.OL.A66J.01 3 0.0000 0.990 0.00 0.00 1.00 0.00
#> TCGA.S3.AA14.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.B6.A0RS.01 4 0.0000 0.959 0.00 0.00 0.00 1.00
#> TCGA.A2.A1G0.01 2 0.0000 0.943 0.00 1.00 0.00 0.00
#> TCGA.XX.A89A.01 4 0.0000 0.959 0.00 0.00 0.00 1.00
#> TCGA.PE.A5DE.01 4 0.0000 0.959 0.00 0.00 0.00 1.00
#> TCGA.D8.A27V.01 3 0.0000 0.990 0.00 0.00 1.00 0.00
#> TCGA.BH.A0BA.01 4 0.0000 0.959 0.00 0.00 0.00 1.00
#> TCGA.E2.A3DX.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.A1.A0SE.01 2 0.0000 0.943 0.00 1.00 0.00 0.00
#> TCGA.MS.A51U.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.D8.A1Y2.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.E2.A1L6.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.D8.A1XY.01 3 0.0000 0.990 0.00 0.00 1.00 0.00
#> TCGA.AR.A1AM.01 2 0.4907 0.206 0.00 0.58 0.00 0.42
#> TCGA.AC.A5XS.01 4 0.0000 0.959 0.00 0.00 0.00 1.00
#> TCGA.E2.A1IF.01 2 0.4277 0.589 0.28 0.72 0.00 0.00
#> TCGA.AR.A24S.01 3 0.0000 0.990 0.00 0.00 1.00 0.00
#> TCGA.A2.A3KD.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.E9.A226.01 2 0.0000 0.943 0.00 1.00 0.00 0.00
#> TCGA.EW.A2FV.01 4 0.0000 0.959 0.00 0.00 0.00 1.00
#> TCGA.BH.A0DV.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.A2.A0YI.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.BH.A0BM.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.D8.A27I.01 2 0.0000 0.943 0.00 1.00 0.00 0.00
#> TCGA.E9.A1NG.01 2 0.0707 0.937 0.00 0.98 0.00 0.02
#> TCGA.C8.A26W.01 3 0.0000 0.990 0.00 0.00 1.00 0.00
#> TCGA.OL.A6VQ.01 1 0.4977 0.104 0.54 0.46 0.00 0.00
#> TCGA.E2.A1LL.01 3 0.0000 0.990 0.00 0.00 1.00 0.00
#> TCGA.BH.A0AU.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.A2.A0T1.01 4 0.0000 0.959 0.00 0.00 0.00 1.00
#> TCGA.AR.A24W.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.AR.A24L.01 4 0.0707 0.946 0.00 0.02 0.00 0.98
#> TCGA.AR.A0TX.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.E9.A1N3.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.AN.A0XL.01 3 0.0000 0.990 0.00 0.00 1.00 0.00
#> TCGA.E9.A24A.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.B6.A0WY.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.E9.A1R4.01 2 0.0707 0.937 0.00 0.98 0.00 0.02
#> TCGA.A7.A5ZW.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.OL.A5RV.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.A7.A426.01 4 0.4855 0.311 0.00 0.40 0.00 0.60
#> TCGA.E9.A1N6.01 2 0.0000 0.943 0.00 1.00 0.00 0.00
#> TCGA.D8.A27L.01 4 0.0000 0.959 0.00 0.00 0.00 1.00
#> TCGA.E2.A1LA.01 3 0.0000 0.990 0.00 0.00 1.00 0.00
#> TCGA.E9.A227.01 2 0.0000 0.943 0.00 1.00 0.00 0.00
#> TCGA.A2.A0YL.01 2 0.0707 0.937 0.00 0.98 0.00 0.02
#> TCGA.AO.A0JF.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.A2.A4S3.01 2 0.1211 0.913 0.00 0.96 0.00 0.04
#> TCGA.BH.A0AZ.01 2 0.0000 0.943 0.00 1.00 0.00 0.00
#> TCGA.A2.A0YH.01 3 0.0000 0.990 0.00 0.00 1.00 0.00
#> TCGA.LL.A5YN.01 4 0.0000 0.959 0.00 0.00 0.00 1.00
#> TCGA.E2.A1IK.01 2 0.0707 0.930 0.02 0.98 0.00 0.00
#> TCGA.A1.A0SI.01 4 0.0000 0.959 0.00 0.00 0.00 1.00
#> TCGA.E9.A1RH.01 3 0.0000 0.990 0.00 0.00 1.00 0.00
#> TCGA.A7.A13H.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.E2.A1IO.01 2 0.0707 0.937 0.00 0.98 0.00 0.02
#> TCGA.C8.A26Y.01 4 0.0707 0.946 0.00 0.02 0.00 0.98
#> TCGA.AN.A0XW.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.E9.A229.01 2 0.0000 0.943 0.00 1.00 0.00 0.00
#> TCGA.D8.A1JK.01 3 0.0000 0.990 0.00 0.00 1.00 0.00
#> TCGA.BH.A208.01 4 0.0000 0.959 0.00 0.00 0.00 1.00
#> TCGA.EW.A1IX.01 2 0.0000 0.943 0.00 1.00 0.00 0.00
#> TCGA.A2.A259.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.E2.A1B1.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.E9.A22E.01 2 0.0000 0.943 0.00 1.00 0.00 0.00
#> TCGA.D8.A1XO.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.A1.A0SH.01 1 0.1637 0.923 0.94 0.06 0.00 0.00
#> TCGA.D8.A1Y0.01 2 0.0000 0.943 0.00 1.00 0.00 0.00
#> TCGA.A2.A0SU.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.E9.A1N4.01 3 0.0000 0.990 0.00 0.00 1.00 0.00
#> TCGA.EW.A1PF.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.BH.A0HF.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.AC.A2QI.01 3 0.0000 0.990 0.00 0.00 1.00 0.00
#> TCGA.GM.A2DA.01 3 0.0000 0.990 0.00 0.00 1.00 0.00
#> TCGA.A7.A4SA.01 2 0.0707 0.937 0.00 0.98 0.00 0.02
#> TCGA.AR.A2LM.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.AR.A1AN.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.GM.A5PV.01 4 0.0000 0.959 0.00 0.00 0.00 1.00
#> TCGA.E9.A1R3.01 2 0.0707 0.937 0.00 0.98 0.00 0.02
#> TCGA.BH.A8G0.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.BH.A0W5.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.B6.A1KI.01 2 0.0000 0.943 0.00 1.00 0.00 0.00
#> TCGA.BH.A0C3.01 2 0.0000 0.943 0.00 1.00 0.00 0.00
#> TCGA.AR.A24O.01 2 0.0000 0.943 0.00 1.00 0.00 0.00
#> TCGA.AC.A3HN.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.D8.A1JE.01 2 0.0707 0.937 0.00 0.98 0.00 0.02
#> TCGA.EW.A2FR.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.BH.A0W4.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.BH.A0BJ.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.E2.A14U.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.D8.A1JH.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.BH.A1EU.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.BH.A1FR.01 2 0.0000 0.943 0.00 1.00 0.00 0.00
#> TCGA.A7.A425.01 4 0.0707 0.942 0.00 0.02 0.00 0.98
#> TCGA.BH.A8FZ.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.AC.A2FG.01 4 0.0000 0.959 0.00 0.00 0.00 1.00
#> TCGA.AR.A1AL.01 2 0.0707 0.937 0.00 0.98 0.00 0.02
#> TCGA.C8.A1HG.01 4 0.3610 0.728 0.00 0.00 0.20 0.80
#> TCGA.D8.A1JU.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
#> TCGA.5L.AAT0.01 2 0.0707 0.930 0.02 0.98 0.00 0.00
#> TCGA.D8.A27E.01 1 0.0000 0.988 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.OL.A66H.01 2 0.2929 0.723 0.00 0.82 0.00 0.00 0.18
#> TCGA.AC.A5EH.01 4 0.4262 0.710 0.00 0.00 0.00 0.56 0.44
#> TCGA.E9.A1R0.01 4 0.1043 0.840 0.00 0.00 0.00 0.96 0.04
#> TCGA.AC.A62Y.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A0JD.01 3 0.0000 0.970 0.00 0.00 1.00 0.00 0.00
#> TCGA.A7.A3IY.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A3Z5.01 5 0.6548 0.765 0.20 0.38 0.00 0.00 0.42
#> TCGA.AC.A3QP.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A2DK.01 1 0.4126 0.144 0.62 0.00 0.00 0.00 0.38
#> TCGA.E2.A1B0.01 3 0.4726 0.307 0.00 0.00 0.58 0.40 0.02
#> TCGA.AO.A03M.01 2 0.2516 0.733 0.00 0.86 0.00 0.00 0.14
#> TCGA.AR.A2LJ.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JB.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BC.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A27P.01 1 0.4767 -0.125 0.56 0.02 0.00 0.00 0.42
#> TCGA.OL.A66J.01 3 0.0000 0.970 0.00 0.00 1.00 0.00 0.00
#> TCGA.S3.AA14.01 1 0.5673 -0.380 0.50 0.08 0.00 0.00 0.42
#> TCGA.B6.A0RS.01 4 0.0000 0.835 0.00 0.00 0.00 1.00 0.00
#> TCGA.A2.A1G0.01 2 0.0609 0.734 0.00 0.98 0.00 0.00 0.02
#> TCGA.XX.A89A.01 4 0.1043 0.840 0.00 0.00 0.00 0.96 0.04
#> TCGA.PE.A5DE.01 4 0.0000 0.835 0.00 0.00 0.00 1.00 0.00
#> TCGA.D8.A27V.01 3 0.0000 0.970 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A0BA.01 4 0.1043 0.840 0.00 0.00 0.00 0.96 0.04
#> TCGA.E2.A3DX.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.A1.A0SE.01 2 0.2280 0.746 0.00 0.88 0.00 0.12 0.00
#> TCGA.MS.A51U.01 1 0.4060 0.219 0.64 0.00 0.00 0.00 0.36
#> TCGA.D8.A1Y2.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1L6.01 1 0.4060 0.219 0.64 0.00 0.00 0.00 0.36
#> TCGA.D8.A1XY.01 3 0.0000 0.970 0.00 0.00 1.00 0.00 0.00
#> TCGA.AR.A1AM.01 2 0.5156 0.552 0.00 0.62 0.00 0.06 0.32
#> TCGA.AC.A5XS.01 4 0.2020 0.827 0.00 0.00 0.00 0.90 0.10
#> TCGA.E2.A1IF.01 5 0.6459 0.722 0.18 0.40 0.00 0.00 0.42
#> TCGA.AR.A24S.01 3 0.0000 0.970 0.00 0.00 1.00 0.00 0.00
#> TCGA.A2.A3KD.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A226.01 2 0.1043 0.744 0.00 0.96 0.00 0.00 0.04
#> TCGA.EW.A2FV.01 4 0.4262 0.710 0.00 0.00 0.00 0.56 0.44
#> TCGA.BH.A0DV.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0YI.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BM.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A27I.01 2 0.1732 0.699 0.00 0.92 0.00 0.00 0.08
#> TCGA.E9.A1NG.01 2 0.3274 0.711 0.00 0.78 0.00 0.22 0.00
#> TCGA.C8.A26W.01 3 0.0000 0.970 0.00 0.00 1.00 0.00 0.00
#> TCGA.OL.A6VQ.01 5 0.6671 0.808 0.24 0.34 0.00 0.00 0.42
#> TCGA.E2.A1LL.01 3 0.0000 0.970 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A0AU.01 1 0.5131 -0.213 0.54 0.04 0.00 0.00 0.42
#> TCGA.A2.A0T1.01 4 0.1732 0.782 0.00 0.08 0.00 0.92 0.00
#> TCGA.AR.A24W.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A24L.01 4 0.4262 0.710 0.00 0.00 0.00 0.56 0.44
#> TCGA.AR.A0TX.01 1 0.4060 0.219 0.64 0.00 0.00 0.00 0.36
#> TCGA.E9.A1N3.01 5 0.6275 0.746 0.30 0.18 0.00 0.00 0.52
#> TCGA.AN.A0XL.01 3 0.0000 0.970 0.00 0.00 1.00 0.00 0.00
#> TCGA.E9.A24A.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0WY.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1R4.01 2 0.3274 0.711 0.00 0.78 0.00 0.22 0.00
#> TCGA.A7.A5ZW.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5RV.01 1 0.4060 0.219 0.64 0.00 0.00 0.00 0.36
#> TCGA.A7.A426.01 2 0.5297 0.479 0.00 0.58 0.00 0.36 0.06
#> TCGA.E9.A1N6.01 2 0.3424 0.685 0.00 0.76 0.00 0.00 0.24
#> TCGA.D8.A27L.01 4 0.0609 0.839 0.00 0.00 0.00 0.98 0.02
#> TCGA.E2.A1LA.01 3 0.0000 0.970 0.00 0.00 1.00 0.00 0.00
#> TCGA.E9.A227.01 2 0.1732 0.748 0.00 0.92 0.00 0.08 0.00
#> TCGA.A2.A0YL.01 2 0.2732 0.734 0.00 0.84 0.00 0.16 0.00
#> TCGA.AO.A0JF.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A4S3.01 2 0.4126 0.581 0.00 0.62 0.00 0.00 0.38
#> TCGA.BH.A0AZ.01 2 0.1732 0.699 0.00 0.92 0.00 0.00 0.08
#> TCGA.A2.A0YH.01 3 0.0000 0.970 0.00 0.00 1.00 0.00 0.00
#> TCGA.LL.A5YN.01 4 0.5783 0.646 0.00 0.10 0.00 0.54 0.36
#> TCGA.E2.A1IK.01 2 0.4829 -0.294 0.02 0.50 0.00 0.00 0.48
#> TCGA.A1.A0SI.01 4 0.0000 0.835 0.00 0.00 0.00 1.00 0.00
#> TCGA.E9.A1RH.01 3 0.0000 0.970 0.00 0.00 1.00 0.00 0.00
#> TCGA.A7.A13H.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1IO.01 2 0.2732 0.733 0.00 0.84 0.00 0.16 0.00
#> TCGA.C8.A26Y.01 4 0.4302 0.684 0.00 0.00 0.00 0.52 0.48
#> TCGA.AN.A0XW.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A229.01 2 0.1043 0.744 0.00 0.96 0.00 0.00 0.04
#> TCGA.D8.A1JK.01 3 0.0000 0.970 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A208.01 4 0.1043 0.840 0.00 0.00 0.00 0.96 0.04
#> TCGA.EW.A1IX.01 2 0.3731 0.728 0.00 0.80 0.00 0.04 0.16
#> TCGA.A2.A259.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1B1.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A22E.01 2 0.3983 0.626 0.00 0.66 0.00 0.00 0.34
#> TCGA.D8.A1XO.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.A1.A0SH.01 5 0.6705 0.802 0.32 0.26 0.00 0.00 0.42
#> TCGA.D8.A1Y0.01 2 0.1732 0.741 0.00 0.92 0.00 0.00 0.08
#> TCGA.A2.A0SU.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1N4.01 3 0.0609 0.951 0.00 0.00 0.98 0.02 0.00
#> TCGA.EW.A1PF.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0HF.01 1 0.5425 -0.297 0.52 0.06 0.00 0.00 0.42
#> TCGA.AC.A2QI.01 3 0.0000 0.970 0.00 0.00 1.00 0.00 0.00
#> TCGA.GM.A2DA.01 3 0.0000 0.970 0.00 0.00 1.00 0.00 0.00
#> TCGA.A7.A4SA.01 2 0.3274 0.711 0.00 0.78 0.00 0.22 0.00
#> TCGA.AR.A2LM.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AN.01 1 0.3109 0.601 0.80 0.00 0.00 0.00 0.20
#> TCGA.GM.A5PV.01 4 0.5083 0.631 0.00 0.16 0.00 0.70 0.14
#> TCGA.E9.A1R3.01 2 0.3274 0.711 0.00 0.78 0.00 0.22 0.00
#> TCGA.BH.A8G0.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0W5.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A1KI.01 2 0.1732 0.699 0.00 0.92 0.00 0.00 0.08
#> TCGA.BH.A0C3.01 2 0.1043 0.744 0.00 0.96 0.00 0.00 0.04
#> TCGA.AR.A24O.01 2 0.1732 0.699 0.00 0.92 0.00 0.00 0.08
#> TCGA.AC.A3HN.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JE.01 2 0.3274 0.711 0.00 0.78 0.00 0.22 0.00
#> TCGA.EW.A2FR.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0W4.01 5 0.6548 0.696 0.38 0.20 0.00 0.00 0.42
#> TCGA.BH.A0BJ.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A14U.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JH.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1EU.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FR.01 2 0.2516 0.710 0.00 0.86 0.00 0.00 0.14
#> TCGA.A7.A425.01 4 0.1043 0.815 0.00 0.04 0.00 0.96 0.00
#> TCGA.BH.A8FZ.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A2FG.01 4 0.0000 0.835 0.00 0.00 0.00 1.00 0.00
#> TCGA.AR.A1AL.01 2 0.5673 -0.163 0.00 0.50 0.00 0.08 0.42
#> TCGA.C8.A1HG.01 4 0.6327 0.581 0.00 0.00 0.20 0.52 0.28
#> TCGA.D8.A1JU.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
#> TCGA.5L.AAT0.01 2 0.5673 -0.439 0.08 0.50 0.00 0.00 0.42
#> TCGA.D8.A27E.01 1 0.0000 0.874 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.OL.A66H.01 2 0.4380 0.5788 0.00 0.70 0.00 0.00 0.22 0.08
#> TCGA.AC.A5EH.01 6 0.2454 0.9284 0.00 0.00 0.00 0.16 0.00 0.84
#> TCGA.E9.A1R0.01 4 0.2631 0.5877 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.AC.A62Y.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AO.A0JD.01 3 0.0000 0.9860 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A7.A3IY.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A3Z5.01 5 0.2728 0.5511 0.04 0.10 0.00 0.00 0.86 0.00
#> TCGA.AC.A3QP.01 1 0.0547 0.9648 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.GM.A2DK.01 5 0.4873 0.5501 0.42 0.00 0.00 0.00 0.52 0.06
#> TCGA.E2.A1B0.01 4 0.5371 0.1107 0.00 0.00 0.36 0.52 0.00 0.12
#> TCGA.AO.A03M.01 2 0.3045 0.6439 0.00 0.84 0.00 0.00 0.10 0.06
#> TCGA.AR.A2LJ.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JB.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BC.01 1 0.0547 0.9648 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.D8.A27P.01 5 0.4806 0.6048 0.38 0.00 0.00 0.00 0.56 0.06
#> TCGA.OL.A66J.01 3 0.0000 0.9860 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S3.AA14.01 5 0.4067 0.6650 0.26 0.00 0.00 0.00 0.70 0.04
#> TCGA.B6.A0RS.01 4 0.0547 0.6652 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.A2.A1G0.01 2 0.3309 0.6668 0.00 0.72 0.00 0.00 0.28 0.00
#> TCGA.XX.A89A.01 4 0.2631 0.5877 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.PE.A5DE.01 4 0.1092 0.6643 0.00 0.02 0.00 0.96 0.00 0.02
#> TCGA.D8.A27V.01 3 0.0000 0.9860 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0BA.01 4 0.2631 0.5877 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.E2.A3DX.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A1.A0SE.01 2 0.4737 0.6056 0.00 0.68 0.00 0.16 0.16 0.00
#> TCGA.MS.A51U.01 5 0.4873 0.5501 0.42 0.00 0.00 0.00 0.52 0.06
#> TCGA.D8.A1Y2.01 1 0.0547 0.9648 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.E2.A1L6.01 5 0.4873 0.5501 0.42 0.00 0.00 0.00 0.52 0.06
#> TCGA.D8.A1XY.01 3 0.0000 0.9860 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A1AM.01 2 0.4067 0.4933 0.00 0.70 0.00 0.04 0.00 0.26
#> TCGA.AC.A5XS.01 4 0.2631 0.5877 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.E2.A1IF.01 5 0.2094 0.5219 0.02 0.08 0.00 0.00 0.90 0.00
#> TCGA.AR.A24S.01 3 0.0000 0.9860 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A3KD.01 1 0.0937 0.9421 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.E9.A226.01 2 0.2790 0.6575 0.00 0.84 0.00 0.00 0.14 0.02
#> TCGA.EW.A2FV.01 6 0.2454 0.9284 0.00 0.00 0.00 0.16 0.00 0.84
#> TCGA.BH.A0DV.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0YI.01 1 0.0547 0.9648 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.BH.A0BM.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A27I.01 2 0.4282 0.5904 0.00 0.56 0.00 0.02 0.42 0.00
#> TCGA.E9.A1NG.01 2 0.5354 0.5338 0.00 0.58 0.00 0.26 0.16 0.00
#> TCGA.C8.A26W.01 3 0.1092 0.9561 0.00 0.00 0.96 0.02 0.00 0.02
#> TCGA.OL.A6VQ.01 5 0.3258 0.5542 0.04 0.10 0.00 0.00 0.84 0.02
#> TCGA.E2.A1LL.01 3 0.1092 0.9561 0.00 0.00 0.96 0.02 0.00 0.02
#> TCGA.BH.A0AU.01 5 0.4552 0.6647 0.30 0.00 0.00 0.00 0.64 0.06
#> TCGA.A2.A0T1.01 4 0.3156 0.5676 0.00 0.18 0.00 0.80 0.02 0.00
#> TCGA.AR.A24W.01 1 0.0547 0.9613 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.AR.A24L.01 6 0.2454 0.9284 0.00 0.00 0.00 0.16 0.00 0.84
#> TCGA.AR.A0TX.01 5 0.4282 0.5546 0.42 0.00 0.00 0.00 0.56 0.02
#> TCGA.E9.A1N3.01 5 0.4265 0.4729 0.02 0.14 0.00 0.00 0.76 0.08
#> TCGA.AN.A0XL.01 3 0.0000 0.9860 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E9.A24A.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0WY.01 1 0.1267 0.9289 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.E9.A1R4.01 2 0.5354 0.5338 0.00 0.58 0.00 0.26 0.16 0.00
#> TCGA.A7.A5ZW.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5RV.01 5 0.4873 0.5501 0.42 0.00 0.00 0.00 0.52 0.06
#> TCGA.A7.A426.01 2 0.4873 0.2857 0.00 0.52 0.00 0.42 0.06 0.00
#> TCGA.E9.A1N6.01 2 0.3156 0.5779 0.00 0.80 0.00 0.00 0.02 0.18
#> TCGA.D8.A27L.01 4 0.3544 0.6305 0.00 0.12 0.00 0.80 0.00 0.08
#> TCGA.E2.A1LA.01 3 0.0000 0.9860 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E9.A227.01 2 0.5039 0.5987 0.00 0.64 0.00 0.18 0.18 0.00
#> TCGA.A2.A0YL.01 2 0.5259 0.5517 0.00 0.60 0.00 0.24 0.16 0.00
#> TCGA.AO.A0JF.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A4S3.01 2 0.3198 0.5004 0.00 0.74 0.00 0.00 0.00 0.26
#> TCGA.BH.A0AZ.01 2 0.3578 0.6321 0.00 0.66 0.00 0.00 0.34 0.00
#> TCGA.A2.A0YH.01 3 0.0000 0.9860 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.LL.A5YN.01 4 0.6380 0.0943 0.00 0.24 0.00 0.44 0.02 0.30
#> TCGA.E2.A1IK.01 5 0.1865 0.4877 0.00 0.04 0.00 0.00 0.92 0.04
#> TCGA.A1.A0SI.01 4 0.0547 0.6652 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.E9.A1RH.01 3 0.0000 0.9860 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A7.A13H.01 1 0.1480 0.9227 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.E2.A1IO.01 2 0.5354 0.5338 0.00 0.58 0.00 0.26 0.16 0.00
#> TCGA.C8.A26Y.01 6 0.2581 0.8768 0.00 0.02 0.00 0.12 0.00 0.86
#> TCGA.AN.A0XW.01 1 0.2190 0.8773 0.90 0.00 0.00 0.00 0.04 0.06
#> TCGA.E9.A229.01 2 0.3163 0.6511 0.00 0.82 0.00 0.00 0.14 0.04
#> TCGA.D8.A1JK.01 3 0.0000 0.9860 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A208.01 4 0.2631 0.5877 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.EW.A1IX.01 2 0.1267 0.6409 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.A2.A259.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1B1.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A22E.01 2 0.3076 0.5166 0.00 0.76 0.00 0.00 0.00 0.24
#> TCGA.D8.A1XO.01 1 0.0547 0.9648 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.A1.A0SH.01 5 0.2728 0.6149 0.10 0.04 0.00 0.00 0.86 0.00
#> TCGA.D8.A1Y0.01 2 0.3045 0.6439 0.00 0.84 0.00 0.00 0.10 0.06
#> TCGA.A2.A0SU.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1N4.01 3 0.2094 0.8874 0.00 0.00 0.90 0.02 0.00 0.08
#> TCGA.EW.A1PF.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0HF.01 5 0.4199 0.6097 0.38 0.00 0.00 0.00 0.60 0.02
#> TCGA.AC.A2QI.01 3 0.0000 0.9860 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.GM.A2DA.01 3 0.0000 0.9860 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A7.A4SA.01 2 0.5354 0.5338 0.00 0.58 0.00 0.26 0.16 0.00
#> TCGA.AR.A2LM.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AN.01 1 0.3819 0.4029 0.70 0.00 0.00 0.00 0.28 0.02
#> TCGA.GM.A5PV.01 4 0.5302 0.1585 0.00 0.36 0.00 0.56 0.04 0.04
#> TCGA.E9.A1R3.01 2 0.5354 0.5338 0.00 0.58 0.00 0.26 0.16 0.00
#> TCGA.BH.A8G0.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0W5.01 1 0.0547 0.9648 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.B6.A1KI.01 2 0.3756 0.5693 0.00 0.60 0.00 0.00 0.40 0.00
#> TCGA.BH.A0C3.01 2 0.3156 0.6662 0.00 0.80 0.00 0.00 0.18 0.02
#> TCGA.AR.A24O.01 2 0.3309 0.6594 0.00 0.72 0.00 0.00 0.28 0.00
#> TCGA.AC.A3HN.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JE.01 2 0.5354 0.5338 0.00 0.58 0.00 0.26 0.16 0.00
#> TCGA.EW.A2FR.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0W4.01 5 0.2981 0.6485 0.16 0.02 0.00 0.00 0.82 0.00
#> TCGA.BH.A0BJ.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A14U.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JH.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1EU.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FR.01 2 0.4552 0.5675 0.00 0.64 0.00 0.00 0.30 0.06
#> TCGA.A7.A425.01 4 0.2981 0.5867 0.00 0.16 0.00 0.82 0.02 0.00
#> TCGA.BH.A8FZ.01 1 0.0547 0.9648 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.AC.A2FG.01 4 0.1814 0.6323 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.AR.A1AL.01 5 0.4067 0.2142 0.00 0.26 0.00 0.04 0.70 0.00
#> TCGA.C8.A1HG.01 6 0.4165 0.7984 0.00 0.00 0.10 0.16 0.00 0.74
#> TCGA.D8.A1JU.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5L.AAT0.01 5 0.1556 0.4865 0.00 0.08 0.00 0.00 0.92 0.00
#> TCGA.D8.A27E.01 1 0.0000 0.9751 1.00 0.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.OL.A66H.01 7 0.5373 0.5738 0.00 0.14 0.00 0.00 0.12 0.10 0.64
#> TCGA.AC.A5EH.01 6 0.3745 0.9198 0.00 0.00 0.00 0.26 0.00 0.70 0.04
#> TCGA.E9.A1R0.01 4 0.0504 0.7352 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.AC.A62Y.01 1 0.0863 0.9221 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.AO.A0JD.01 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A3IY.01 1 0.1166 0.9196 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.D8.A3Z5.01 5 0.3494 0.6841 0.06 0.12 0.00 0.00 0.80 0.02 0.00
#> TCGA.AC.A3QP.01 1 0.1505 0.9100 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.GM.A2DK.01 5 0.4795 0.7300 0.28 0.00 0.00 0.00 0.62 0.08 0.02
#> TCGA.E2.A1B0.01 4 0.3863 0.4305 0.00 0.00 0.20 0.74 0.04 0.00 0.02
#> TCGA.AO.A03M.01 7 0.2945 0.7665 0.00 0.26 0.00 0.00 0.00 0.00 0.74
#> TCGA.AR.A2LJ.01 1 0.1166 0.9196 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.D8.A1JB.01 1 0.1166 0.9196 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.BH.A0BC.01 1 0.1505 0.9100 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.D8.A27P.01 5 0.4377 0.7528 0.24 0.00 0.00 0.00 0.68 0.06 0.02
#> TCGA.OL.A66J.01 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S3.AA14.01 5 0.3388 0.7575 0.20 0.00 0.00 0.00 0.76 0.04 0.00
#> TCGA.B6.A0RS.01 4 0.4589 0.7187 0.00 0.22 0.00 0.68 0.06 0.00 0.04
#> TCGA.A2.A1G0.01 2 0.5281 0.1261 0.00 0.60 0.00 0.00 0.08 0.06 0.26
#> TCGA.XX.A89A.01 4 0.1006 0.7279 0.00 0.02 0.00 0.96 0.02 0.00 0.00
#> TCGA.PE.A5DE.01 4 0.2708 0.7491 0.00 0.22 0.00 0.78 0.00 0.00 0.00
#> TCGA.D8.A27V.01 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BA.01 4 0.0504 0.7352 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.E2.A3DX.01 1 0.1006 0.9178 0.96 0.00 0.00 0.00 0.02 0.02 0.00
#> TCGA.A1.A0SE.01 2 0.2569 0.5003 0.00 0.84 0.00 0.00 0.00 0.02 0.14
#> TCGA.MS.A51U.01 5 0.4718 0.6853 0.32 0.00 0.00 0.00 0.60 0.06 0.02
#> TCGA.D8.A1Y2.01 1 0.1505 0.9100 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.E2.A1L6.01 5 0.4649 0.7157 0.30 0.00 0.00 0.00 0.62 0.06 0.02
#> TCGA.D8.A1XY.01 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AM.01 7 0.3606 0.7379 0.00 0.30 0.00 0.00 0.00 0.02 0.68
#> TCGA.AC.A5XS.01 4 0.0504 0.7352 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.E2.A1IF.01 5 0.3494 0.6841 0.06 0.12 0.00 0.00 0.80 0.02 0.00
#> TCGA.AR.A24S.01 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A3KD.01 1 0.1433 0.9059 0.92 0.00 0.00 0.00 0.00 0.08 0.00
#> TCGA.E9.A226.01 7 0.4795 0.6764 0.00 0.28 0.00 0.00 0.02 0.08 0.62
#> TCGA.EW.A2FV.01 6 0.4305 0.9068 0.00 0.00 0.00 0.28 0.02 0.66 0.04
#> TCGA.BH.A0DV.01 1 0.1006 0.9178 0.96 0.00 0.00 0.00 0.02 0.02 0.00
