Date: 2021-07-22 19:46:35 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 376162 rows and 580 columns.
#> Performed in total 134400 partitions.
#> There are 66 groups under the following parameters:
#> - min_samples: 6
#> - 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, 580 cols
#> |-- 01, 90 cols, 4660 signatures
#> | |-- 011, 27 cols, 3188 signatures
#> | | |-- 0111, 7 cols (b)
#> | | |-- 0112, 15 cols, 832 signatures (c)
#> | | `-- 0113, 5 cols (b)
#> | |-- 012, 38 cols, 2836 signatures
#> | | |-- 0121, 13 cols, 2262 signatures
#> | | | |-- 01211, 5 cols (b)
#> | | | |-- 01212, 3 cols (b)
#> | | | `-- 01213, 5 cols (b)
#> | | `-- 0122, 25 cols, 9384 signatures
#> | | |-- 01221, 7 cols (b)
#> | | |-- 01222, 11 cols (b)
#> | | `-- 01223, 7 cols (b)
#> | `-- 013, 25 cols, 203 signatures (c)
#> |-- 02, 268 cols, 4027 signatures
#> | |-- 021, 90 cols, 4522 signatures
#> | | |-- 0211, 28 cols, 7761 signatures
#> | | | |-- 02111, 11 cols (b)
#> | | | |-- 02112, 4 cols (b)
#> | | | |-- 02113, 8 cols (b)
#> | | | `-- 02114, 5 cols (b)
#> | | |-- 0212, 34 cols, 30719 signatures
#> | | | |-- 02121, 14 cols, 803 signatures (c)
#> | | | |-- 02122, 4 cols (b)
#> | | | |-- 02123, 6 cols (b)
#> | | | `-- 02124, 10 cols (b)
#> | | `-- 0213, 28 cols, 8755 signatures
#> | | |-- 02131, 10 cols (b)
#> | | |-- 02132, 13 cols, 1269 signatures
#> | | | |-- 021321, 8 cols (b)
#> | | | `-- 021322, 5 cols (b)
#> | | `-- 02133, 5 cols (b)
#> | |-- 022, 109 cols, 24546 signatures
#> | | |-- 0221, 25 cols, 10841 signatures
#> | | | |-- 02211, 10 cols (b)
#> | | | |-- 02212, 8 cols (b)
#> | | | `-- 02213, 7 cols (b)
#> | | |-- 0222, 28 cols, 2489 signatures
#> | | | |-- 02221, 12 cols, 557 signatures (c)
#> | | | |-- 02222, 13 cols, 0 signatures (c)
#> | | | `-- 02223, 3 cols (b)
#> | | |-- 0223, 28 cols, 4864 signatures
#> | | | |-- 02231, 9 cols (b)
#> | | | |-- 02232, 12 cols, 230 signatures (c)
#> | | | `-- 02233, 7 cols (b)
#> | | |-- 0224, 23 cols, 1526 signatures
#> | | | |-- 02241, 7 cols (b)
#> | | | |-- 02242, 9 cols (b)
#> | | | `-- 02243, 7 cols (b)
#> | | `-- 0225, 5 cols (b)
#> | `-- 023, 69 cols, 20003 signatures
#> | |-- 0231, 10 cols (b)
#> | |-- 0232, 29 cols, 1622 signatures
#> | | |-- 02321, 4 cols (b)
#> | | |-- 02322, 17 cols, 156 signatures (c)
#> | | `-- 02323, 8 cols (b)
#> | |-- 0233, 19 cols, 69 signatures (c)
#> | `-- 0234, 11 cols (b)
#> |-- 03, 55 cols, 5547 signatures
#> | |-- 031, 19 cols, 987 signatures (c)
#> | |-- 032, 12 cols, 93 signatures (c)
#> | |-- 033, 16 cols, 2279 signatures
#> | | |-- 0331, 7 cols (b)
#> | | |-- 0332, 3 cols (b)
#> | | `-- 0333, 6 cols (b)
#> | `-- 034, 8 cols (b)
#> |-- 04, 68 cols, 3867 signatures
#> | |-- 041, 26 cols, 70 signatures (c)
#> | |-- 042, 21 cols, 235 signatures (c)
#> | `-- 043, 21 cols, 1540 signatures
#> | |-- 0431, 7 cols (b)
#> | |-- 0432, 5 cols (b)
#> | `-- 0433, 9 cols (b)
#> `-- 05, 99 cols, 6152 signatures
#> |-- 051, 41 cols, 1469 signatures
#> | |-- 0511, 15 cols, 7175 signatures
#> | | |-- 05111, 2 cols (b)
#> | | |-- 05112, 9 cols (b)
#> | | |-- 05113, 2 cols (b)
#> | | `-- 05114, 2 cols (b)
#> | `-- 0512, 26 cols, 8181 signatures
#> | |-- 05121, 12 cols, 1619 signatures
#> | | |-- 051211, 10 cols (b)
#> | | `-- 051212, 2 cols (b)
#> | |-- 05122, 5 cols (b)
#> | `-- 05123, 9 cols (b)
#> |-- 052, 37 cols, 5764 signatures
#> | |-- 0521, 9 cols (b)
#> | |-- 0522, 19 cols, 2775 signatures
#> | | |-- 05221, 8 cols (b)
#> | | `-- 05222, 11 cols (b)
#> | |-- 0523, 1 cols (b)
#> | `-- 0524, 8 cols (b)
#> `-- 053, 21 cols, 712 signatures (c)
#> 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] 376162 580
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" "012" "0121" "01211" "01212"
#> [11] "01213" "0122" "01221" "01222" "01223" "013" "02" "021" "0211" "02111"
#> [21] "02112" "02113" "02114" "0212" "02121" "02122" "02123" "02124" "0213" "02131"
#> [31] "02132" "021321" "021322" "02133" "022" "0221" "02211" "02212" "02213" "0222"
#> [41] "02221" "02222" "02223" "0223" "02231" "02232" "02233" "0224" "02241" "02242"
#> [51] "02243" "0225" "023" "0231" "0232" "02321" "02322" "02323" "0233" "0234"
#> [61] "03" "031" "032" "033" "0331" "0332" "0333" "034" "04" "041"
#> [71] "042" "043" "0431" "0432" "0433" "05" "051" "0511" "05111" "05112"
#> [81] "05113" "05114" "0512" "05121" "051211" "051212" "05122" "05123" "052" "0521"
#> [91] "0522" "05221" "05222" "0523" "0524" "053"
all_leaves(res_rh)
#> [1] "0111" "0112" "0113" "01211" "01212" "01213" "01221" "01222" "01223" "013"
#> [11] "02111" "02112" "02113" "02114" "02121" "02122" "02123" "02124" "02131" "021321"
#> [21] "021322" "02133" "02211" "02212" "02213" "02221" "02222" "02223" "02231" "02232"
#> [31] "02233" "02241" "02242" "02243" "0225" "0231" "02321" "02322" "02323" "0233"
#> [41] "0234" "031" "032" "0331" "0332" "0333" "034" "041" "042" "0431"
#> [51] "0432" "0433" "05111" "05112" "05113" "05114" "051211" "051212" "05122" "05123"
#> [61] "0521" "05221" "05222" "0523" "0524" "053"
node_info(res_rh)
#> id best_method depth best_k n_columns n_signatures p_signatures is_leaf
#> 1 0 SD:skmeans 1 5 580 63548 0.168938 FALSE
#> 2 01 ATC:skmeans 2 3 90 4660 0.012388 FALSE
#> 3 011 ATC:skmeans 3 3 27 3188 0.008475 FALSE
#> 4 0111 not applied 4 NA 7 NA NA TRUE
#> 5 0112 ATC:kmeans 4 2 15 832 0.002212 TRUE
#> 6 0113 not applied 4 NA 5 NA NA TRUE
#> 7 012 SD:kmeans 3 2 38 2836 0.007539 FALSE
#> 8 0121 ATC:kmeans 4 3 13 2262 0.006013 FALSE
#> 9 01211 not applied 5 NA 5 NA NA TRUE
#> 10 01212 not applied 5 NA 3 NA NA TRUE
#> 11 01213 not applied 5 NA 5 NA NA TRUE
#> 12 0122 ATC:kmeans 4 3 25 9384 0.024947 FALSE
#> 13 01221 not applied 5 NA 7 NA NA TRUE
#> 14 01222 not applied 5 NA 11 NA NA TRUE
#> 15 01223 not applied 5 NA 7 NA NA TRUE
#> 16 013 ATC:kmeans 3 2 25 203 0.000540 TRUE
#> 17 02 SD:kmeans 2 3 268 4027 0.010705 FALSE
#> 18 021 SD:kmeans 3 3 90 4522 0.012021 FALSE
#> 19 0211 ATC:kmeans 4 4 28 7761 0.020632 FALSE
#> 20 02111 not applied 5 NA 11 NA NA TRUE
#> 21 02112 not applied 5 NA 4 NA NA TRUE
#> 22 02113 not applied 5 NA 8 NA NA TRUE
#> 23 02114 not applied 5 NA 5 NA NA TRUE
#> 24 0212 ATC:kmeans 4 4 34 30719 0.081664 FALSE
#> 25 02121 ATC:kmeans 5 3 14 803 0.002135 TRUE
#> 26 02122 not applied 5 NA 4 NA NA TRUE
#> 27 02123 not applied 5 NA 6 NA NA TRUE
#> 28 02124 not applied 5 NA 10 NA NA TRUE
#> 29 0213 ATC:skmeans 4 3 28 8755 0.023275 FALSE
#> 30 02131 not applied 5 NA 10 NA NA TRUE
#> 31 02132 ATC:kmeans 5 2 13 1269 0.003374 FALSE
#> 32 021321 not applied 6 NA 8 NA NA TRUE
#> 33 021322 not applied 6 NA 5 NA NA TRUE
#> 34 02133 not applied 5 NA 5 NA NA TRUE
#> 35 022 ATC:skmeans 3 5 109 24546 0.065254 FALSE
#> 36 0221 ATC:skmeans 4 3 25 10841 0.028820 FALSE
#> 37 02211 not applied 5 NA 10 NA NA TRUE
#> 38 02212 not applied 5 NA 8 NA NA TRUE
#> 39 02213 not applied 5 NA 7 NA NA TRUE
#> 40 0222 ATC:skmeans 4 3 28 2489 0.006617 FALSE
#> 41 02221 ATC:kmeans 5 2 12 557 0.001481 TRUE
#> 42 02222 ATC:kmeans 5 2 13 0 0.000000 TRUE
#> 43 02223 not applied 5 NA 3 NA NA TRUE
#> 44 0223 ATC:kmeans 4 3 28 4864 0.012931 FALSE
#> 45 02231 not applied 5 NA 9 NA NA TRUE
#> 46 02232 ATC:kmeans 5 2 12 230 0.000611 TRUE
#> 47 02233 not applied 5 NA 7 NA NA TRUE
#> 48 0224 ATC:kmeans 4 3 23 1526 0.004057 FALSE
#> 49 02241 not applied 5 NA 7 NA NA TRUE
#> 50 02242 not applied 5 NA 9 NA NA TRUE
#> 51 02243 not applied 5 NA 7 NA NA TRUE
#> 52 0225 not applied 4 NA 5 NA NA TRUE
#> 53 023 ATC:skmeans 3 4 69 20003 0.053177 FALSE
#> 54 0231 not applied 4 NA 10 NA NA TRUE
#> 55 0232 ATC:kmeans 4 3 29 1622 0.004312 FALSE
#> 56 02321 not applied 5 NA 4 NA NA TRUE
#> 57 02322 ATC:kmeans 5 3 17 156 0.000415 TRUE
#> 58 02323 not applied 5 NA 8 NA NA TRUE
#> 59 0233 ATC:skmeans 4 2 19 69 0.000183 TRUE
#> 60 0234 not applied 4 NA 11 NA NA TRUE
#> 61 03 SD:skmeans 2 4 55 5547 0.014746 FALSE
#> 62 031 ATC:skmeans 3 3 19 987 0.002624 TRUE
#> 63 032 SD:skmeans 3 2 12 93 0.000247 TRUE
#> 64 033 ATC:skmeans 3 3 16 2279 0.006059 FALSE
#> 65 0331 not applied 4 NA 7 NA NA TRUE
#> 66 0332 not applied 4 NA 3 NA NA TRUE
#> 67 0333 not applied 4 NA 6 NA NA TRUE
#> 68 034 not applied 3 NA 8 NA NA TRUE
#> 69 04 ATC:kmeans 2 3 68 3867 0.010280 FALSE
#> 70 041 ATC:skmeans 3 2 26 70 0.000186 TRUE
#> 71 042 ATC:kmeans 3 2 21 235 0.000625 TRUE
#> 72 043 ATC:kmeans 3 3 21 1540 0.004094 FALSE
#> 73 0431 not applied 4 NA 7 NA NA TRUE
#> 74 0432 not applied 4 NA 5 NA NA TRUE
#> 75 0433 not applied 4 NA 9 NA NA TRUE
#> 76 05 ATC:skmeans 2 3 99 6152 0.016355 FALSE
#> 77 051 ATC:kmeans 3 2 41 1469 0.003905 FALSE
#> 78 0511 ATC:kmeans 4 4 15 7175 0.019074 FALSE
#> 79 05111 not applied 5 NA 2 NA NA TRUE
#> 80 05112 not applied 5 NA 9 NA NA TRUE
#> 81 05113 not applied 5 NA 2 NA NA TRUE
#> 82 05114 not applied 5 NA 2 NA NA TRUE
#> 83 0512 ATC:kmeans 4 3 26 8181 0.021749 FALSE
#> 84 05121 ATC:kmeans 5 2 12 1619 0.004304 FALSE
#> 85 051211 not applied 6 NA 10 NA NA TRUE
#> 86 051212 not applied 6 NA 2 NA NA TRUE
#> 87 05122 not applied 5 NA 5 NA NA TRUE
#> 88 05123 not applied 5 NA 9 NA NA TRUE
#> 89 052 ATC:skmeans 3 4 37 5764 0.015323 FALSE
#> 90 0521 not applied 4 NA 9 NA NA TRUE
#> 91 0522 SD:kmeans 4 2 19 2775 0.007377 FALSE
#> 92 05221 not applied 5 NA 8 NA NA TRUE
#> 93 05222 not applied 5 NA 11 NA NA TRUE
#> 94 0523 not applied 4 NA 1 NA NA TRUE
#> 95 0524 not applied 4 NA 8 NA NA TRUE
#> 96 053 ATC:kmeans 3 2 21 712 0.001893 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 | 5 | 0.99 | 0.95 | 0.98 | 580 | ** | |
| Node01 | ATC:skmeans | 3 | 1.00 | 0.98 | 0.99 | 90 | ** | |
| Node011 | ATC:skmeans | 3 | 1.00 | 1.00 | 1.00 | 27 | ** | |
| Node0111-leaf | not applied | ✓ (b) | 7 | |||||
| Node0112-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 15 | ** |
| Node0113-leaf | not applied | ✓ (b) | 5 | |||||
| Node012 | SD:kmeans | 2 | 1.00 | 1.00 | 1.00 | 38 | ** | |
| Node0121 | ATC:kmeans | 5 | 1.00 | 0.97 | 0.98 | 13 | ** | |
| Node01211-leaf | not applied | ✓ (b) | 5 | |||||
| Node01212-leaf | not applied | ✓ (b) | 3 | |||||
| Node01213-leaf | not applied | ✓ (b) | 5 | |||||
| Node0122 | ATC:kmeans | 3 | 1.00 | 1.00 | 1.00 | 25 | ** | |
| Node01221-leaf | not applied | ✓ (b) | 7 | |||||
| Node01222-leaf | not applied | ✓ (b) | 11 | |||||
| Node01223-leaf | not applied | ✓ (b) | 7 | |||||
| Node013-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 25 | ** |
| Node02 | SD:kmeans | 3 | 1.00 | 0.98 | 0.98 | 268 | ** | |
| Node021 | SD:kmeans | 3 | 1.00 | 0.96 | 0.98 | 90 | ** | |
| Node0211 | ATC:kmeans | 4 | 1.00 | 1.00 | 1.00 | 28 | ** | |
| Node02111-leaf | not applied | ✓ (b) | 11 | |||||
| Node02112-leaf | not applied | ✓ (b) | 4 | |||||
| Node02113-leaf | not applied | ✓ (b) | 8 | |||||
| Node02114-leaf | not applied | ✓ (b) | 5 | |||||
| Node0212 | ATC:kmeans | 4 | 1.00 | 1.00 | 1.00 | 34 | ** | |
| Node02121-leaf | ATC:kmeans | ✓ (c) | 3 | 1.00 | 1.00 | 1.00 | 14 | ** |
| Node02122-leaf | not applied | ✓ (b) | 4 | |||||
| Node02123-leaf | not applied | ✓ (b) | 6 | |||||
| Node02124-leaf | not applied | ✓ (b) | 10 | |||||
| Node0213 | ATC:skmeans | 5 | 0.97 | 0.89 | 0.95 | 28 | ** | |
| Node02131-leaf | not applied | ✓ (b) | 10 | |||||
| Node02132 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 13 | ** | |
| Node021321-leaf | not applied | ✓ (b) | 8 | |||||
| Node021322-leaf | not applied | ✓ (b) | 5 | |||||
| Node02133-leaf | not applied | ✓ (b) | 5 | |||||
| Node022 | ATC:skmeans | 5 | 1.00 | 0.96 | 0.98 | 109 | ** | |
| Node0221 | ATC:skmeans | 5 | 0.93 | 0.79 | 0.93 | 25 | * | |
| Node02211-leaf | not applied | ✓ (b) | 10 | |||||
| Node02212-leaf | not applied | ✓ (b) | 8 | |||||
| Node02213-leaf | not applied | ✓ (b) | 7 | |||||
| Node0222 | ATC:skmeans | 5 | 0.94 | 0.95 | 0.96 | 28 | * | |
| Node02221-leaf | ATC:kmeans | ✓ (c) | 8 | 0.91 | 0.48 | 0.90 | 12 | * |
| Node02222-leaf | ATC:kmeans | ✓ (c) | 4 | 1.00 | 0.91 | 0.99 | 13 | ** |
| Node02223-leaf | not applied | ✓ (b) | 3 | |||||
| Node0223 | ATC:kmeans | 3 | 1.00 | 0.99 | 0.99 | 28 | ** | |