#> TCGA.A2.A0YI.01 1 0.1505 0.9100 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.BH.A0BM.01 1 0.0863 0.9225 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.D8.A27I.01 2 0.4969 0.3846 0.00 0.66 0.00 0.00 0.20 0.06 0.08
#> TCGA.E9.A1NG.01 2 0.0504 0.6026 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.C8.A26W.01 3 0.1928 0.9038 0.00 0.00 0.90 0.08 0.00 0.00 0.02
#> TCGA.OL.A6VQ.01 5 0.3879 0.7073 0.08 0.10 0.00 0.00 0.78 0.04 0.00
#> TCGA.E2.A1LL.01 3 0.1928 0.9038 0.00 0.00 0.90 0.08 0.00 0.00 0.02
#> TCGA.BH.A0AU.01 5 0.4708 0.7421 0.26 0.00 0.00 0.00 0.64 0.08 0.02
#> TCGA.A2.A0T1.01 2 0.3459 -0.1063 0.00 0.60 0.00 0.40 0.00 0.00 0.00
#> TCGA.AR.A24W.01 1 0.1166 0.9179 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.AR.A24L.01 6 0.3745 0.9198 0.00 0.00 0.00 0.26 0.00 0.70 0.04
#> TCGA.AR.A0TX.01 5 0.3984 0.7363 0.28 0.00 0.00 0.00 0.68 0.02 0.02
#> TCGA.E9.A1N3.01 5 0.5868 0.4137 0.08 0.00 0.00 0.00 0.56 0.20 0.16
#> TCGA.AN.A0XL.01 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A24A.01 1 0.1166 0.9196 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.B6.A0WY.01 1 0.2159 0.8862 0.90 0.00 0.00 0.00 0.02 0.06 0.02
#> TCGA.E9.A1R4.01 2 0.0000 0.6095 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A5ZW.01 1 0.1166 0.9196 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.OL.A5RV.01 5 0.4718 0.6853 0.32 0.00 0.00 0.00 0.60 0.06 0.02
#> TCGA.A7.A426.01 2 0.3867 0.4026 0.00 0.74 0.00 0.14 0.00 0.00 0.12
#> TCGA.E9.A1N6.01 7 0.2422 0.7484 0.00 0.18 0.00 0.00 0.00 0.00 0.82
#> TCGA.D8.A27L.01 4 0.2572 0.6970 0.00 0.20 0.00 0.80 0.00 0.00 0.00
#> TCGA.E2.A1LA.01 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A227.01 2 0.1006 0.5959 0.00 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.A2.A0YL.01 2 0.0504 0.6035 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.AO.A0JF.01 1 0.1006 0.9178 0.96 0.00 0.00 0.00 0.02 0.02 0.00
#> TCGA.A2.A4S3.01 7 0.2708 0.7564 0.00 0.22 0.00 0.00 0.00 0.00 0.78
#> TCGA.BH.A0AZ.01 2 0.5922 0.1373 0.00 0.52 0.00 0.00 0.16 0.06 0.26
#> TCGA.A2.A0YH.01 3 0.0504 0.9608 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.LL.A5YN.01 2 0.5619 -0.0864 0.00 0.38 0.00 0.32 0.00 0.00 0.30
#> TCGA.E2.A1IK.01 5 0.4145 0.5198 0.00 0.10 0.00 0.00 0.74 0.14 0.02
#> TCGA.A1.A0SI.01 4 0.2708 0.7491 0.00 0.22 0.00 0.78 0.00 0.00 0.00
#> TCGA.E9.A1RH.01 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A13H.01 1 0.2159 0.8761 0.90 0.00 0.00 0.00 0.06 0.02 0.02
#> TCGA.E2.A1IO.01 2 0.0000 0.6095 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A26Y.01 6 0.5086 0.7959 0.00 0.00 0.00 0.16 0.02 0.62 0.20
#> TCGA.AN.A0XW.01 1 0.3289 0.7755 0.82 0.00 0.00 0.00 0.10 0.06 0.02
#> TCGA.E9.A229.01 7 0.4524 0.6638 0.00 0.34 0.00 0.00 0.02 0.04 0.60
#> TCGA.D8.A1JK.01 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A208.01 4 0.1363 0.7170 0.00 0.02 0.00 0.94 0.04 0.00 0.00
#> TCGA.EW.A1IX.01 7 0.3139 0.7483 0.00 0.30 0.00 0.00 0.00 0.00 0.70
#> TCGA.A2.A259.01 1 0.1166 0.9196 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.E2.A1B1.01 1 0.1166 0.9196 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.E9.A22E.01 7 0.2745 0.7313 0.00 0.16 0.00 0.00 0.00 0.02 0.82
#> TCGA.D8.A1XO.01 1 0.1505 0.9100 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.A1.A0SH.01 5 0.3011 0.6968 0.06 0.12 0.00 0.00 0.82 0.00 0.00
#> TCGA.D8.A1Y0.01 7 0.2945 0.7665 0.00 0.26 0.00 0.00 0.00 0.00 0.74
#> TCGA.A2.A0SU.01 1 0.1166 0.9196 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.E9.A1N4.01 3 0.2745 0.8108 0.00 0.00 0.82 0.16 0.00 0.00 0.02
#> TCGA.EW.A1PF.01 1 0.1006 0.9177 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.BH.A0HF.01 5 0.3661 0.7573 0.22 0.00 0.00 0.00 0.74 0.02 0.02
#> TCGA.AC.A2QI.01 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A2DA.01 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A4SA.01 2 0.0504 0.6026 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.AR.A2LM.01 1 0.1006 0.9244 0.96 0.00 0.00 0.00 0.02 0.02 0.00
#> TCGA.AR.A1AN.01 1 0.4212 0.2319 0.62 0.00 0.00 0.00 0.34 0.02 0.02
#> TCGA.GM.A5PV.01 2 0.3770 0.4129 0.00 0.74 0.00 0.18 0.00 0.00 0.08
#> TCGA.E9.A1R3.01 2 0.0000 0.6095 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A8G0.01 1 0.0000 0.9238 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0W5.01 1 0.1505 0.9100 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.B6.A1KI.01 2 0.5961 0.1593 0.00 0.52 0.00 0.00 0.18 0.06 0.24
#> TCGA.BH.A0C3.01 2 0.5577 -0.1665 0.00 0.50 0.00 0.00 0.08 0.06 0.36
#> TCGA.AR.A24O.01 2 0.5922 0.1373 0.00 0.52 0.00 0.00 0.16 0.06 0.26
#> TCGA.AC.A3HN.01 1 0.1166 0.9196 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.D8.A1JE.01 2 0.1363 0.5846 0.00 0.94 0.00 0.00 0.02 0.00 0.04
#> TCGA.EW.A2FR.01 1 0.1505 0.9100 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.BH.A0W4.01 5 0.3011 0.7341 0.12 0.06 0.00 0.00 0.82 0.00 0.00
#> TCGA.BH.A0BJ.01 1 0.1166 0.9196 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.E2.A14U.01 1 0.1166 0.9196 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.D8.A1JH.01 1 0.1166 0.9196 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.BH.A1EU.01 1 0.0000 0.9238 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1FR.01 7 0.6805 0.1876 0.00 0.24 0.00 0.00 0.20 0.16 0.40
#> TCGA.A7.A425.01 4 0.4524 0.6246 0.00 0.34 0.00 0.60 0.02 0.00 0.04
#> TCGA.BH.A8FZ.01 1 0.1505 0.9100 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.AC.A2FG.01 4 0.3139 0.6971 0.00 0.30 0.00 0.70 0.00 0.00 0.00
#> TCGA.AR.A1AL.01 2 0.3943 0.2195 0.00 0.56 0.00 0.00 0.42 0.02 0.00
#> TCGA.C8.A1HG.01 6 0.3841 0.8768 0.00 0.00 0.04 0.28 0.00 0.68 0.00
#> TCGA.D8.A1JU.01 1 0.0504 0.9219 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.5L.AAT0.01 5 0.3386 0.5861 0.02 0.18 0.00 0.00 0.78 0.02 0.00
#> TCGA.D8.A27E.01 1 0.1166 0.9196 0.94 0.00 0.00 0.00 0.00 0.06 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.OL.A66H.01 7 0.4403 -0.1688 0.00 0.08 0.00 0.00 0.00 0.00 0.48 0.44
#> TCGA.AC.A5EH.01 6 0.2224 0.9244 0.00 0.00 0.00 0.12 0.00 0.86 0.02 0.00
#> TCGA.E9.A1R0.01 4 0.1091 0.7730 0.00 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.AC.A62Y.01 1 0.2224 0.8225 0.86 0.02 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.AO.A0JD.01 3 0.0000 0.9544 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A3IY.01 1 0.1741 0.8282 0.92 0.02 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.D8.A3Z5.01 5 0.4077 0.5389 0.02 0.04 0.00 0.00 0.76 0.08 0.00 0.10
#> TCGA.AC.A3QP.01 1 0.3227 0.7713 0.78 0.00 0.00 0.00 0.08 0.00 0.00 0.14
#> TCGA.GM.A2DK.01 5 0.3660 0.5612 0.24 0.00 0.00 0.00 0.70 0.00 0.00 0.06
#> TCGA.E2.A1B0.01 4 0.5874 0.3396 0.00 0.00 0.22 0.54 0.02 0.08 0.00 0.14
#> TCGA.AO.A03M.01 7 0.1947 0.7120 0.00 0.14 0.00 0.00 0.00 0.00 0.86 0.00
#> TCGA.AR.A2LJ.01 1 0.1741 0.8282 0.92 0.02 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.D8.A1JB.01 1 0.1741 0.8282 0.92 0.02 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.BH.A0BC.01 1 0.3934 0.6976 0.70 0.00 0.00 0.00 0.16 0.00 0.00 0.14
#> TCGA.D8.A27P.01 5 0.1947 0.6136 0.14 0.00 0.00 0.00 0.86 0.00 0.00 0.00
#> TCGA.OL.A66J.01 3 0.0000 0.9544 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S3.AA14.01 5 0.2674 0.5960 0.06 0.00 0.00 0.00 0.86 0.04 0.00 0.04
#> TCGA.B6.A0RS.01 4 0.3048 0.7691 0.00 0.08 0.00 0.84 0.02 0.02 0.00 0.04
#> TCGA.A2.A1G0.01 2 0.5960 0.2857 0.00 0.56 0.00 0.00 0.08 0.04 0.18 0.14
#> TCGA.XX.A89A.01 4 0.1341 0.7672 0.00 0.00 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.PE.A5DE.01 4 0.1341 0.7840 0.00 0.08 0.00 0.92 0.00 0.00 0.00 0.00
#> TCGA.D8.A27V.01 3 0.0000 0.9544 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BA.01 4 0.1091 0.7730 0.00 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.E2.A3DX.01 1 0.1887 0.8282 0.90 0.00 0.00 0.00 0.04 0.00 0.00 0.06
#> TCGA.A1.A0SE.01 2 0.2680 0.5185 0.00 0.84 0.00 0.02 0.00 0.00 0.12 0.02
#> TCGA.MS.A51U.01 5 0.3404 0.5764 0.24 0.00 0.00 0.00 0.72 0.00 0.00 0.04
#> TCGA.D8.A1Y2.01 1 0.3619 0.7341 0.74 0.00 0.00 0.00 0.12 0.00 0.00 0.14
#> TCGA.E2.A1L6.01 5 0.3404 0.5764 0.24 0.00 0.00 0.00 0.72 0.00 0.00 0.04
#> TCGA.D8.A1XY.01 3 0.0000 0.9544 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AM.01 7 0.3449 0.6037 0.00 0.32 0.00 0.00 0.00 0.00 0.66 0.02
#> TCGA.AC.A5XS.01 4 0.1091 0.7730 0.00 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.E2.A1IF.01 5 0.4540 0.5123 0.02 0.06 0.00 0.00 0.72 0.10 0.00 0.10
#> TCGA.AR.A24S.01 3 0.0000 0.9544 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A3KD.01 1 0.1275 0.8333 0.94 0.00 0.00 0.00 0.04 0.00 0.00 0.02
#> TCGA.E9.A226.01 7 0.3528 0.5684 0.00 0.18 0.00 0.00 0.00 0.00 0.74 0.08
#> TCGA.EW.A2FV.01 6 0.3627 0.8994 0.00 0.00 0.00 0.14 0.02 0.78 0.02 0.04
#> TCGA.BH.A0DV.01 1 0.1887 0.8282 0.90 0.00 0.00 0.00 0.04 0.00 0.00 0.06
#> TCGA.A2.A0YI.01 1 0.3227 0.7713 0.78 0.00 0.00 0.00 0.08 0.00 0.00 0.14
#> TCGA.BH.A0BM.01 1 0.0000 0.8413 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A27I.01 2 0.5024 0.3839 0.00 0.66 0.00 0.00 0.16 0.06 0.02 0.10
#> TCGA.E9.A1NG.01 2 0.1765 0.6229 0.00 0.88 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.C8.A26W.01 3 0.3454 0.8106 0.00 0.00 0.80 0.04 0.02 0.02 0.00 0.12
#> TCGA.OL.A6VQ.01 5 0.3369 0.5758 0.04 0.02 0.00 0.00 0.82 0.04 0.00 0.08
#> TCGA.E2.A1LL.01 3 0.3454 0.8106 0.00 0.00 0.80 0.04 0.02 0.02 0.00 0.12
#> TCGA.BH.A0AU.01 5 0.3404 0.5764 0.24 0.00 0.00 0.00 0.72 0.00 0.00 0.04
#> TCGA.A2.A0T1.01 2 0.3272 0.1591 0.00 0.58 0.00 0.42 0.00 0.00 0.00 0.00
#> TCGA.AR.A24W.01 1 0.0941 0.8391 0.96 0.00 0.00 0.00 0.02 0.00 0.00 0.02
#> TCGA.AR.A24L.01 6 0.2224 0.9244 0.00 0.00 0.00 0.12 0.00 0.86 0.02 0.00
#> TCGA.AR.A0TX.01 5 0.5277 0.4916 0.20 0.00 0.00 0.00 0.56 0.04 0.00 0.20
#> TCGA.E9.A1N3.01 8 0.5496 0.3044 0.02 0.02 0.00 0.00 0.32 0.00 0.14 0.50
#> TCGA.AN.A0XL.01 3 0.0000 0.9544 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A24A.01 1 0.0471 0.8395 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.B6.A0WY.01 1 0.4033 0.6555 0.68 0.00 0.00 0.00 0.20 0.00 0.00 0.12
#> TCGA.E9.A1R4.01 2 0.1765 0.6229 0.00 0.88 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.A7.A5ZW.01 1 0.1741 0.8282 0.92 0.02 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.OL.A5RV.01 5 0.3404 0.5764 0.24 0.00 0.00 0.00 0.72 0.00 0.00 0.04
#> TCGA.A7.A426.01 2 0.4757 0.3126 0.00 0.56 0.00 0.24 0.00 0.00 0.20 0.00
#> TCGA.E9.A1N6.01 7 0.1091 0.6702 0.00 0.06 0.00 0.00 0.00 0.00 0.94 0.00
#> TCGA.D8.A27L.01 4 0.2856 0.6705 0.00 0.20 0.00 0.78 0.00 0.02 0.00 0.00
#> TCGA.E2.A1LA.01 3 0.0000 0.9544 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A227.01 2 0.1887 0.5652 0.00 0.90 0.00 0.00 0.00 0.00 0.04 0.06
#> TCGA.A2.A0YL.01 2 0.1341 0.6204 0.00 0.92 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.AO.A0JF.01 1 0.1887 0.8282 0.90 0.00 0.00 0.00 0.04 0.00 0.00 0.06
#> TCGA.A2.A4S3.01 7 0.1765 0.7036 0.00 0.12 0.00 0.00 0.00 0.00 0.88 0.00
#> TCGA.BH.A0AZ.01 2 0.6312 0.2413 0.00 0.52 0.00 0.00 0.14 0.04 0.16 0.14
#> TCGA.A2.A0YH.01 3 0.0000 0.9544 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LL.A5YN.01 7 0.5281 -0.0289 0.00 0.34 0.00 0.32 0.00 0.00 0.34 0.00
#> TCGA.E2.A1IK.01 5 0.5082 0.1625 0.00 0.06 0.00 0.00 0.56 0.08 0.00 0.30
#> TCGA.A1.A0SI.01 4 0.1341 0.7840 0.00 0.08 0.00 0.92 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RH.01 3 0.0000 0.9544 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A13H.01 1 0.4059 0.5678 0.64 0.00 0.00 0.00 0.28 0.00 0.00 0.08
#> TCGA.E2.A1IO.01 2 0.2025 0.6222 0.00 0.88 0.00 0.10 0.02 0.00 0.00 0.00
#> TCGA.C8.A26Y.01 6 0.4774 0.8023 0.00 0.00 0.00 0.10 0.02 0.68 0.16 0.04
#> TCGA.AN.A0XW.01 1 0.3907 0.3785 0.58 0.00 0.00 0.00 0.38 0.00 0.00 0.04
#> TCGA.E9.A229.01 7 0.4096 0.5990 0.00 0.24 0.00 0.00 0.02 0.00 0.68 0.06
#> TCGA.D8.A1JK.01 3 0.0000 0.9544 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A208.01 4 0.2591 0.7382 0.00 0.00 0.00 0.86 0.02 0.08 0.00 0.04
#> TCGA.EW.A1IX.01 7 0.2534 0.6859 0.00 0.22 0.00 0.00 0.00 0.00 0.78 0.00
#> TCGA.A2.A259.01 1 0.1741 0.8282 0.92 0.02 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.E2.A1B1.01 1 0.1741 0.8282 0.92 0.02 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.E9.A22E.01 7 0.0808 0.6505 0.00 0.04 0.00 0.00 0.00 0.00 0.96 0.00
#> TCGA.D8.A1XO.01 1 0.4069 0.6748 0.68 0.00 0.00 0.00 0.18 0.00 0.00 0.14
#> TCGA.A1.A0SH.01 5 0.4282 0.5598 0.04 0.02 0.00 0.00 0.74 0.10 0.00 0.10
#> TCGA.D8.A1Y0.01 7 0.1947 0.7120 0.00 0.14 0.00 0.00 0.00 0.00 0.86 0.00
#> TCGA.A2.A0SU.01 1 0.1741 0.8282 0.92 0.02 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.E9.A1N4.01 3 0.4262 0.7432 0.00 0.00 0.74 0.08 0.02 0.04 0.00 0.12
#> TCGA.EW.A1PF.01 1 0.2132 0.8218 0.88 0.00 0.00 0.00 0.04 0.00 0.00 0.08
#> TCGA.BH.A0HF.01 5 0.3630 0.6024 0.08 0.00 0.00 0.00 0.78 0.04 0.00 0.10
#> TCGA.AC.A2QI.01 3 0.0000 0.9544 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A2DA.01 3 0.0000 0.9544 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A4SA.01 2 0.1765 0.6229 0.00 0.88 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.AR.A2LM.01 1 0.0941 0.8402 0.96 0.00 0.00 0.00 0.02 0.00 0.00 0.02
#> TCGA.AR.A1AN.01 1 0.5886 -0.1000 0.40 0.00 0.00 0.00 0.34 0.06 0.00 0.20
#> TCGA.GM.A5PV.01 2 0.4857 0.2946 0.00 0.52 0.00 0.30 0.00 0.00 0.18 0.00
#> TCGA.E9.A1R3.01 2 0.1765 0.6229 0.00 0.88 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.BH.A8G0.01 1 0.0471 0.8419 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.BH.A0W5.01 1 0.3227 0.7713 0.78 0.00 0.00 0.00 0.08 0.00 0.00 0.14
#> TCGA.B6.A1KI.01 2 0.6638 0.1946 0.00 0.48 0.00 0.00 0.18 0.06 0.14 0.14
#> TCGA.BH.A0C3.01 2 0.5917 -0.0600 0.00 0.44 0.00 0.00 0.06 0.02 0.36 0.12
#> TCGA.AR.A24O.01 2 0.6151 0.2762 0.00 0.54 0.00 0.00 0.12 0.04 0.18 0.12
#> TCGA.AC.A3HN.01 1 0.1741 0.8282 0.92 0.02 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.D8.A1JE.01 2 0.3002 0.6037 0.00 0.82 0.00 0.12 0.00 0.00 0.02 0.04
#> TCGA.EW.A2FR.01 1 0.2818 0.7947 0.82 0.00 0.00 0.00 0.06 0.00 0.00 0.12
#> TCGA.BH.A0W4.01 5 0.3637 0.5887 0.04 0.02 0.00 0.00 0.80 0.06 0.00 0.08
#> TCGA.BH.A0BJ.01 1 0.1741 0.8282 0.92 0.02 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.E2.A14U.01 1 0.1741 0.8282 0.92 0.02 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.D8.A1JH.01 1 0.1741 0.8282 0.92 0.02 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.BH.A1EU.01 1 0.0808 0.8419 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.BH.A1FR.01 8 0.4921 0.2005 0.00 0.22 0.00 0.00 0.00 0.00 0.26 0.52
#> TCGA.A7.A425.01 4 0.3537 0.6388 0.00 0.24 0.00 0.72 0.00 0.00 0.02 0.02
#> TCGA.BH.A8FZ.01 1 0.3227 0.7713 0.78 0.00 0.00 0.00 0.08 0.00 0.00 0.14
#> TCGA.AC.A2FG.01 4 0.2406 0.7071 0.00 0.20 0.00 0.80 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AL.01 2 0.6129 0.1652 0.00 0.48 0.00 0.04 0.30 0.10 0.00 0.08
#> TCGA.C8.A1HG.01 6 0.2224 0.9125 0.00 0.00 0.02 0.12 0.00 0.86 0.00 0.00
#> TCGA.D8.A1JU.01 1 0.0471 0.8419 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.5L.AAT0.01 5 0.4998 0.3646 0.00 0.16 0.00 0.00 0.64 0.10 0.00 0.10
#> TCGA.D8.A27E.01 1 0.1408 0.8325 0.94 0.02 0.00 0.00 0.00 0.02 0.00 0.02
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node041. Child nodes: Node02121-leaf , Node02122-leaf , Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02214-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02321-leaf , Node02322-leaf , Node02421-leaf , Node02422-leaf , Node02423-leaf , Node04111-leaf , Node04112-leaf , Node04113 , Node04131-leaf , Node04132-leaf , Node04133-leaf , Node04221-leaf , Node04222-leaf , Node04331-leaf , Node04332-leaf , Node04333-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0411"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 54 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.990 0.995 0.3777 0.628 0.628
#> 3 3 0.904 0.956 0.972 0.6517 0.614 0.443
#> 4 4 0.534 0.405 0.627 0.0982 0.785 0.506
#> 5 5 0.698 0.602 0.801 0.0972 0.748 0.385
#> 6 6 0.695 0.611 0.805 0.0457 0.876 0.591
#> 7 7 0.710 0.560 0.771 0.0402 0.877 0.501
#> 8 8 0.723 0.563 0.691 0.0216 0.934 0.664
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.AC.A62Y.01 2 0.000 1.000 0.00 1.00
#> TCGA.A7.A3IY.01 2 0.000 1.000 0.00 1.00
#> TCGA.D8.A3Z5.01 1 0.000 0.993 1.00 0.00
#> TCGA.AC.A3QP.01 1 0.000 0.993 1.00 0.00
#> TCGA.GM.A2DK.01 1 0.000 0.993 1.00 0.00
#> TCGA.AR.A2LJ.01 1 0.000 0.993 1.00 0.00
#> TCGA.D8.A1JB.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A0BC.01 1 0.000 0.993 1.00 0.00
#> TCGA.D8.A27P.01 2 0.000 1.000 0.00 1.00
#> TCGA.S3.AA14.01 1 0.000 0.993 1.00 0.00
#> TCGA.E2.A3DX.01 1 0.000 0.993 1.00 0.00
#> TCGA.MS.A51U.01 1 0.000 0.993 1.00 0.00
#> TCGA.D8.A1Y2.01 2 0.000 1.000 0.00 1.00
#> TCGA.E2.A1L6.01 1 0.000 0.993 1.00 0.00
#> TCGA.E2.A1IF.01 2 0.000 1.000 0.00 1.00
#> TCGA.A2.A3KD.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A0DV.01 1 0.000 0.993 1.00 0.00
#> TCGA.A2.A0YI.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A0BM.01 1 0.000 0.993 1.00 0.00
#> TCGA.OL.A6VQ.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A0AU.01 1 0.000 0.993 1.00 0.00
#> TCGA.AR.A24W.01 2 0.000 1.000 0.00 1.00
#> TCGA.AR.A0TX.01 1 0.000 0.993 1.00 0.00
#> TCGA.E9.A1N3.01 2 0.000 1.000 0.00 1.00
#> TCGA.E9.A24A.01 2 0.000 1.000 0.00 1.00
#> TCGA.B6.A0WY.01 1 0.000 0.993 1.00 0.00
#> TCGA.A7.A5ZW.01 1 0.000 0.993 1.00 0.00
#> TCGA.OL.A5RV.01 1 0.000 0.993 1.00 0.00
#> TCGA.AO.A0JF.01 1 0.000 0.993 1.00 0.00
#> TCGA.E2.A1IK.01 2 0.000 1.000 0.00 1.00
#> TCGA.A7.A13H.01 1 0.000 0.993 1.00 0.00
#> TCGA.AN.A0XW.01 1 0.000 0.993 1.00 0.00
#> TCGA.A2.A259.01 1 0.000 0.993 1.00 0.00
#> TCGA.E2.A1B1.01 2 0.000 1.000 0.00 1.00
#> TCGA.D8.A1XO.01 1 0.000 0.993 1.00 0.00
#> TCGA.A1.A0SH.01 1 0.000 0.993 1.00 0.00
#> TCGA.A2.A0SU.01 2 0.000 1.000 0.00 1.00
#> TCGA.EW.A1PF.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A0HF.01 1 0.000 0.993 1.00 0.00
#> TCGA.AR.A2LM.01 1 0.000 0.993 1.00 0.00
#> TCGA.AR.A1AN.01 2 0.000 1.000 0.00 1.00
#> TCGA.BH.A8G0.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A0W5.01 1 0.000 0.993 1.00 0.00
#> TCGA.AC.A3HN.01 1 0.000 0.993 1.00 0.00
#> TCGA.EW.A2FR.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A0W4.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A0BJ.01 1 0.529 0.868 0.88 0.12
#> TCGA.E2.A14U.01 1 0.529 0.868 0.88 0.12
#> TCGA.D8.A1JH.01 1 0.000 0.993 1.00 0.00
#> TCGA.BH.A1EU.01 1 0.141 0.975 0.98 0.02
#> TCGA.BH.A8FZ.01 1 0.000 0.993 1.00 0.00
#> TCGA.D8.A1JU.01 1 0.000 0.993 1.00 0.00
#> TCGA.5L.AAT0.01 1 0.000 0.993 1.00 0.00
#> TCGA.D8.A27E.01 2 0.000 1.000 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.AC.A62Y.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.A7.A3IY.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D8.A3Z5.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.AC.A3QP.01 3 0.0892 0.945 0.02 0.00 0.98
#> TCGA.GM.A2DK.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.AR.A2LJ.01 3 0.4291 0.814 0.18 0.00 0.82
#> TCGA.D8.A1JB.01 3 0.0892 0.945 0.02 0.00 0.98
#> TCGA.BH.A0BC.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.D8.A27P.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.S3.AA14.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.E2.A3DX.01 3 0.0892 0.945 0.02 0.00 0.98
#> TCGA.MS.A51U.01 3 0.0892 0.945 0.02 0.00 0.98
#> TCGA.D8.A1Y2.01 3 0.0892 0.931 0.00 0.02 0.98
#> TCGA.E2.A1L6.01 3 0.3686 0.857 0.14 0.00 0.86
#> TCGA.E2.A1IF.01 3 0.0892 0.931 0.00 0.02 0.98
#> TCGA.A2.A3KD.01 3 0.0892 0.945 0.02 0.00 0.98
#> TCGA.BH.A0DV.01 3 0.4002 0.837 0.16 0.00 0.84
#> TCGA.A2.A0YI.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.BH.A0BM.01 3 0.0892 0.945 0.02 0.00 0.98
#> TCGA.OL.A6VQ.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.BH.A0AU.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.AR.A24W.01 3 0.0892 0.931 0.00 0.02 0.98
#> TCGA.AR.A0TX.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.E9.A1N3.01 2 0.0892 0.986 0.00 0.98 0.02
#> TCGA.E9.A24A.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.B6.A0WY.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.A7.A5ZW.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.OL.A5RV.01 3 0.0892 0.945 0.02 0.00 0.98
#> TCGA.AO.A0JF.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.E2.A1IK.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.A7.A13H.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.AN.A0XW.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.A2.A259.01 3 0.0892 0.945 0.02 0.00 0.98
#> TCGA.E2.A1B1.01 3 0.0892 0.931 0.00 0.02 0.98
#> TCGA.D8.A1XO.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.A1.A0SH.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.A2.A0SU.01 3 0.5706 0.532 0.00 0.32 0.68
#> TCGA.EW.A1PF.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.BH.A0HF.01 3 0.3686 0.857 0.14 0.00 0.86
#> TCGA.AR.A2LM.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.AR.A1AN.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.BH.A8G0.01 3 0.0892 0.945 0.02 0.00 0.98
#> TCGA.BH.A0W5.01 1 0.0892 0.975 0.98 0.00 0.02
#> TCGA.AC.A3HN.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.EW.A2FR.01 3 0.0892 0.945 0.02 0.00 0.98
#> TCGA.BH.A0W4.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.BH.A0BJ.01 3 0.0892 0.945 0.02 0.00 0.98
#> TCGA.E2.A14U.01 3 0.0892 0.945 0.02 0.00 0.98
#> TCGA.D8.A1JH.01 3 0.4002 0.838 0.16 0.00 0.84
#> TCGA.BH.A1EU.01 3 0.0892 0.945 0.02 0.00 0.98
#> TCGA.BH.A8FZ.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.D8.A1JU.01 3 0.0892 0.945 0.02 0.00 0.98
#> TCGA.5L.AAT0.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.D8.A27E.01 2 0.0000 0.998 0.00 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.AC.A62Y.01 2 0.2647 0.83060 0.00 0.88 0.00 0.12
#> TCGA.A7.A3IY.01 2 0.0000 0.85885 0.00 1.00 0.00 0.00
#> TCGA.D8.A3Z5.01 1 0.4907 0.54863 0.58 0.00 0.42 0.00
#> TCGA.AC.A3QP.01 3 0.0707 0.47729 0.00 0.00 0.98 0.02
#> TCGA.GM.A2DK.01 1 0.2921 0.72196 0.86 0.00 0.14 0.00
#> TCGA.AR.A2LJ.01 3 0.2011 0.51662 0.08 0.00 0.92 0.00
#> TCGA.D8.A1JB.01 3 0.4855 -0.32525 0.00 0.00 0.60 0.40
#> TCGA.BH.A0BC.01 1 0.0000 0.74319 1.00 0.00 0.00 0.00
#> TCGA.D8.A27P.01 2 0.4948 0.64350 0.00 0.56 0.00 0.44
#> TCGA.S3.AA14.01 1 0.0000 0.74319 1.00 0.00 0.00 0.00
#> TCGA.E2.A3DX.01 3 0.3172 0.28728 0.00 0.00 0.84 0.16
#> TCGA.MS.A51U.01 3 0.3172 0.25020 0.00 0.00 0.84 0.16
#> TCGA.D8.A1Y2.01 4 0.4977 0.56507 0.00 0.00 0.46 0.54
#> TCGA.E2.A1L6.01 3 0.2706 0.50737 0.08 0.00 0.90 0.02
#> TCGA.E2.A1IF.01 4 0.4948 0.57321 0.00 0.00 0.44 0.56
#> TCGA.A2.A3KD.01 3 0.4277 -0.00279 0.00 0.00 0.72 0.28
#> TCGA.BH.A0DV.01 3 0.2011 0.51662 0.08 0.00 0.92 0.00
#> TCGA.A2.A0YI.01 1 0.0000 0.74319 1.00 0.00 0.00 0.00
#> TCGA.BH.A0BM.01 4 0.4907 0.21513 0.00 0.00 0.42 0.58
#> TCGA.OL.A6VQ.01 1 0.4790 0.59521 0.62 0.00 0.38 0.00
#> TCGA.BH.A0AU.01 1 0.0000 0.74319 1.00 0.00 0.00 0.00
#> TCGA.AR.A24W.01 4 0.3975 0.55655 0.00 0.00 0.24 0.76
#> TCGA.AR.A0TX.01 1 0.4994 0.43049 0.52 0.00 0.48 0.00
#> TCGA.E9.A1N3.01 4 0.5428 -0.59711 0.00 0.38 0.02 0.60
#> TCGA.E9.A24A.01 2 0.0000 0.85885 0.00 1.00 0.00 0.00
#> TCGA.B6.A0WY.01 1 0.0000 0.74319 1.00 0.00 0.00 0.00
#> TCGA.A7.A5ZW.01 3 0.4977 -0.33509 0.46 0.00 0.54 0.00
#> TCGA.OL.A5RV.01 3 0.0000 0.48027 0.00 0.00 1.00 0.00
#> TCGA.AO.A0JF.01 3 0.4907 -0.21457 0.42 0.00 0.58 0.00
#> TCGA.E2.A1IK.01 2 0.0000 0.85885 0.00 1.00 0.00 0.00
#> TCGA.A7.A13H.01 3 0.4948 -0.27218 0.44 0.00 0.56 0.00
#> TCGA.AN.A0XW.01 1 0.3172 0.71596 0.84 0.00 0.16 0.00
#> TCGA.A2.A259.01 3 0.4855 -0.32525 0.00 0.00 0.60 0.40
#> TCGA.E2.A1B1.01 4 0.5000 0.52687 0.00 0.00 0.50 0.50