| Node02231-leaf | not applied | ✓ (b) | 9 | |||||
| Node02232-leaf | ATC:kmeans | ✓ (c) | 4 | 1.00 | 0.75 | 1.00 | 12 | ** |
| Node02233-leaf | not applied | ✓ (b) | 7 | |||||
| Node0224 | ATC:kmeans | 3 | 1.00 | 0.98 | 0.99 | 23 | ** | |
| Node02241-leaf | not applied | ✓ (b) | 7 | |||||
| Node02242-leaf | not applied | ✓ (b) | 9 | |||||
| Node02243-leaf | not applied | ✓ (b) | 7 | |||||
| Node0225-leaf | not applied | ✓ (b) | 5 | |||||
| Node023 | ATC:skmeans | 4 | 1.00 | 0.98 | 0.99 | 69 | ** | |
| Node0231-leaf | not applied | ✓ (b) | 10 | |||||
| Node0232 | ATC:kmeans | 3 | 1.00 | 0.99 | 1.00 | 29 | ** | |
| Node02321-leaf | not applied | ✓ (b) | 4 | |||||
| Node02322-leaf | ATC:kmeans | ✓ (c) | 8 | 0.90 | 0.69 | 0.89 | 17 | |
| Node02323-leaf | not applied | ✓ (b) | 8 | |||||
| Node0233-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 0.99 | 0.99 | 19 | ** |
| Node0234-leaf | not applied | ✓ (b) | 11 | |||||
| Node03 | SD:skmeans | 4 | 0.97 | 0.96 | 0.98 | 55 | ** | |
| Node031-leaf | ATC:skmeans | ✓ (c) | 7 | 0.93 | 0.87 | 0.94 | 19 | * |
| Node032-leaf | SD:skmeans | ✓ (c) | 8 | 0.91 | 0.45 | 0.96 | 12 | * |
| Node033 | ATC:skmeans | 3 | 1.00 | 1.00 | 1.00 | 16 | ** | |
| Node0331-leaf | not applied | ✓ (b) | 7 | |||||
| Node0332-leaf | not applied | ✓ (b) | 3 | |||||
| Node0333-leaf | not applied | ✓ (b) | 6 | |||||
| Node034-leaf | not applied | ✓ (b) | 8 | |||||
| Node04 | ATC:kmeans | 3 | 0.98 | 0.97 | 0.98 | 68 | ** | |
| Node041-leaf | ATC:skmeans | ✓ (c) | 2 | 0.62 | 0.93 | 0.96 | 26 | |
| Node042-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 21 | ** |
| Node043 | ATC:kmeans | 3 | 1.00 | 1.00 | 1.00 | 21 | ** | |
| Node0431-leaf | not applied | ✓ (b) | 7 | |||||
| Node0432-leaf | not applied | ✓ (b) | 5 | |||||
| Node0433-leaf | not applied | ✓ (b) | 9 | |||||
| Node05 | ATC:skmeans | 5 | 0.90 | 0.84 | 0.93 | 99 | * | |
| Node051 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 41 | ** | |
| Node0511 | ATC:kmeans | 8 | 0.90 | 0.73 | 0.85 | 15 | * | |
| Node05111-leaf | not applied | ✓ (b) | 2 | |||||
| Node05112-leaf | not applied | ✓ (b) | 9 | |||||
| Node05113-leaf | not applied | ✓ (b) | 2 | |||||
| Node05114-leaf | not applied | ✓ (b) | 2 | |||||
| Node0512 | ATC:kmeans | 3 | 1.00 | 1.00 | 1.00 | 26 | ** | |
| Node05121 | ATC:kmeans | 7 | 0.91 | 0.65 | 0.94 | 12 | * | |
| Node051211-leaf | not applied | ✓ (b) | 10 | |||||
| Node051212-leaf | not applied | ✓ (b) | 2 | |||||
| Node05122-leaf | not applied | ✓ (b) | 5 | |||||
| Node05123-leaf | not applied | ✓ (b) | 9 | |||||
| Node052 | ATC:skmeans | 4 | 1.00 | 0.95 | 0.99 | 37 | ** | |
| Node0521-leaf | not applied | ✓ (b) | 9 | |||||
| Node0522 | SD:kmeans | 2 | 1.00 | 1.00 | 1.00 | 19 | ** | |
| Node05221-leaf | not applied | ✓ (b) | 8 | |||||
| Node05222-leaf | not applied | ✓ (b) | 11 | |||||
| Node0523-leaf | not applied | ✓ (b) | 1 | |||||
| Node0524-leaf | not applied | ✓ (b) | 8 | |||||
| Node053-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 21 | ** |
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 = 1269))
#> Error in structure(1, members = 1, height = 0, label = label[ind], leaf = TRUE, : object 'ind' not found
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1469))
#> Error in structure(1, members = 1, height = 0, label = label[ind], leaf = TRUE, : object 'ind' not found
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1526))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1540))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1619))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1622))
#> Error in structure(1, members = 1, height = 0, label = label[ind], leaf = TRUE, : object 'ind' not found
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2262))
#> Error in structure(1, members = 1, height = 0, label = label[ind], leaf = TRUE, : object 'ind' not found
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2279))
#> Error in structure(1, members = 1, height = 0, label = label[ind], leaf = TRUE, : object 'ind' not found
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2489))
#> Error in structure(1, members = 1, height = 0, label = label[ind], leaf = TRUE, : object 'ind' not found
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2775))
#> Error in structure(1, members = 1, height = 0, label = label[ind], leaf = TRUE, : object 'ind' not found
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2836))
#> Error in structure(1, members = 1, height = 0, label = label[ind], leaf = TRUE, : object 'ind' not found
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3188))
#> Error in structure(1, members = 1, height = 0, label = label[ind], leaf = TRUE, : object 'ind' not found
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3867))
#> Error in structure(1, members = 1, height = 0, label = label[ind], leaf = TRUE, : object 'ind' not found
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4027))
#> Error in structure(1, members = 1, height = 0, label = label[ind], leaf = TRUE, : object 'ind' not found
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4522))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4660))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4864))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5547))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5764))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6152))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7175))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7761))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8181))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8755))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 9384))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 10841))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 20003))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 24546))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 30719))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 63548))
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 = 1269))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "05222" "02113" "0333" "02242" "02222" "0521"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02131" "02242" "041" "02212" "0112" "02322"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "02242" "05221" "02122" "034" "02114" "02111"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "034" "02113" "02213" "053" "02241" "0333"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "031" "02111" "0234" "0233" "031" "031"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "0233" "0233" "021322" "02222" "02243" "02233"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02122" "0112" "021322" "05112" "02211" "01212"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "05122" "02222" "032" "013" "0524" "0331"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "02243" "013" "031" "0112" "02242" "02232"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "041" "05122" "02233" "032" "0112"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "0331" "0233" "0111" "031" "02211" "021322"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "0521" "0113" "0234" "053" "0523" "0112"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01223" "02121" "02121" "053" "02322" "02123"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "032" "032" "02222" "02111" "013"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "031" "031" "02322" "041" "02321" "02222"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "013" "02213" "0333" "0333" "02122" "0225"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "013" "0432" "0225" "0231" "0111" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "032" "032" "02123" "02243" "0332" "041"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02113" "042" "034" "0112" "01223" "05112"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "0233" "0521" "0111" "032" "05221" "021321"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "05123" "0433" "032" "0233" "05221" "01221"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02112" "041" "0524" "02131" "013" "0233"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "0233" "034" "021321" "02233" "02121" "05113"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02124" "05222" "032" "02113" "02221" "0521"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02221" "02121" "013" "031" "042" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "0112" "01213" "013" "05221" "0331" "02221"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "02322" "0332" "02131" "02121" "051211" "0234"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "05112" "013" "042" "02231" "0234" "02232"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "053" "02111" "031" "02133" "0431" "031"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "05222" "031" "0331" "01222" "05114" "02114"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "0432" "05111" "02322" "02121" "042" "013"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "032" "02113" "034" "05123" "042" "02231"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "0331" "0431" "0331" "053" "02232" "034"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01222" "0233" "0225" "021321" "02112" "01223"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02124" "0111" "05123" "0231" "02232" "02121"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "0113" "02124" "042" "051211" "034" "02222"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "031" "01221" "0231" "02212" "0333" "053"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "0234" "02242" "0231" "032" "02121" "02121"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "031" "02211" "053" "02113" "02231" "0331"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "013" "0433" "041" "02221" "013" "02222"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "031" "05122" "051211" "0431" "021321" "034"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02131" "02322" "02121" "02222" "05221" "021321"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "051211" "01211" "02233" "02131" "013" "02231"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02231" "051212" "02111" "042" "0233" "02241"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02221" "02121" "02111" "02121" "02121" "031"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "042" "02322" "032" "0231" "031" "041"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "0233" "041" "02221" "02322" "053"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "02243" "0113" "031" "02131" "02242" "021321"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "02241" "02231" "02323" "02232" "0333" "02133"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "042" "02233" "041" "0233" "0332" "051211"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "05123" "02322" "042" "05222" "053" "01223"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "053" "02124" "02122" "0233" "05123" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02114" "02232" "0521" "053" "02221" "02231"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01222" "02322" "02241" "02322" "02131" "01223"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "0432" "02323" "0521" "041" "0431" "013"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01222" "05221" "0225" "02221" "02123" "02322"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "05123" "01222" "0234" "02124" "0433" "02221"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "021322" "02124" "02124" "02111" "01213" "01222"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "053" "013" "02123" "02242" "02222" "0524"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02232" "02222" "02211" "041" "02223" "02321"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "0225" "053" "05222" "02321" "02131" "041"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "01213" "02212" "0112" "0433" "042" "02241"