#> TCGA.D8.A1XO.01 1 0.4855 0.57506 0.60 0.00 0.40 0.00
#> TCGA.A1.A0SH.01 1 0.0000 0.74319 1.00 0.00 0.00 0.00
#> TCGA.A2.A0SU.01 4 0.4553 0.52517 0.00 0.04 0.18 0.78
#> TCGA.EW.A1PF.01 1 0.4977 0.47835 0.54 0.00 0.46 0.00
#> TCGA.BH.A0HF.01 3 0.3198 0.49968 0.08 0.00 0.88 0.04
#> TCGA.AR.A2LM.01 1 0.0000 0.74319 1.00 0.00 0.00 0.00
#> TCGA.AR.A1AN.01 2 0.4948 0.64350 0.00 0.56 0.00 0.44
#> TCGA.BH.A8G0.01 3 0.4855 -0.32525 0.00 0.00 0.60 0.40
#> TCGA.BH.A0W5.01 3 0.4406 0.17332 0.30 0.00 0.70 0.00
#> TCGA.AC.A3HN.01 3 0.4948 -0.27218 0.44 0.00 0.56 0.00
#> TCGA.EW.A2FR.01 3 0.4855 -0.32525 0.00 0.00 0.60 0.40
#> TCGA.BH.A0W4.01 1 0.0000 0.74319 1.00 0.00 0.00 0.00
#> TCGA.BH.A0BJ.01 4 0.5000 0.52687 0.00 0.00 0.50 0.50
#> TCGA.E2.A14U.01 4 0.5000 0.52687 0.00 0.00 0.50 0.50
#> TCGA.D8.A1JH.01 3 0.1637 0.51123 0.06 0.00 0.94 0.00
#> TCGA.BH.A1EU.01 3 0.4977 -0.49864 0.00 0.00 0.54 0.46
#> TCGA.BH.A8FZ.01 1 0.4977 0.47835 0.54 0.00 0.46 0.00
#> TCGA.D8.A1JU.01 3 0.0707 0.47729 0.00 0.00 0.98 0.02
#> TCGA.5L.AAT0.01 1 0.4790 0.59521 0.62 0.00 0.38 0.00
#> TCGA.D8.A27E.01 2 0.0000 0.85885 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.AC.A62Y.01 2 0.3561 0.7483 0.00 0.74 0.00 0.00 0.26
#> TCGA.A7.A3IY.01 2 0.4227 0.7752 0.00 0.58 0.00 0.00 0.42
#> TCGA.D8.A3Z5.01 3 0.3796 0.5016 0.00 0.00 0.70 0.00 0.30
#> TCGA.AC.A3QP.01 3 0.5579 0.3479 0.00 0.00 0.60 0.10 0.30
#> TCGA.GM.A2DK.01 3 0.4262 -0.1342 0.44 0.00 0.56 0.00 0.00
#> TCGA.AR.A2LJ.01 3 0.1410 0.6057 0.00 0.00 0.94 0.06 0.00
#> TCGA.D8.A1JB.01 4 0.1410 0.8488 0.00 0.00 0.06 0.94 0.00
#> TCGA.BH.A0BC.01 1 0.1410 0.9535 0.94 0.00 0.06 0.00 0.00
#> TCGA.D8.A27P.01 2 0.1410 0.6113 0.00 0.94 0.00 0.06 0.00
#> TCGA.S3.AA14.01 1 0.1410 0.9535 0.94 0.00 0.06 0.00 0.00
#> TCGA.E2.A3DX.01 3 0.5394 -0.0256 0.00 0.00 0.54 0.40 0.06
#> TCGA.MS.A51U.01 3 0.6778 -0.2493 0.00 0.00 0.38 0.28 0.34
#> TCGA.D8.A1Y2.01 4 0.1648 0.8336 0.04 0.00 0.00 0.94 0.02
#> TCGA.E2.A1L6.01 3 0.5232 0.3864 0.00 0.00 0.60 0.06 0.34
#> TCGA.E2.A1IF.01 4 0.0000 0.8567 0.00 0.00 0.00 1.00 0.00
#> TCGA.A2.A3KD.01 4 0.6386 -0.3161 0.00 0.00 0.18 0.48 0.34
#> TCGA.BH.A0DV.01 3 0.2438 0.6082 0.00 0.00 0.90 0.06 0.04
#> TCGA.A2.A0YI.01 1 0.1410 0.9535 0.94 0.00 0.06 0.00 0.00
#> TCGA.BH.A0BM.01 5 0.7973 0.0000 0.00 0.36 0.16 0.12 0.36
#> TCGA.OL.A6VQ.01 3 0.4644 0.4955 0.04 0.00 0.68 0.00 0.28
#> TCGA.BH.A0AU.01 1 0.1410 0.9535 0.94 0.00 0.06 0.00 0.00
#> TCGA.AR.A24W.01 4 0.0609 0.8496 0.00 0.02 0.00 0.98 0.00
#> TCGA.AR.A0TX.01 3 0.0609 0.6176 0.02 0.00 0.98 0.00 0.00
#> TCGA.E9.A1N3.01 2 0.5005 0.4346 0.02 0.72 0.00 0.06 0.20
#> TCGA.E9.A24A.01 2 0.4227 0.7752 0.00 0.58 0.00 0.00 0.42
#> TCGA.B6.A0WY.01 1 0.3895 0.6413 0.68 0.00 0.32 0.00 0.00
#> TCGA.A7.A5ZW.01 3 0.0000 0.6220 0.00 0.00 1.00 0.00 0.00
#> TCGA.OL.A5RV.01 3 0.5558 0.3013 0.00 0.00 0.56 0.08 0.36
#> TCGA.AO.A0JF.01 3 0.3684 0.5210 0.00 0.00 0.72 0.00 0.28
#> TCGA.E2.A1IK.01 2 0.4227 0.7752 0.00 0.58 0.00 0.00 0.42
#> TCGA.A7.A13H.01 3 0.0000 0.6220 0.00 0.00 1.00 0.00 0.00
#> TCGA.AN.A0XW.01 3 0.4227 -0.0633 0.42 0.00 0.58 0.00 0.00
#> TCGA.A2.A259.01 4 0.3037 0.7892 0.00 0.00 0.10 0.86 0.04
#> TCGA.E2.A1B1.01 4 0.1648 0.8336 0.04 0.00 0.00 0.94 0.02
#> TCGA.D8.A1XO.01 3 0.4360 0.4905 0.02 0.00 0.68 0.00 0.30
#> TCGA.A1.A0SH.01 1 0.1410 0.9535 0.94 0.00 0.06 0.00 0.00
#> TCGA.A2.A0SU.01 4 0.2249 0.8169 0.04 0.02 0.00 0.92 0.02
#> TCGA.EW.A1PF.01 3 0.0609 0.6176 0.02 0.00 0.98 0.00 0.00
#> TCGA.BH.A0HF.01 3 0.4990 0.3856 0.00 0.00 0.60 0.04 0.36
#> TCGA.AR.A2LM.01 1 0.1410 0.9535 0.94 0.00 0.06 0.00 0.00
#> TCGA.AR.A1AN.01 2 0.1410 0.6113 0.00 0.94 0.00 0.06 0.00
#> TCGA.BH.A8G0.01 4 0.3390 0.7704 0.00 0.00 0.10 0.84 0.06
#> TCGA.BH.A0W5.01 3 0.0609 0.6190 0.00 0.00 0.98 0.02 0.00
#> TCGA.AC.A3HN.01 3 0.2280 0.6022 0.00 0.00 0.88 0.00 0.12
#> TCGA.EW.A2FR.01 4 0.2012 0.8483 0.00 0.00 0.06 0.92 0.02
#> TCGA.BH.A0W4.01 1 0.1410 0.9535 0.94 0.00 0.06 0.00 0.00
#> TCGA.BH.A0BJ.01 4 0.1410 0.8339 0.00 0.00 0.00 0.94 0.06
#> TCGA.E2.A14U.01 4 0.0000 0.8567 0.00 0.00 0.00 1.00 0.00
#> TCGA.D8.A1JH.01 3 0.1410 0.6057 0.00 0.00 0.94 0.06 0.00
#> TCGA.BH.A1EU.01 4 0.1410 0.8488 0.00 0.00 0.06 0.94 0.00
#> TCGA.BH.A8FZ.01 3 0.0609 0.6176 0.02 0.00 0.98 0.00 0.00
#> TCGA.D8.A1JU.01 3 0.5487 0.3799 0.00 0.00 0.62 0.10 0.28
#> TCGA.5L.AAT0.01 3 0.4096 0.5513 0.04 0.00 0.76 0.00 0.20
#> TCGA.D8.A27E.01 2 0.4227 0.7752 0.00 0.58 0.00 0.00 0.42
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.AC.A62Y.01 6 0.3869 0.4849 0.00 0.50 0.00 0.00 0.00 0.50
#> TCGA.A7.A3IY.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A3Z5.01 5 0.4337 0.0668 0.02 0.00 0.48 0.00 0.50 0.00
#> TCGA.AC.A3QP.01 3 0.4764 -0.1913 0.00 0.00 0.54 0.02 0.42 0.02
#> TCGA.GM.A2DK.01 3 0.3460 0.5016 0.22 0.00 0.76 0.00 0.00 0.02
#> TCGA.AR.A2LJ.01 3 0.1092 0.6547 0.00 0.00 0.96 0.02 0.00 0.02
#> TCGA.D8.A1JB.01 4 0.0937 0.8463 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.BH.A0BC.01 1 0.0547 0.8871 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.D8.A27P.01 6 0.4078 0.7343 0.00 0.34 0.00 0.02 0.00 0.64
#> TCGA.S3.AA14.01 1 0.1480 0.8771 0.94 0.00 0.02 0.00 0.04 0.00
#> TCGA.E2.A3DX.01 4 0.5288 0.2282 0.00 0.00 0.38 0.54 0.06 0.02
#> TCGA.MS.A51U.01 5 0.5883 0.5356 0.00 0.00 0.18 0.24 0.56 0.02
#> TCGA.D8.A1Y2.01 4 0.3460 0.7062 0.00 0.00 0.00 0.76 0.22 0.02
#> TCGA.E2.A1L6.01 5 0.4199 0.4380 0.00 0.00 0.38 0.02 0.60 0.00
#> TCGA.E2.A1IF.01 4 0.0000 0.8495 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A2.A3KD.01 5 0.5501 0.4893 0.00 0.00 0.10 0.30 0.58 0.02
#> TCGA.BH.A0DV.01 3 0.3111 0.5888 0.00 0.00 0.84 0.02 0.12 0.02
#> TCGA.A2.A0YI.01 1 0.0547 0.8871 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.BH.A0BM.01 5 0.5390 0.3886 0.00 0.00 0.02 0.18 0.64 0.16
#> TCGA.OL.A6VQ.01 3 0.4902 -0.1308 0.06 0.00 0.48 0.00 0.46 0.00
#> TCGA.BH.A0AU.01 1 0.0547 0.8871 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.AR.A24W.01 4 0.0000 0.8495 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AR.A0TX.01 3 0.1480 0.6586 0.04 0.00 0.94 0.00 0.00 0.02
#> TCGA.E9.A1N3.01 6 0.2938 0.5301 0.02 0.04 0.00 0.02 0.04 0.88
#> TCGA.E9.A24A.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0WY.01 1 0.4337 0.1361 0.50 0.00 0.48 0.00 0.00 0.02
#> TCGA.A7.A5ZW.01 3 0.1480 0.6591 0.00 0.00 0.94 0.00 0.04 0.02
#> TCGA.OL.A5RV.01 5 0.5609 0.5455 0.00 0.00 0.28 0.12 0.58 0.02
#> TCGA.AO.A0JF.01 3 0.3647 0.1878 0.00 0.00 0.64 0.00 0.36 0.00
#> TCGA.E2.A1IK.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A13H.01 3 0.1814 0.6351 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.AN.A0XW.01 3 0.3315 0.5237 0.20 0.00 0.78 0.00 0.00 0.02
#> TCGA.A2.A259.01 4 0.3688 0.7281 0.00 0.00 0.14 0.80 0.04 0.02
#> TCGA.E2.A1B1.01 4 0.1807 0.8281 0.00 0.00 0.00 0.92 0.06 0.02
#> TCGA.D8.A1XO.01 5 0.4892 0.1115 0.06 0.00 0.44 0.00 0.50 0.00
#> TCGA.A1.A0SH.01 1 0.0547 0.8871 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.A2.A0SU.01 4 0.3821 0.6818 0.00 0.00 0.00 0.74 0.22 0.04
#> TCGA.EW.A1PF.01 3 0.1480 0.6586 0.04 0.00 0.94 0.00 0.00 0.02
#> TCGA.BH.A0HF.01 5 0.3409 0.5095 0.00 0.00 0.30 0.00 0.70 0.00
#> TCGA.AR.A2LM.01 1 0.1480 0.8771 0.94 0.00 0.02 0.00 0.04 0.00
#> TCGA.AR.A1AN.01 6 0.4078 0.7343 0.00 0.34 0.00 0.02 0.00 0.64
#> TCGA.BH.A8G0.01 4 0.3997 0.7100 0.00 0.00 0.14 0.78 0.06 0.02
#> TCGA.BH.A0W5.01 3 0.0547 0.6654 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.AC.A3HN.01 3 0.2454 0.5924 0.00 0.00 0.84 0.00 0.16 0.00
#> TCGA.EW.A2FR.01 4 0.1480 0.8450 0.00 0.00 0.04 0.94 0.02 0.00
#> TCGA.BH.A0W4.01 1 0.1480 0.8771 0.94 0.00 0.02 0.00 0.04 0.00
#> TCGA.BH.A0BJ.01 4 0.1267 0.8286 0.00 0.00 0.00 0.94 0.06 0.00
#> TCGA.E2.A14U.01 4 0.0000 0.8495 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D8.A1JH.01 3 0.1092 0.6547 0.00 0.00 0.96 0.02 0.00 0.02
#> TCGA.BH.A1EU.01 4 0.0000 0.8495 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A8FZ.01 3 0.1480 0.6586 0.04 0.00 0.94 0.00 0.00 0.02
#> TCGA.D8.A1JU.01 3 0.6019 -0.3270 0.00 0.00 0.46 0.14 0.38 0.02
#> TCGA.5L.AAT0.01 3 0.4700 0.2945 0.06 0.00 0.60 0.00 0.34 0.00
#> TCGA.D8.A27E.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.AC.A62Y.01 6 0.336 0.7040 0.00 0.36 0.00 0.00 0.00 0.64 0.00
#> TCGA.A7.A3IY.01 2 0.000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A3Z5.01 5 0.294 0.6901 0.00 0.00 0.26 0.00 0.74 0.00 0.00
#> TCGA.AC.A3QP.01 5 0.563 0.1557 0.00 0.00 0.34 0.30 0.36 0.00 0.00
#> TCGA.GM.A2DK.01 3 0.208 0.6215 0.14 0.00 0.86 0.00 0.00 0.00 0.00
#> TCGA.AR.A2LJ.01 3 0.324 0.6275 0.00 0.00 0.78 0.18 0.04 0.00 0.00
#> TCGA.D8.A1JB.01 4 0.324 0.2010 0.00 0.00 0.04 0.78 0.00 0.00 0.18
#> TCGA.BH.A0BC.01 1 0.117 0.9515 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.D8.A27P.01 6 0.369 0.7445 0.00 0.32 0.00 0.00 0.00 0.66 0.02
#> TCGA.S3.AA14.01 1 0.000 0.9798 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A3DX.01 4 0.364 0.3023 0.00 0.00 0.24 0.72 0.04 0.00 0.00
#> TCGA.MS.A51U.01 4 0.558 -0.0186 0.00 0.00 0.08 0.50 0.36 0.00 0.06
#> TCGA.D8.A1Y2.01 7 0.350 1.0000 0.00 0.00 0.00 0.42 0.00 0.00 0.58
#> TCGA.E2.A1L6.01 5 0.454 0.6649 0.00 0.00 0.14 0.08 0.72 0.00 0.06
#> TCGA.E2.A1IF.01 4 0.331 0.0343 0.00 0.00 0.00 0.74 0.02 0.00 0.24
#> TCGA.A2.A3KD.01 4 0.468 0.2157 0.00 0.00 0.00 0.58 0.32 0.00 0.10
#> TCGA.BH.A0DV.01 3 0.474 0.4371 0.00 0.00 0.62 0.22 0.16 0.00 0.00
#> TCGA.A2.A0YI.01 1 0.166 0.9365 0.92 0.00 0.02 0.00 0.00 0.00 0.06
#> TCGA.BH.A0BM.01 5 0.470 0.4495 0.00 0.00 0.00 0.04 0.68 0.08 0.20
#> TCGA.OL.A6VQ.01 5 0.342 0.6901 0.02 0.00 0.26 0.00 0.72 0.00 0.00
#> TCGA.BH.A0AU.01 1 0.000 0.9798 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A24W.01 4 0.331 0.0343 0.00 0.00 0.00 0.74 0.02 0.00 0.24
#> TCGA.AR.A0TX.01 3 0.000 0.7085 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1N3.01 6 0.345 0.4230 0.00 0.00 0.00 0.00 0.08 0.78 0.14
#> TCGA.E9.A24A.01 2 0.000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0WY.01 3 0.329 0.3259 0.34 0.00 0.66 0.00 0.00 0.00 0.00
#> TCGA.A7.A5ZW.01 3 0.387 0.5742 0.00 0.00 0.74 0.12 0.14 0.00 0.00
#> TCGA.OL.A5RV.01 5 0.539 0.5786 0.00 0.00 0.14 0.18 0.62 0.00 0.06
#> TCGA.AO.A0JF.01 5 0.329 0.6054 0.00 0.00 0.34 0.00 0.66 0.00 0.00
#> TCGA.E2.A1IK.01 2 0.000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A13H.01 3 0.362 0.5751 0.00 0.00 0.76 0.08 0.16 0.00 0.00
#> TCGA.AN.A0XW.01 3 0.291 0.6027 0.14 0.00 0.82 0.00 0.00 0.00 0.04
#> TCGA.A2.A259.01 4 0.272 0.3369 0.00 0.00 0.12 0.84 0.04 0.00 0.00
#> TCGA.E2.A1B1.01 4 0.305 -0.0623 0.00 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.D8.A1XO.01 5 0.378 0.6917 0.02 0.00 0.24 0.00 0.72 0.00 0.02
#> TCGA.A1.A0SH.01 1 0.000 0.9798 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0SU.01 7 0.350 1.0000 0.00 0.00 0.00 0.42 0.00 0.00 0.58
#> TCGA.EW.A1PF.01 3 0.000 0.7085 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0HF.01 5 0.470 0.5987 0.00 0.00 0.08 0.04 0.68 0.00 0.20
#> TCGA.AR.A2LM.01 1 0.000 0.9798 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AN.01 6 0.369 0.7445 0.00 0.32 0.00 0.00 0.00 0.66 0.02
#> TCGA.BH.A8G0.01 4 0.228 0.3350 0.00 0.00 0.08 0.88 0.04 0.00 0.00
#> TCGA.BH.A0W5.01 3 0.000 0.7085 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A3HN.01 3 0.407 0.2033 0.00 0.00 0.62 0.04 0.34 0.00 0.00
#> TCGA.EW.A2FR.01 4 0.339 0.1587 0.00 0.00 0.04 0.76 0.00 0.00 0.20
#> TCGA.BH.A0W4.01 1 0.000 0.9798 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BJ.01 4 0.291 0.1717 0.00 0.00 0.00 0.80 0.02 0.00 0.18
#> TCGA.E2.A14U.01 4 0.319 0.0859 0.00 0.00 0.00 0.76 0.02 0.00 0.22
#> TCGA.D8.A1JH.01 3 0.364 0.5722 0.00 0.00 0.72 0.24 0.04 0.00 0.00
#> TCGA.BH.A1EU.01 4 0.305 0.1303 0.00 0.00 0.00 0.78 0.02 0.00 0.20
#> TCGA.BH.A8FZ.01 3 0.000 0.7085 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JU.01 4 0.552 -0.2466 0.00 0.00 0.34 0.42 0.24 0.00 0.00
#> TCGA.5L.AAT0.01 5 0.352 0.6720 0.02 0.00 0.28 0.00 0.70 0.00 0.00
#> TCGA.D8.A27E.01 2 0.000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.AC.A62Y.01 6 0.2756 0.911 0.00 0.26 0.00 0.00 0.00 0.74 0.00 0.00
#> TCGA.A7.A3IY.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A3Z5.01 5 0.6501 0.563 0.00 0.00 0.20 0.00 0.38 0.04 0.06 0.32
#> TCGA.AC.A3QP.01 8 0.3528 0.325 0.00 0.00 0.18 0.00 0.08 0.00 0.00 0.74
#> TCGA.GM.A2DK.01 3 0.0808 0.692 0.04 0.00 0.96 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A2LJ.01 3 0.3083 0.430 0.00 0.00 0.66 0.00 0.00 0.00 0.00 0.34
#> TCGA.D8.A1JB.01 4 0.2719 0.684 0.00 0.00 0.02 0.80 0.00 0.00 0.00 0.18
#> TCGA.BH.A0BC.01 1 0.2724 0.882 0.86 0.00 0.02 0.00 0.02 0.02 0.08 0.00
#> TCGA.D8.A27P.01 6 0.2981 0.934 0.00 0.22 0.00 0.00 0.02 0.76 0.00 0.00
#> TCGA.S3.AA14.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A3DX.01 4 0.4562 0.318 0.00 0.00 0.10 0.46 0.00 0.00 0.00 0.44
#> TCGA.MS.A51U.01 8 0.4758 0.171 0.00 0.00 0.02 0.26 0.12 0.00 0.00 0.60
#> TCGA.D8.A1Y2.01 4 0.6453 0.240 0.00 0.00 0.00 0.48 0.04 0.10 0.18 0.20
#> TCGA.E2.A1L6.01 5 0.4999 0.426 0.00 0.00 0.18 0.00 0.42 0.00 0.00 0.40
#> TCGA.E2.A1IF.01 4 0.0471 0.683 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.A2.A3KD.01 4 0.5618 0.283 0.00 0.00 0.00 0.50 0.18 0.02 0.02 0.28
#> TCGA.BH.A0DV.01 8 0.3318 -0.140 0.00 0.00 0.46 0.00 0.00 0.00 0.00 0.54
#> TCGA.A2.A0YI.01 1 0.2724 0.882 0.86 0.00 0.02 0.00 0.02 0.02 0.08 0.00
#> TCGA.BH.A0BM.01 5 0.2807 0.163 0.00 0.00 0.00 0.00 0.84 0.04 0.02 0.10
#> TCGA.OL.A6VQ.01 5 0.6501 0.563 0.00 0.00 0.20 0.00 0.38 0.04 0.06 0.32
#> TCGA.BH.A0AU.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A24W.01 4 0.0941 0.669 0.00 0.00 0.00 0.96 0.00 0.02 0.02 0.00
#> TCGA.AR.A0TX.01 3 0.0000 0.709 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A1N3.01 7 0.3514 0.000 0.00 0.02 0.00 0.00 0.00 0.34 0.64 0.00
#> TCGA.E9.A24A.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0WY.01 3 0.1947 0.599 0.14 0.00 0.86 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A5ZW.01 3 0.3808 0.366 0.00 0.00 0.62 0.00 0.04 0.00 0.00 0.34
#> TCGA.OL.A5RV.01 8 0.4723 -0.240 0.00 0.00 0.14 0.00 0.34 0.00 0.00 0.52
#> TCGA.AO.A0JF.01 8 0.5798 -0.398 0.00 0.00 0.24 0.00 0.34 0.00 0.04 0.38
#> TCGA.E2.A1IK.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A13H.01 3 0.3907 0.254 0.00 0.00 0.58 0.00 0.04 0.00 0.00 0.38
#> TCGA.AN.A0XW.01 3 0.2204 0.675 0.04 0.00 0.90 0.00 0.02 0.02 0.02 0.00
#> TCGA.A2.A259.01 4 0.3714 0.454 0.00 0.00 0.02 0.54 0.00 0.00 0.00 0.44
#> TCGA.E2.A1B1.01 4 0.2350 0.681 0.00 0.00 0.00 0.86 0.00 0.00 0.04 0.10
#> TCGA.D8.A1XO.01 5 0.6501 0.563 0.00 0.00 0.20 0.00 0.38 0.04 0.06 0.32
#> TCGA.A1.A0SH.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0SU.01 4 0.6582 0.199 0.00 0.00 0.00 0.48 0.06 0.10 0.18 0.18
#> TCGA.EW.A1PF.01 3 0.0000 0.709 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0HF.01 5 0.3021 0.300 0.00 0.00 0.00 0.00 0.80 0.02 0.02 0.16
#> TCGA.AR.A2LM.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A1AN.01 6 0.2534 0.942 0.00 0.22 0.00 0.00 0.00 0.78 0.00 0.00
#> TCGA.BH.A8G0.01 4 0.3658 0.504 0.00 0.00 0.02 0.58 0.00 0.00 0.00 0.40
#> TCGA.BH.A0W5.01 3 0.0808 0.700 0.00 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.AC.A3HN.01 3 0.4622 0.246 0.00 0.00 0.56 0.00 0.14 0.00 0.00 0.30
#> TCGA.EW.A2FR.01 4 0.2981 0.666 0.00 0.00 0.02 0.76 0.00 0.00 0.00 0.22
#> TCGA.BH.A0W4.01 1 0.0000 0.955 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BJ.01 4 0.2025 0.692 0.00 0.00 0.00 0.88 0.02 0.00 0.00 0.10
#> TCGA.E2.A14U.01 4 0.0941 0.669 0.00 0.00 0.00 0.96 0.00 0.02 0.02 0.00
#> TCGA.D8.A1JH.01 3 0.3237 0.334 0.00 0.00 0.60 0.00 0.00 0.00 0.00 0.40
#> TCGA.BH.A1EU.01 4 0.1408 0.676 0.00 0.00 0.00 0.94 0.00 0.02 0.02 0.02
#> TCGA.BH.A8FZ.01 3 0.0000 0.709 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JU.01 8 0.3785 0.398 0.00 0.00 0.14 0.14 0.00 0.00 0.00 0.72
#> TCGA.5L.AAT0.01 5 0.6555 0.536 0.00 0.00 0.22 0.00 0.36 0.04 0.06 0.32
#> TCGA.D8.A27E.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0411. Child nodes: Node041131-leaf , Node041132-leaf , Node041133-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["04113"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 24 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.994 0.993 0.5055 0.493 0.493
#> 3 3 1.000 0.996 0.998 0.1762 0.623 0.409
#> 4 4 0.758 0.758 0.838 0.1114 0.986 0.964
#> 5 5 0.762 0.737 0.863 0.0924 0.859 0.658
#> 6 6 0.684 0.767 0.897 0.0449 0.960 0.864
#> 7 7 0.623 0.627 0.797 0.0273 0.993 0.971
#> 8 8 0.700 0.488 0.797 0.0469 0.848 0.462
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.AC.A3QP.01 2 0.141 0.991 0.02 0.98
#> TCGA.AR.A2LJ.01 1 0.000 1.000 1.00 0.00
#> TCGA.D8.A1JB.01 1 0.000 1.000 1.00 0.00
#> TCGA.E2.A3DX.01 1 0.000 1.000 1.00 0.00
#> TCGA.MS.A51U.01 2 0.000 0.988 0.00 1.00
#> TCGA.D8.A1Y2.01 1 0.000 1.000 1.00 0.00
#> TCGA.E2.A1L6.01 2 0.000 0.988 0.00 1.00
#> TCGA.E2.A1IF.01 2 0.141 0.991 0.02 0.98
#> TCGA.A2.A3KD.01 2 0.000 0.988 0.00 1.00
#> TCGA.BH.A0DV.01 2 0.141 0.991 0.02 0.98
#> TCGA.BH.A0BM.01 2 0.000 0.988 0.00 1.00
#> TCGA.AR.A24W.01 2 0.141 0.991 0.02 0.98
#> TCGA.OL.A5RV.01 2 0.141 0.991 0.02 0.98
#> TCGA.A2.A259.01 1 0.000 1.000 1.00 0.00
#> TCGA.E2.A1B1.01 1 0.000 1.000 1.00 0.00
#> TCGA.A2.A0SU.01 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A0HF.01 2 0.000 0.988 0.00 1.00
#> TCGA.BH.A8G0.01 2 0.141 0.991 0.02 0.98
#> TCGA.EW.A2FR.01 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A0BJ.01 2 0.000 0.988 0.00 1.00
#> TCGA.E2.A14U.01 1 0.000 1.000 1.00 0.00
#> TCGA.D8.A1JH.01 1 0.000 1.000 1.00 0.00
#> TCGA.BH.A1EU.01 2 0.141 0.991 0.02 0.98
#> TCGA.D8.A1JU.01 2 0.141 0.991 0.02 0.98
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.AC.A3QP.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.AR.A2LJ.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D8.A1JB.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.E2.A3DX.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.MS.A51U.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D8.A1Y2.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.E2.A1L6.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.E2.A1IF.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.A2.A3KD.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.BH.A0DV.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.BH.A0BM.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.AR.A24W.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.OL.A5RV.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.A2.A259.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.E2.A1B1.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.A2.A0SU.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.BH.A0HF.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.BH.A8G0.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.EW.A2FR.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.BH.A0BJ.01 2 0.0892 0.980 0.00 0.98 0.02
#> TCGA.E2.A14U.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D8.A1JH.01 1 0.0892 0.971 0.98 0.02 0.00
#> TCGA.BH.A1EU.01 2 0.0000 0.998 0.00 1.00 0.00
#> TCGA.D8.A1JU.01 2 0.0000 0.998 0.00 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.AC.A3QP.01 2 0.0000 0.848 0.00 1.00 0.00 0.00
#> TCGA.AR.A2LJ.01 2 0.4948 0.517 0.00 0.56 0.44 0.00
#> TCGA.D8.A1JB.01 1 0.4855 0.707 0.60 0.00 0.40 0.00
#> TCGA.E2.A3DX.01 2 0.4134 0.717 0.00 0.74 0.26 0.00
#> TCGA.MS.A51U.01 2 0.2011 0.805 0.00 0.92 0.00 0.08
#> TCGA.D8.A1Y2.01 1 0.0000 0.706 1.00 0.00 0.00 0.00
#> TCGA.E2.A1L6.01 4 0.0000 0.543 0.00 0.00 0.00 1.00
#> TCGA.E2.A1IF.01 2 0.0000 0.848 0.00 1.00 0.00 0.00
#> TCGA.A2.A3KD.01 4 0.2921 0.629 0.00 0.14 0.00 0.86
#> TCGA.BH.A0DV.01 2 0.1211 0.846 0.00 0.96 0.04 0.00
#> TCGA.BH.A0BM.01 3 0.4977 1.000 0.00 0.00 0.54 0.46
#> TCGA.AR.A24W.01 2 0.0000 0.848 0.00 1.00 0.00 0.00
#> TCGA.OL.A5RV.01 2 0.1211 0.833 0.00 0.96 0.00 0.04
#> TCGA.A2.A259.01 2 0.4948 0.517 0.00 0.56 0.44 0.00
#> TCGA.E2.A1B1.01 1 0.4855 0.707 0.60 0.00 0.40 0.00
#> TCGA.A2.A0SU.01 1 0.0000 0.706 1.00 0.00 0.00 0.00
#> TCGA.BH.A0HF.01 3 0.4977 1.000 0.00 0.00 0.54 0.46
#> TCGA.BH.A8G0.01 2 0.1211 0.846 0.00 0.96 0.04 0.00
#> TCGA.EW.A2FR.01 1 0.0000 0.706 1.00 0.00 0.00 0.00
#> TCGA.BH.A0BJ.01 2 0.2335 0.807 0.00 0.92 0.02 0.06
#> TCGA.E2.A14U.01 2 0.4277 0.701 0.00 0.72 0.28 0.00
#> TCGA.D8.A1JH.01 1 0.5570 0.658 0.54 0.02 0.44 0.00
#> TCGA.BH.A1EU.01 2 0.0707 0.841 0.00 0.98 0.00 0.02
#> TCGA.D8.A1JU.01 2 0.1211 0.846 0.00 0.96 0.04 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.AC.A3QP.01 2 0.0000 0.845 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A2LJ.01 1 0.3274 0.641 0.78 0.22 0.00 0.00 0.00
#> TCGA.D8.A1JB.01 1 0.2516 0.559 0.86 0.00 0.00 0.00 0.14
#> TCGA.E2.A3DX.01 2 0.4262 0.212 0.44 0.56 0.00 0.00 0.00
#> TCGA.MS.A51U.01 2 0.0609 0.837 0.00 0.98 0.00 0.02 0.00
#> TCGA.D8.A1Y2.01 5 0.3109 0.962 0.20 0.00 0.00 0.00 0.80
#> TCGA.E2.A1L6.01 4 0.1410 0.840 0.00 0.00 0.06 0.94 0.00
#> TCGA.E2.A1IF.01 2 0.0000 0.845 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A3KD.01 4 0.1732 0.847 0.00 0.08 0.00 0.92 0.00
#> TCGA.BH.A0DV.01 2 0.1043 0.833 0.04 0.96 0.00 0.00 0.00
#> TCGA.BH.A0BM.01 3 0.1732 1.000 0.00 0.00 0.92 0.08 0.00
#> TCGA.AR.A24W.01 2 0.0000 0.845 0.00 1.00 0.00 0.00 0.00
#> TCGA.OL.A5RV.01 2 0.0000 0.845 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A259.01 1 0.3274 0.641 0.78 0.22 0.00 0.00 0.00
#> TCGA.E2.A1B1.01 1 0.3424 0.402 0.76 0.00 0.00 0.00 0.24
#> TCGA.A2.A0SU.01 5 0.2929 0.954 0.18 0.00 0.00 0.00 0.82
#> TCGA.BH.A0HF.01 3 0.1732 1.000 0.00 0.00 0.92 0.08 0.00
#> TCGA.BH.A8G0.01 2 0.1732 0.808 0.08 0.92 0.00 0.00 0.00
#> TCGA.EW.A2FR.01 5 0.3424 0.936 0.24 0.00 0.00 0.00 0.76
#> TCGA.BH.A0BJ.01 2 0.8439 0.170 0.04 0.48 0.14 0.16 0.18
#> TCGA.E2.A14U.01 2 0.4182 0.332 0.40 0.60 0.00 0.00 0.00
#> TCGA.D8.A1JH.01 1 0.0000 0.644 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1EU.01 2 0.0609 0.839 0.00 0.98 0.02 0.00 0.00
#> TCGA.D8.A1JU.01 2 0.0609 0.841 0.02 0.98 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.AC.A3QP.01 2 0.0000 0.852 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A2LJ.01 1 0.2631 0.664 0.82 0.18 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JB.01 1 0.3460 0.618 0.76 0.00 0.00 0.00 0.22 0.02
#> TCGA.E2.A3DX.01 2 0.3499 0.613 0.32 0.68 0.00 0.00 0.00 0.00
#> TCGA.MS.A51U.01 2 0.1807 0.811 0.00 0.92 0.00 0.06 0.00 0.02
#> TCGA.D8.A1Y2.01 5 0.1267 0.908 0.06 0.00 0.00 0.00 0.94 0.00
#> TCGA.E2.A1L6.01 4 0.1092 0.911 0.00 0.00 0.02 0.96 0.00 0.02
#> TCGA.E2.A1IF.01 2 0.0000 0.852 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A3KD.01 4 0.0937 0.910 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.BH.A0DV.01 2 0.1814 0.840 0.10 0.90 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BM.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A24W.01 2 0.0547 0.845 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.OL.A5RV.01 2 0.1480 0.827 0.00 0.94 0.00 0.04 0.00 0.02
#> TCGA.A2.A259.01 1 0.2260 0.696 0.86 0.14 0.00 0.00 0.00 0.00
#> TCGA.E2.A1B1.01 1 0.3592 0.592 0.74 0.00 0.00 0.00 0.24 0.02
#> TCGA.A2.A0SU.01 5 0.0937 0.854 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.BH.A0HF.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A8G0.01 2 0.2048 0.830 0.12 0.88 0.00 0.00 0.00 0.00
#> TCGA.EW.A2FR.01 5 0.2350 0.881 0.10 0.00 0.00 0.00 0.88 0.02
#> TCGA.BH.A0BJ.01 6 0.1556 0.000 0.00 0.08 0.00 0.00 0.00 0.92
#> TCGA.E2.A14U.01 2 0.3578 0.549 0.34 0.66 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JH.01 1 0.0547 0.711 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.BH.A1EU.01 2 0.1814 0.807 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.D8.A1JU.01 2 0.1814 0.840 0.10 0.90 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.AC.A3QP.01 2 0.1006 0.8312 0.02 0.96 0 0.02 0.00 0.00 0.00
#> TCGA.AR.A2LJ.01 1 0.3139 0.3733 0.70 0.30 0 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JB.01 1 0.3558 0.1121 0.52 0.00 0 0.00 0.48 0.00 0.00
#> TCGA.E2.A3DX.01 2 0.3221 0.5237 0.32 0.68 0 0.00 0.00 0.00 0.00
#> TCGA.MS.A51U.01 2 0.3772 0.7428 0.02 0.80 0 0.10 0.00 0.02 0.06
#> TCGA.D8.A1Y2.01 5 0.0504 0.8609 0.00 0.00 0 0.00 0.98 0.00 0.02
#> TCGA.E2.A1L6.01 4 0.1671 0.8976 0.00 0.00 0 0.90 0.00 0.00 0.10
#> TCGA.E2.A1IF.01 2 0.1006 0.8270 0.00 0.96 0 0.02 0.00 0.00 0.02
#> TCGA.A2.A3KD.01 4 0.0000 0.8978 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.BH.A0DV.01 2 0.1166 0.8236 0.06 0.94 0 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BM.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.AR.A24W.01 2 0.1860 0.8165 0.00 0.92 0 0.04 0.00 0.02 0.02
#> TCGA.OL.A5RV.01 2 0.3257 0.7727 0.02 0.84 0 0.08 0.00 0.02 0.04
#> TCGA.A2.A259.01 1 0.2422 0.5008 0.82 0.18 0 0.00 0.00 0.00 0.00
#> TCGA.E2.A1B1.01 1 0.3562 0.0634 0.50 0.00 0 0.00 0.50 0.00 0.00
#> TCGA.A2.A0SU.01 7 0.2945 0.0000 0.00 0.00 0 0.00 0.26 0.00 0.74
#> TCGA.BH.A0HF.01 3 0.0000 1.0000 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.BH.A8G0.01 2 0.1166 0.8236 0.06 0.94 0 0.00 0.00 0.00 0.00
#> TCGA.EW.A2FR.01 5 0.1166 0.8705 0.06 0.00 0 0.00 0.94 0.00 0.00
#> TCGA.BH.A0BJ.01 6 0.0000 0.0000 0.00 0.00 0 0.00 0.00 1.00 0.00
#> TCGA.E2.A14U.01 2 0.3496 0.3134 0.42 0.58 0 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JH.01 1 0.3000 0.3944 0.84 0.00 0 0.00 0.04 0.02 0.10
#> TCGA.BH.A1EU.01 2 0.1671 0.7877 0.00 0.90 0 0.00 0.00 0.10 0.00
#> TCGA.D8.A1JU.01 2 0.1664 0.8267 0.06 0.92 0 0.00 0.00 0.00 0.02
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.AC.A3QP.01 2 0.1091 0.722 0.06 0.94 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A2LJ.01 1 0.4998 0.412 0.64 0.16 0.00 0.00 0.10 0.00 0.00 0.10
#> TCGA.D8.A1JB.01 5 0.3385 0.607 0.16 0.00 0.00 0.00 0.76 0.00 0.00 0.08
#> TCGA.E2.A3DX.01 1 0.3618 0.289 0.60 0.38 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.MS.A51U.01 2 0.2348 0.709 0.04 0.88 0.00 0.02 0.00 0.00 0.00 0.06
#> TCGA.D8.A1Y2.01 5 0.3794 0.462 0.04 0.00 0.00 0.00 0.74 0.00 0.18 0.04
#> TCGA.E2.A1L6.01 4 0.0000 0.677 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1IF.01 2 0.0808 0.737 0.04 0.96 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A3KD.01 4 0.4963 0.678 0.08 0.06 0.00 0.66 0.00 0.00 0.02 0.18
#> TCGA.BH.A0DV.01 2 0.3658 0.235 0.40 0.58 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.BH.A0BM.01 3 0.0471 0.984 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.AR.A24W.01 2 0.1607 0.732 0.04 0.92 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.OL.A5RV.01 2 0.1275 0.705 0.02 0.94 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.A2.A259.01 1 0.4514 0.073 0.68 0.04 0.00 0.00 0.16 0.00 0.00 0.12
#> TCGA.E2.A1B1.01 5 0.2994 0.650 0.14 0.00 0.00 0.00 0.80 0.00 0.00 0.06
#> TCGA.A2.A0SU.01 7 0.0808 0.000 0.00 0.00 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.BH.A0HF.01 3 0.0000 0.984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A8G0.01 1 0.3333 -0.138 0.50 0.50 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A2FR.01 5 0.1091 0.651 0.00 0.00 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.BH.A0BJ.01 6 0.0000 0.000 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E2.A14U.01 1 0.4673 0.493 0.56 0.34 0.00 0.00 0.02 0.00 0.00 0.08
#> TCGA.D8.A1JH.01 8 0.3431 0.000 0.20 0.00 0.00 0.00 0.06 0.00 0.00 0.74
#> TCGA.BH.A1EU.01 2 0.3744 0.617 0.18 0.74 0.00 0.00 0.00 0.06 0.00 0.02
#> TCGA.D8.A1JU.01 2 0.3449 0.433 0.32 0.66 0.00 0.00 0.00 0.00 0.00 0.02
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node041. Child nodes: Node02121-leaf , Node02122-leaf , Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02214-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02321-leaf , Node02322-leaf , Node02421-leaf , Node02422-leaf , Node02423-leaf , Node04111-leaf , Node04112-leaf , Node04113 , Node04131-leaf , Node04132-leaf , Node04133-leaf , Node04221-leaf , Node04222-leaf , Node04331-leaf , Node04332-leaf , Node04333-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0413"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 18 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 7.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4254 0.575 0.575
#> 3 3 1.000 1.000 1.000 0.5525 0.765 0.591
#> 4 4 0.974 0.919 0.990 0.0368 0.974 0.923
#> 5 5 1.000 0.872 0.989 0.0341 0.980 0.938
#> 6 6 0.915 0.779 0.953 0.0619 0.948 0.822
#> 7 7 0.915 0.642 0.918 0.0617 0.935 0.737
#> 8 8 0.980 0.625 0.950 0.0226 0.980 0.900
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 7
#> attr(,"optional")
#> [1] 2 3 6
There is also optional best \(k\) = 2 3 6 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.AC.A5EH.01 2 0 1 0 1
#> TCGA.AO.A0JD.01 1 0 1 1 0
#> TCGA.E2.A1B0.01 2 0 1 0 1
#> TCGA.OL.A66J.01 1 0 1 1 0
#> TCGA.D8.A27V.01 1 0 1 1 0
#> TCGA.D8.A1XY.01 1 0 1 1 0
#> TCGA.AR.A24S.01 1 0 1 1 0
#> TCGA.C8.A26W.01 1 0 1 1 0
#> TCGA.E2.A1LL.01 2 0 1 0 1
#> TCGA.AN.A0XL.01 1 0 1 1 0
#> TCGA.E2.A1LA.01 1 0 1 1 0
#> TCGA.A2.A0YH.01 1 0 1 1 0
#> TCGA.E9.A1RH.01 2 0 1 0 1
#> TCGA.D8.A1JK.01 2 0 1 0 1
#> TCGA.E9.A1N4.01 1 0 1 1 0
#> TCGA.AC.A2QI.01 1 0 1 1 0
#> TCGA.GM.A2DA.01 1 0 1 1 0
#> TCGA.C8.A1HG.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.AC.A5EH.01 2 0 1 0 1 0
#> TCGA.AO.A0JD.01 1 0 1 1 0 0
#> TCGA.E2.A1B0.01 2 0 1 0 1 0
#> TCGA.OL.A66J.01 1 0 1 1 0 0
#> TCGA.D8.A27V.01 1 0 1 1 0 0
#> TCGA.D8.A1XY.01 1 0 1 1 0 0
#> TCGA.AR.A24S.01 3 0 1 0 0 1
#> TCGA.C8.A26W.01 3 0 1 0 0 1
#> TCGA.E2.A1LL.01 2 0 1 0 1 0
#> TCGA.AN.A0XL.01 1 0 1 1 0 0
#> TCGA.E2.A1LA.01 1 0 1 1 0 0
#> TCGA.A2.A0YH.01 3 0 1 0 0 1
#> TCGA.E9.A1RH.01 2 0 1 0 1 0
#> TCGA.D8.A1JK.01 2 0 1 0 1 0
#> TCGA.E9.A1N4.01 1 0 1 1 0 0
#> TCGA.AC.A2QI.01 1 0 1 1 0 0
#> TCGA.GM.A2DA.01 1 0 1 1 0 0
#> TCGA.C8.A1HG.01 3 0 1 0 0 1
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.AC.A5EH.01 4 0.000 0.000 0.00 0 0.00 1.0
#> TCGA.AO.A0JD.01 1 0.000 1.000 1.00 0 0.00 0.0
#> TCGA.E2.A1B0.01 2 0.000 1.000 0.00 1 0.00 0.0
#> TCGA.OL.A66J.01 1 0.000 1.000 1.00 0 0.00 0.0
#> TCGA.D8.A27V.01 1 0.000 1.000 1.00 0 0.00 0.0
#> TCGA.D8.A1XY.01 1 0.000 1.000 1.00 0 0.00 0.0
#> TCGA.AR.A24S.01 3 0.000 0.919 0.00 0 1.00 0.0
#> TCGA.C8.A26W.01 3 0.201 0.848 0.08 0 0.92 0.0
#> TCGA.E2.A1LL.01 2 0.000 1.000 0.00 1 0.00 0.0
#> TCGA.AN.A0XL.01 1 0.000 1.000 1.00 0 0.00 0.0
#> TCGA.E2.A1LA.01 1 0.000 1.000 1.00 0 0.00 0.0
#> TCGA.A2.A0YH.01 3 0.000 0.919 0.00 0 1.00 0.0
#> TCGA.E9.A1RH.01 2 0.000 1.000 0.00 1 0.00 0.0
#> TCGA.D8.A1JK.01 2 0.000 1.000 0.00 1 0.00 0.0
#> TCGA.E9.A1N4.01 1 0.000 1.000 1.00 0 0.00 0.0
#> TCGA.AC.A2QI.01 1 0.000 1.000 1.00 0 0.00 0.0
#> TCGA.GM.A2DA.01 1 0.000 1.000 1.00 0 0.00 0.0
#> TCGA.C8.A1HG.01 3 0.234 0.863 0.00 0 0.90 0.1
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.AC.A5EH.01 4 0.0000 0.000 0.00 0 0.00 1.00 0.00
#> TCGA.AO.A0JD.01 1 0.1648 0.940 0.94 0 0.02 0.00 0.04
#> TCGA.E2.A1B0.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.OL.A66J.01 1 0.0000 0.993 1.00 0 0.00 0.00 0.00
#> TCGA.D8.A27V.01 1 0.0000 0.993 1.00 0 0.00 0.00 0.00
#> TCGA.D8.A1XY.01 1 0.0000 0.993 1.00 0 0.00 0.00 0.00
#> TCGA.AR.A24S.01 3 0.1043 0.938 0.00 0 0.96 0.00 0.04
#> TCGA.C8.A26W.01 3 0.1216 0.935 0.02 0 0.96 0.00 0.02
#> TCGA.E2.A1LL.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.AN.A0XL.01 1 0.0000 0.993 1.00 0 0.00 0.00 0.00
#> TCGA.E2.A1LA.01 1 0.0000 0.993 1.00 0 0.00 0.00 0.00
#> TCGA.A2.A0YH.01 3 0.0609 0.947 0.00 0 0.98 0.00 0.02
#> TCGA.E9.A1RH.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.D8.A1JK.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.E9.A1N4.01 1 0.0000 0.993 1.00 0 0.00 0.00 0.00
#> TCGA.AC.A2QI.01 1 0.0000 0.993 1.00 0 0.00 0.00 0.00
#> TCGA.GM.A2DA.01 1 0.0000 0.993 1.00 0 0.00 0.00 0.00
#> TCGA.C8.A1HG.01 5 0.1216 0.000 0.00 0 0.02 0.02 0.96
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.AC.A5EH.01 4 0.0000 0.000 0.00 0 0.00 1 0.00 0.00
#> TCGA.AO.A0JD.01 6 0.3819 0.000 0.28 0 0.02 0 0.00 0.70
#> TCGA.E2.A1B0.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.OL.A66J.01 1 0.0937 0.952 0.96 0 0.00 0 0.00 0.04
#> TCGA.D8.A27V.01 1 0.0547 0.967 0.98 0 0.00 0 0.00 0.02
#> TCGA.D8.A1XY.01 1 0.0000 0.973 1.00 0 0.00 0 0.00 0.00
#> TCGA.AR.A24S.01 3 0.2048 0.780 0.00 0 0.88 0 0.00 0.12
#> TCGA.C8.A26W.01 3 0.3163 0.755 0.04 0 0.82 0 0.00 0.14
#> TCGA.E2.A1LL.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.AN.A0XL.01 1 0.0547 0.967 0.98 0 0.00 0 0.00 0.02
#> TCGA.E2.A1LA.01 1 0.0000 0.973 1.00 0 0.00 0 0.00 0.00
#> TCGA.A2.A0YH.01 3 0.2094 0.796 0.00 0 0.90 0 0.02 0.08
#> TCGA.E9.A1RH.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.D8.A1JK.01 2 0.0000 1.000 0.00 1 0.00 0 0.00 0.00
#> TCGA.E9.A1N4.01 1 0.1267 0.911 0.94 0 0.00 0 0.00 0.06
#> TCGA.AC.A2QI.01 1 0.0000 0.973 1.00 0 0.00 0 0.00 0.00
#> TCGA.GM.A2DA.01 1 0.0000 0.973 1.00 0 0.00 0 0.00 0.00
#> TCGA.C8.A1HG.01 5 0.0000 0.000 0.00 0 0.00 0 1.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.AC.A5EH.01 4 0.0000 0.0000 0.00 0 0.00 1 0 0.00 0.00
#> TCGA.AO.A0JD.01 6 0.0863 0.0000 0.04 0 0.00 0 0 0.96 0.00
#> TCGA.E2.A1B0.01 2 0.0000 1.0000 0.00 1 0.00 0 0 0.00 0.00
#> TCGA.OL.A66J.01 1 0.0863 0.9460 0.96 0 0.00 0 0 0.00 0.04
#> TCGA.D8.A27V.01 1 0.0000 0.9742 1.00 0 0.00 0 0 0.00 0.00
#> TCGA.D8.A1XY.01 1 0.1006 0.9643 0.96 0 0.00 0 0 0.02 0.02
#> TCGA.AR.A24S.01 3 0.0000 0.5194 0.00 0 1.00 0 0 0.00 0.00
#> TCGA.C8.A26W.01 7 0.5338 -0.2847 0.00 0 0.32 0 0 0.20 0.48
#> TCGA.E2.A1LL.01 2 0.0000 1.0000 0.00 1 0.00 0 0 0.00 0.00
#> TCGA.AN.A0XL.01 1 0.1006 0.9643 0.96 0 0.00 0 0 0.02 0.02
#> TCGA.E2.A1LA.01 1 0.0000 0.9742 1.00 0 0.00 0 0 0.00 0.00
#> TCGA.A2.A0YH.01 3 0.4244 0.4813 0.00 0 0.54 0 0 0.04 0.42
#> TCGA.E9.A1RH.01 2 0.0000 1.0000 0.00 1 0.00 0 0 0.00 0.00
#> TCGA.D8.A1JK.01 2 0.0000 1.0000 0.00 1 0.00 0 0 0.00 0.00
#> TCGA.E9.A1N4.01 7 0.5128 0.0724 0.32 0 0.00 0 0 0.16 0.52
#> TCGA.AC.A2QI.01 1 0.0504 0.9701 0.98 0 0.00 0 0 0.02 0.00
#> TCGA.GM.A2DA.01 1 0.0000 0.9742 1.00 0 0.00 0 0 0.00 0.00
#> TCGA.C8.A1HG.01 5 0.0000 0.0000 0.00 0 0.00 0 1 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.AC.A5EH.01 4 0.0000 0.0000 0.00 0 0.00 1 0 0.00 0.00 0.00
#> TCGA.AO.A0JD.01 6 0.0000 0.0000 0.00 0 0.00 0 0 1.00 0.00 0.00
#> TCGA.E2.A1B0.01 2 0.0000 1.0000 0.00 1 0.00 0 0 0.00 0.00 0.00
#> TCGA.OL.A66J.01 1 0.0471 0.9791 0.98 0 0.00 0 0 0.00 0.00 0.02
#> TCGA.D8.A27V.01 1 0.0000 0.9966 1.00 0 0.00 0 0 0.00 0.00 0.00
#> TCGA.D8.A1XY.01 1 0.0000 0.9966 1.00 0 0.00 0 0 0.00 0.00 0.00
#> TCGA.AR.A24S.01 3 0.0000 0.0000 0.00 0 1.00 0 0 0.00 0.00 0.00
#> TCGA.C8.A26W.01 7 0.3227 0.0428 0.00 0 0.14 0 0 0.08 0.78 0.00
#> TCGA.E2.A1LL.01 2 0.0000 1.0000 0.00 1 0.00 0 0 0.00 0.00 0.00
#> TCGA.AN.A0XL.01 1 0.0000 0.9966 1.00 0 0.00 0 0 0.00 0.00 0.00
#> TCGA.E2.A1LA.01 1 0.0000 0.9966 1.00 0 0.00 0 0 0.00 0.00 0.00
#> TCGA.A2.A0YH.01 7 0.4302 0.2466 0.00 0 0.08 0 0 0.00 0.56 0.36
#> TCGA.E9.A1RH.01 2 0.0000 1.0000 0.00 1 0.00 0 0 0.00 0.00 0.00
#> TCGA.D8.A1JK.01 2 0.0000 1.0000 0.00 1 0.00 0 0 0.00 0.00 0.00
#> TCGA.E9.A1N4.01 8 0.4174 0.0000 0.04 0 0.00 0 0 0.02 0.32 0.62
#> TCGA.AC.A2QI.01 1 0.0000 0.9966 1.00 0 0.00 0 0 0.00 0.00 0.00
#> TCGA.GM.A2DA.01 1 0.0000 0.9966 1.00 0 0.00 0 0 0.00 0.00 0.00
#> TCGA.C8.A1HG.01 5 0.0000 0.0000 0.00 0 0.00 0 1 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node04. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0115-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0151-leaf , Node0152-leaf , Node0153-leaf , Node0154-leaf , Node0211-leaf , Node0212 , Node0213 , Node0221 , Node0222 , Node0231-leaf , Node0232 , Node0233-leaf , Node0241-leaf , Node0242 , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0331-leaf , Node0332-leaf , Node0341-leaf , Node0342-leaf , Node0343-leaf , Node0411 , Node0412-leaf , Node0413 , Node0421-leaf , Node0422 , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["042"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 67 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.998 0.999 0.4267 0.575 0.575
#> 3 3 1.000 0.995 0.998 0.3118 0.862 0.761
#> 4 4 0.885 0.900 0.950 0.1195 0.925 0.835
#> 5 5 0.825 0.821 0.922 0.1384 0.896 0.738
#> 6 6 0.766 0.713 0.849 0.0550 0.953 0.844
#> 7 7 0.726 0.615 0.819 0.0181 0.957 0.839
#> 8 8 0.686 0.564 0.741 0.0226 0.947 0.796
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.3C.AALK.01 1 0.000 0.998 1.00 0.00
#> TCGA.AR.A255.01 2 0.000 1.000 0.00 1.00
#> TCGA.A8.A0A6.01 1 0.000 0.998 1.00 0.00
#> TCGA.BH.A1EY.01 1 0.000 0.998 1.00 0.00
#> TCGA.A2.A4RW.01 1 0.000 0.998 1.00 0.00
#> TCGA.AQ.A1H3.01 1 0.000 0.998 1.00 0.00
#> TCGA.BH.A1EW.01 1 0.000 0.998 1.00 0.00
#> TCGA.EW.A2FS.01 2 0.000 1.000 0.00 1.00
#> TCGA.AR.A1AT.01 1 0.000 0.998 1.00 0.00
#> TCGA.AC.A3OD.01 1 0.000 0.998 1.00 0.00
#> TCGA.AR.A5QM.01 2 0.000 1.000 0.00 1.00
#> TCGA.AC.A23H.01 2 0.000 1.000 0.00 1.00
#> TCGA.BH.AB28.01 1 0.000 0.998 1.00 0.00
#> TCGA.OL.A5D6.01 1 0.000 0.998 1.00 0.00
#> TCGA.A2.A0T4.01 1 0.000 0.998 1.00 0.00
#> TCGA.BH.A0DG.01 1 0.000 0.998 1.00 0.00
#> TCGA.D8.A27G.01 2 0.000 1.000 0.00 1.00
#> TCGA.AR.A0TQ.01 2 0.000 1.000 0.00 1.00
#> TCGA.AO.A0JE.01 1 0.000 0.998 1.00 0.00
#> TCGA.E9.A228.01 2 0.000 1.000 0.00 1.00
#> TCGA.LL.A740.01 1 0.000 0.998 1.00 0.00
#> TCGA.BH.A0BZ.01 2 0.000 1.000 0.00 1.00
#> TCGA.BH.A0C0.01 1 0.000 0.998 1.00 0.00
#> TCGA.EW.A1IW.01 1 0.000 0.998 1.00 0.00
#> TCGA.JL.A3YW.01 1 0.000 0.998 1.00 0.00
#> TCGA.AN.A0XN.01 1 0.000 0.998 1.00 0.00
#> TCGA.D8.A1JF.01 2 0.000 1.000 0.00 1.00
#> TCGA.OL.A66N.01 1 0.000 0.998 1.00 0.00
#> TCGA.A7.A4SC.01 1 0.000 0.998 1.00 0.00
#> TCGA.GM.A2DL.01 1 0.000 0.998 1.00 0.00
#> TCGA.E9.A22B.01 2 0.000 1.000 0.00 1.00
#> TCGA.A2.A3XV.01 1 0.000 0.998 1.00 0.00
#> TCGA.AC.A6IX.01 1 0.000 0.998 1.00 0.00
#> TCGA.E9.A22D.01 1 0.000 0.998 1.00 0.00
#> TCGA.E9.A1NF.01 1 0.000 0.998 1.00 0.00
#> TCGA.A1.A0SM.01 1 0.000 0.998 1.00 0.00
#> TCGA.D8.A1JG.01 1 0.000 0.998 1.00 0.00
#> TCGA.C8.A8HQ.01 2 0.000 1.000 0.00 1.00
#> TCGA.E2.A1LE.01 1 0.000 0.998 1.00 0.00
#> TCGA.C8.A275.01 1 0.000 0.998 1.00 0.00
#> TCGA.AO.A12E.01 2 0.000 1.000 0.00 1.00
#> TCGA.AR.A5QN.01 1 0.000 0.998 1.00 0.00
#> TCGA.D8.A27N.01 1 0.000 0.998 1.00 0.00
#> TCGA.BH.A202.01 1 0.000 0.998 1.00 0.00
#> TCGA.A1.A0SN.01 2 0.000 1.000 0.00 1.00
#> TCGA.E9.A295.01 2 0.000 1.000 0.00 1.00
#> TCGA.AC.A8OP.01 2 0.000 1.000 0.00 1.00
#> TCGA.GI.A2C8.01 2 0.000 1.000 0.00 1.00
#> TCGA.AR.A24T.01 1 0.000 0.998 1.00 0.00
#> TCGA.AC.A2FE.01 1 0.000 0.998 1.00 0.00
#> TCGA.S3.AA17.01 1 0.000 0.998 1.00 0.00
#> TCGA.A2.A3KC.01 1 0.000 0.998 1.00 0.00
#> TCGA.OL.A66L.01 2 0.000 1.000 0.00 1.00
#> TCGA.OK.A5Q2.01 1 0.000 0.998 1.00 0.00
#> TCGA.AR.A254.01 1 0.000 0.998 1.00 0.00
#> TCGA.A2.A0T6.01 1 0.000 0.998 1.00 0.00
#> TCGA.EW.A3E8.01 1 0.000 0.998 1.00 0.00
#> TCGA.WT.AB41.01 1 0.000 0.998 1.00 0.00
#> TCGA.LL.A5YL.01 1 0.000 0.998 1.00 0.00
#> TCGA.C8.A26X.01 1 0.000 0.998 1.00 0.00
#> TCGA.D8.A1Y3.01 2 0.000 1.000 0.00 1.00
#> TCGA.BH.A0DK.01 2 0.000 1.000 0.00 1.00
#> TCGA.BH.A203.01 1 0.000 0.998 1.00 0.00
#> TCGA.B6.A0IK.01 1 0.000 0.998 1.00 0.00
#> TCGA.E9.A1RF.01 2 0.000 1.000 0.00 1.00
#> TCGA.BH.A1EO.01 1 0.402 0.913 0.92 0.08
#> TCGA.BH.A0DI.01 1 0.000 0.998 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.3C.AALK.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.AR.A255.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.A8.A0A6.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.BH.A1EY.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.A2.A4RW.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.AQ.A1H3.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.BH.A1EW.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.EW.A2FS.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AR.A1AT.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.AC.A3OD.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.AR.A5QM.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AC.A23H.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.BH.AB28.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.OL.A5D6.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.A2.A0T4.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.BH.A0DG.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.D8.A27G.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AR.A0TQ.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AO.A0JE.01 1 0.0892 0.978 0.98 0.00 0.02
#> TCGA.E9.A228.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.LL.A740.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.BH.A0BZ.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.BH.A0C0.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.EW.A1IW.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.JL.A3YW.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.AN.A0XN.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.D8.A1JF.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.OL.A66N.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.A7.A4SC.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.GM.A2DL.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.E9.A22B.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.A2.A3XV.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.AC.A6IX.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.E9.A22D.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.E9.A1NF.01 1 0.1529 0.959 0.96 0.00 0.04
#> TCGA.A1.A0SM.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.D8.A1JG.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.C8.A8HQ.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.E2.A1LE.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.C8.A275.01 1 0.2537 0.917 0.92 0.00 0.08
#> TCGA.AO.A12E.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AR.A5QN.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.D8.A27N.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.BH.A202.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.A1.A0SN.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.E9.A295.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AC.A8OP.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.GI.A2C8.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AR.A24T.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.AC.A2FE.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.S3.AA17.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.A2.A3KC.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.OL.A66L.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.OK.A5Q2.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.AR.A254.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.A2.A0T6.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.EW.A3E8.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.WT.AB41.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.LL.A5YL.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.C8.A26X.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.D8.A1Y3.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.BH.A0DK.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.BH.A203.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.B6.A0IK.01 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.E9.A1RF.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.BH.A1EO.01 1 0.0892 0.976 0.98 0.02 0.00
#> TCGA.BH.A0DI.01 1 0.0000 0.996 1.00 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.3C.AALK.01 1 0.2345 0.879 0.90 0.10 0.00 0.00
#> TCGA.AR.A255.01 2 0.4948 0.290 0.00 0.56 0.00 0.44
#> TCGA.A8.A0A6.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.BH.A1EY.01 1 0.1211 0.944 0.96 0.00 0.00 0.04
#> TCGA.A2.A4RW.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.AQ.A1H3.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.BH.A1EW.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.EW.A2FS.01 2 0.1637 0.846 0.00 0.94 0.00 0.06
#> TCGA.AR.A1AT.01 1 0.1211 0.944 0.96 0.00 0.00 0.04
#> TCGA.AC.A3OD.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.AR.A5QM.01 2 0.0000 0.880 0.00 1.00 0.00 0.00
#> TCGA.AC.A23H.01 4 0.1211 1.000 0.00 0.04 0.00 0.96
#> TCGA.BH.AB28.01 1 0.0707 0.947 0.98 0.02 0.00 0.00
#> TCGA.OL.A5D6.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.A2.A0T4.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.BH.A0DG.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.D8.A27G.01 2 0.0000 0.880 0.00 1.00 0.00 0.00
#> TCGA.AR.A0TQ.01 2 0.0000 0.880 0.00 1.00 0.00 0.00
#> TCGA.AO.A0JE.01 1 0.5755 0.766 0.76 0.10 0.10 0.04
#> TCGA.E9.A228.01 2 0.4790 0.444 0.00 0.62 0.00 0.38
#> TCGA.LL.A740.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.BH.A0BZ.01 4 0.1211 1.000 0.00 0.04 0.00 0.96
#> TCGA.BH.A0C0.01 1 0.1211 0.944 0.96 0.00 0.00 0.04
#> TCGA.EW.A1IW.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.JL.A3YW.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.AN.A0XN.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.D8.A1JF.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.OL.A66N.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.A7.A4SC.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.GM.A2DL.01 1 0.4284 0.756 0.78 0.20 0.00 0.02
#> TCGA.E9.A22B.01 2 0.1211 0.857 0.04 0.96 0.00 0.00
#> TCGA.A2.A3XV.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.AC.A6IX.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.E9.A22D.01 2 0.1637 0.834 0.06 0.94 0.00 0.00
#> TCGA.E9.A1NF.01 1 0.1913 0.933 0.94 0.00 0.02 0.04
#> TCGA.A1.A0SM.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.D8.A1JG.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.C8.A8HQ.01 2 0.4713 0.481 0.00 0.64 0.00 0.36
#> TCGA.E2.A1LE.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.C8.A275.01 1 0.3821 0.838 0.84 0.00 0.12 0.04
#> TCGA.AO.A12E.01 2 0.0000 0.880 0.00 1.00 0.00 0.00
#> TCGA.AR.A5QN.01 1 0.1637 0.916 0.94 0.06 0.00 0.00
#> TCGA.D8.A27N.01 1 0.1411 0.945 0.96 0.02 0.00 0.02
#> TCGA.BH.A202.01 1 0.1211 0.944 0.96 0.00 0.00 0.04
#> TCGA.A1.A0SN.01 2 0.3801 0.693 0.00 0.78 0.00 0.22
#> TCGA.E9.A295.01 2 0.0000 0.880 0.00 1.00 0.00 0.00
#> TCGA.AC.A8OP.01 4 0.1211 1.000 0.00 0.04 0.00 0.96
#> TCGA.GI.A2C8.01 2 0.0000 0.880 0.00 1.00 0.00 0.00
#> TCGA.AR.A24T.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.AC.A2FE.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.S3.AA17.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.A2.A3KC.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.OL.A66L.01 2 0.0707 0.871 0.02 0.98 0.00 0.00
#> TCGA.OK.A5Q2.01 1 0.0707 0.952 0.98 0.00 0.00 0.02
#> TCGA.AR.A254.01 1 0.0707 0.952 0.98 0.00 0.00 0.02
#> TCGA.A2.A0T6.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.EW.A3E8.01 1 0.4713 0.478 0.64 0.36 0.00 0.00
#> TCGA.WT.AB41.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.LL.A5YL.01 1 0.0000 0.958 1.00 0.00 0.00 0.00
#> TCGA.C8.A26X.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.D8.A1Y3.01 2 0.0000 0.880 0.00 1.00 0.00 0.00
#> TCGA.BH.A0DK.01 2 0.0707 0.871 0.02 0.98 0.00 0.00
#> TCGA.BH.A203.01 1 0.1211 0.944 0.96 0.00 0.00 0.04
#> TCGA.B6.A0IK.01 1 0.1913 0.933 0.94 0.00 0.02 0.04
#> TCGA.E9.A1RF.01 4 0.1211 1.000 0.00 0.04 0.00 0.96
#> TCGA.BH.A1EO.01 2 0.1211 0.857 0.04 0.96 0.00 0.00
#> TCGA.BH.A0DI.01 1 0.0707 0.952 0.98 0.00 0.00 0.02