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02221" "041" "02222" "01223" "042" "02322"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "02243" "0231" "0234" "0112" "05222" "041"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "0112" "053" "0431" "02114" "02323" "01213"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01222" "02211" "02212" "02232" "02111" "01221"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "05222" "01222" "02232" "0233" "05221" "01221"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "021321" "0233" "053" "0231" "02121" "0112"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "041" "02213" "05112" "05123" "02243"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "0112" "0432" "013" "013" "02124" "051211"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02124" "02232" "02133" "041" "02112" "02241"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02222" "02223" "013" "02111" "041" "02321"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "042" "0233" "021322" "02322" "013" "0521"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "041" "05112" "0524" "02243" "01213" "0431"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02131" "0111" "013" "01212" "0524" "02322"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "041" "01211" "0112" "05123" "02233" "02131"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "02323" "05222" "02114" "042" "042" "0432"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "041" "05112" "02242" "051211" "02113"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02123" "0433" "02112" "051211" "01222" "02323"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02133" "05112" "02232" "05112" "013" "041"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "0433" "051212" "042" "02124" "0233" "053"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "042" "05122" "041" "0231" "02322" "0231"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02231" "05221" "02213" "02111" "0234" "0231"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "042" "02113" "02323" "02223" "0233" "0113"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "021321" "05113" "0433" "0112" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "0521" "02221" "0112" "01222" "02233" "0233"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02123" "05111" "013" "02323" "01211" "01221"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "05114" "02231" "05112" "02211" "02111" "05222"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "02242" "0111" "053" "0234" "05222" "031"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "041" "02232" "031" "0234" "05123" "0433"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "053" "01223" "0524" "051211" "01221"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "05222" "01212" "0524" "013" "02241" "02323"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "053" "042" "013" "01211" "05122" "02322"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "042" "041" "01211" "0234" "041" "0111"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02133" "041" "053" "053" "0521" "01222"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01221" "0433" "0524" "02221" "042" "0431"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02222" "0113" "051211" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1469))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "05222" "02113" "0333" "02242" "02222" "0521"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02131" "02242" "041" "02212" "0112" "02322"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "02242" "05221" "02122" "034" "02114" "02111"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "034" "02113" "02213" "053" "02241" "0333"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "031" "02111" "0234" "0233" "031" "031"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "0233" "0233" "02132" "02222" "02243" "02233"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02122" "0112" "02132" "05112" "02211" "01212"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "05122" "02222" "032" "013" "0524" "0331"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "02243" "013" "031" "0112" "02242" "02232"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "041" "05122" "02233" "032" "0112"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "0331" "0233" "0111" "031" "02211" "02132"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "0521" "0113" "0234" "053" "0523" "0112"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01223" "02121" "02121" "053" "02322" "02123"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "032" "032" "02222" "02111" "013"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "031" "031" "02322" "041" "02321" "02222"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "013" "02213" "0333" "0333" "02122" "0225"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "013" "0432" "0225" "0231" "0111" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "032" "032" "02123" "02243" "0332" "041"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02113" "042" "034" "0112" "01223" "05112"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "0233" "0521" "0111" "032" "05221" "02132"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "05123" "0433" "032" "0233" "05221" "01221"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02112" "041" "0524" "02131" "013" "0233"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "0233" "034" "02132" "02233" "02121" "05113"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02124" "05222" "032" "02113" "02221" "0521"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02221" "02121" "013" "031" "042" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "0112" "01213" "013" "05221" "0331" "02221"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "02322" "0332" "02131" "02121" "051211" "0234"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "05112" "013" "042" "02231" "0234" "02232"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "053" "02111" "031" "02133" "0431" "031"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "05222" "031" "0331" "01222" "05114" "02114"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "0432" "05111" "02322" "02121" "042" "013"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "032" "02113" "034" "05123" "042" "02231"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "0331" "0431" "0331" "053" "02232" "034"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01222" "0233" "0225" "02132" "02112" "01223"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02124" "0111" "05123" "0231" "02232" "02121"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "0113" "02124" "042" "051211" "034" "02222"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "031" "01221" "0231" "02212" "0333" "053"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "0234" "02242" "0231" "032" "02121" "02121"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "031" "02211" "053" "02113" "02231" "0331"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "013" "0433" "041" "02221" "013" "02222"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "031" "05122" "051211" "0431" "02132" "034"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02131" "02322" "02121" "02222" "05221" "02132"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "051211" "01211" "02233" "02131" "013" "02231"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02231" "051212" "02111" "042" "0233" "02241"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02221" "02121" "02111" "02121" "02121" "031"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "042" "02322" "032" "0231" "031" "041"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "0233" "041" "02221" "02322" "053"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "02243" "0113" "031" "02131" "02242" "02132"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "02241" "02231" "02323" "02232" "0333" "02133"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "042" "02233" "041" "0233" "0332" "051211"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "05123" "02322" "042" "05222" "053" "01223"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "053" "02124" "02122" "0233" "05123" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02114" "02232" "0521" "053" "02221" "02231"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01222" "02322" "02241" "02322" "02131" "01223"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "0432" "02323" "0521" "041" "0431" "013"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01222" "05221" "0225" "02221" "02123" "02322"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "05123" "01222" "0234" "02124" "0433" "02221"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02132" "02124" "02124" "02111" "01213" "01222"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "053" "013" "02123" "02242" "02222" "0524"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02232" "02222" "02211" "041" "02223" "02321"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "0225" "053" "05222" "02321" "02131" "041"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "01213" "02212" "0112" "0433" "042" "02241"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02221" "041" "02222" "01223" "042" "02322"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "02243" "0231" "0234" "0112" "05222" "041"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "0112" "053" "0431" "02114" "02323" "01213"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01222" "02211" "02212" "02232" "02111" "01221"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "05222" "01222" "02232" "0233" "05221" "01221"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02132" "0233" "053" "0231" "02121" "0112"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "041" "02213" "05112" "05123" "02243"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "0112" "0432" "013" "013" "02124" "051211"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02124" "02232" "02133" "041" "02112" "02241"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02222" "02223" "013" "02111" "041" "02321"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "042" "0233" "02132" "02322" "013" "0521"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "041" "05112" "0524" "02243" "01213" "0431"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02131" "0111" "013" "01212" "0524" "02322"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "041" "01211" "0112" "05123" "02233" "02131"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "02323" "05222" "02114" "042" "042" "0432"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "041" "05112" "02242" "051211" "02113"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02123" "0433" "02112" "051211" "01222" "02323"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02133" "05112" "02232" "05112" "013" "041"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "0433" "051212" "042" "02124" "0233" "053"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "042" "05122" "041" "0231" "02322" "0231"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02231" "05221" "02213" "02111" "0234" "0231"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "042" "02113" "02323" "02223" "0233" "0113"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02132" "05113" "0433" "0112" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "0521" "02221" "0112" "01222" "02233" "0233"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02123" "05111" "013" "02323" "01211" "01221"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "05114" "02231" "05112" "02211" "02111" "05222"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "02242" "0111" "053" "0234" "05222" "031"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "041" "02232" "031" "0234" "05123" "0433"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "053" "01223" "0524" "051211" "