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.3C.AALK.01 1 0.1043 0.8959 0.96 0.00 0.00 0.00 0.04
#> TCGA.AR.A255.01 2 0.4132 0.6407 0.00 0.72 0.00 0.26 0.02
#> TCGA.A8.A0A6.01 1 0.0000 0.9241 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1EY.01 5 0.2020 0.7765 0.10 0.00 0.00 0.00 0.90
#> TCGA.A2.A4RW.01 1 0.0000 0.9241 1.00 0.00 0.00 0.00 0.00
#> TCGA.AQ.A1H3.01 1 0.0000 0.9241 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1EW.01 1 0.0000 0.9241 1.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A2FS.01 2 0.0609 0.8780 0.00 0.98 0.00 0.00 0.02
#> TCGA.AR.A1AT.01 1 0.3561 0.5874 0.74 0.00 0.00 0.00 0.26
#> TCGA.AC.A3OD.01 1 0.0000 0.9241 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A5QM.01 2 0.0000 0.8842 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A23H.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00
#> TCGA.BH.AB28.01 1 0.0609 0.9118 0.98 0.00 0.00 0.00 0.02
#> TCGA.OL.A5D6.01 5 0.4262 -0.0332 0.00 0.00 0.44 0.00 0.56
#> TCGA.A2.A0T4.01 1 0.0000 0.9241 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DG.01 1 0.0000 0.9241 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A27G.01 2 0.0609 0.8827 0.00 0.98 0.00 0.00 0.02
#> TCGA.AR.A0TQ.01 2 0.0000 0.8842 0.00 1.00 0.00 0.00 0.00
#> TCGA.AO.A0JE.01 5 0.2280 0.7302 0.12 0.00 0.00 0.00 0.88
#> TCGA.E9.A228.01 2 0.4540 0.5103 0.00 0.64 0.00 0.34 0.02
#> TCGA.LL.A740.01 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A0BZ.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00
#> TCGA.BH.A0C0.01 1 0.4262 0.0896 0.56 0.00 0.00 0.00 0.44
#> TCGA.EW.A1IW.01 1 0.0609 0.9118 0.98 0.00 0.00 0.00 0.02
#> TCGA.JL.A3YW.01 3 0.1043 0.9812 0.00 0.00 0.96 0.00 0.04
#> TCGA.AN.A0XN.01 1 0.0000 0.9241 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JF.01 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00
#> TCGA.OL.A66N.01 1 0.0000 0.9241 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A4SC.01 1 0.0000 0.9241 1.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A2DL.01 1 0.5136 0.5105 0.66 0.08 0.00 0.00 0.26
#> TCGA.E9.A22B.01 2 0.1648 0.8681 0.02 0.94 0.00 0.00 0.04
#> TCGA.A2.A3XV.01 3 0.0000 0.9748 0.00 0.00 1.00 0.00 0.00
#> TCGA.AC.A6IX.01 1 0.0000 0.9241 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A22D.01 2 0.4748 0.4524 0.30 0.66 0.00 0.00 0.04
#> TCGA.E9.A1NF.01 5 0.1410 0.7520 0.06 0.00 0.00 0.00 0.94
#> TCGA.A1.A0SM.01 1 0.0000 0.9241 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JG.01 3 0.1043 0.9812 0.00 0.00 0.96 0.00 0.04
#> TCGA.C8.A8HQ.01 2 0.4360 0.5803 0.00 0.68 0.00 0.30 0.02
#> TCGA.E2.A1LE.01 3 0.1043 0.9812 0.00 0.00 0.96 0.00 0.04
#> TCGA.C8.A275.01 5 0.1648 0.7286 0.04 0.00 0.02 0.00 0.94
#> TCGA.AO.A12E.01 2 0.0000 0.8842 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A5QN.01 1 0.1043 0.8959 0.96 0.00 0.00 0.00 0.04
#> TCGA.D8.A27N.01 1 0.4182 0.2861 0.60 0.00 0.00 0.00 0.40
#> TCGA.BH.A202.01 5 0.4302 0.1306 0.48 0.00 0.00 0.00 0.52
#> TCGA.A1.A0SN.01 2 0.2012 0.8419 0.00 0.92 0.00 0.06 0.02
#> TCGA.E9.A295.01 2 0.0000 0.8842 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A8OP.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00
#> TCGA.GI.A2C8.01 2 0.1043 0.8788 0.00 0.96 0.00 0.00 0.04
#> TCGA.AR.A24T.01 1 0.0609 0.9118 0.98 0.00 0.00 0.00 0.02
#> TCGA.AC.A2FE.01 1 0.0000 0.9241 1.00 0.00 0.00 0.00 0.00
#> TCGA.S3.AA17.01 1 0.0000 0.9241 1.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A3KC.01 1 0.0000 0.9241 1.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A66L.01 2 0.0000 0.8842 0.00 1.00 0.00 0.00 0.00
#> TCGA.OK.A5Q2.01 1 0.0000 0.9241 1.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A254.01 1 0.0609 0.9098 0.98 0.00 0.00 0.00 0.02
#> TCGA.A2.A0T6.01 1 0.0000 0.9241 1.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A3E8.01 1 0.3922 0.6802 0.78 0.18 0.00 0.00 0.04
#> TCGA.WT.AB41.01 1 0.0000 0.9241 1.00 0.00 0.00 0.00 0.00
#> TCGA.LL.A5YL.01 1 0.0000 0.9241 1.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A26X.01 3 0.1043 0.9812 0.00 0.00 0.96 0.00 0.04
#> TCGA.D8.A1Y3.01 2 0.1043 0.8788 0.00 0.96 0.00 0.00 0.04
#> TCGA.BH.A0DK.01 2 0.1043 0.8788 0.00 0.96 0.00 0.00 0.04
#> TCGA.BH.A203.01 5 0.2280 0.7684 0.12 0.00 0.00 0.00 0.88
#> TCGA.B6.A0IK.01 5 0.2020 0.7765 0.10 0.00 0.00 0.00 0.90
#> TCGA.E9.A1RF.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00
#> TCGA.BH.A1EO.01 2 0.1043 0.8788 0.00 0.96 0.00 0.00 0.04
#> TCGA.BH.A0DI.01 1 0.2280 0.8124 0.88 0.00 0.00 0.00 0.12
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.3C.AALK.01 1 0.3916 0.2864 0.68 0.02 0.00 0.00 0.00 0.30
#> TCGA.AR.A255.01 2 0.2793 0.5639 0.00 0.80 0.00 0.20 0.00 0.00
#> TCGA.A8.A0A6.01 1 0.0937 0.8745 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.BH.A1EY.01 5 0.1807 0.6993 0.02 0.00 0.00 0.00 0.92 0.06
#> TCGA.A2.A4RW.01 1 0.0547 0.8874 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.AQ.A1H3.01 1 0.0000 0.8918 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A1EW.01 1 0.0547 0.8874 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EW.A2FS.01 2 0.1480 0.7067 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.AR.A1AT.01 1 0.2941 0.6415 0.78 0.00 0.00 0.00 0.22 0.00
#> TCGA.AC.A3OD.01 1 0.0000 0.8918 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A5QM.01 2 0.0937 0.7112 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.AC.A23H.01 4 0.1556 0.9533 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.BH.AB28.01 1 0.0547 0.8806 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.OL.A5D6.01 5 0.3828 0.0450 0.00 0.00 0.44 0.00 0.56 0.00
#> TCGA.A2.A0T4.01 1 0.0000 0.8918 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DG.01 1 0.0547 0.8874 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.D8.A27G.01 2 0.3706 0.6168 0.00 0.62 0.00 0.00 0.00 0.38
#> TCGA.AR.A0TQ.01 2 0.2454 0.7199 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.AO.A0JE.01 5 0.4576 0.2574 0.04 0.00 0.00 0.00 0.56 0.40
#> TCGA.E9.A228.01 2 0.5150 0.4892 0.00 0.62 0.00 0.22 0.00 0.16
#> TCGA.LL.A740.01 3 0.1814 0.9142 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.BH.A0BZ.01 4 0.0000 0.9742 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A0C0.01 1 0.4310 0.0876 0.54 0.00 0.00 0.00 0.44 0.02
#> TCGA.EW.A1IW.01 1 0.1814 0.7925 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.JL.A3YW.01 3 0.0547 0.9575 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.AN.A0XN.01 1 0.1267 0.8465 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.D8.A1JF.01 3 0.2260 0.8807 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.OL.A66N.01 1 0.0000 0.8918 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A4SC.01 1 0.0547 0.8874 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.GM.A2DL.01 6 0.6496 0.4789 0.22 0.06 0.00 0.00 0.20 0.52
#> TCGA.E9.A22B.01 2 0.4144 0.5794 0.02 0.62 0.00 0.00 0.00 0.36
#> TCGA.A2.A3XV.01 3 0.0547 0.9472 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.AC.A6IX.01 1 0.0547 0.8874 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.E9.A22D.01 6 0.5987 0.2766 0.26 0.30 0.00 0.00 0.00 0.44
#> TCGA.E9.A1NF.01 5 0.0937 0.7020 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.A1.A0SM.01 1 0.0000 0.8918 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JG.01 3 0.0547 0.9575 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.C8.A8HQ.01 2 0.2454 0.6166 0.00 0.84 0.00 0.16 0.00 0.00
#> TCGA.E2.A1LE.01 3 0.0547 0.9575 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.C8.A275.01 5 0.0547 0.7020 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.AO.A12E.01 2 0.2260 0.7209 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.AR.A5QN.01 1 0.3647 0.1432 0.64 0.00 0.00 0.00 0.00 0.36
#> TCGA.D8.A27N.01 6 0.5992 0.2581 0.24 0.00 0.00 0.00 0.34 0.42
#> TCGA.BH.A202.01 5 0.3828 0.0423 0.44 0.00 0.00 0.00 0.56 0.00
#> TCGA.A1.A0SN.01 2 0.1556 0.6678 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.E9.A295.01 2 0.2260 0.7209 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.AC.A8OP.01 4 0.0000 0.9742 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.GI.A2C8.01 2 0.3864 0.5180 0.00 0.52 0.00 0.00 0.00 0.48
#> TCGA.AR.A24T.01 1 0.0937 0.8647 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.AC.A2FE.01 1 0.0000 0.8918 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S3.AA17.01 1 0.1267 0.8465 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.A2.A3KC.01 1 0.0000 0.8918 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A66L.01 2 0.2048 0.7132 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.OK.A5Q2.01 1 0.1267 0.8577 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.AR.A254.01 1 0.1267 0.8577 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.A2.A0T6.01 1 0.0000 0.8918 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A3E8.01 6 0.5698 0.5160 0.40 0.16 0.00 0.00 0.00 0.44
#> TCGA.WT.AB41.01 1 0.0000 0.8918 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LL.A5YL.01 1 0.0000 0.8918 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A26X.01 3 0.0547 0.9575 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.D8.A1Y3.01 2 0.3828 0.5623 0.00 0.56 0.00 0.00 0.00 0.44
#> TCGA.BH.A0DK.01 2 0.3797 0.5778 0.00 0.58 0.00 0.00 0.00 0.42
#> TCGA.BH.A203.01 5 0.1814 0.6260 0.10 0.00 0.00 0.00 0.90 0.00
#> TCGA.B6.A0IK.01 5 0.0000 0.7027 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.E9.A1RF.01 4 0.0937 0.9699 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.BH.A1EO.01 2 0.4651 0.4144 0.04 0.48 0.00 0.00 0.00 0.48
#> TCGA.BH.A0DI.01 1 0.2260 0.7656 0.86 0.00 0.00 0.00 0.14 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.3C.AALK.01 1 0.4547 0.2670 0.58 0.00 0.00 0.00 0.00 0.34 0.08
#> TCGA.AR.A255.01 2 0.1928 0.6615 0.00 0.90 0.00 0.08 0.00 0.00 0.02
#> TCGA.A8.A0A6.01 1 0.1363 0.8634 0.94 0.00 0.00 0.00 0.04 0.02 0.00
#> TCGA.BH.A1EY.01 5 0.3404 0.6444 0.06 0.00 0.00 0.00 0.82 0.08 0.04
#> TCGA.A2.A4RW.01 1 0.0000 0.8832 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AQ.A1H3.01 1 0.1006 0.8743 0.96 0.00 0.00 0.00 0.02 0.02 0.00
#> TCGA.BH.A1EW.01 1 0.1006 0.8743 0.96 0.00 0.00 0.00 0.02 0.02 0.00
#> TCGA.EW.A2FS.01 2 0.1928 0.7095 0.00 0.90 0.00 0.00 0.00 0.08 0.02
#> TCGA.AR.A1AT.01 1 0.3606 0.5109 0.68 0.00 0.00 0.00 0.30 0.02 0.00
#> TCGA.AC.A3OD.01 1 0.0000 0.8832 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AR.A5QM.01 2 0.0863 0.7085 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.AC.A23H.01 4 0.1363 0.9508 0.00 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.BH.AB28.01 1 0.1928 0.8228 0.90 0.00 0.00 0.00 0.00 0.08 0.02
#> TCGA.OL.A5D6.01 3 0.4426 0.1471 0.00 0.00 0.56 0.00 0.38 0.00 0.06
#> TCGA.A2.A0T4.01 1 0.0000 0.8832 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DG.01 1 0.0504 0.8793 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.D8.A27G.01 6 0.3943 0.1634 0.00 0.42 0.00 0.00 0.00 0.56 0.02
#> TCGA.AR.A0TQ.01 2 0.2708 0.6493 0.00 0.78 0.00 0.00 0.00 0.22 0.00
#> TCGA.AO.A0JE.01 5 0.6211 0.1814 0.00 0.00 0.06 0.00 0.42 0.34 0.18
#> TCGA.E9.A228.01 2 0.6814 0.1855 0.00 0.40 0.00 0.22 0.00 0.22 0.16
#> TCGA.LL.A740.01 3 0.3795 0.1542 0.00 0.00 0.72 0.00 0.00 0.06 0.22
#> TCGA.BH.A0BZ.01 4 0.0000 0.9727 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0C0.01 1 0.3909 0.2658 0.58 0.00 0.00 0.00 0.40 0.02 0.00
#> TCGA.EW.A1IW.01 1 0.3307 0.6054 0.74 0.00 0.00 0.00 0.00 0.24 0.02
#> TCGA.JL.A3YW.01 3 0.0504 0.6699 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.AN.A0XN.01 1 0.1166 0.8526 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.D8.A1JF.01 7 0.3525 0.0000 0.00 0.00 0.44 0.00 0.00 0.00 0.56
#> TCGA.OL.A66N.01 1 0.1006 0.8743 0.96 0.00 0.00 0.00 0.02 0.02 0.00
#> TCGA.A7.A4SC.01 1 0.0504 0.8793 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.GM.A2DL.01 6 0.4461 0.4195 0.22 0.02 0.00 0.00 0.04 0.70 0.02
#> TCGA.E9.A22B.01 6 0.5901 0.2395 0.06 0.36 0.00 0.00 0.00 0.46 0.12
#> TCGA.A2.A3XV.01 3 0.3494 0.4481 0.00 0.00 0.80 0.00 0.02 0.06 0.12
#> TCGA.AC.A6IX.01 1 0.0504 0.8801 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.E9.A22D.01 6 0.6037 0.4272 0.22 0.12 0.00 0.00 0.00 0.54 0.12
#> TCGA.E9.A1NF.01 5 0.2016 0.6334 0.00 0.00 0.00 0.00 0.90 0.06 0.04
#> TCGA.A1.A0SM.01 1 0.0000 0.8832 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JG.01 3 0.1006 0.6635 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.C8.A8HQ.01 2 0.3000 0.6421 0.00 0.84 0.00 0.10 0.00 0.02 0.04
#> TCGA.E2.A1LE.01 3 0.1006 0.6635 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.C8.A275.01 5 0.2016 0.6202 0.00 0.00 0.04 0.00 0.90 0.00 0.06
#> TCGA.AO.A12E.01 2 0.2422 0.6687 0.00 0.82 0.00 0.00 0.00 0.18 0.00
#> TCGA.AR.A5QN.01 1 0.3909 0.2305 0.58 0.00 0.00 0.00 0.00 0.40 0.02
#> TCGA.D8.A27N.01 6 0.5665 0.0244 0.40 0.00 0.00 0.00 0.16 0.42 0.02
#> TCGA.BH.A202.01 5 0.3968 0.1195 0.44 0.00 0.00 0.00 0.54 0.02 0.00
#> TCGA.A1.A0SN.01 2 0.1860 0.6899 0.00 0.92 0.00 0.04 0.00 0.02 0.02
#> TCGA.E9.A295.01 2 0.2572 0.6515 0.00 0.80 0.00 0.00 0.00 0.20 0.00
#> TCGA.AC.A8OP.01 4 0.0000 0.9727 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.GI.A2C8.01 2 0.3562 -0.0464 0.00 0.50 0.00 0.00 0.00 0.50 0.00
#> TCGA.AR.A24T.01 1 0.2163 0.8017 0.88 0.00 0.00 0.00 0.00 0.10 0.02
#> TCGA.AC.A2FE.01 1 0.0000 0.8832 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S3.AA17.01 1 0.0863 0.8657 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.A2.A3KC.01 1 0.0000 0.8832 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A66L.01 2 0.2569 0.6738 0.00 0.84 0.00 0.00 0.00 0.14 0.02
#> TCGA.OK.A5Q2.01 1 0.1363 0.8634 0.94 0.00 0.00 0.00 0.04 0.02 0.00
#> TCGA.AR.A254.01 1 0.2163 0.8204 0.88 0.00 0.00 0.00 0.10 0.02 0.00
#> TCGA.A2.A0T6.01 1 0.0000 0.8832 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A3E8.01 6 0.4649 0.4464 0.30 0.06 0.00 0.00 0.00 0.62 0.02
#> TCGA.WT.AB41.01 1 0.0000 0.8832 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LL.A5YL.01 1 0.0000 0.8832 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A26X.01 3 0.0504 0.6699 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.D8.A1Y3.01 6 0.4127 0.2428 0.00 0.36 0.00 0.00 0.00 0.60 0.04
#> TCGA.BH.A0DK.01 6 0.3413 0.2664 0.00 0.38 0.00 0.00 0.00 0.62 0.00
#> TCGA.BH.A203.01 5 0.1886 0.6282 0.12 0.00 0.00 0.00 0.88 0.00 0.00
#> TCGA.B6.A0IK.01 5 0.1860 0.6391 0.00 0.00 0.02 0.00 0.92 0.02 0.04
#> TCGA.E9.A1RF.01 4 0.1006 0.9618 0.00 0.02 0.00 0.96 0.00 0.02 0.00
#> TCGA.BH.A1EO.01 6 0.3459 0.2559 0.00 0.40 0.00 0.00 0.00 0.60 0.00
#> TCGA.BH.A0DI.01 1 0.2376 0.7928 0.86 0.00 0.00 0.00 0.12 0.02 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.3C.AALK.01 1 0.4642 0.3118 0.60 0.00 0.00 0.00 0.00 0.30 0.06 0.04
#> TCGA.AR.A255.01 2 0.3970 0.4984 0.00 0.72 0.00 0.18 0.00 0.02 0.08 0.00
#> TCGA.A8.A0A6.01 1 0.2132 0.8144 0.88 0.00 0.00 0.00 0.08 0.00 0.04 0.00
#> TCGA.BH.A1EY.01 5 0.3928 0.4834 0.04 0.00 0.00 0.00 0.74 0.02 0.18 0.02
#> TCGA.A2.A4RW.01 1 0.0471 0.8640 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.AQ.A1H3.01 1 0.0471 0.8634 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.BH.A1EW.01 1 0.1887 0.8310 0.90 0.00 0.00 0.00 0.06 0.00 0.04 0.00
#> TCGA.EW.A2FS.01 2 0.1741 0.6107 0.00 0.92 0.00 0.04 0.00 0.02 0.02 0.00
#> TCGA.AR.A1AT.01 1 0.4199 0.3185 0.60 0.00 0.00 0.00 0.32 0.00 0.08 0.00
#> TCGA.AC.A3OD.01 1 0.0471 0.8640 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.AR.A5QM.01 2 0.1275 0.6101 0.00 0.94 0.00 0.00 0.00 0.04 0.02 0.00
#> TCGA.AC.A23H.01 4 0.3660 0.7361 0.00 0.00 0.00 0.70 0.00 0.00 0.24 0.06
#> TCGA.BH.AB28.01 1 0.1341 0.8248 0.92 0.00 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.OL.A5D6.01 3 0.4125 0.1186 0.00 0.00 0.52 0.00 0.44 0.00 0.02 0.02
#> TCGA.A2.A0T4.01 1 0.0000 0.8636 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DG.01 1 0.1607 0.8443 0.92 0.00 0.00 0.00 0.04 0.00 0.04 0.00
#> TCGA.D8.A27G.01 2 0.3941 0.4958 0.00 0.68 0.00 0.00 0.00 0.26 0.02 0.04
#> TCGA.AR.A0TQ.01 2 0.1765 0.6072 0.00 0.88 0.00 0.00 0.00 0.12 0.00 0.00
#> TCGA.AO.A0JE.01 6 0.5996 -0.0740 0.00 0.04 0.00 0.00 0.34 0.42 0.18 0.02
#> TCGA.E9.A228.01 2 0.7409 0.2000 0.00 0.34 0.00 0.22 0.00 0.16 0.16 0.12
#> TCGA.LL.A740.01 3 0.3922 0.1633 0.00 0.00 0.64 0.00 0.00 0.00 0.06 0.30
#> TCGA.BH.A0BZ.01 4 0.0471 0.8529 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.BH.A0C0.01 5 0.4619 0.1422 0.44 0.00 0.00 0.00 0.48 0.02 0.06 0.00
#> TCGA.EW.A1IW.01 1 0.2569 0.7307 0.82 0.00 0.00 0.00 0.02 0.16 0.00 0.00
#> TCGA.JL.A3YW.01 3 0.0000 0.7059 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AN.A0XN.01 1 0.2025 0.7965 0.88 0.00 0.00 0.00 0.02 0.10 0.00 0.00
#> TCGA.D8.A1JF.01 8 0.3015 0.0000 0.00 0.00 0.32 0.00 0.00 0.00 0.00 0.68
#> TCGA.OL.A66N.01 1 0.1275 0.8541 0.94 0.00 0.00 0.00 0.02 0.00 0.04 0.00
#> TCGA.A7.A4SC.01 1 0.1275 0.8528 0.94 0.00 0.00 0.00 0.04 0.00 0.02 0.00
#> TCGA.GM.A2DL.01 6 0.7024 0.2877 0.16 0.06 0.00 0.00 0.18 0.46 0.12 0.02
#> TCGA.E9.A22B.01 2 0.6407 0.1074 0.06 0.42 0.00 0.00 0.00 0.34 0.08 0.10
#> TCGA.A2.A3XV.01 3 0.3675 0.5192 0.00 0.00 0.76 0.00 0.00 0.02 0.08 0.14
#> TCGA.AC.A6IX.01 1 0.0941 0.8599 0.96 0.00 0.00 0.00 0.02 0.00 0.02 0.00
#> TCGA.E9.A22D.01 6 0.6846 0.1883 0.24 0.24 0.00 0.00 0.00 0.38 0.08 0.06
#> TCGA.E9.A1NF.01 5 0.2569 0.4816 0.00 0.00 0.00 0.00 0.82 0.02 0.16 0.00
#> TCGA.A1.A0SM.01 1 0.0000 0.8636 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1JG.01 3 0.0000 0.7059 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A8HQ.01 2 0.5018 0.3677 0.00 0.60 0.00 0.26 0.00 0.02 0.10 0.02
#> TCGA.E2.A1LE.01 3 0.0000 0.7059 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A275.01 5 0.1874 0.5035 0.00 0.00 0.02 0.00 0.92 0.02 0.02 0.02
#> TCGA.AO.A12E.01 2 0.2404 0.5963 0.00 0.84 0.00 0.00 0.00 0.14 0.02 0.00
#> TCGA.AR.A5QN.01 1 0.4995 0.3067 0.60 0.00 0.00 0.00 0.04 0.28 0.06 0.02
#> TCGA.D8.A27N.01 5 0.6241 -0.0729 0.18 0.00 0.00 0.00 0.36 0.34 0.12 0.00
#> TCGA.BH.A202.01 5 0.4403 0.1579 0.44 0.00 0.00 0.00 0.48 0.00 0.08 0.00
#> TCGA.A1.A0SN.01 2 0.3270 0.5480 0.00 0.80 0.00 0.12 0.00 0.02 0.06 0.00
#> TCGA.E9.A295.01 2 0.2725 0.5895 0.00 0.82 0.00 0.00 0.00 0.14 0.04 0.00
#> TCGA.AC.A8OP.01 4 0.0000 0.8631 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GI.A2C8.01 2 0.4370 0.2948 0.00 0.52 0.00 0.00 0.00 0.40 0.08 0.00
#> TCGA.AR.A24T.01 1 0.1765 0.7920 0.88 0.00 0.00 0.00 0.00 0.12 0.00 0.00
#> TCGA.AC.A2FE.01 1 0.0471 0.8603 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.S3.AA17.01 1 0.1804 0.8147 0.90 0.00 0.00 0.00 0.02 0.08 0.00 0.00
#> TCGA.A2.A3KC.01 1 0.0000 0.8636 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A66L.01 2 0.2807 0.5815 0.00 0.84 0.00 0.00 0.00 0.10 0.02 0.04
#> TCGA.OK.A5Q2.01 1 0.2350 0.7961 0.86 0.00 0.00 0.00 0.10 0.00 0.04 0.00
#> TCGA.AR.A254.01 1 0.3227 0.7086 0.78 0.00 0.00 0.00 0.14 0.00 0.08 0.00
#> TCGA.A2.A0T6.01 1 0.0471 0.8634 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.EW.A3E8.01 6 0.5943 0.3947 0.30 0.14 0.00 0.00 0.02 0.48 0.06 0.00
#> TCGA.WT.AB41.01 1 0.0000 0.8636 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LL.A5YL.01 1 0.0471 0.8588 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.C8.A26X.01 3 0.0000 0.7059 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A1Y3.01 2 0.5026 0.3466 0.00 0.50 0.00 0.00 0.00 0.38 0.04 0.08
#> TCGA.BH.A0DK.01 2 0.4077 0.3781 0.00 0.56 0.00 0.00 0.00 0.40 0.02 0.02
#> TCGA.BH.A203.01 5 0.1341 0.5488 0.08 0.00 0.00 0.00 0.92 0.00 0.00 0.00
#> TCGA.B6.A0IK.01 5 0.0941 0.5233 0.00 0.00 0.00 0.00 0.96 0.02 0.00 0.02
#> TCGA.E9.A1RF.01 4 0.2132 0.8514 0.00 0.00 0.00 0.88 0.00 0.00 0.08 0.04
#> TCGA.BH.A1EO.01 6 0.4607 -0.2730 0.02 0.42 0.00 0.00 0.00 0.50 0.06 0.00
#> TCGA.BH.A0DI.01 1 0.2981 0.6769 0.76 0.00 0.00 0.00 0.22 0.00 0.02 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node042. Child nodes: Node02121-leaf , Node02122-leaf , Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02214-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02321-leaf , Node02322-leaf , Node02421-leaf , Node02422-leaf , Node02423-leaf , Node04111-leaf , Node04112-leaf , Node04113 , Node04131-leaf , Node04132-leaf , Node04133-leaf , Node04221-leaf , Node04222-leaf , Node04331-leaf , Node04332-leaf , Node04333-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0422"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 19 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4099 0.591 0.591
#> 3 3 0.643 0.914 0.881 0.5271 0.719 0.525
#> 4 4 0.614 0.447 0.664 0.1224 0.766 0.420
#> 5 5 0.637 0.778 0.774 0.0798 0.836 0.472
#> 6 6 0.649 0.676 0.793 0.0652 0.947 0.769
#> 7 7 0.760 0.642 0.795 0.0483 0.883 0.487
#> 8 8 0.754 0.549 0.708 0.0247 0.942 0.630
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.AR.A255.01 2 0 1 0 1
#> TCGA.EW.A2FS.01 2 0 1 0 1
#> TCGA.AR.A5QM.01 2 0 1 0 1
#> TCGA.AC.A23H.01 1 0 1 1 0
#> TCGA.D8.A27G.01 2 0 1 0 1
#> TCGA.AR.A0TQ.01 2 0 1 0 1
#> TCGA.E9.A228.01 1 0 1 1 0
#> TCGA.BH.A0BZ.01 2 0 1 0 1
#> TCGA.E9.A22B.01 1 0 1 1 0
#> TCGA.C8.A8HQ.01 2 0 1 0 1
#> TCGA.AO.A12E.01 2 0 1 0 1
#> TCGA.A1.A0SN.01 2 0 1 0 1
#> TCGA.E9.A295.01 2 0 1 0 1
#> TCGA.AC.A8OP.01 2 0 1 0 1
#> TCGA.GI.A2C8.01 2 0 1 0 1
#> TCGA.OL.A66L.01 2 0 1 0 1
#> TCGA.D8.A1Y3.01 1 0 1 1 0
#> TCGA.BH.A0DK.01 2 0 1 0 1
#> TCGA.E9.A1RF.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.AR.A255.01 2 0.5016 0.952 0.00 0.76 0.24
#> TCGA.EW.A2FS.01 2 0.5216 0.961 0.00 0.74 0.26
#> TCGA.AR.A5QM.01 3 0.4291 0.765 0.00 0.18 0.82
#> TCGA.AC.A23H.01 1 0.4002 0.914 0.84 0.16 0.00
#> TCGA.D8.A27G.01 3 0.2066 0.886 0.00 0.06 0.94
#> TCGA.AR.A0TQ.01 3 0.0000 0.896 0.00 0.00 1.00
#> TCGA.E9.A228.01 1 0.0000 0.941 1.00 0.00 0.00
#> TCGA.BH.A0BZ.01 2 0.4291 0.903 0.00 0.82 0.18
#> TCGA.E9.A22B.01 1 0.0000 0.941 1.00 0.00 0.00
#> TCGA.C8.A8HQ.01 2 0.5216 0.961 0.00 0.74 0.26
#> TCGA.AO.A12E.01 2 0.5216 0.961 0.00 0.74 0.26
#> TCGA.A1.A0SN.01 3 0.0000 0.896 0.00 0.00 1.00
#> TCGA.E9.A295.01 2 0.5216 0.961 0.00 0.74 0.26
#> TCGA.AC.A8OP.01 2 0.4291 0.903 0.00 0.82 0.18
#> TCGA.GI.A2C8.01 2 0.5216 0.961 0.00 0.74 0.26
#> TCGA.OL.A66L.01 3 0.3686 0.825 0.00 0.14 0.86
#> TCGA.D8.A1Y3.01 1 0.0892 0.935 0.98 0.02 0.00
#> TCGA.BH.A0DK.01 3 0.0000 0.896 0.00 0.00 1.00
#> TCGA.E9.A1RF.01 1 0.4002 0.914 0.84 0.16 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.AR.A255.01 2 0.4855 0.3100 0.00 0.60 0.40 0.00
#> TCGA.EW.A2FS.01 2 0.4977 0.1162 0.00 0.54 0.46 0.00
#> TCGA.AR.A5QM.01 3 0.1211 0.4788 0.00 0.04 0.96 0.00
#> TCGA.AC.A23H.01 1 0.4949 0.8385 0.76 0.06 0.00 0.18
#> TCGA.D8.A27G.01 3 0.1211 0.4112 0.00 0.00 0.96 0.04
#> TCGA.AR.A0TQ.01 3 0.4134 -0.2520 0.00 0.00 0.74 0.26
#> TCGA.E9.A228.01 1 0.0000 0.8820 1.00 0.00 0.00 0.00
#> TCGA.BH.A0BZ.01 2 0.2011 0.5666 0.00 0.92 0.08 0.00
#> TCGA.E9.A22B.01 1 0.0000 0.8820 1.00 0.00 0.00 0.00
#> TCGA.C8.A8HQ.01 3 0.6586 -0.2044 0.00 0.42 0.50 0.08
#> TCGA.AO.A12E.01 3 0.4907 -0.0329 0.00 0.42 0.58 0.00
#> TCGA.A1.A0SN.01 4 0.4522 1.0000 0.00 0.00 0.32 0.68
#> TCGA.E9.A295.01 3 0.4977 -0.1254 0.00 0.46 0.54 0.00
#> TCGA.AC.A8OP.01 2 0.2011 0.5666 0.00 0.92 0.08 0.00
#> TCGA.GI.A2C8.01 3 0.4977 -0.1254 0.00 0.46 0.54 0.00
#> TCGA.OL.A66L.01 3 0.0707 0.4782 0.00 0.02 0.98 0.00
#> TCGA.D8.A1Y3.01 1 0.2335 0.8552 0.92 0.02 0.00 0.06
#> TCGA.BH.A0DK.01 4 0.4522 1.0000 0.00 0.00 0.32 0.68
#> TCGA.E9.A1RF.01 1 0.4949 0.8385 0.76 0.06 0.00 0.18
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.AR.A255.01 3 0.000 0.856 0.00 0.00 1.00 0.00 0.00
#> TCGA.EW.A2FS.01 3 0.000 0.856 0.00 0.00 1.00 0.00 0.00
#> TCGA.AR.A5QM.01 5 0.483 0.506 0.00 0.02 0.48 0.00 0.50
#> TCGA.AC.A23H.01 1 0.548 0.745 0.64 0.24 0.00 0.00 0.12