01221"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "05222" "01212" "0524" "013" "02241" "02323"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "053" "042" "013" "01211" "05122" "02322"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "042" "041" "01211" "0234" "041" "0111"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02133" "041" "053" "053" "0521" "01222"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01221" "0433" "0524" "02221" "042" "0431"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02222" "0113" "051211" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1526))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "05222" "02113" "0333" "02242" "02222" "0521"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02131" "02242" "041" "02212" "0112" "02322"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "02242" "05221" "02122" "034" "02114" "02111"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "034" "02113" "02213" "053" "02241" "0333"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "031" "02111" "0234" "0233" "031" "031"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "0233" "0233" "02132" "02222" "02243" "02233"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02122" "0112" "02132" "051" "02211" "01212"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "051" "02222" "032" "013" "0524" "0331"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "02243" "013" "031" "0112" "02242" "02232"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "041" "051" "02233" "032" "0112"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "0331" "0233" "0111" "031" "02211" "02132"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "0521" "0113" "0234" "053" "0523" "0112"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01223" "02121" "02121" "053" "02322" "02123"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "032" "032" "02222" "02111" "013"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "031" "031" "02322" "041" "02321" "02222"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "013" "02213" "0333" "0333" "02122" "0225"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "013" "0432" "0225" "0231" "0111" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "032" "032" "02123" "02243" "0332" "041"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02113" "042" "034" "0112" "01223" "051"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "0233" "0521" "0111" "032" "05221" "02132"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "051" "0433" "032" "0233" "05221" "01221"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02112" "041" "0524" "02131" "013" "0233"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "0233" "034" "02132" "02233" "02121" "051"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02124" "05222" "032" "02113" "02221" "0521"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02221" "02121" "013" "031" "042" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "0112" "01213" "013" "05221" "0331" "02221"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "02322" "0332" "02131" "02121" "051211" "0234"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "051" "013" "042" "02231" "0234" "02232"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "053" "02111" "031" "02133" "0431" "031"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "05222" "031" "0331" "01222" "051" "02114"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "0432" "051" "02322" "02121" "042" "013"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "032" "02113" "034" "051" "042" "02231"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "0331" "0431" "0331" "053" "02232" "034"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01222" "0233" "0225" "02132" "02112" "01223"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02124" "0111" "051" "0231" "02232" "02121"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "0113" "02124" "042" "051211" "034" "02222"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "031" "01221" "0231" "02212" "0333" "053"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "0234" "02242" "0231" "032" "02121" "02121"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "031" "02211" "053" "02113" "02231" "0331"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "013" "0433" "041" "02221" "013" "02222"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "031" "051" "051211" "0431" "02132" "034"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02131" "02322" "02121" "02222" "05221" "02132"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "051211" "01211" "02233" "02131" "013" "02231"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02231" "051212" "02111" "042" "0233" "02241"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02221" "02121" "02111" "02121" "02121" "031"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "042" "02322" "032" "0231" "031" "041"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "0233" "041" "02221" "02322" "053"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "02243" "0113" "031" "02131" "02242" "02132"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "02241" "02231" "02323" "02232" "0333" "02133"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "042" "02233" "041" "0233" "0332" "051211"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "051" "02322" "042" "05222" "053" "01223"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "053" "02124" "02122" "0233" "051" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02114" "02232" "0521" "053" "02221" "02231"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01222" "02322" "02241" "02322" "02131" "01223"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "0432" "02323" "0521" "041" "0431" "013"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01222" "05221" "0225" "02221" "02123" "02322"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "051" "01222" "0234" "02124" "0433" "02221"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02132" "02124" "02124" "02111" "01213" "01222"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "053" "013" "02123" "02242" "02222" "0524"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02232" "02222" "02211" "041" "02223" "02321"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "0225" "053" "05222" "02321" "02131" "041"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "01213" "02212" "0112" "0433" "042" "02241"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02221" "041" "02222" "01223" "042" "02322"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "02243" "0231" "0234" "0112" "05222" "041"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "0112" "053" "0431" "02114" "02323" "01213"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01222" "02211" "02212" "02232" "02111" "01221"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "05222" "01222" "02232" "0233" "05221" "01221"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02132" "0233" "053" "0231" "02121" "0112"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "041" "02213" "051" "051" "02243"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "0112" "0432" "013" "013" "02124" "051211"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02124" "02232" "02133" "041" "02112" "02241"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02222" "02223" "013" "02111" "041" "02321"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "042" "0233" "02132" "02322" "013" "0521"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "041" "051" "0524" "02243" "01213" "0431"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02131" "0111" "013" "01212" "0524" "02322"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "041" "01211" "0112" "051" "02233" "02131"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "02323" "05222" "02114" "042" "042" "0432"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "041" "051" "02242" "051211" "02113"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02123" "0433" "02112" "051211" "01222" "02323"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02133" "051" "02232" "051" "013" "041"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "0433" "051212" "042" "02124" "0233" "053"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "042" "051" "041" "0231" "02322" "0231"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02231" "05221" "02213" "02111" "0234" "0231"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "042" "02113" "02323" "02223" "0233" "0113"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02132" "051" "0433" "0112" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "0521" "02221" "0112" "01222" "02233" "0233"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02123" "051" "013" "02323" "01211" "01221"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "051" "02231" "051" "02211" "02111" "05222"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "02242" "0111" "053" "0234" "05222" "031"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "041" "02232" "031" "0234" "051" "0433"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "053" "01223" "0524" "051211" "01221"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "05222" "01212" "0524" "013" "02241" "02323"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "053" "042" "013" "01211" "051" "02322"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "042" "041" "01211" "0234" "041" "0111"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02133" "041" "053" "053" "0521" "01222"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01221" "0433" "0524" "02221" "042" "0431"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02222" "0113" "051211" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1540))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "05222" "02113" "0333" "0224" "02222" "0521"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02131" "0224" "041" "02212" "0112" "02322"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "0224" "05221" "02122" "034" "02114" "02111"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "034" "02113" "02213" "053" "0224" "0333"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "031" "02111" "0234" "0233" "031" "031"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "0233" "0233" "02132" "02222" "0224" "02233"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02122" "0112" "02132" "051" "02211" "01212"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "051" "02222" "032" "013" "0524" "0331"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "0224" "013" "031" "0112" "0224" "02232"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "041" "051" "02233" "032" "0112"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "0331" "0233" "0111" "031" "02211" "02132"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "0521" "0113" "0234" "053" "0523" "0112"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01223" "02121" "02121" "053" "02322" "02123"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "032" "032" "02222" "02111" "013"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "031" "031" "02322" "041" "02321" "02222"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "013" "02213" "0333" "0333" "02122" "0225"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "013" "0432" "0225" "0231" "0111" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "032" "032" "02123" "0224" "0332" "041"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02113" "042" "034" "0112" "01223" "051"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "0233" "0521" "0111" "032" "05221" "02132"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "051" "0433" "032" "0233" "05221" "01221"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02112" "041" "0524" "02131" "013" "0233"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "0233" "034" "02132" "02233" "02121" "051"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