#> TCGA.D8.A27G.01 5 0.400 0.683 0.00 0.00 0.24 0.02 0.74
#> TCGA.AR.A0TQ.01 5 0.464 0.555 0.00 0.00 0.16 0.10 0.74
#> TCGA.E9.A228.01 1 0.000 0.801 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BZ.01 2 0.477 0.984 0.00 0.56 0.42 0.00 0.02
#> TCGA.E9.A22B.01 1 0.000 0.801 1.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A8HQ.01 3 0.453 0.645 0.00 0.12 0.78 0.02 0.08
#> TCGA.AO.A12E.01 3 0.287 0.757 0.00 0.02 0.86 0.00 0.12
#> TCGA.A1.A0SN.01 4 0.273 0.866 0.00 0.00 0.00 0.84 0.16
#> TCGA.E9.A295.01 3 0.104 0.868 0.00 0.00 0.96 0.00 0.04
#> TCGA.AC.A8OP.01 2 0.423 0.984 0.00 0.58 0.42 0.00 0.00
#> TCGA.GI.A2C8.01 3 0.104 0.868 0.00 0.00 0.96 0.00 0.04
#> TCGA.OL.A66L.01 5 0.473 0.644 0.00 0.02 0.40 0.00 0.58
#> TCGA.D8.A1Y3.01 1 0.369 0.753 0.82 0.02 0.00 0.14 0.02
#> TCGA.BH.A0DK.01 4 0.464 0.861 0.00 0.04 0.00 0.68 0.28
#> TCGA.E9.A1RF.01 1 0.548 0.745 0.64 0.24 0.00 0.00 0.12
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.AR.A255.01 6 0.4055 0.714 0.00 0.14 0.04 0.00 0.04 0.78
#> TCGA.EW.A2FS.01 6 0.4055 0.714 0.00 0.14 0.04 0.00 0.04 0.78
#> TCGA.AR.A5QM.01 6 0.4938 -0.115 0.00 0.00 0.08 0.00 0.34 0.58
#> TCGA.AC.A23H.01 1 0.4002 0.739 0.66 0.02 0.32 0.00 0.00 0.00
#> TCGA.D8.A27G.01 5 0.2631 0.766 0.00 0.00 0.00 0.00 0.82 0.18
#> TCGA.AR.A0TQ.01 5 0.3321 0.686 0.00 0.00 0.00 0.08 0.82 0.10
#> TCGA.E9.A228.01 1 0.0000 0.791 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0BZ.01 2 0.1556 1.000 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.E9.A22B.01 1 0.0000 0.791 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A8HQ.01 6 0.5420 0.298 0.00 0.04 0.44 0.00 0.04 0.48
#> TCGA.AO.A12E.01 6 0.0547 0.661 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.A1.A0SN.01 4 0.0547 0.693 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.E9.A295.01 6 0.1814 0.719 0.00 0.10 0.00 0.00 0.00 0.90
#> TCGA.AC.A8OP.01 2 0.1556 1.000 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.GI.A2C8.01 6 0.1814 0.719 0.00 0.10 0.00 0.00 0.00 0.90
#> TCGA.OL.A66L.01 5 0.4758 0.572 0.00 0.00 0.06 0.00 0.58 0.36
#> TCGA.D8.A1Y3.01 1 0.4516 0.697 0.76 0.02 0.06 0.02 0.14 0.00
#> TCGA.BH.A0DK.01 4 0.5422 0.667 0.00 0.02 0.12 0.62 0.24 0.00
#> TCGA.E9.A1RF.01 1 0.3578 0.739 0.66 0.00 0.34 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.AR.A255.01 6 0.367 0.678 0.00 0.00 0.10 0.00 0.14 0.76 0.00
#> TCGA.EW.A2FS.01 6 0.367 0.678 0.00 0.00 0.10 0.00 0.14 0.76 0.00
#> TCGA.AR.A5QM.01 5 0.393 0.243 0.00 0.00 0.04 0.00 0.66 0.30 0.00
#> TCGA.AC.A23H.01 7 0.000 1.000 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D8.A27G.01 5 0.533 0.528 0.04 0.00 0.02 0.36 0.54 0.04 0.00
#> TCGA.AR.A0TQ.01 5 0.458 0.538 0.00 0.00 0.02 0.36 0.58 0.04 0.00
#> TCGA.E9.A228.01 1 0.355 0.746 0.54 0.00 0.00 0.00 0.00 0.00 0.46
#> TCGA.BH.A0BZ.01 2 0.143 0.969 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.E9.A22B.01 1 0.355 0.746 0.54 0.00 0.00 0.00 0.00 0.00 0.46
#> TCGA.C8.A8HQ.01 3 0.425 0.000 0.00 0.00 0.66 0.00 0.08 0.26 0.00
#> TCGA.AO.A12E.01 6 0.143 0.734 0.00 0.00 0.00 0.00 0.08 0.92 0.00
#> TCGA.A1.A0SN.01 4 0.699 0.422 0.30 0.04 0.14 0.42 0.10 0.00 0.00
#> TCGA.E9.A295.01 6 0.000 0.773 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AC.A8OP.01 2 0.242 0.969 0.02 0.88 0.02 0.00 0.00 0.08 0.00
#> TCGA.GI.A2C8.01 6 0.000 0.773 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.OL.A66L.01 5 0.272 0.507 0.04 0.00 0.00 0.00 0.84 0.12 0.00
#> TCGA.D8.A1Y3.01 1 0.633 0.503 0.42 0.04 0.16 0.00 0.02 0.00 0.36
#> TCGA.BH.A0DK.01 4 0.000 0.396 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E9.A1RF.01 7 0.000 1.000 0.00 0.00 0.00 0.00 0.00 0.00 1.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.AR.A255.01 6 0.3763 0.587 0.02 0.00 0.10 0.00 0.02 0.78 0.00 0.08
#> TCGA.EW.A2FS.01 6 0.3763 0.587 0.02 0.00 0.10 0.00 0.02 0.78 0.00 0.08
#> TCGA.AR.A5QM.01 6 0.8158 -0.221 0.04 0.02 0.10 0.12 0.26 0.30 0.00 0.16
#> TCGA.AC.A23H.01 7 0.1557 0.922 0.00 0.02 0.06 0.00 0.00 0.00 0.92 0.00
#> TCGA.D8.A27G.01 5 0.0000 0.582 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A0TQ.01 5 0.2025 0.577 0.02 0.00 0.00 0.00 0.88 0.00 0.00 0.10
#> TCGA.E9.A228.01 1 0.5865 0.910 0.44 0.00 0.06 0.00 0.00 0.00 0.22 0.28
#> TCGA.BH.A0BZ.01 2 0.1091 0.935 0.00 0.94 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.E9.A22B.01 1 0.4983 0.910 0.50 0.00 0.00 0.00 0.00 0.00 0.22 0.28
#> TCGA.C8.A8HQ.01 3 0.2981 0.000 0.00 0.00 0.76 0.00 0.02 0.22 0.00 0.00
#> TCGA.AO.A12E.01 6 0.0941 0.630 0.00 0.02 0.02 0.00 0.00 0.96 0.00 0.00
#> TCGA.A1.A0SN.01 4 0.4751 0.306 0.38 0.02 0.08 0.52 0.00 0.00 0.00 0.00
#> TCGA.E9.A295.01 6 0.0471 0.642 0.02 0.00 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.AC.A8OP.01 2 0.2624 0.935 0.06 0.86 0.02 0.00 0.00 0.06 0.00 0.00
#> TCGA.GI.A2C8.01 6 0.0471 0.642 0.02 0.00 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.OL.A66L.01 5 0.6404 0.340 0.00 0.02 0.10 0.12 0.56 0.14 0.00 0.06
#> TCGA.D8.A1Y3.01 8 0.2114 0.000 0.00 0.00 0.00 0.00 0.00 0.00 0.16 0.84
#> TCGA.BH.A0DK.01 4 0.3083 0.218 0.00 0.00 0.00 0.66 0.34 0.00 0.00 0.00
#> TCGA.E9.A1RF.01 7 0.0000 0.922 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node04. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0114-leaf , Node0115-leaf , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0131-leaf , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0151-leaf , Node0152-leaf , Node0153-leaf , Node0154-leaf , Node0211-leaf , Node0212 , Node0213 , Node0221 , Node0222 , Node0231-leaf , Node0232 , Node0233-leaf , Node0241-leaf , Node0242 , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0331-leaf , Node0332-leaf , Node0341-leaf , Node0342-leaf , Node0343-leaf , Node0411 , Node0412-leaf , Node0413 , Node0421-leaf , Node0422 , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["043"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 104 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.976 0.990 0.3112 0.686 0.686
#> 3 3 1.000 0.966 0.986 0.9127 0.654 0.519
#> 4 4 0.873 0.847 0.938 0.1468 0.887 0.729
#> 5 5 0.826 0.829 0.911 0.0408 0.931 0.790
#> 6 6 0.707 0.729 0.863 0.0211 0.978 0.924
#> 7 7 0.730 0.718 0.852 0.0242 0.989 0.960
#> 8 8 0.658 0.554 0.786 0.0234 0.990 0.963
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.E9.A1R2.01 1 0.000 0.995 1.00 0.00
#> TCGA.E9.A3X8.01 1 0.000 0.995 1.00 0.00
#> TCGA.E2.A10B.01 1 0.000 0.995 1.00 0.00
#> TCGA.E9.A1RD.01 1 0.000 0.995 1.00 0.00
#> TCGA.LD.A66U.01 1 0.000 0.995 1.00 0.00
#> TCGA.AC.A8OS.01 1 0.000 0.995 1.00 0.00
#> TCGA.GM.A2DN.01 1 0.000 0.995 1.00 0.00
#> TCGA.AC.A6IV.01 1 0.000 0.995 1.00 0.00
#> TCGA.LL.A7SZ.01 2 0.000 0.967 0.00 1.00
#> TCGA.GM.A2DH.01 2 0.141 0.955 0.02 0.98
#> TCGA.AR.A2LO.01 1 0.000 0.995 1.00 0.00
#> TCGA.BH.A201.01 1 0.000 0.995 1.00 0.00
#> TCGA.UU.A93S.01 2 0.000 0.967 0.00 1.00
#> TCGA.A2.A1FZ.01 1 0.000 0.995 1.00 0.00
#> TCGA.D8.A27R.01 1 0.000 0.995 1.00 0.00
#> TCGA.D8.A1XT.01 1 0.000 0.995 1.00 0.00
#> TCGA.C8.A1HI.01 1 0.000 0.995 1.00 0.00
#> TCGA.C8.A3M7.01 1 0.000 0.995 1.00 0.00
#> TCGA.4H.AAAK.01 1 0.000 0.995 1.00 0.00
#> TCGA.AC.A2FO.01 1 0.000 0.995 1.00 0.00
#> TCGA.D8.A1X8.01 1 0.000 0.995 1.00 0.00
#> TCGA.A2.A0T5.01 1 0.000 0.995 1.00 0.00
#> TCGA.LD.A74U.01 1 0.000 0.995 1.00 0.00
#> TCGA.E9.A1RA.01 1 0.000 0.995 1.00 0.00
#> TCGA.A2.A0YD.01 1 0.000 0.995 1.00 0.00
#> TCGA.E9.A6HE.01 1 0.000 0.995 1.00 0.00
#> TCGA.BH.A0DP.01 1 0.000 0.995 1.00 0.00
#> TCGA.AR.A2LN.01 1 0.000 0.995 1.00 0.00
#> TCGA.AR.A0TT.01 2 0.000 0.967 0.00 1.00
#> TCGA.AC.A3W6.01 1 0.000 0.995 1.00 0.00
#> TCGA.OL.A66P.01 2 0.000 0.967 0.00 1.00
#> TCGA.BH.A0H3.01 1 0.000 0.995 1.00 0.00
#> TCGA.EW.A1IZ.01 2 0.000 0.967 0.00 1.00
#> TCGA.AO.A0JA.01 1 0.000 0.995 1.00 0.00
#> TCGA.AO.A0JG.01 1 0.000 0.995 1.00 0.00
#> TCGA.GM.A2DB.01 2 0.000 0.967 0.00 1.00
#> TCGA.AC.A6IX.06 1 0.000 0.995 1.00 0.00
#> TCGA.EW.A1J2.01 1 0.000 0.995 1.00 0.00
#> TCGA.BH.A0GY.01 2 0.000 0.967 0.00 1.00
#> TCGA.W8.A86G.01 1 0.000 0.995 1.00 0.00
#> TCGA.C8.A1HF.01 1 0.000 0.995 1.00 0.00
#> TCGA.A2.A0T7.01 1 0.000 0.995 1.00 0.00
#> TCGA.AO.A0JJ.01 1 0.000 0.995 1.00 0.00
#> TCGA.B6.A0X7.01 1 0.000 0.995 1.00 0.00
#> TCGA.E2.A1BC.01 1 0.000 0.995 1.00 0.00
#> TCGA.A1.A0SF.01 1 0.000 0.995 1.00 0.00
#> TCGA.EW.A6SD.01 1 0.000 0.995 1.00 0.00
#> TCGA.AR.A1AU.01 1 0.000 0.995 1.00 0.00
#> TCGA.LD.A7W5.01 2 0.141 0.955 0.02 0.98
#> TCGA.BH.A42V.01 1 0.000 0.995 1.00 0.00
#> TCGA.E9.A5FK.01 1 0.000 0.995 1.00 0.00
#> TCGA.D8.A1XB.01 1 0.000 0.995 1.00 0.00
#> TCGA.A7.A5ZX.01 1 0.000 0.995 1.00 0.00
#> TCGA.AC.A2B8.01 1 0.000 0.995 1.00 0.00
#> TCGA.A2.A0CO.01 1 0.000 0.995 1.00 0.00
#> TCGA.AC.A23G.01 1 0.000 0.995 1.00 0.00
#> TCGA.GM.A3XN.01 1 0.000 0.995 1.00 0.00
#> TCGA.AQ.A7U7.01 1 0.000 0.995 1.00 0.00
#> TCGA.A2.A25A.01 1 0.000 0.995 1.00 0.00
#> TCGA.A2.A25D.01 1 0.000 0.995 1.00 0.00
#> TCGA.BH.A0AW.01 2 0.000 0.967 0.00 1.00
#> TCGA.BH.A0B6.01 1 0.000 0.995 1.00 0.00
#> TCGA.GM.A5PX.01 1 0.000 0.995 1.00 0.00
#> TCGA.GM.A2DD.01 2 0.000 0.967 0.00 1.00
#> TCGA.D8.A73U.01 2 0.242 0.939 0.04 0.96
#> TCGA.OL.A5RX.01 1 0.000 0.995 1.00 0.00
#> TCGA.AC.A23C.01 2 0.943 0.457 0.36 0.64
#> TCGA.A7.A56D.01 2 0.680 0.782 0.18 0.82
#> TCGA.AR.A5QP.01 1 0.000 0.995 1.00 0.00
#> TCGA.BH.A2L8.01 1 0.000 0.995 1.00 0.00
#> TCGA.EW.A1OV.01 2 0.000 0.967 0.00 1.00
#> TCGA.AR.A24P.01 1 0.000 0.995 1.00 0.00
#> TCGA.BH.A0B2.01 1 0.000 0.995 1.00 0.00
#> TCGA.XX.A899.01 1 0.000 0.995 1.00 0.00
#> TCGA.E9.A1N9.01 1 0.958 0.349 0.62 0.38
#> TCGA.AO.A03L.01 2 0.000 0.967 0.00 1.00
#> TCGA.A2.A4S2.01 1 0.000 0.995 1.00 0.00
#> TCGA.E2.A10C.01 2 0.000 0.967 0.00 1.00
#> TCGA.5L.AAT1.01 1 0.000 0.995 1.00 0.00
#> TCGA.HN.A2OB.01 1 0.000 0.995 1.00 0.00
#> TCGA.E2.A1IJ.01 1 0.000 0.995 1.00 0.00
#> TCGA.AR.A0TW.01 2 0.000 0.967 0.00 1.00
#> TCGA.B6.A401.01 1 0.000 0.995 1.00 0.00
#> TCGA.E2.A1LB.01 1 0.000 0.995 1.00 0.00
#> TCGA.AC.A3W7.01 1 0.000 0.995 1.00 0.00
#> TCGA.AC.A3W5.01 2 0.000 0.967 0.00 1.00
#> TCGA.E9.A1RI.01 1 0.000 0.995 1.00 0.00
#> TCGA.OL.A5RU.01 1 0.000 0.995 1.00 0.00
#> TCGA.E2.A10F.01 1 0.000 0.995 1.00 0.00
#> TCGA.B6.A0RV.01 1 0.000 0.995 1.00 0.00
#> TCGA.E2.A1IH.01 1 0.000 0.995 1.00 0.00
#> TCGA.EW.A1IY.01 1 0.000 0.995 1.00 0.00
#> TCGA.C8.A278.01 2 0.000 0.967 0.00 1.00
#> TCGA.AC.A3BB.01 1 0.000 0.995 1.00 0.00
#> TCGA.BH.A1FE.01 1 0.000 0.995 1.00 0.00
#> TCGA.A2.A0EN.01 1 0.000 0.995 1.00 0.00
#> TCGA.BH.A0BF.01 1 0.000 0.995 1.00 0.00
#> TCGA.AR.A1AK.01 1 0.000 0.995 1.00 0.00
#> TCGA.A7.A3J1.01 1 0.000 0.995 1.00 0.00
#> TCGA.D8.A1XM.01 1 0.000 0.995 1.00 0.00
#> TCGA.BH.A0HP.01 1 0.000 0.995 1.00 0.00
#> TCGA.D8.A27K.01 1 0.000 0.995 1.00 0.00
#> TCGA.A2.A0YK.01 1 0.000 0.995 1.00 0.00
#> TCGA.E2.A107.01 1 0.000 0.995 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.E9.A1R2.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.E9.A3X8.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.E2.A10B.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.E9.A1RD.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.LD.A66U.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.AC.A8OS.01 3 0.1529 0.930 0.04 0.00 0.96
#> TCGA.GM.A2DN.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.AC.A6IV.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.LL.A7SZ.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.GM.A2DH.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.AR.A2LO.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.BH.A201.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.UU.A93S.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.A2.A1FZ.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.D8.A27R.01 3 0.1529 0.928 0.04 0.00 0.96
#> TCGA.D8.A1XT.01 3 0.5216 0.615 0.26 0.00 0.74
#> TCGA.C8.A1HI.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.C8.A3M7.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.4H.AAAK.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.AC.A2FO.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.D8.A1X8.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.A2.A0T5.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.LD.A74U.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.E9.A1RA.01 1 0.0892 0.970 0.98 0.00 0.02
#> TCGA.A2.A0YD.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.E9.A6HE.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.BH.A0DP.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.AR.A2LN.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.AR.A0TT.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AC.A3W6.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.OL.A66P.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.BH.A0H3.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.EW.A1IZ.01 3 0.4002 0.801 0.00 0.16 0.84
#> TCGA.AO.A0JA.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.AO.A0JG.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.GM.A2DB.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AC.A6IX.06 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.EW.A1J2.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.BH.A0GY.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.W8.A86G.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.C8.A1HF.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.A2.A0T7.01 1 0.0892 0.970 0.98 0.00 0.02
#> TCGA.AO.A0JJ.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.B6.A0X7.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.E2.A1BC.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.A1.A0SF.01 3 0.0892 0.950 0.02 0.00 0.98
#> TCGA.EW.A6SD.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.AR.A1AU.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.LD.A7W5.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.BH.A42V.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.E9.A5FK.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.D8.A1XB.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.A7.A5ZX.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.AC.A2B8.01 3 0.5216 0.618 0.26 0.00 0.74
#> TCGA.A2.A0CO.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.AC.A23G.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.GM.A3XN.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.AQ.A7U7.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.A2.A25A.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.A2.A25D.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.BH.A0AW.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.BH.A0B6.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.GM.A5PX.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.GM.A2DD.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.D8.A73U.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.OL.A5RX.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.AC.A23C.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.A7.A56D.01 3 0.2947 0.906 0.02 0.06 0.92
#> TCGA.AR.A5QP.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.BH.A2L8.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.EW.A1OV.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AR.A24P.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.BH.A0B2.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.XX.A899.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.E9.A1N9.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.AO.A03L.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.A2.A4S2.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.E2.A10C.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.5L.AAT1.01 3 0.0892 0.950 0.02 0.00 0.98
#> TCGA.HN.A2OB.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.E2.A1IJ.01 1 0.4002 0.800 0.84 0.00 0.16
#> TCGA.AR.A0TW.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.B6.A401.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.E2.A1LB.01 1 0.0892 0.970 0.98 0.00 0.02
#> TCGA.AC.A3W7.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.AC.A3W5.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.E9.A1RI.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.OL.A5RU.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.E2.A10F.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.B6.A0RV.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.E2.A1IH.01 1 0.0892 0.970 0.98 0.00 0.02
#> TCGA.EW.A1IY.01 1 0.2066 0.927 0.94 0.00 0.06
#> TCGA.C8.A278.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.AC.A3BB.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.BH.A1FE.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.A2.A0EN.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.BH.A0BF.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.AR.A1AK.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.A7.A3J1.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.D8.A1XM.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.BH.A0HP.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.D8.A27K.01 1 0.0000 0.988 1.00 0.00 0.00
#> TCGA.A2.A0YK.01 3 0.0000 0.967 0.00 0.00 1.00
#> TCGA.E2.A107.01 1 0.5216 0.645 0.74 0.00 0.26
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.E9.A1R2.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.E9.A3X8.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.E2.A10B.01 4 0.2345 0.7204 0.10 0.0 0.00 0.90
#> TCGA.E9.A1RD.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.LD.A66U.01 1 0.5000 -0.1287 0.50 0.0 0.00 0.50
#> TCGA.AC.A8OS.01 4 0.3606 0.7530 0.02 0.0 0.14 0.84
#> TCGA.GM.A2DN.01 3 0.0000 0.9726 0.00 0.0 1.00 0.00
#> TCGA.AC.A6IV.01 3 0.0000 0.9726 0.00 0.0 1.00 0.00
#> TCGA.LL.A7SZ.01 2 0.0000 0.9939 0.00 1.0 0.00 0.00
#> TCGA.GM.A2DH.01 3 0.0000 0.9726 0.00 0.0 1.00 0.00
#> TCGA.AR.A2LO.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.BH.A201.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.UU.A93S.01 2 0.0000 0.9939 0.00 1.0 0.00 0.00
#> TCGA.A2.A1FZ.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.D8.A27R.01 3 0.0000 0.9726 0.00 0.0 1.00 0.00
#> TCGA.D8.A1XT.01 3 0.3400 0.6864 0.18 0.0 0.82 0.00
#> TCGA.C8.A1HI.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.C8.A3M7.01 3 0.0000 0.9726 0.00 0.0 1.00 0.00
#> TCGA.4H.AAAK.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.AC.A2FO.01 3 0.3975 0.6526 0.00 0.0 0.76 0.24
#> TCGA.D8.A1X8.01 4 0.4977 0.1905 0.46 0.0 0.00 0.54
#> TCGA.A2.A0T5.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.LD.A74U.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.E9.A1RA.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.A2.A0YD.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.E9.A6HE.01 1 0.0707 0.9174 0.98 0.0 0.00 0.02
#> TCGA.BH.A0DP.01 1 0.4948 0.1017 0.56 0.0 0.00 0.44
#> TCGA.AR.A2LN.01 4 0.5000 0.0529 0.50 0.0 0.00 0.50
#> TCGA.AR.A0TT.01 2 0.0000 0.9939 0.00 1.0 0.00 0.00
#> TCGA.AC.A3W6.01 3 0.0000 0.9726 0.00 0.0 1.00 0.00
#> TCGA.OL.A66P.01 2 0.0000 0.9939 0.00 1.0 0.00 0.00
#> TCGA.BH.A0H3.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.EW.A1IZ.01 3 0.2345 0.8670 0.00 0.1 0.90 0.00
#> TCGA.AO.A0JA.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.AO.A0JG.01 4 0.2345 0.7526 0.00 0.0 0.10 0.90
#> TCGA.GM.A2DB.01 2 0.0000 0.9939 0.00 1.0 0.00 0.00
#> TCGA.AC.A6IX.06 3 0.0000 0.9726 0.00 0.0 1.00 0.00
#> TCGA.EW.A1J2.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.BH.A0GY.01 2 0.2345 0.9160 0.00 0.9 0.00 0.10
#> TCGA.W8.A86G.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.C8.A1HF.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.A2.A0T7.01 4 0.0707 0.7195 0.02 0.0 0.00 0.98
#> TCGA.AO.A0JJ.01 1 0.4994 -0.0558 0.52 0.0 0.00 0.48
#> TCGA.B6.A0X7.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.E2.A1BC.01 1 0.0707 0.9174 0.98 0.0 0.00 0.02
#> TCGA.A1.A0SF.01 4 0.4797 0.6377 0.02 0.0 0.26 0.72
#> TCGA.EW.A6SD.01 3 0.0000 0.9726 0.00 0.0 1.00 0.00
#> TCGA.AR.A1AU.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.LD.A7W5.01 3 0.0000 0.9726 0.00 0.0 1.00 0.00
#> TCGA.BH.A42V.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.E9.A5FK.01 3 0.0000 0.9726 0.00 0.0 1.00 0.00
#> TCGA.D8.A1XB.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.A7.A5ZX.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.AC.A2B8.01 4 0.3198 0.7585 0.04 0.0 0.08 0.88
#> TCGA.A2.A0CO.01 4 0.3400 0.7252 0.00 0.0 0.18 0.82
#> TCGA.AC.A23G.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.GM.A3XN.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.AQ.A7U7.01 3 0.0000 0.9726 0.00 0.0 1.00 0.00
#> TCGA.A2.A25A.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.A2.A25D.01 3 0.0000 0.9726 0.00 0.0 1.00 0.00
#> TCGA.BH.A0AW.01 2 0.0000 0.9939 0.00 1.0 0.00 0.00
#> TCGA.BH.A0B6.01 4 0.2345 0.7526 0.00 0.0 0.10 0.90
#> TCGA.GM.A5PX.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.GM.A2DD.01 2 0.0000 0.9939 0.00 1.0 0.00 0.00
#> TCGA.D8.A73U.01 3 0.0000 0.9726 0.00 0.0 1.00 0.00
#> TCGA.OL.A5RX.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.AC.A23C.01 4 0.4855 0.3283 0.00 0.0 0.40 0.60
#> TCGA.A7.A56D.01 4 0.0000 0.7162 0.00 0.0 0.00 1.00
#> TCGA.AR.A5QP.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.BH.A2L8.01 3 0.0000 0.9726 0.00 0.0 1.00 0.00
#> TCGA.EW.A1OV.01 2 0.0000 0.9939 0.00 1.0 0.00 0.00
#> TCGA.AR.A24P.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.BH.A0B2.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.XX.A899.01 3 0.0000 0.9726 0.00 0.0 1.00 0.00
#> TCGA.E9.A1N9.01 4 0.2011 0.7161 0.00 0.0 0.08 0.92
#> TCGA.AO.A03L.01 2 0.0000 0.9939 0.00 1.0 0.00 0.00
#> TCGA.A2.A4S2.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.E2.A10C.01 2 0.0000 0.9939 0.00 1.0 0.00 0.00
#> TCGA.5L.AAT1.01 4 0.3975 0.6725 0.00 0.0 0.24 0.76
#> TCGA.HN.A2OB.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.E2.A1IJ.01 4 0.5987 0.2459 0.44 0.0 0.04 0.52
#> TCGA.AR.A0TW.01 2 0.0000 0.9939 0.00 1.0 0.00 0.00
#> TCGA.B6.A401.01 3 0.0000 0.9726 0.00 0.0 1.00 0.00
#> TCGA.E2.A1LB.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.AC.A3W7.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.AC.A3W5.01 2 0.0000 0.9939 0.00 1.0 0.00 0.00
#> TCGA.E9.A1RI.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.OL.A5RU.01 3 0.0000 0.9726 0.00 0.0 1.00 0.00
#> TCGA.E2.A10F.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.B6.A0RV.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.E2.A1IH.01 1 0.0707 0.9146 0.98 0.0 0.02 0.00
#> TCGA.EW.A1IY.01 1 0.4624 0.4183 0.66 0.0 0.34 0.00
#> TCGA.C8.A278.01 2 0.0000 0.9939 0.00 1.0 0.00 0.00
#> TCGA.AC.A3BB.01 3 0.0000 0.9726 0.00 0.0 1.00 0.00
#> TCGA.BH.A1FE.01 3 0.0000 0.9726 0.00 0.0 1.00 0.00
#> TCGA.A2.A0EN.01 3 0.0000 0.9726 0.00 0.0 1.00 0.00
#> TCGA.BH.A0BF.01 3 0.0000 0.9726 0.00 0.0 1.00 0.00
#> TCGA.AR.A1AK.01 1 0.4855 0.2302 0.60 0.0 0.00 0.40
#> TCGA.A7.A3J1.01 1 0.4624 0.4021 0.66 0.0 0.00 0.34
#> TCGA.D8.A1XM.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.BH.A0HP.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.D8.A27K.01 1 0.0000 0.9359 1.00 0.0 0.00 0.00
#> TCGA.A2.A0YK.01 3 0.0000 0.9726 0.00 0.0 1.00 0.00
#> TCGA.E2.A107.01 4 0.2335 0.7411 0.06 0.0 0.02 0.92
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.E9.A1R2.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A3X8.01 1 0.0609 0.9563 0.98 0.00 0.02 0.00 0.00
#> TCGA.E2.A10B.01 4 0.2754 0.5031 0.04 0.00 0.00 0.88 0.08
#> TCGA.E9.A1RD.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.LD.A66U.01 4 0.3895 0.5539 0.32 0.00 0.00 0.68 0.00
#> TCGA.AC.A8OS.01 4 0.3037 0.4670 0.00 0.00 0.10 0.86 0.04
#> TCGA.GM.A2DN.01 3 0.0000 0.9107 0.00 0.00 1.00 0.00 0.00