02124" "05222" "032" "02113" "02221" "0521"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02221" "02121" "013" "031" "042" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "0112" "01213" "013" "05221" "0331" "02221"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "02322" "0332" "02131" "02121" "051211" "0234"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "051" "013" "042" "02231" "0234" "02232"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "053" "02111" "031" "02133" "0431" "031"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "05222" "031" "0331" "01222" "051" "02114"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "0432" "051" "02322" "02121" "042" "013"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "032" "02113" "034" "051" "042" "02231"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "0331" "0431" "0331" "053" "02232" "034"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01222" "0233" "0225" "02132" "02112" "01223"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02124" "0111" "051" "0231" "02232" "02121"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "0113" "02124" "042" "051211" "034" "02222"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "031" "01221" "0231" "02212" "0333" "053"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "0234" "0224" "0231" "032" "02121" "02121"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "031" "02211" "053" "02113" "02231" "0331"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "013" "0433" "041" "02221" "013" "02222"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "031" "051" "051211" "0431" "02132" "034"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02131" "02322" "02121" "02222" "05221" "02132"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "051211" "01211" "02233" "02131" "013" "02231"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02231" "051212" "02111" "042" "0233" "0224"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02221" "02121" "02111" "02121" "02121" "031"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "042" "02322" "032" "0231" "031" "041"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "0233" "041" "02221" "02322" "053"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "0224" "0113" "031" "02131" "0224" "02132"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "0224" "02231" "02323" "02232" "0333" "02133"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "042" "02233" "041" "0233" "0332" "051211"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "051" "02322" "042" "05222" "053" "01223"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "053" "02124" "02122" "0233" "051" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02114" "02232" "0521" "053" "02221" "02231"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01222" "02322" "0224" "02322" "02131" "01223"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "0432" "02323" "0521" "041" "0431" "013"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01222" "05221" "0225" "02221" "02123" "02322"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "051" "01222" "0234" "02124" "0433" "02221"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02132" "02124" "02124" "02111" "01213" "01222"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "053" "013" "02123" "0224" "02222" "0524"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02232" "02222" "02211" "041" "02223" "02321"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "0225" "053" "05222" "02321" "02131" "041"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "01213" "02212" "0112" "0433" "042" "0224"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02221" "041" "02222" "01223" "042" "02322"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "0224" "0231" "0234" "0112" "05222" "041"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "0112" "053" "0431" "02114" "02323" "01213"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01222" "02211" "02212" "02232" "02111" "01221"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "05222" "01222" "02232" "0233" "05221" "01221"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02132" "0233" "053" "0231" "02121" "0112"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "041" "02213" "051" "051" "0224"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "0112" "0432" "013" "013" "02124" "051211"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02124" "02232" "02133" "041" "02112" "0224"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02222" "02223" "013" "02111" "041" "02321"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "042" "0233" "02132" "02322" "013" "0521"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "041" "051" "0524" "0224" "01213" "0431"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02131" "0111" "013" "01212" "0524" "02322"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "041" "01211" "0112" "051" "02233" "02131"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "02323" "05222" "02114" "042" "042" "0432"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "041" "051" "0224" "051211" "02113"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02123" "0433" "02112" "051211" "01222" "02323"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02133" "051" "02232" "051" "013" "041"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "0433" "051212" "042" "02124" "0233" "053"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "042" "051" "041" "0231" "02322" "0231"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02231" "05221" "02213" "02111" "0234" "0231"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "042" "02113" "02323" "02223" "0233" "0113"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02132" "051" "0433" "0112" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "0521" "02221" "0112" "01222" "02233" "0233"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02123" "051" "013" "02323" "01211" "01221"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "051" "02231" "051" "02211" "02111" "05222"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "0224" "0111" "053" "0234" "05222" "031"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "041" "02232" "031" "0234" "051" "0433"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "053" "01223" "0524" "051211" "01221"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "05222" "01212" "0524" "013" "0224" "02323"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "053" "042" "013" "01211" "051" "02322"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "042" "041" "01211" "0234" "041" "0111"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02133" "041" "053" "053" "0521" "01222"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01221" "0433" "0524" "02221" "042" "0431"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02222" "0113" "051211" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1619))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "05222" "02113" "0333" "0224" "02222" "0521"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02131" "0224" "041" "02212" "0112" "02322"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "0224" "05221" "02122" "034" "02114" "02111"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "034" "02113" "02213" "053" "0224" "0333"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "031" "02111" "0234" "0233" "031" "031"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "0233" "0233" "02132" "02222" "0224" "02233"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02122" "0112" "02132" "051" "02211" "01212"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "051" "02222" "032" "013" "0524" "0331"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "0224" "013" "031" "0112" "0224" "02232"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "041" "051" "02233" "032" "0112"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "0331" "0233" "0111" "031" "02211" "02132"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "0521" "0113" "0234" "053" "0523" "0112"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01223" "02121" "02121" "053" "02322" "02123"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "032" "032" "02222" "02111" "013"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "031" "031" "02322" "041" "02321" "02222"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "013" "02213" "0333" "0333" "02122" "0225"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "013" "043" "0225" "0231" "0111" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "032" "032" "02123" "0224" "0332" "041"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02113" "042" "034" "0112" "01223" "051"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "0233" "0521" "0111" "032" "05221" "02132"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "051" "043" "032" "0233" "05221" "01221"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02112" "041" "0524" "02131" "013" "0233"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "0233" "034" "02132" "02233" "02121" "051"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02124" "05222" "032" "02113" "02221" "0521"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02221" "02121" "013" "031" "042" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "0112" "01213" "013" "05221" "0331" "02221"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "02322" "0332" "02131" "02121" "051211" "0234"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "051" "013" "042" "02231" "0234" "02232"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "053" "02111" "031" "02133" "043" "031"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "05222" "031" "0331" "01222" "051" "02114"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "043" "051" "02322" "02121" "042" "013"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "032" "02113" "034" "051" "042" "02231"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "0331" "043" "0331" "053" "02232" "034"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01222" "0233" "0225" "02132" "02112" "01223"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02124" "0111" "051" "0231" "02232" "02121"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "0113" "02124" "042" "051211" "034" "02222"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "031" "01221" "0231" "02212" "0333" "053"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "0234" "0224" "0231" "032" "02121" "02121"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "031" "02211" "053" "02113" "02231" "0331"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "013" "043" "041" "02221" "013" "02222"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "031" "051" "051211" "043" "02132" "034"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02131" "02322" "02121" "02222" "05221" "02132"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "051211" "01211" "02233" "02131" "013" "02231"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02231" "051212" "02111" "042" "0233" "0224"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02221" "02121" "02111" "02121" "02121" "031"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "042" "02322" "032" "0231" "031" "041"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "0233" "041" "02221" "02322" "053"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "0224" "0113" "031" "02131" "0224" "02132"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "0224" "02231" "02323" "02232" "0333" "02133"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "042" "02233" "041" "0233" "0332" "051211"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "051" "02322" "042" "05222" "053" "01223"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "053" "02124" "02122" "0233" "051" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02114" "02232" "0521" "053" "02221" "02231"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