#> TCGA.AC.A6IV.01 3 0.0609 0.9033 0.00 0.00 0.98 0.02 0.00
#> TCGA.LL.A7SZ.01 2 0.0000 0.9459 0.00 1.00 0.00 0.00 0.00
#> TCGA.GM.A2DH.01 3 0.2797 0.8820 0.00 0.00 0.88 0.06 0.06
#> TCGA.AR.A2LO.01 1 0.2020 0.8676 0.90 0.00 0.10 0.00 0.00
#> TCGA.BH.A201.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.UU.A93S.01 2 0.3513 0.8206 0.00 0.80 0.00 0.02 0.18
#> TCGA.A2.A1FZ.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A27R.01 3 0.0609 0.9047 0.00 0.00 0.98 0.00 0.02
#> TCGA.D8.A1XT.01 3 0.4281 0.7196 0.08 0.00 0.80 0.02 0.10
#> TCGA.C8.A1HI.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A3M7.01 3 0.3037 0.8646 0.00 0.00 0.86 0.10 0.04
#> TCGA.4H.AAAK.01 1 0.0609 0.9535 0.98 0.00 0.00 0.02 0.00
#> TCGA.AC.A2FO.01 3 0.2280 0.8424 0.00 0.00 0.88 0.12 0.00
#> TCGA.D8.A1X8.01 4 0.3109 0.6008 0.20 0.00 0.00 0.80 0.00
#> TCGA.A2.A0T5.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.LD.A74U.01 1 0.1043 0.9368 0.96 0.00 0.00 0.04 0.00
#> TCGA.E9.A1RA.01 1 0.2020 0.8676 0.90 0.00 0.10 0.00 0.00
#> TCGA.A2.A0YD.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A6HE.01 1 0.1410 0.9107 0.94 0.00 0.00 0.06 0.00
#> TCGA.BH.A0DP.01 4 0.4182 0.4814 0.40 0.00 0.00 0.60 0.00
#> TCGA.AR.A2LN.01 4 0.4798 0.4389 0.44 0.00 0.00 0.54 0.02
#> TCGA.AR.A0TT.01 2 0.0000 0.9459 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A3W6.01 3 0.2438 0.8906 0.00 0.00 0.90 0.06 0.04
#> TCGA.OL.A66P.01 2 0.0000 0.9459 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A0H3.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1IZ.01 3 0.4675 0.3940 0.00 0.38 0.60 0.02 0.00
#> TCGA.AO.A0JA.01 1 0.1216 0.9423 0.96 0.00 0.02 0.02 0.00
#> TCGA.AO.A0JG.01 4 0.2616 0.4437 0.00 0.00 0.02 0.88 0.10
#> TCGA.GM.A2DB.01 2 0.0000 0.9459 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A6IX.06 3 0.0000 0.9107 0.00 0.00 1.00 0.00 0.00
#> TCGA.EW.A1J2.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0GY.01 5 0.4456 0.4727 0.00 0.32 0.00 0.02 0.66
#> TCGA.W8.A86G.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A1HF.01 1 0.0609 0.9563 0.98 0.00 0.02 0.00 0.00
#> TCGA.A2.A0T7.01 5 0.4254 0.7522 0.04 0.00 0.00 0.22 0.74
#> TCGA.AO.A0JJ.01 4 0.3274 0.6031 0.22 0.00 0.00 0.78 0.00
#> TCGA.B6.A0X7.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1BC.01 1 0.0609 0.9544 0.98 0.00 0.00 0.02 0.00
#> TCGA.A1.A0SF.01 4 0.6983 0.0417 0.06 0.00 0.38 0.46 0.10
#> TCGA.EW.A6SD.01 3 0.1410 0.8947 0.00 0.00 0.94 0.00 0.06
#> TCGA.AR.A1AU.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.LD.A7W5.01 3 0.0609 0.9110 0.00 0.00 0.98 0.02 0.00
#> TCGA.BH.A42V.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A5FK.01 3 0.0000 0.9107 0.00 0.00 1.00 0.00 0.00
#> TCGA.D8.A1XB.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A5ZX.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A2B8.01 4 0.3034 0.5493 0.06 0.00 0.02 0.88 0.04
#> TCGA.A2.A0CO.01 4 0.3037 0.4670 0.00 0.00 0.10 0.86 0.04
#> TCGA.AC.A23G.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A3XN.01 1 0.0609 0.9563 0.98 0.00 0.02 0.00 0.00
#> TCGA.AQ.A7U7.01 3 0.0609 0.9110 0.00 0.00 0.98 0.02 0.00
#> TCGA.A2.A25A.01 1 0.1043 0.9348 0.96 0.00 0.00 0.04 0.00
#> TCGA.A2.A25D.01 3 0.2438 0.8906 0.00 0.00 0.90 0.06 0.04
#> TCGA.BH.A0AW.01 2 0.1410 0.9239 0.00 0.94 0.00 0.00 0.06
#> TCGA.BH.A0B6.01 4 0.4254 0.3426 0.00 0.00 0.22 0.74 0.04
#> TCGA.GM.A5PX.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A2DD.01 2 0.0000 0.9459 0.00 1.00 0.00 0.00 0.00
#> TCGA.D8.A73U.01 3 0.2438 0.8906 0.00 0.00 0.90 0.06 0.04
#> TCGA.OL.A5RX.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A23C.01 3 0.5892 0.4148 0.00 0.00 0.60 0.22 0.18
#> TCGA.A7.A56D.01 5 0.3424 0.7689 0.00 0.00 0.00 0.24 0.76
#> TCGA.AR.A5QP.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A2L8.01 3 0.0000 0.9107 0.00 0.00 1.00 0.00 0.00
#> TCGA.EW.A1OV.01 2 0.0000 0.9459 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A24P.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0B2.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.XX.A899.01 3 0.0000 0.9107 0.00 0.00 1.00 0.00 0.00
#> TCGA.E9.A1N9.01 5 0.3922 0.7618 0.00 0.00 0.04 0.18 0.78
#> TCGA.AO.A03L.01 2 0.1043 0.9332 0.00 0.96 0.00 0.00 0.04
#> TCGA.A2.A4S2.01 1 0.0609 0.9544 0.98 0.00 0.00 0.02 0.00
#> TCGA.E2.A10C.01 2 0.2012 0.9109 0.00 0.92 0.00 0.02 0.06
#> TCGA.5L.AAT1.01 4 0.3348 0.5265 0.04 0.00 0.08 0.86 0.02
#> TCGA.HN.A2OB.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1IJ.01 4 0.3274 0.6053 0.22 0.00 0.00 0.78 0.00
#> TCGA.AR.A0TW.01 2 0.3852 0.7882 0.00 0.76 0.00 0.02 0.22
#> TCGA.B6.A401.01 3 0.1410 0.9039 0.00 0.00 0.94 0.06 0.00
#> TCGA.E2.A1LB.01 1 0.0609 0.9563 0.98 0.00 0.02 0.00 0.00
#> TCGA.AC.A3W7.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A3W5.01 2 0.1732 0.9133 0.00 0.92 0.00 0.00 0.08
#> TCGA.E9.A1RI.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5RU.01 3 0.0000 0.9107 0.00 0.00 1.00 0.00 0.00
#> TCGA.E2.A10F.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.B6.A0RV.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1IH.01 1 0.2516 0.8112 0.86 0.00 0.14 0.00 0.00
#> TCGA.EW.A1IY.01 1 0.4060 0.3961 0.64 0.00 0.36 0.00 0.00
#> TCGA.C8.A278.01 2 0.0000 0.9459 0.00 1.00 0.00 0.00 0.00
#> TCGA.AC.A3BB.01 3 0.2754 0.8782 0.00 0.00 0.88 0.08 0.04
#> TCGA.BH.A1FE.01 3 0.0609 0.9110 0.00 0.00 0.98 0.02 0.00
#> TCGA.A2.A0EN.01 3 0.0000 0.9107 0.00 0.00 1.00 0.00 0.00
#> TCGA.BH.A0BF.01 3 0.0609 0.9110 0.00 0.00 0.98 0.02 0.00
#> TCGA.AR.A1AK.01 4 0.4307 0.2869 0.50 0.00 0.00 0.50 0.00
#> TCGA.A7.A3J1.01 4 0.3684 0.5744 0.28 0.00 0.00 0.72 0.00
#> TCGA.D8.A1XM.01 1 0.0609 0.9563 0.98 0.00 0.02 0.00 0.00
#> TCGA.BH.A0HP.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A27K.01 1 0.0000 0.9690 1.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0YK.01 3 0.2438 0.8906 0.00 0.00 0.90 0.06 0.04
#> TCGA.E2.A107.01 4 0.2331 0.4880 0.02 0.00 0.00 0.90 0.08
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.E9.A1R2.01 1 0.0000 0.9222 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A3X8.01 1 0.2345 0.8665 0.90 0.00 0.02 0.00 0.02 0.06
#> TCGA.E2.A10B.01 4 0.4926 0.5132 0.14 0.00 0.00 0.72 0.08 0.06
#> TCGA.E9.A1RD.01 1 0.0000 0.9222 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LD.A66U.01 4 0.3756 0.4976 0.40 0.00 0.00 0.60 0.00 0.00
#> TCGA.AC.A8OS.01 4 0.4516 0.4365 0.02 0.00 0.14 0.76 0.02 0.06
#> TCGA.GM.A2DN.01 3 0.1480 0.8545 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.AC.A6IV.01 3 0.2725 0.8239 0.00 0.00 0.88 0.02 0.04 0.06
#> TCGA.LL.A7SZ.01 2 0.0937 0.7028 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.GM.A2DH.01 3 0.3382 0.8215 0.00 0.00 0.84 0.04 0.08 0.04
#> TCGA.AR.A2LO.01 1 0.3045 0.8234 0.86 0.00 0.06 0.00 0.02 0.06
#> TCGA.BH.A201.01 1 0.0000 0.9222 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UU.A93S.01 6 0.3499 0.7167 0.00 0.32 0.00 0.00 0.00 0.68
#> TCGA.A2.A1FZ.01 1 0.0547 0.9149 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.D8.A27R.01 3 0.4221 0.7494 0.04 0.00 0.80 0.02 0.08 0.06
#> TCGA.D8.A1XT.01 3 0.6565 0.4612 0.10 0.00 0.60 0.04 0.18 0.08
#> TCGA.C8.A1HI.01 1 0.1480 0.8959 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.C8.A3M7.01 3 0.4468 0.7592 0.00 0.00 0.76 0.12 0.06 0.06
#> TCGA.4H.AAAK.01 1 0.1814 0.8392 0.90 0.00 0.00 0.10 0.00 0.00
#> TCGA.AC.A2FO.01 3 0.2793 0.7225 0.00 0.00 0.80 0.20 0.00 0.00
#> TCGA.D8.A1X8.01 4 0.4798 0.5378 0.30 0.00 0.00 0.62 0.00 0.08
#> TCGA.A2.A0T5.01 1 0.0000 0.9222 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LD.A74U.01 1 0.0937 0.9021 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.E9.A1RA.01 1 0.2725 0.8379 0.88 0.00 0.06 0.00 0.02 0.04
#> TCGA.A2.A0YD.01 1 0.0000 0.9222 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A6HE.01 1 0.2793 0.7000 0.80 0.00 0.00 0.20 0.00 0.00
#> TCGA.BH.A0DP.01 4 0.4534 0.4864 0.38 0.00 0.00 0.58 0.00 0.04
#> TCGA.AR.A2LN.01 4 0.4576 0.4691 0.40 0.00 0.00 0.56 0.00 0.04
#> TCGA.AR.A0TT.01 2 0.0547 0.7127 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AC.A3W6.01 3 0.2784 0.8390 0.00 0.00 0.88 0.04 0.04 0.04
#> TCGA.OL.A66P.01 2 0.0000 0.7137 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0H3.01 1 0.0000 0.9222 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1IZ.01 2 0.3647 0.1237 0.00 0.64 0.36 0.00 0.00 0.00
#> TCGA.AO.A0JA.01 1 0.2725 0.8546 0.88 0.00 0.00 0.02 0.04 0.06
#> TCGA.AO.A0JG.01 4 0.5018 0.3038 0.00 0.00 0.08 0.72 0.10 0.10
#> TCGA.GM.A2DB.01 2 0.0547 0.7127 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AC.A6IX.06 3 0.0547 0.8678 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EW.A1J2.01 1 0.0547 0.9152 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.BH.A0GY.01 5 0.4144 0.1310 0.00 0.36 0.00 0.00 0.62 0.02
#> TCGA.W8.A86G.01 1 0.0000 0.9222 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A1HF.01 1 0.0547 0.9149 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.A2.A0T7.01 5 0.3475 0.6267 0.06 0.00 0.00 0.14 0.80 0.00
#> TCGA.AO.A0JJ.01 4 0.4711 0.5438 0.28 0.00 0.00 0.64 0.00 0.08
#> TCGA.B6.A0X7.01 1 0.0000 0.9222 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1BC.01 1 0.2048 0.8159 0.88 0.00 0.00 0.12 0.00 0.00
#> TCGA.A1.A0SF.01 4 0.6757 0.2560 0.06 0.00 0.20 0.58 0.08 0.08
#> TCGA.EW.A6SD.01 3 0.3854 0.8205 0.00 0.00 0.80 0.04 0.12 0.04
#> TCGA.AR.A1AU.01 1 0.0000 0.9222 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LD.A7W5.01 3 0.0000 0.8688 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BH.A42V.01 1 0.0000 0.9222 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A5FK.01 3 0.0547 0.8678 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.D8.A1XB.01 1 0.0000 0.9222 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A5ZX.01 1 0.0000 0.9222 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A2B8.01 4 0.3420 0.4929 0.04 0.00 0.06 0.84 0.00 0.06
#> TCGA.A2.A0CO.01 4 0.2794 0.4462 0.00 0.00 0.08 0.86 0.00 0.06
#> TCGA.AC.A23G.01 1 0.0547 0.9149 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.GM.A3XN.01 1 0.1807 0.8817 0.92 0.00 0.00 0.00 0.02 0.06
#> TCGA.AQ.A7U7.01 3 0.0000 0.8688 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A25A.01 1 0.2790 0.7879 0.84 0.00 0.00 0.14 0.00 0.02
#> TCGA.A2.A25D.01 3 0.4008 0.7939 0.00 0.00 0.80 0.08 0.06 0.06
#> TCGA.BH.A0AW.01 2 0.5327 0.3406 0.00 0.68 0.00 0.06 0.10 0.16
#> TCGA.BH.A0B6.01 4 0.4552 0.2362 0.00 0.00 0.30 0.64 0.06 0.00
#> TCGA.GM.A5PX.01 1 0.1480 0.8955 0.94 0.00 0.00 0.04 0.00 0.02
#> TCGA.GM.A2DD.01 2 0.0937 0.7056 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.D8.A73U.01 3 0.2938 0.8413 0.00 0.02 0.88 0.04 0.02 0.04
#> TCGA.OL.A5RX.01 1 0.0000 0.9222 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A23C.01 3 0.5150 0.4939 0.00 0.00 0.62 0.22 0.16 0.00
#> TCGA.A7.A56D.01 5 0.2793 0.6240 0.00 0.00 0.00 0.20 0.80 0.00
#> TCGA.AR.A5QP.01 1 0.0000 0.9222 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A2L8.01 3 0.1092 0.8624 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.EW.A1OV.01 2 0.0547 0.7127 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AR.A24P.01 1 0.0000 0.9222 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0B2.01 1 0.0000 0.9222 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XX.A899.01 3 0.1092 0.8624 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.E9.A1N9.01 5 0.3324 0.5973 0.00 0.00 0.06 0.08 0.84 0.02
#> TCGA.AO.A03L.01 2 0.4306 0.5244 0.00 0.76 0.00 0.02 0.12 0.10
#> TCGA.A2.A4S2.01 1 0.2350 0.8242 0.88 0.00 0.00 0.10 0.00 0.02
#> TCGA.E2.A10C.01 2 0.3309 0.2244 0.00 0.72 0.00 0.00 0.00 0.28
#> TCGA.5L.AAT1.01 4 0.3475 0.4395 0.00 0.00 0.14 0.80 0.00 0.06
#> TCGA.HN.A2OB.01 1 0.0000 0.9222 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1IJ.01 4 0.4042 0.5634 0.18 0.00 0.02 0.76 0.00 0.04
#> TCGA.AR.A0TW.01 6 0.5371 0.6936 0.00 0.36 0.00 0.00 0.12 0.52
#> TCGA.B6.A401.01 3 0.2020 0.8542 0.00 0.00 0.92 0.02 0.02 0.04
#> TCGA.E2.A1LB.01 1 0.3420 0.7942 0.84 0.00 0.04 0.00 0.06 0.06
#> TCGA.AC.A3W7.01 1 0.0000 0.9222 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A3W5.01 2 0.5190 0.3325 0.00 0.68 0.00 0.04 0.10 0.18
#> TCGA.E9.A1RI.01 1 0.0000 0.9222 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5RU.01 3 0.1480 0.8545 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.E2.A10F.01 1 0.0547 0.9152 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.B6.A0RV.01 1 0.0000 0.9222 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1IH.01 1 0.3942 0.7470 0.80 0.00 0.10 0.00 0.04 0.06
#> TCGA.EW.A1IY.01 1 0.4844 0.3804 0.62 0.00 0.32 0.00 0.02 0.04
#> TCGA.C8.A278.01 2 0.1480 0.6914 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.AC.A3BB.01 3 0.4213 0.7725 0.00 0.00 0.78 0.10 0.04 0.08
#> TCGA.BH.A1FE.01 3 0.0000 0.8688 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A2.A0EN.01 3 0.0547 0.8678 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.BH.A0BF.01 3 0.0000 0.8688 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AR.A1AK.01 1 0.4534 0.0812 0.58 0.00 0.00 0.38 0.00 0.04
#> TCGA.A7.A3J1.01 4 0.4806 0.4841 0.38 0.00 0.00 0.56 0.00 0.06
#> TCGA.D8.A1XM.01 1 0.1807 0.8817 0.92 0.00 0.00 0.00 0.02 0.06
#> TCGA.BH.A0HP.01 1 0.0937 0.8984 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.D8.A27K.01 1 0.0000 0.9222 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0YK.01 3 0.2784 0.8390 0.00 0.00 0.88 0.04 0.04 0.04
#> TCGA.E2.A107.01 4 0.3942 0.4239 0.04 0.00 0.00 0.80 0.06 0.10
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.E9.A1R2.01 1 0.0000 0.9335 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A3X8.01 1 0.1363 0.9006 0.94 0.00 0.04 0.00 0.00 0.00 0.02
#> TCGA.E2.A10B.01 4 0.1664 0.4914 0.00 0.00 0.00 0.92 0.06 0.02 0.00
#> TCGA.E9.A1RD.01 1 0.0000 0.9335 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LD.A66U.01 4 0.3841 0.4922 0.28 0.00 0.04 0.68 0.00 0.00 0.00
#> TCGA.AC.A8OS.01 4 0.5755 0.4363 0.00 0.00 0.22 0.56 0.06 0.00 0.16
#> TCGA.GM.A2DN.01 7 0.0863 0.8594 0.00 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.AC.A6IV.01 7 0.3635 0.7827 0.00 0.00 0.06 0.04 0.02 0.06 0.82
#> TCGA.LL.A7SZ.01 2 0.1718 0.6513 0.00 0.92 0.04 0.00 0.00 0.04 0.00
#> TCGA.GM.A2DH.01 7 0.3208 0.8075 0.00 0.02 0.12 0.00 0.04 0.00 0.82
#> TCGA.AR.A2LO.01 1 0.2213 0.8708 0.90 0.00 0.04 0.00 0.00 0.02 0.04
#> TCGA.BH.A201.01 1 0.0000 0.9335 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UU.A93S.01 6 0.2259 0.5061 0.00 0.16 0.00 0.00 0.00 0.84 0.00
#> TCGA.A2.A1FZ.01 1 0.0504 0.9260 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.D8.A27R.01 7 0.4171 0.7504 0.00 0.00 0.06 0.02 0.08 0.06 0.78
#> TCGA.D8.A1XT.01 7 0.6556 0.4253 0.06 0.00 0.08 0.02 0.22 0.06 0.56
#> TCGA.C8.A1HI.01 1 0.1006 0.9169 0.96 0.00 0.02 0.02 0.00 0.00 0.00
#> TCGA.C8.A3M7.01 7 0.3396 0.7891 0.00 0.00 0.14 0.02 0.04 0.00 0.80
#> TCGA.4H.AAAK.01 1 0.1363 0.9008 0.94 0.00 0.02 0.04 0.00 0.00 0.00
#> TCGA.AC.A2FO.01 7 0.3404 0.7599 0.00 0.00 0.04 0.08 0.06 0.00 0.82
#> TCGA.D8.A1X8.01 4 0.2864 0.5329 0.12 0.00 0.00 0.84 0.02 0.02 0.00
#> TCGA.A2.A0T5.01 1 0.0000 0.9335 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LD.A74U.01 1 0.3541 0.7494 0.80 0.00 0.08 0.10 0.02 0.00 0.00
#> TCGA.E9.A1RA.01 1 0.2278 0.8460 0.88 0.00 0.04 0.00 0.00 0.00 0.08
#> TCGA.A2.A0YD.01 1 0.0000 0.9335 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A6HE.01 1 0.2708 0.7033 0.78 0.00 0.00 0.22 0.00 0.00 0.00
#> TCGA.BH.A0DP.01 4 0.5086 0.5086 0.20 0.00 0.16 0.62 0.02 0.00 0.00
#> TCGA.AR.A2LN.01 4 0.5604 0.3768 0.34 0.00 0.16 0.48 0.02 0.00 0.00
#> TCGA.AR.A0TT.01 2 0.1006 0.6666 0.00 0.96 0.00 0.00 0.02 0.02 0.00
#> TCGA.AC.A3W6.01 7 0.1433 0.8503 0.00 0.00 0.08 0.00 0.00 0.00 0.92
#> TCGA.OL.A66P.01 2 0.1363 0.6691 0.00 0.94 0.02 0.00 0.00 0.04 0.00
#> TCGA.BH.A0H3.01 1 0.0000 0.9335 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1IZ.01 2 0.3755 0.1613 0.00 0.64 0.02 0.00 0.00 0.00 0.34
#> TCGA.AO.A0JA.01 1 0.3439 0.8010 0.82 0.00 0.06 0.06 0.00 0.06 0.00
#> TCGA.AO.A0JG.01 4 0.4022 0.4625 0.00 0.00 0.08 0.78 0.10 0.02 0.02
#> TCGA.GM.A2DB.01 2 0.1664 0.6653 0.00 0.92 0.02 0.00 0.00 0.06 0.00
#> TCGA.AC.A6IX.06 7 0.0504 0.8640 0.00 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.EW.A1J2.01 1 0.0000 0.9335 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0GY.01 5 0.5460 0.1893 0.00 0.24 0.14 0.00 0.58 0.04 0.00
#> TCGA.W8.A86G.01 1 0.0000 0.9335 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C8.A1HF.01 1 0.0504 0.9260 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.A2.A0T7.01 5 0.2912 0.6604 0.00 0.00 0.04 0.14 0.82 0.00 0.00
#> TCGA.AO.A0JJ.01 4 0.2376 0.5353 0.12 0.00 0.00 0.86 0.00 0.02 0.00
#> TCGA.B6.A0X7.01 1 0.0000 0.9335 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1BC.01 1 0.2803 0.7973 0.84 0.00 0.06 0.10 0.00 0.00 0.00
#> TCGA.A1.A0SF.01 4 0.6833 0.2926 0.02 0.00 0.24 0.42 0.08 0.00 0.24
#> TCGA.EW.A6SD.01 7 0.4033 0.6604 0.00 0.00 0.08 0.00 0.22 0.00 0.70
#> TCGA.AR.A1AU.01 1 0.0000 0.9335 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LD.A7W5.01 7 0.1006 0.8637 0.00 0.00 0.02 0.00 0.00 0.02 0.96
#> TCGA.BH.A42V.01 1 0.0504 0.9265 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.E9.A5FK.01 7 0.0504 0.8640 0.00 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.D8.A1XB.01 1 0.0000 0.9335 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A7.A5ZX.01 1 0.0000 0.9335 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A2B8.01 4 0.5166 0.5128 0.02 0.00 0.20 0.66 0.08 0.00 0.04
#> TCGA.A2.A0CO.01 4 0.5173 0.4871 0.00 0.00 0.20 0.64 0.06 0.00 0.10
#> TCGA.AC.A23G.01 1 0.0000 0.9335 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GM.A3XN.01 1 0.0504 0.9260 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.AQ.A7U7.01 7 0.0504 0.8615 0.00 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.A2.A25A.01 1 0.1433 0.8839 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.A2.A25D.01 7 0.3055 0.8038 0.00 0.00 0.14 0.02 0.02 0.00 0.82
#> TCGA.BH.A0AW.01 2 0.6333 -0.1679 0.00 0.42 0.36 0.00 0.04 0.16 0.02
#> TCGA.BH.A0B6.01 4 0.5462 0.3919 0.00 0.00 0.06 0.60 0.12 0.00 0.22
#> TCGA.GM.A5PX.01 1 0.0504 0.9258 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.GM.A2DD.01 2 0.1166 0.6606 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.D8.A73U.01 7 0.2163 0.8391 0.00 0.02 0.10 0.00 0.00 0.00 0.88
#> TCGA.OL.A5RX.01 1 0.0000 0.9335 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A23C.01 7 0.7294 0.0999 0.00 0.02 0.16 0.14 0.22 0.02 0.44
#> TCGA.A7.A56D.01 5 0.3927 0.6298 0.00 0.00 0.08 0.14 0.76 0.02 0.00
#> TCGA.AR.A5QP.01 1 0.0000 0.9335 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A2L8.01 7 0.0863 0.8594 0.00 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.EW.A1OV.01 2 0.1664 0.6529 0.00 0.92 0.02 0.00 0.00 0.06 0.00
#> TCGA.AR.A24P.01 1 0.0000 0.9335 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A0B2.01 1 0.0000 0.9335 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XX.A899.01 7 0.0863 0.8594 0.00 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.E9.A1N9.01 5 0.2213 0.6261 0.00 0.00 0.04 0.02 0.90 0.00 0.04
#> TCGA.AO.A03L.01 2 0.4358 0.4268 0.00 0.74 0.08 0.00 0.06 0.12 0.00
#> TCGA.A2.A4S2.01 1 0.1664 0.8847 0.92 0.00 0.02 0.06 0.00 0.00 0.00
#> TCGA.E2.A10C.01 2 0.3221 0.3538 0.00 0.68 0.00 0.00 0.00 0.32 0.00
#> TCGA.5L.AAT1.01 4 0.5287 0.5266 0.02 0.00 0.16 0.66 0.04 0.00 0.12
#> TCGA.HN.A2OB.01 1 0.0000 0.9335 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E2.A1IJ.01 4 0.2509 0.5709 0.06 0.00 0.02 0.88 0.00 0.00 0.04
#> TCGA.AR.A0TW.01 6 0.6816 0.4431 0.00 0.26 0.22 0.00 0.14 0.38 0.00
#> TCGA.B6.A401.01 7 0.1664 0.8518 0.00 0.00 0.02 0.06 0.00 0.00 0.92
#> TCGA.E2.A1LB.01 1 0.4295 0.6695 0.74 0.00 0.06 0.00 0.14 0.00 0.06
#> TCGA.AC.A3W7.01 1 0.0504 0.9256 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.AC.A3W5.01 2 0.6337 -0.1182 0.00 0.44 0.30 0.00 0.08 0.18 0.00
#> TCGA.E9.A1RI.01 1 0.0000 0.9335 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5RU.01 7 0.1363 0.8512 0.00 0.00 0.04 0.00 0.00 0.02 0.94
#> TCGA.E2.A10F.01 1 0.0863 0.9139 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.B6.A0RV.01 1 0.1006 0.9141 0.96 0.00 0.02 0.02 0.00 0.00 0.00
#> TCGA.E2.A1IH.01 1 0.4767 0.6504 0.72 0.00 0.06 0.02 0.00 0.06 0.14
#> TCGA.EW.A1IY.01 1 0.4461 0.4327 0.62 0.00 0.04 0.00 0.00 0.02 0.32
#> TCGA.C8.A278.01 2 0.0504 0.6644 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.AC.A3BB.01 7 0.2864 0.8113 0.00 0.00 0.12 0.02 0.02 0.00 0.84
#> TCGA.BH.A1FE.01 7 0.0000 0.8648 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.A2.A0EN.01 7 0.0504 0.8640 0.00 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.BH.A0BF.01 7 0.0000 0.8648 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AR.A1AK.01 4 0.5132 0.3060 0.44 0.00 0.08 0.46 0.02 0.00 0.00
#> TCGA.A7.A3J1.01 4 0.2945 0.4863 0.26 0.00 0.00 0.74 0.00 0.00 0.00
#> TCGA.D8.A1XM.01 1 0.2159 0.8745 0.90 0.00 0.06 0.00 0.00 0.02 0.02
#> TCGA.BH.A0HP.01 1 0.0000 0.9335 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A27K.01 1 0.0000 0.9335 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0YK.01 7 0.1433 0.8503 0.00 0.00 0.08 0.00 0.00 0.00 0.92
#> TCGA.E2.A107.01 4 0.3208 0.4660 0.00 0.00 0.12 0.82 0.04 0.02 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.E9.A1R2.01 1 0.0000 0.86828 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A3X8.01 1 0.1741 0.84487 0.92 0.00 0.02 0.02 0.00 0.00 0.04 0.00
#> TCGA.E2.A10B.01 4 0.3720 0.48256 0.06 0.00 0.04 0.80 0.04 0.00 0.00 0.06
#> TCGA.E9.A1RD.01 1 0.0471 0.86886 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.LD.A66U.01 4 0.3746 0.48562 0.32 0.00 0.04 0.64 0.00 0.00 0.00 0.00
#> TCGA.AC.A8OS.01 4 0.5623 0.18003 0.00 0.00 0.36 0.48 0.02 0.00 0.08 0.06
#> TCGA.GM.A2DN.01 7 0.0000 0.68088 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AC.A6IV.01 7 0.2348 0.59917 0.00 0.00 0.06 0.04 0.02 0.00 0.88 0.00
#> TCGA.LL.A7SZ.01 2 0.4019 0.47291 0.00 0.74 0.14 0.00 0.00 0.06 0.00 0.06
#> TCGA.GM.A2DH.01 7 0.4458 0.09568 0.00 0.02 0.38 0.00 0.00 0.02 0.56 0.02
#> TCGA.AR.A2LO.01 1 0.3303 0.67601 0.76 0.00 0.02 0.02 0.00 0.00 0.20 0.00
#> TCGA.BH.A201.01 1 0.0808 0.86583 0.96 0.00 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.UU.A93S.01 6 0.2623 0.00000 0.00 0.10 0.00 0.00 0.00 0.84 0.00 0.06
#> TCGA.A2.A1FZ.01 1 0.0000 0.86828 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D8.A27R.01 7 0.4906 0.36278 0.02 0.00 0.10 0.04 0.18 0.00 0.66 0.00
#> TCGA.D8.A1XT.01 7 0.6234 0.18006 0.06 0.00 0.10 0.04 0.26 0.00 0.52 0.02
#> TCGA.C8.A1HI.01 1 0.1275 0.86044 0.94 0.00 0.00 0.04 0.02 0.00 0.00 0.00
#> TCGA.C8.A3M7.01 3 0.4137 -0.13082 0.00 0.00 0.50 0.00 0.00 0.02 0.46 0.02
#> TCGA.4H.AAAK.01 1 0.3735 0.65096 0.72 0.00 0.04 0.22 0.00 0.00 0.00 0.02
#> TCGA.AC.A2FO.01 7 0.2204 0.62798 0.00 0.00 0.04 0.02 0.02 0.00 0.90 0.02
#> TCGA.D8.A1X8.01 4 0.3941 0.54577 0.14 0.00 0.04 0.76 0.02 0.00 0.00 0.04
#> TCGA.A2.A0T5.01 1 0.0471 0.86886 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.LD.A74U.01 1 0.3785 0.63012 0.72 0.00 0.14 0.14 0.00 0.00 0.00 0.00
#> TCGA.E9.A1RA.01 1 0.3537 0.61362 0.72 0.00 0.02 0.02 0.00 0.00 0.24 0.00
#> TCGA.A2.A0YD.01 1 0.0471 0.86555 0.98 0.00 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.E9.A6HE.01 1 0.3193 0.45351 0.62 0.00 0.00 0.38 0.00 0.00 0.00 0.00
#> TCGA.BH.A0DP.01 4 0.5171 0.49867 0.20 0.00 0.18 0.58 0.00 0.00 0.00 0.04
#> TCGA.AR.A2LN.01 4 0.5704 0.44748 0.28 0.00 0.18 0.48 0.00 0.00 0.00 0.06
#> TCGA.AR.A0TT.01 2 0.0941 0.62846 0.00 0.96 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.AC.A3W6.01 7 0.3142 0.24392 0.00 0.00 0.36 0.00 0.00 0.00 0.64 0.00
#> TCGA.OL.A66P.01 2 0.0471 0.62936 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.BH.A0H3.01 1 0.0000 0.86828 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EW.A1IZ.01 2 0.3995 0.13878 0.00 0.60 0.02 0.00 0.00 0.00 0.36 0.02
#> TCGA.AO.A0JA.01 1 0.4339 0.68854 0.74 0.00 0.08 0.06 0.10 0.00 0.02 0.00
#> TCGA.AO.A0JG.01 4 0.6295 0.12446 0.00 0.00 0.14 0.56 0.06 0.02 0.06 0.16
#> TCGA.GM.A2DB.01 2 0.0471 0.63132 0.00 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A6IX.06 7 0.0808 0.67696 0.00 0.00 0.04 0.00 0.00 0.00 0.96 0.00
#> TCGA.EW.A1J2.01 1 0.1091 0.85873 0.94 0.00 0.00 0.06 0.00 0.00 0.00 0.00
#> TCGA.BH.A0GY.01 5 0.6722 0.19430 0.00 0.22 0.08 0.00 0.46 0.10 0.00 0.14
#> TCGA.W8.A86G.01 1 0.0471 0.86886 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.C8.A1HF.01 1 0.0941 0.86098 0.96 0.00 0.02 0.00 0.00 0.00 0.02 0.00
#> TCGA.A2.A0T7.01 5 0.3131 0.56442 0.04 0.00 0.02 0.06 0.84 0.00 0.00 0.04
#> TCGA.AO.A0JJ.01 4 0.3770 0.54713 0.12 0.00 0.02 0.78 0.04 0.00 0.00 0.04
#> TCGA.B6.A0X7.01 1 0.0471 0.86886 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.E2.A1BC.01 1 0.3594 0.57549 0.68 0.00 0.04 0.28 0.00 0.00 0.00 0.00
#> TCGA.A1.A0SF.01 3 0.6322 0.10597 0.00 0.00 0.46 0.26 0.04 0.02 0.20 0.02
#> TCGA.EW.A6SD.01 7 0.4644 0.37659 0.00 0.00 0.16 0.00 0.18 0.02 0.64 0.00
#> TCGA.AR.A1AU.01 1 0.0471 0.86886 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.LD.A7W5.01 7 0.1091 0.66457 0.00 0.00 0.06 0.00 0.00 0.00 0.94 0.00
#> TCGA.BH.A42V.01 1 0.2350 0.81336 0.86 0.00 0.04 0.10 0.00 0.00 0.00 0.00
#> TCGA.E9.A5FK.01 7 0.0000 0.68088 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D8.A1XB.01 1 0.1765 0.82159 0.88 0.00 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.A7.A5ZX.01 1 0.0471 0.86886 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.AC.A2B8.01 4 0.5129 0.39315 0.02 0.00 0.28 0.60 0.02 0.00 0.02 0.06
#> TCGA.A2.A0CO.01 4 0.4983 0.25217 0.00 0.00 0.36 0.54 0.02 0.00 0.04 0.04
#> TCGA.AC.A23G.01 1 0.1887 0.84101 0.90 0.00 0.04 0.06 0.00 0.00 0.00 0.00
#> TCGA.GM.A3XN.01 1 0.1408 0.85475 0.94 0.00 0.02 0.02 0.00 0.00 0.02 0.00
#> TCGA.AQ.A7U7.01 7 0.1091 0.67061 0.00 0.00 0.06 0.00 0.00 0.00 0.94 0.00
#> TCGA.A2.A25A.01 1 0.2856 0.76943 0.78 0.00 0.02 0.20 0.00 0.00 0.00 0.00
#> TCGA.A2.A25D.01 7 0.4141 -0.24403 0.00 0.02 0.48 0.00 0.00 0.02 0.48 0.00
#> TCGA.BH.A0AW.01 2 0.4541 -0.44588 0.00 0.48 0.02 0.00 0.02 0.02 0.00 0.46
#> TCGA.BH.A0B6.01 4 0.5449 -0.02009 0.00 0.00 0.04 0.52 0.06 0.00 0.34 0.04
#> TCGA.GM.A5PX.01 1 0.2114 0.81172 0.84 0.00 0.00 0.16 0.00 0.00 0.00 0.00
#> TCGA.GM.A2DD.01 2 0.1341 0.59527 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.D8.A73U.01 7 0.4417 0.14517 0.00 0.02 0.36 0.00 0.00 0.02 0.58 0.02
#> TCGA.OL.A5RX.01 1 0.0000 0.86828 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AC.A23C.01 7 0.6476 -0.00295 0.00 0.00 0.08 0.02 0.24 0.02 0.48 0.16
#> TCGA.A7.A56D.01 5 0.3185 0.55678 0.00 0.00 0.04 0.08 0.82 0.00 0.00 0.06
#> TCGA.AR.A5QP.01 1 0.0000 0.86828 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BH.A2L8.01 7 0.0471 0.68118 0.00 0.00 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.EW.A1OV.01 2 0.0471 0.63174 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.AR.A24P.01 1 0.0471 0.86886 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.BH.A0B2.01 1 0.0471 0.86555 0.98 0.00 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.XX.A899.01 7 0.0471 0.68118 0.00 0.00 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.E9.A1N9.01 5 0.4230 0.55920 0.00 0.00 0.16 0.04 0.74 0.02 0.02 0.02
#> TCGA.AO.A03L.01 2 0.4313 0.34613 0.00 0.70 0.02 0.00 0.06 0.02 0.00 0.20
#> TCGA.A2.A4S2.01 1 0.2888 0.73921 0.80 0.00 0.04 0.16 0.00 0.00 0.00 0.00
#> TCGA.E2.A10C.01 2 0.5137 0.10420 0.00 0.54 0.08 0.00 0.00 0.32 0.00 0.06
#> TCGA.5L.AAT1.01 4 0.5195 0.26493 0.00 0.00 0.18 0.60 0.02 0.00 0.18 0.02
#> TCGA.HN.A2OB.01 1 0.0471 0.86886 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.E2.A1IJ.01 4 0.3951 0.55220 0.12 0.00 0.02 0.76 0.00 0.00 0.08 0.02
#> TCGA.AR.A0TW.01 8 0.6735 -0.00571 0.00 0.18 0.04 0.00 0.16 0.18 0.00 0.44
#> TCGA.B6.A401.01 7 0.2404 0.61669 0.00 0.00 0.14 0.00 0.00 0.00 0.84 0.02
#> TCGA.E2.A1LB.01 1 0.3397 0.74064 0.80 0.00 0.10 0.00 0.04 0.00 0.06 0.00
#> TCGA.AC.A3W7.01 1 0.0941 0.86208 0.96 0.00 0.02 0.02 0.00 0.00 0.00 0.00
#> TCGA.AC.A3W5.01 8 0.4954 0.16894 0.00 0.42 0.00 0.00 0.10 0.02 0.00 0.46
#> TCGA.E9.A1RI.01 1 0.0000 0.86828 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OL.A5RU.01 7 0.0000 0.68088 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.E2.A10F.01 1 0.1804 0.84752 0.90 0.00 0.02 0.08 0.00 0.00 0.00 0.00
#> TCGA.B6.A0RV.01 1 0.2350 0.80039 0.86 0.00 0.04 0.10 0.00 0.00 0.00 0.00
#> TCGA.E2.A1IH.01 1 0.5284 0.37801 0.58 0.00 0.04 0.04 0.06 0.00 0.28 0.00
#> TCGA.EW.A1IY.01 1 0.3618 0.36605 0.60 0.00 0.02 0.00 0.00 0.00 0.38 0.00
#> TCGA.C8.A278.01 2 0.2025 0.56875 0.00 0.88 0.02 0.00 0.00 0.00 0.00 0.10
#> TCGA.AC.A3BB.01 7 0.3272 -0.00946 0.00 0.00 0.42 0.00 0.00 0.00 0.58 0.00
#> TCGA.BH.A1FE.01 7 0.0808 0.67419 0.00 0.00 0.04 0.00 0.00 0.00 0.96 0.00
#> TCGA.A2.A0EN.01 7 0.0000 0.68088 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BH.A0BF.01 7 0.0808 0.66427 0.00 0.00 0.04 0.00 0.00 0.00 0.96 0.00
#> TCGA.AR.A1AK.01 4 0.4619 0.22131 0.44 0.00 0.06 0.48 0.00 0.00 0.00 0.02
#> TCGA.A7.A3J1.01 4 0.3170 0.54747 0.20 0.00 0.00 0.76 0.00 0.00 0.00 0.04
#> TCGA.D8.A1XM.01 1 0.2071 0.84623 0.90 0.00 0.02 0.04 0.00 0.00 0.04 0.00
#> TCGA.BH.A0HP.01 1 0.1765 0.82159 0.88 0.00 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.D8.A27K.01 1 0.0000 0.86828 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A2.A0YK.01 7 0.3083 0.29138 0.00 0.00 0.34 0.00 0.00 0.00 0.66 0.00
#> TCGA.E2.A107.01 4 0.3535 0.42399 0.02 0.00 0.06 0.82 0.02 0.02 0.00 0.06
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node043. Child nodes: Node02121-leaf , Node02122-leaf , Node02131-leaf , Node02132-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02214-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02321-leaf , Node02322-leaf , Node02421-leaf , Node02422-leaf , Node02423-leaf , Node04111-leaf , Node04112-leaf , Node04113 , Node04131-leaf , Node04132-leaf , Node04133-leaf , Node04221-leaf , Node04222-leaf , Node04331-leaf , Node04332-leaf , Node04333-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0433"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 35 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.984 0.993 0.2196 0.792 0.792
#> 3 3 1.000 0.956 0.982 1.1821 0.748 0.682
#> 4 4 0.744 0.757 0.880 0.3033 0.817 0.680
#> 5 5 0.727 0.869 0.923 0.1265 0.755 0.479
#> 6 6 0.704 0.766 0.891 0.0419 0.945 0.812
#> 7 7 0.650 0.740 0.895 0.0459 0.976 0.911
#> 8 8 0.677 0.708 0.862 0.0318 0.963 0.855
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.AC.A8OS.01 2 0.000 0.992 0.00 1.00
#> TCGA.GM.A2DN.01 2 0.000 0.992 0.00 1.00
#> TCGA.AC.A6IV.01 2 0.000 0.992 0.00 1.00
#> TCGA.GM.A2DH.01 2 0.795 0.684 0.24 0.76
#> TCGA.D8.A27R.01 1 0.000 1.000 1.00 0.00
#> TCGA.D8.A1XT.01 1 0.000 1.000 1.00 0.00
#> TCGA.C8.A3M7.01 2 0.000 0.992 0.00 1.00
#> TCGA.AC.A2FO.01 2 0.000 0.992 0.00 1.00
#> TCGA.AC.A3W6.01 2 0.000 0.992 0.00 1.00
#> TCGA.EW.A1IZ.01 2 0.000 0.992 0.00 1.00
#> TCGA.AO.A0JG.01 2 0.000 0.992 0.00 1.00
#> TCGA.AC.A6IX.06 2 0.000 0.992 0.00 1.00
#> TCGA.A1.A0SF.01 2 0.000 0.992 0.00 1.00
#> TCGA.EW.A6SD.01 1 0.000 1.000 1.00 0.00
#> TCGA.LD.A7W5.01 2 0.000 0.992 0.00 1.00
#> TCGA.E9.A5FK.01 2 0.000 0.992 0.00 1.00
#> TCGA.AC.A2B8.01 2 0.000 0.992 0.00 1.00
#> TCGA.A2.A0CO.01 2 0.000 0.992 0.00 1.00
#> TCGA.AQ.A7U7.01 2 0.000 0.992 0.00 1.00
#> TCGA.A2.A25D.01 2 0.000 0.992 0.00 1.00
#> TCGA.BH.A0B6.01 2 0.000 0.992 0.00 1.00
#> TCGA.D8.A73U.01 2 0.000 0.992 0.00 1.00
#> TCGA.AC.A23C.01 2 0.000 0.992 0.00 1.00
#> TCGA.A7.A56D.01 2 0.000 0.992 0.00 1.00
#> TCGA.BH.A2L8.01 2 0.000 0.992 0.00 1.00
#> TCGA.XX.A899.01 2 0.000 0.992 0.00 1.00
#> TCGA.E9.A1N9.01 1 0.000 1.000 1.00 0.00
#> TCGA.5L.AAT1.01 2 0.000 0.992 0.00 1.00
#> TCGA.B6.A401.01 2 0.000 0.992 0.00 1.00
#> TCGA.OL.A5RU.01 2 0.000 0.992 0.00 1.00
#> TCGA.AC.A3BB.01 2 0.000 0.992 0.00 1.00
#> TCGA.BH.A1FE.01 2 0.000 0.992 0.00 1.00
#> TCGA.A2.A0EN.01 2 0.000 0.992 0.00 1.00
#> TCGA.BH.A0BF.01 2 0.000 0.992 0.00 1.00
#> TCGA.A2.A0YK.01 2 0.000 0.992 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.AC.A8OS.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.GM.A2DN.01 2 0.000 0.972 0 1.00 0.00
#> TCGA.AC.A6IV.01 2 0.000 0.972 0 1.00 0.00
#> TCGA.GM.A2DH.01 2 0.000 0.972 0 1.00 0.00
#> TCGA.D8.A27R.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.D8.A1XT.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.C8.A3M7.01 2 0.000 0.972 0 1.00 0.00
#> TCGA.AC.A2FO.01 2 0.000 0.972 0 1.00 0.00
#> TCGA.AC.A3W6.01 2 0.000 0.972 0 1.00 0.00
#> TCGA.EW.A1IZ.01 2 0.000 0.972 0 1.00 0.00
#> TCGA.AO.A0JG.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.AC.A6IX.06 2 0.000 0.972 0 1.00 0.00
#> TCGA.A1.A0SF.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.EW.A6SD.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.LD.A7W5.01 2 0.000 0.972 0 1.00 0.00
#> TCGA.E9.A5FK.01 2 0.000 0.972 0 1.00 0.00
#> TCGA.AC.A2B8.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.A2.A0CO.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.AQ.A7U7.01 2 0.000 0.972 0 1.00 0.00
#> TCGA.A2.A25D.01 2 0.000 0.972 0 1.00 0.00
#> TCGA.BH.A0B6.01 2 0.000 0.972 0 1.00 0.00
#> TCGA.D8.A73U.01 2 0.000 0.972 0 1.00 0.00
#> TCGA.AC.A23C.01 2 0.000 0.972 0 1.00 0.00
#> TCGA.A7.A56D.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.BH.A2L8.01 2 0.000 0.972 0 1.00 0.00
#> TCGA.XX.A899.01 2 0.000 0.972 0 1.00 0.00
#> TCGA.E9.A1N9.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.5L.AAT1.01 2 0.571 0.549 0 0.68 0.32
#> TCGA.B6.A401.01 2 0.571 0.549 0 0.68 0.32
#> TCGA.OL.A5RU.01 2 0.000 0.972 0 1.00 0.00
#> TCGA.AC.A3BB.01 2 0.000 0.972 0 1.00 0.00
#> TCGA.BH.A1FE.01 2 0.000 0.972 0 1.00 0.00
#> TCGA.A2.A0EN.01 2 0.000 0.972 0 1.00 0.00
#> TCGA.BH.A0BF.01 2 0.000 0.972 0 1.00 0.00
#> TCGA.A2.A0YK.01 2 0.000 0.972 0 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.AC.A8OS.01 3 0.4522 0.659 0 0.00 0.68 0.32
#> TCGA.GM.A2DN.01 2 0.0000 0.866 0 1.00 0.00 0.00
#> TCGA.AC.A6IV.01 2 0.0000 0.866 0 1.00 0.00 0.00
#> TCGA.GM.A2DH.01 2 0.0707 0.854 0 0.98 0.00 0.02
#> TCGA.D8.A27R.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.D8.A1XT.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.C8.A3M7.01 2 0.0000 0.866 0 1.00 0.00 0.00
#> TCGA.AC.A2FO.01 3 0.1211 0.629 0 0.04 0.96 0.00
#> TCGA.AC.A3W6.01 2 0.0000 0.866 0 1.00 0.00 0.00
#> TCGA.EW.A1IZ.01 2 0.4522 0.689 0 0.68 0.32 0.00
#> TCGA.AO.A0JG.01 3 0.4522 0.659 0 0.00 0.68 0.32
#> TCGA.AC.A6IX.06 2 0.0707 0.854 0 0.98 0.00 0.02
#> TCGA.A1.A0SF.01 3 0.4522 0.659 0 0.00 0.68 0.32
#> TCGA.EW.A6SD.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.LD.A7W5.01 2 0.4522 0.689 0 0.68 0.32 0.00
#> TCGA.E9.A5FK.01 2 0.0000 0.866 0 1.00 0.00 0.00
#> TCGA.AC.A2B8.01 3 0.4522 0.659 0 0.00 0.68 0.32
#> TCGA.A2.A0CO.01 3 0.4522 0.659 0 0.00 0.68 0.32
#> TCGA.AQ.A7U7.01 2 0.0000 0.866 0 1.00 0.00 0.00
#> TCGA.A2.A25D.01 2 0.4277 0.713 0 0.72 0.28 0.00
#> TCGA.BH.A0B6.01 2 0.4907 0.559 0 0.58 0.42 0.00
#> TCGA.D8.A73U.01 2 0.0000 0.866 0 1.00 0.00 0.00
#> TCGA.AC.A23C.01 2 0.4790 0.621 0 0.62 0.38 0.00
#> TCGA.A7.A56D.01 4 0.0707 0.000 0 0.00 0.02 0.98
#> TCGA.BH.A2L8.01 2 0.0707 0.854 0 0.98 0.00 0.02
#> TCGA.XX.A899.01 2 0.0000 0.866 0 1.00 0.00 0.00
#> TCGA.E9.A1N9.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.5L.AAT1.01 3 0.0707 0.644 0 0.02 0.98 0.00
#> TCGA.B6.A401.01 3 0.0707 0.644 0 0.02 0.98 0.00
#> TCGA.OL.A5RU.01 2 0.0000 0.866 0 1.00 0.00 0.00
#> TCGA.AC.A3BB.01 2 0.4855 0.592 0 0.60 0.40 0.00
#> TCGA.BH.A1FE.01 2 0.0000 0.866 0 1.00 0.00 0.00
#> TCGA.A2.A0EN.01 2 0.4134 0.731 0 0.74 0.26 0.00
#> TCGA.BH.A0BF.01 3 0.1637 0.604 0 0.06 0.94 0.00
#> TCGA.A2.A0YK.01 2 0.0000 0.866 0 1.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.AC.A8OS.01 3 0.0000 1.000 0 0.00 1.00 0.00 0.00
#> TCGA.GM.A2DN.01 2 0.0000 0.949 0 1.00 0.00 0.00 0.00
#> TCGA.AC.A6IV.01 2 0.0000 0.949 0 1.00 0.00 0.00 0.00
#> TCGA.GM.A2DH.01 2 0.1732 0.891 0 0.92 0.00 0.00 0.08
#> TCGA.D8.A27R.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
#> TCGA.D8.A1XT.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
#> TCGA.C8.A3M7.01 2 0.0000 0.949 0 1.00 0.00 0.00 0.00
#> TCGA.AC.A2FO.01 5 0.3421 0.814 0 0.08 0.08 0.00 0.84
#> TCGA.AC.A3W6.01 2 0.1410 0.918 0 0.94 0.00 0.00 0.06
#> TCGA.EW.A1IZ.01 5 0.2732 0.851 0 0.16 0.00 0.00 0.84
#> TCGA.AO.A0JG.01 3 0.0000 1.000 0 0.00 1.00 0.00 0.00
#> TCGA.AC.A6IX.06 2 0.1732 0.891 0 0.92 0.00 0.00 0.08
#> TCGA.A1.A0SF.01 3 0.0000 1.000 0 0.00 1.00 0.00 0.00
#> TCGA.EW.A6SD.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
#> TCGA.LD.A7W5.01 5 0.2732 0.851 0 0.16 0.00 0.00 0.84
#> TCGA.E9.A5FK.01 2 0.0000 0.949 0 1.00 0.00 0.00 0.00
#> TCGA.AC.A2B8.01 3 0.0000 1.000 0 0.00 1.00 0.00 0.00
#> TCGA.A2.A0CO.01 3 0.0000 1.000 0 0.00 1.00 0.00 0.00
#> TCGA.AQ.A7U7.01 2 0.1410 0.918 0 0.94 0.00 0.00 0.06
#> TCGA.A2.A25D.01 5 0.4675 0.462 0 0.38 0.00 0.02 0.60
#> TCGA.BH.A0B6.01 5 0.2732 0.851 0 0.16 0.00 0.00 0.84
#> TCGA.D8.A73U.01 2 0.1043 0.934 0 0.96 0.00 0.00 0.04
#> TCGA.AC.A23C.01 5 0.3274 0.816 0 0.22 0.00 0.00 0.78
#> TCGA.A7.A56D.01 4 0.0609 0.000 0 0.00 0.02 0.98 0.00
#> TCGA.BH.A2L8.01 2 0.1732 0.891 0 0.92 0.00 0.00 0.08
#> TCGA.XX.A899.01 2 0.0000 0.949 0 1.00 0.00 0.00 0.00
#> TCGA.E9.A1N9.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
#> TCGA.5L.AAT1.01 5 0.3106 0.740 0 0.02 0.14 0.00 0.84
#> TCGA.B6.A401.01 5 0.3390 0.795 0 0.06 0.10 0.00 0.84
#> TCGA.OL.A5RU.01 2 0.0000 0.949 0 1.00 0.00 0.00 0.00
#> TCGA.AC.A3BB.01 5 0.2929 0.844 0 0.18 0.00 0.00 0.82
#> TCGA.BH.A1FE.01 2 0.1732 0.892 0 0.92 0.00 0.00 0.08
#> TCGA.A2.A0EN.01 5 0.4126 0.606 0 0.38 0.00 0.00 0.62
#> TCGA.BH.A0BF.01 5 0.3390 0.829 0 0.10 0.06 0.00 0.84
#> TCGA.A2.A0YK.01 2 0.1043 0.934 0 0.96 0.00 0.00 0.04
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.AC.A8OS.01 3 0.0000 0.995 0 0.00 1.00 0 0.00 0.00
#> TCGA.GM.A2DN.01 2 0.0000 0.833 0 1.00 0.00 0 0.00 0.00
#> TCGA.AC.A6IV.01 2 0.0547 0.823 0 0.98 0.00 0 0.02 0.00
#> TCGA.GM.A2DH.01 2 0.5150 0.423 0 0.62 0.00 0 0.16 0.22
#> TCGA.D8.A27R.01 1 0.0000 1.000 1 0.00 0.00 0 0.00 0.00
#> TCGA.D8.A1XT.01 1 0.0000 1.000 1 0.00 0.00 0 0.00 0.00
#> TCGA.C8.A3M7.01 2 0.1480 0.827 0 0.94 0.00 0 0.04 0.02
#> TCGA.AC.A2FO.01 5 0.2790 0.879 0 0.14 0.02 0 0.84 0.00
#> TCGA.AC.A3W6.01 2 0.1807 0.806 0 0.92 0.00 0 0.06 0.02
#> TCGA.EW.A1IZ.01 5 0.2454 0.881 0 0.16 0.00 0 0.84 0.00
#> TCGA.AO.A0JG.01 3 0.0547 0.982 0 0.00 0.98 0 0.00 0.02
#> TCGA.AC.A6IX.06 2 0.4377 0.567 0 0.72 0.00 0 0.16 0.12
#> TCGA.A1.A0SF.01 3 0.0000 0.995 0 0.00 1.00 0 0.00 0.00
#> TCGA.EW.A6SD.01 1 0.0000 1.000 1 0.00 0.00 0 0.00 0.00
#> TCGA.LD.A7W5.01 5 0.2631 0.873 0 0.18 0.00 0 0.82 0.00
#> TCGA.E9.A5FK.01 2 0.0000 0.833 0 1.00 0.00 0 0.00 0.00
#> TCGA.AC.A2B8.01 3 0.0000 0.995 0 0.00 1.00 0 0.00 0.00
#> TCGA.A2.A0CO.01 3 0.0000 0.995 0 0.00 1.00 0 0.00 0.00
#> TCGA.AQ.A7U7.01 2 0.1807 0.806 0 0.92 0.00 0 0.06 0.02
#> TCGA.A2.A25D.01 6 0.3746 0.000 0 0.14 0.00 0 0.08 0.78
#> TCGA.BH.A0B6.01 5 0.2454 0.881 0 0.16 0.00 0 0.84 0.00
#> TCGA.D8.A73U.01 2 0.1092 0.830 0 0.96 0.00 0 0.02 0.02
#> TCGA.AC.A23C.01 5 0.4360 0.708 0 0.26 0.00 0 0.68 0.06
#> TCGA.A7.A56D.01 4 0.0000 0.000 0 0.00 0.00 1 0.00 0.00
#> TCGA.BH.A2L8.01 2 0.4004 0.625 0 0.76 0.00 0 0.12 0.12
#> TCGA.XX.A899.01 2 0.0547 0.832 0 0.98 0.00 0 0.00 0.02
#> TCGA.E9.A1N9.01 1 0.0000 1.000 1 0.00 0.00 0 0.00 0.00
#> TCGA.5L.AAT1.01 5 0.3592 0.604 0 0.02 0.24 0 0.74 0.00
#> TCGA.B6.A401.01 5 0.3321 0.805 0 0.08 0.10 0 0.82 0.00
#> TCGA.OL.A5RU.01 2 0.0000 0.833 0 1.00 0.00 0 0.00 0.00
#> TCGA.AC.A3BB.01 5 0.2941 0.836 0 0.22 0.00 0 0.78 0.00
#> TCGA.BH.A1FE.01 2 0.0937 0.821 0 0.96 0.00 0 0.04 0.00
#> TCGA.A2.A0EN.01 2 0.3851 -0.173 0 0.54 0.00 0 0.46 0.00
#> TCGA.BH.A0BF.01 5 0.2790 0.879 0 0.14 0.02 0 0.84 0.00
#> TCGA.A2.A0YK.01 2 0.1480 0.819 0 0.94 0.00 0 0.04 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.AC.A8OS.01 3 0.0000 0.985 0 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.GM.A2DN.01 2 0.0863 0.821 0 0.96 0.00 0 0.00 0.00 0.04
#> TCGA.AC.A6IV.01 2 0.2163 0.777 0 0.88 0.00 0 0.02 0.00 0.10
#> TCGA.GM.A2DH.01 7 0.2512 0.000 0 0.10 0.00 0 0.00 0.04 0.86
#> TCGA.D8.A27R.01 1 0.0000 1.000 1 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.D8.A1XT.01 1 0.0000 1.000 1 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.C8.A3M7.01 2 0.3404 0.782 0 0.82 0.00 0 0.08 0.04 0.06
#> TCGA.AC.A2FO.01 5 0.1718 0.810 0 0.04 0.04 0 0.92 0.00 0.00
#> TCGA.AC.A3W6.01 2 0.2278 0.819 0 0.88 0.00 0 0.08 0.00 0.04
#> TCGA.EW.A1IZ.01 5 0.2906 0.784 0 0.18 0.00 0 0.80 0.00 0.02
#> TCGA.AO.A0JG.01 3 0.1006 0.958 0 0.00 0.96 0 0.02 0.00 0.02
#> TCGA.AC.A6IX.06 2 0.3517 0.491 0 0.70 0.00 0 0.02 0.00 0.28
#> TCGA.A1.A0SF.01 3 0.0504 0.974 0 0.00 0.98 0 0.00 0.02 0.00
#> TCGA.EW.A6SD.01 1 0.0000 1.000 1 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.LD.A7W5.01 5 0.2259 0.812 0 0.16 0.00 0 0.84 0.00 0.00
#> TCGA.E9.A5FK.01 2 0.0000 0.823 0 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.AC.A2B8.01 3 0.0000 0.985 0 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.A2.A0CO.01 3 0.0000 0.985 0 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.AQ.A7U7.01 2 0.2163 0.811 0 0.88 0.00 0 0.10 0.00 0.02
#> TCGA.A2.A25D.01 6 0.0000 0.000 0 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.BH.A0B6.01 5 0.2163 0.823 0 0.10 0.00 0 0.88 0.00 0.02
#> TCGA.D8.A73U.01 2 0.1718 0.826 0 0.92 0.00 0 0.04 0.00 0.04
#> TCGA.AC.A23C.01 5 0.4884 0.500 0 0.28 0.00 0 0.62 0.06 0.04
#> TCGA.A7.A56D.01 4 0.0000 0.000 0 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.BH.A2L8.01 2 0.3186 0.586 0 0.76 0.00 0 0.02 0.00 0.22
#> TCGA.XX.A899.01 2 0.0000 0.823 0 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.E9.A1N9.01 1 0.0000 1.000 1 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.5L.AAT1.01 5 0.2832 0.649 0 0.00 0.24 0 0.76 0.00 0.00
#> TCGA.B6.A401.01 5 0.2569 0.758 0 0.02 0.14 0 0.84 0.00 0.00
#> TCGA.OL.A5RU.01 2 0.0504 0.816 0 0.98 0.00 0 0.00 0.00 0.02
#> TCGA.AC.A3BB.01 5 0.3055 0.813 0 0.14 0.00 0 0.82 0.02 0.02
#> TCGA.BH.A1FE.01 2 0.1886 0.806 0 0.88 0.00 0 0.12 0.00 0.00
#> TCGA.A2.A0EN.01 2 0.3459 0.261 0 0.60 0.00 0 0.40 0.00 0.00
#> TCGA.BH.A0BF.01 5 0.1664 0.820 0 0.06 0.02 0 0.92 0.00 0.00
#> TCGA.A2.A0YK.01 2 0.2512 0.806 0 0.86 0.00 0 0.10 0.00 0.04
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.AC.A8OS.01 3 0.0000 0.901 0.00 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.GM.A2DN.01 8 0.0471 0.837 0.00 0.02 0.00 0 0.00 0.00 0.00 0.98
#> TCGA.AC.A6IV.01 8 0.1741 0.815 0.00 0.04 0.00 0 0.00 0.02 0.02 0.92
#> TCGA.GM.A2DH.01 7 0.0471 0.000 0.00 0.00 0.00 0 0.00 0.00 0.98 0.02
#> TCGA.D8.A27R.01 1 0.0471 0.988 0.98 0.02 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.D8.A1XT.01 1 0.0471 0.988 0.98 0.02 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.C8.A3M7.01 8 0.4540 0.748 0.00 0.10 0.00 0 0.06 0.02 0.10 0.72
#> TCGA.AC.A2FO.01 5 0.1408 0.734 0.00 0.02 0.02 0 0.94 0.00 0.00 0.02
#> TCGA.AC.A3W6.01 8 0.3970 0.783 0.00 0.10 0.00 0 0.10 0.02 0.02 0.76
#> TCGA.EW.A1IZ.01 5 0.2648 0.752 0.00 0.08 0.00 0 0.84 0.00 0.00 0.08
#> TCGA.AO.A0JG.01 3 0.3015 0.628 0.00 0.32 0.68 0 0.00 0.00 0.00 0.00
#> TCGA.AC.A6IX.06 8 0.3873 0.631 0.00 0.06 0.00 0 0.00 0.02 0.20 0.72
#> TCGA.A1.A0SF.01 3 0.0808 0.887 0.00 0.04 0.96 0 0.00 0.00 0.00 0.00
#> TCGA.EW.A6SD.01 1 0.0000 0.988 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.LD.A7W5.01 5 0.2807 0.751 0.00 0.04 0.00 0 0.84 0.02 0.00 0.10
#> TCGA.E9.A5FK.01 8 0.0941 0.840 0.00 0.00 0.00 0 0.02 0.02 0.00 0.96
#> TCGA.AC.A2B8.01 3 0.0471 0.903 0.00 0.02 0.98 0 0.00 0.00 0.00 0.00
#> TCGA.A2.A0CO.01 3 0.0471 0.903 0.00 0.02 0.98 0 0.00 0.00 0.00 0.00
#> TCGA.AQ.A7U7.01 8 0.3078 0.812 0.00 0.06 0.00 0 0.10 0.02 0.00 0.82
#> TCGA.A2.A25D.01 6 0.0471 0.000 0.00 0.00 0.00 0 0.00 0.98 0.00 0.02
#> TCGA.BH.A0B6.01 5 0.2648 0.752 0.00 0.08 0.00 0 0.84 0.00 0.00 0.08
#> TCGA.D8.A73U.01 8 0.3078 0.823 0.00 0.10 0.00 0 0.06 0.02 0.00 0.82
#> TCGA.AC.A23C.01 5 0.4906 0.364 0.00 0.32 0.00 0 0.56 0.04 0.00 0.08
#> TCGA.A7.A56D.01 4 0.0000 0.000 0.00 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.BH.A2L8.01 8 0.3002 0.727 0.00 0.04 0.00 0 0.00 0.02 0.12 0.82
#> TCGA.XX.A899.01 8 0.0471 0.841 0.00 0.00 0.00 0 0.02 0.00 0.00 0.98
#> TCGA.E9.A1N9.01 1 0.0000 0.988 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.5L.AAT1.01 5 0.4578 0.613 0.00 0.08 0.16 0 0.70 0.04 0.00 0.02
#> TCGA.B6.A401.01 5 0.3503 0.669 0.00 0.08 0.12 0 0.78 0.00 0.00 0.02
#> TCGA.OL.A5RU.01 8 0.1091 0.830 0.00 0.06 0.00 0 0.00 0.00 0.00 0.94
#> TCGA.AC.A3BB.01 5 0.4467 0.631 0.00 0.12 0.00 0 0.66 0.02 0.00 0.20
#> TCGA.BH.A1FE.01 8 0.3483 0.729 0.00 0.04 0.00 0 0.18 0.02 0.00 0.76
#> TCGA.A2.A0EN.01 5 0.4325 0.366 0.00 0.04 0.00 0 0.56 0.02 0.00 0.38
#> TCGA.BH.A0BF.01 5 0.1275 0.751 0.00 0.02 0.00 0 0.94 0.00 0.00 0.04
#> TCGA.A2.A0YK.01 8 0.3554 0.812 0.00 0.08 0.00 0 0.08 0.02 0.02 0.80
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
sessionInfo()
#> R version 4.1.0 (2021-05-18)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: CentOS Linux 7 (Core)
#>
#> Matrix products: default
#> BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
#> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
#> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] grid stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] genefilter_1.74.0 ComplexHeatmap_2.8.0 markdown_1.1 knitr_1.33
#> [5] matrixStats_0.59.0 cola_1.9.4
#>
#> loaded via a namespace (and not attached):
#> [1] bitops_1.0-7 bit64_4.0.5 doParallel_1.0.16 RColorBrewer_1.1-2
#> [5] httr_1.4.2 GenomeInfoDb_1.28.1 data.tree_1.0.0 tools_4.1.0
#> [9] utf8_1.2.1 R6_2.5.0 irlba_2.3.3 DBI_1.1.1
#> [13] BiocGenerics_0.38.0 colorspace_2.0-2 GetoptLong_1.0.5 gridExtra_2.3
#> [17] tidyselect_1.1.1 bit_4.0.4 compiler_4.1.0 Biobase_2.52.0
#> [21] Cairo_1.5-12.2 xml2_1.3.2 microbenchmark_1.4-7 slam_0.1-48
#> [25] scales_1.1.1 askpass_1.1 stringr_1.4.0 digest_0.6.27
#> [29] XVector_0.32.0 pkgconfig_2.0.3 umap_0.2.7.0 fastmap_1.1.0
#> [33] highr_0.9 rlang_0.4.11 GlobalOptions_0.1.2 rstudioapi_0.13
#> [37] RSQLite_2.2.7 impute_1.66.0 generics_0.1.0 shape_1.4.6
#> [41] jsonlite_1.7.2 mclust_5.4.7 dplyr_1.0.7 dendextend_1.15.1
#> [45] RCurl_1.98-1.3 magrittr_2.0.1 GenomeInfoDbData_1.2.6 Matrix_1.3-4
#> [49] fansi_0.5.0 Rcpp_1.0.7 munsell_0.5.0 S4Vectors_0.30.0
#> [53] viridis_0.6.1 reticulate_1.20 lifecycle_1.0.0 scatterplot3d_0.3-41
#> [57] stringi_1.7.3 zlibbioc_1.38.0 blob_1.2.1 parallel_4.1.0
#> [61] crayon_1.4.1 lattice_0.20-44 Biostrings_2.60.1 splines_4.1.0
#> [65] annotate_1.70.0 circlize_0.4.13 KEGGREST_1.32.0 polylabelr_0.2.0
#> [69] pillar_1.6.1 rjson_0.2.20 codetools_0.2-18 stats4_4.1.0
#> [73] XML_3.99-0.6 glue_1.4.2 evaluate_0.14 png_0.1-7
#> [77] vctrs_0.3.8 foreach_1.5.1 polyclip_1.10-0 purrr_0.3.4
#> [81] gtable_0.3.0 openssl_1.4.4 assertthat_0.2.1 clue_0.3-59
#> [85] cachem_1.0.5 ggplot2_3.3.5 xfun_0.24 eulerr_6.1.0
#> [89] xtable_1.8-4 skmeans_0.2-13 RSpectra_0.16-0 viridisLite_0.4.0
#> [93] survival_3.2-11 tibble_3.1.2 Polychrome_1.3.1 iterators_1.0.13
#> [97] AnnotationDbi_1.54.1 memoise_2.0.0 IRanges_2.26.0 cluster_2.1.2
#> [101] ellipsis_0.3.2 brew_1.0-6