01222" "02322" "0224" "02322" "02131" "01223"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "043" "02323" "0521" "041" "043" "013"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01222" "05221" "0225" "02221" "02123" "02322"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "051" "01222" "0234" "02124" "043" "02221"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02132" "02124" "02124" "02111" "01213" "01222"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "053" "013" "02123" "0224" "02222" "0524"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02232" "02222" "02211" "041" "02223" "02321"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "0225" "053" "05222" "02321" "02131" "041"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "01213" "02212" "0112" "043" "042" "0224"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02221" "041" "02222" "01223" "042" "02322"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "0224" "0231" "0234" "0112" "05222" "041"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "0112" "053" "043" "02114" "02323" "01213"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01222" "02211" "02212" "02232" "02111" "01221"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "05222" "01222" "02232" "0233" "05221" "01221"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02132" "0233" "053" "0231" "02121" "0112"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "041" "02213" "051" "051" "0224"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "0112" "043" "013" "013" "02124" "051211"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02124" "02232" "02133" "041" "02112" "0224"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02222" "02223" "013" "02111" "041" "02321"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "042" "0233" "02132" "02322" "013" "0521"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "041" "051" "0524" "0224" "01213" "043"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02131" "0111" "013" "01212" "0524" "02322"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "041" "01211" "0112" "051" "02233" "02131"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "02323" "05222" "02114" "042" "042" "043"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "041" "051" "0224" "051211" "02113"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02123" "043" "02112" "051211" "01222" "02323"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02133" "051" "02232" "051" "013" "041"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "043" "051212" "042" "02124" "0233" "053"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "042" "051" "041" "0231" "02322" "0231"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02231" "05221" "02213" "02111" "0234" "0231"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "042" "02113" "02323" "02223" "0233" "0113"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02132" "051" "043" "0112" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "0521" "02221" "0112" "01222" "02233" "0233"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02123" "051" "013" "02323" "01211" "01221"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "051" "02231" "051" "02211" "02111" "05222"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "0224" "0111" "053" "0234" "05222" "031"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "041" "02232" "031" "0234" "051" "043"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "053" "01223" "0524" "051211" "01221"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "05222" "01212" "0524" "013" "0224" "02323"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "053" "042" "013" "01211" "051" "02322"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "042" "041" "01211" "0234" "041" "0111"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02133" "041" "053" "053" "0521" "01222"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01221" "043" "0524" "02221" "042" "043"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02222" "0113" "051211" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1622))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "05222" "02113" "0333" "0224" "02222" "0521"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02131" "0224" "041" "02212" "0112" "02322"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "0224" "05221" "02122" "034" "02114" "02111"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "034" "02113" "02213" "053" "0224" "0333"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "031" "02111" "0234" "0233" "031" "031"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "0233" "0233" "02132" "02222" "0224" "02233"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02122" "0112" "02132" "051" "02211" "01212"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "051" "02222" "032" "013" "0524" "0331"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "0224" "013" "031" "0112" "0224" "02232"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "041" "051" "02233" "032" "0112"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "0331" "0233" "0111" "031" "02211" "02132"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "0521" "0113" "0234" "053" "0523" "0112"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01223" "02121" "02121" "053" "02322" "02123"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "032" "032" "02222" "02111" "013"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "031" "031" "02322" "041" "02321" "02222"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "013" "02213" "0333" "0333" "02122" "0225"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "013" "043" "0225" "0231" "0111" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "032" "032" "02123" "0224" "0332" "041"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02113" "042" "034" "0112" "01223" "051"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "0233" "0521" "0111" "032" "05221" "02132"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "051" "043" "032" "0233" "05221" "01221"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02112" "041" "0524" "02131" "013" "0233"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "0233" "034" "02132" "02233" "02121" "051"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02124" "05222" "032" "02113" "02221" "0521"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02221" "02121" "013" "031" "042" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "0112" "01213" "013" "05221" "0331" "02221"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "02322" "0332" "02131" "02121" "051" "0234"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "051" "013" "042" "02231" "0234" "02232"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "053" "02111" "031" "02133" "043" "031"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "05222" "031" "0331" "01222" "051" "02114"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "043" "051" "02322" "02121" "042" "013"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "032" "02113" "034" "051" "042" "02231"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "0331" "043" "0331" "053" "02232" "034"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01222" "0233" "0225" "02132" "02112" "01223"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02124" "0111" "051" "0231" "02232" "02121"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "0113" "02124" "042" "051" "034" "02222"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "031" "01221" "0231" "02212" "0333" "053"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "0234" "0224" "0231" "032" "02121" "02121"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "031" "02211" "053" "02113" "02231" "0331"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "013" "043" "041" "02221" "013" "02222"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "031" "051" "051" "043" "02132" "034"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02131" "02322" "02121" "02222" "05221" "02132"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "051" "01211" "02233" "02131" "013" "02231"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02231" "051" "02111" "042" "0233" "0224"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02221" "02121" "02111" "02121" "02121" "031"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "042" "02322" "032" "0231" "031" "041"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "0233" "041" "02221" "02322" "053"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "0224" "0113" "031" "02131" "0224" "02132"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "0224" "02231" "02323" "02232" "0333" "02133"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "042" "02233" "041" "0233" "0332" "051"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "051" "02322" "042" "05222" "053" "01223"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "053" "02124" "02122" "0233" "051" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02114" "02232" "0521" "053" "02221" "02231"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01222" "02322" "0224" "02322" "02131" "01223"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "043" "02323" "0521" "041" "043" "013"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01222" "05221" "0225" "02221" "02123" "02322"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "051" "01222" "0234" "02124" "043" "02221"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02132" "02124" "02124" "02111" "01213" "01222"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "053" "013" "02123" "0224" "02222" "0524"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02232" "02222" "02211" "041" "02223" "02321"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "0225" "053" "05222" "02321" "02131" "041"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "01213" "02212" "0112" "043" "042" "0224"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02221" "041" "02222" "01223" "042" "02322"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "0224" "0231" "0234" "0112" "05222" "041"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "0112" "053" "043" "02114" "02323" "01213"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01222" "02211" "02212" "02232" "02111" "01221"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "05222" "01222" "02232" "0233" "05221" "01221"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02132" "0233" "053" "0231" "02121" "0112"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "041" "02213" "051" "051" "0224"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "0112" "043" "013" "013" "02124" "051"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02124" "02232" "02133" "041" "02112" "0224"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02222" "02223" "013" "02111" "041" "02321"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "042" "0233" "02132" "02322" "013" "0521"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "041" "051" "0524" "0224" "01213" "043"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02131" "0111" "013" "01212" "0524" "02322"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "041" "01211" "0112" "051" "02233" "02131"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "02323" "05222" "02114" "042" "042" "043"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "041" "051" "0224" "051" "02113"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02123" "043" "02112" "051" "01222" "02323"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02133" "051" "02232" "051" "013" "041"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "043" "051" "042" "02124" "0233" "053"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "042" "051" "041" "0231" "02322" "0231"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02231" "05221" "02213" "02111" "0234" "0231"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "042" "02113" "02323" "02223" "0233" "0113"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02132" "051" "043" "0112" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "0521" "02221" "0112" "01222" "02233" "0233"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02123" "051" "013" "02323" "01211" "01221"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "051" "02231" "051" "02211" "02111" "05222"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "0224" "0111" "053" "0234" "05222" "031"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "041" "02232" "031" "0234" "051" "043"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "053" "01223" "0524" "051" "01221"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "05222" "01212" "0524" "013" "0224" "02323"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "053" "042" "013" "01211" "051" "02322"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "042" "041" "01211" "0234" "041" "0111"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02133" "041" "053" "053" "0521" "01222"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01221" "043" "0524" "02221" "042" "043"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02222" "0113" "051" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2262))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "05222" "02113" "0333" "0224" "02222" "0521"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02131" "0224" "041" "02212" "0112" "0232"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "0224" "05221" "02122" "034" "02114" "02111"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "034" "02113" "02213" "053" "0224" "0333"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "031" "02111" "0234" "0233" "031" "031"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "0233" "0233" "02132" "02222" "0224" "02233"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02122" "0112" "02132" "051" "02211" "01212"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "051" "02222" "032" "013" "0524" "0331"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "0224" "013" "031" "0112" "0224" "02232"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "041" "051" "02233" "032" "0112"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "0331" "0233" "0111" "031" "02211" "02132"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "0521" "0113" "0234" "053" "0523" "0112"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01223" "02121" "02121" "053" "0232" "02123"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "032" "032" "02222" "02111" "013"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "031" "031" "0232" "041" "0232" "02222"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "013" "02213" "0333" "0333" "02122" "0225"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "013" "043" "0225" "0231" "0111" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "032" "032" "02123" "0224" "0332" "041"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02113" "042" "034" "0112" "01223" "051"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "0233" "0521" "0111" "032" "05221" "02132"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "051" "043" "032" "0233" "05221" "01221"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02112" "041" "0524" "02131" "013" "0233"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "0233" "034" "02132" "02233" "02121" "051"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02124" "05222" "032" "02113" "02221" "0521"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02221" "02121" "013" "031" "042" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "0112" "01213" "013" "05221" "0331" "02221"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "0232" "0332" "02131" "02121" "051" "0234"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "051" "013" "042" "02231" "0234" "02232"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "053" "02111" "031" "02133" "043" "031"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "05222" "031" "0331" "01222" "051" "02114"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "043" "051" "0232" "02121" "042" "013"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "032" "02113" "034" "051" "042" "02231"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "0331" "043" "0331" "053" "02232" "034"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01222" "0233" "0225" "02132" "02112" "01223"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02124" "0111" "051" "0231" "02232" "02121"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "0113" "02124" "042" "051" "034" "02222"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "031" "01221" "0231" "02212" "0333" "053"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "0234" "0224" "0231" "032" "02121" "02121"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "031" "02211" "053" "02113" "02231" "0331"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "013" "043" "041" "02221" "013" "02222"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "031" "051" "051" "043" "02132" "034"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02131" "0232" "02121" "02222" "05221" "02132"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "051" "01211" "02233" "02131" "013" "02231"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02231" "051" "02111" "042" "0233" "0224"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02221" "02121" "02111" "02121" "02121" "031"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "042" "0232" "032" "0231" "031" "041"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "0233" "041" "02221" "0232" "053"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "0224" "0113" "031" "02131" "0224" "02132"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "0224" "02231" "0232" "02232" "0333" "02133"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "042" "02233" "041" "0233" "0332" "051"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "051" "0232" "042" "05222" "053" "01223"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "053" "02124" "02122" "0233" "051" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02114" "02232" "0521" "053" "02221" "02231"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01222" "0232" "0224" "0232" "02131" "01223"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "043" "0232" "0521" "041" "043" "013"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01222" "05221" "0225" "02221" "02123" "0232"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "051" "01222" "0234" "02124" "043" "02221"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02132" "02124" "02124" "02111" "01213" "01222"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "053" "013" "02123" "0224" "02222" "0524"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02232" "02222" "02211" "041" "02223" "0232"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "0225" "053" "05222" "0232" "02131" "041"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "01213" "02212" "0112" "043" "042" "0224"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02221" "041" "02222" "01223" "042" "0232"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "0224" "0231" "0234" "0112" "05222" "041"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "0112" "053" "043" "02114" "0232" "01213"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01222" "02211" "02212" "02232" "02111" "01221"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "05222" "01222" "02232" "0233" "05221" "01221"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02132" "0233" "053" "0231" "02121" "0112"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "041" "02213" "051" "051" "0224"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "0112" "043" "013" "013" "02124" "051"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02124" "02232" "02133" "041" "02112" "0224"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02222" "02223" "013" "02111" "041" "0232"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "042" "0233" "02132" "0232" "013" "0521"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "041" "051" "0524" "0224" "01213" "043"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02131" "0111" "013" "01212" "0524" "0232"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "041" "01211" "0112" "051" "02233" "02131"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "0232" "05222" "02114" "042" "042" "043"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "041" "051" "0224" "051" "02113"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02123" "043" "02112" "051" "01222" "0232"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02133" "051" "02232" "051" "013" "041"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "043" "051" "042" "02124" "0233" "053"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "042" "051" "041" "0231" "0232" "0231"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02231" "05221" "02213" "02111" "0234" "0231"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "042" "02113" "0232" "02223" "0233" "0113"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02132" "051" "043" "0112" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "0521" "02221" "0112" "01222" "02233" "0233"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02123" "051" "013" "0232" "01211" "01221"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "051" "02231" "051" "02211" "02111" "05222"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "0224" "0111" "053" "0234" "05222" "031"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "041" "02232" "031" "0234" "051" "043"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "053" "01223" "0524" "051" "01221"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "05222" "01212" "0524" "013" "0224" "0232"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "053" "042" "013" "01211" "051" "0232"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "042" "041" "01211" "0234" "041" "0111"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02133" "041" "053" "053" "0521" "01222"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01221" "043" "0524" "02221" "042" "043"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02222" "0113" "051" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2279))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "05222" "02113" "0333" "0224" "02222" "0521"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02131" "0224" "041" "02212" "0112" "0232"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "0224" "05221" "02122" "034" "02114" "02111"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "034" "02113" "02213" "053" "0224" "0333"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "031" "02111" "0234" "0233" "031" "031"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "0233" "0233" "02132" "02222" "0224" "02233"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02122" "0112" "02132" "051" "02211" "0121"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "051" "02222" "032" "013" "0524" "0331"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "0224" "013" "031" "0112" "0224" "02232"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "041" "051" "02233" "032" "0112"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "0331" "0233" "0111" "031" "02211" "02132"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "0521" "0113" "0234" "053" "0523" "0112"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01223" "02121" "02121" "053" "0232" "02123"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "032" "032" "02222" "02111" "013"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "031" "031" "0232" "041" "0232" "02222"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "013" "02213" "0333" "0333" "02122" "0225"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "013" "043" "0225" "0231" "0111" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "032" "032" "02123" "0224" "0332" "041"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02113" "042" "034" "0112" "01223" "051"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "0233" "0521" "0111" "032" "05221" "02132"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "051" "043" "032" "0233" "05221" "01221"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02112" "041" "0524" "02131" "013" "0233"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "0233" "034" "02132" "02233" "02121" "051"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02124" "05222" "032" "02113" "02221" "0521"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02221" "02121" "013" "031" "042" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "0112" "0121" "013" "05221" "0331" "02221"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "0232" "0332" "02131" "02121" "051" "0234"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "051" "013" "042" "02231" "0234" "02232"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "053" "02111" "031" "02133" "043" "031"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "05222" "031" "0331" "01222" "051" "02114"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "043" "051" "0232" "02121" "042" "013"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "032" "02113" "034" "051" "042" "02231"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "0331" "043" "0331" "053" "02232" "034"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01222" "0233" "0225" "02132" "02112" "01223"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02124" "0111" "051" "0231" "02232" "02121"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "0113" "02124" "042" "051" "034" "02222"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "031" "01221" "0231" "02212" "0333" "053"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "0234" "0224" "0231" "032" "02121" "02121"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "031" "02211" "053" "02113" "02231" "0331"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "013" "043" "041" "02221" "013" "02222"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "031" "051" "051" "043" "02132" "034"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02131" "0232" "02121" "02222" "05221" "02132"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "051" "0121" "02233" "02131" "013" "02231"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02231" "051" "02111" "042" "0233" "0224"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02221" "02121" "02111" "02121" "02121" "031"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "042" "0232" "032" "0231" "031" "041"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "0233" "041" "02221" "0232" "053"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "0224" "0113" "031" "02131" "0224" "02132"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "0224" "02231" "0232" "02232" "0333" "02133"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "042" "02233" "041" "0233" "0332" "051"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "051" "0232" "042" "05222" "053" "01223"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "053" "02124" "02122" "0233" "051" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02114" "02232" "0521" "053" "02221" "02231"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01222" "0232" "0224" "0232" "02131" "01223"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "043" "0232" "0521" "041" "043" "013"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01222" "05221" "0225" "02221" "02123" "0232"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "051" "01222" "0234" "02124" "043" "02221"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02132" "02124" "02124" "02111" "0121" "01222"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "053" "013" "02123" "0224" "02222" "0524"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02232" "02222" "02211" "041" "02223" "0232"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "0225" "053" "05222" "0232" "02131" "041"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "0121" "02212" "0112" "043" "042" "0224"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02221" "041" "02222" "01223" "042" "0232"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "0224" "0231" "0234" "0112" "05222" "041"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "0112" "053" "043" "02114" "0232" "0121"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01222" "02211" "02212" "02232" "02111" "01221"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "05222" "01222" "02232" "0233" "05221" "01221"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02132" "0233" "053" "0231" "02121" "0112"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "041" "02213" "051" "051" "0224"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "0112" "043" "013" "013" "02124" "051"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02124" "02232" "02133" "041" "02112" "0224"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02222" "02223" "013" "02111" "041" "0232"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "042" "0233" "02132" "0232" "013" "0521"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "041" "051" "0524" "0224" "0121" "043"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02131" "0111" "013" "0121" "0524" "0232"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "041" "0121" "0112" "051" "02233" "02131"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "0232" "05222" "02114" "042" "042" "043"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "041" "051" "0224" "051" "02113"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02123" "043" "02112" "051" "01222" "0232"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02133" "051" "02232" "051" "013" "041"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "043" "051" "042" "02124" "0233" "053"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "042" "051" "041" "0231" "0232" "0231"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02231" "05221" "02213" "02111" "0234" "0231"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "042" "02113" "0232" "02223" "0233" "0113"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02132" "051" "043" "0112" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "0521" "02221" "0112" "01222" "02233" "0233"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02123" "051" "013" "0232" "0121" "01221"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "051" "02231" "051" "02211" "02111" "05222"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "0224" "0111" "053" "0234" "05222" "031"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "041" "02232" "031" "0234" "051" "043"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "053" "01223" "0524" "051" "01221"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "05222" "0121" "0524" "013" "0224" "0232"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "053" "042" "013" "0121" "051" "0232"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "042" "041" "0121" "0234" "041" "0111"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02133" "041" "053" "053" "0521" "01222"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01221" "043" "0524" "02221" "042" "043"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02222" "0113" "051" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2489))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "05222" "02113" "033" "0224" "02222" "0521"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02131" "0224" "041" "02212" "0112" "0232"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "0224" "05221" "02122" "034" "02114" "02111"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "034" "02113" "02213" "053" "0224" "033"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "031" "02111" "0234" "0233" "031" "031"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "0233" "0233" "02132" "02222" "0224" "02233"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02122" "0112" "02132" "051" "02211" "0121"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "051" "02222" "032" "013" "0524" "033"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "0224" "013" "031" "0112" "0224" "02232"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "041" "051" "02233" "032" "0112"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "033" "0233" "0111" "031" "02211" "02132"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "0521" "0113" "0234" "053" "0523" "0112"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01223" "02121" "02121" "053" "0232" "02123"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "032" "032" "02222" "02111" "013"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "031" "031" "0232" "041" "0232" "02222"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "013" "02213" "033" "033" "02122" "0225"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "013" "043" "0225" "0231" "0111" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "032" "032" "02123" "0224" "033" "041"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02113" "042" "034" "0112" "01223" "051"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "0233" "0521" "0111" "032" "05221" "02132"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "051" "043" "032" "0233" "05221" "01221"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02112" "041" "0524" "02131" "013" "0233"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "0233" "034" "02132" "02233" "02121" "051"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02124" "05222" "032" "02113" "02221" "0521"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02221" "02121" "013" "031" "042" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "0112" "0121" "013" "05221" "033" "02221"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "0232" "033" "02131" "02121" "051" "0234"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "051" "013" "042" "02231" "0234" "02232"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "053" "02111" "031" "02133" "043" "031"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "05222" "031" "033" "01222" "051" "02114"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "043" "051" "0232" "02121" "042" "013"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "032" "02113" "034" "051" "042" "02231"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "033" "043" "033" "053" "02232" "034"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01222" "0233" "0225" "02132" "02112" "01223"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02124" "0111" "051" "0231" "02232" "02121"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "0113" "02124" "042" "051" "034" "02222"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "031" "01221" "0231" "02212" "033" "053"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "0234" "0224" "0231" "032" "02121" "02121"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "031" "02211" "053" "02113" "02231" "033"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "013" "043" "041" "02221" "013" "02222"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "031" "051" "051" "043" "02132" "034"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02131" "0232" "02121" "02222" "05221" "02132"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "051" "0121" "02233" "02131" "013" "02231"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02231" "051" "02111" "042" "0233" "0224"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02221" "02121" "02111" "02121" "02121" "031"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "042" "0232" "032" "0231" "031" "041"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "0233" "041" "02221" "0232" "053"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "0224" "0113" "031" "02131" "0224" "02132"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "0224" "02231" "0232" "02232" "033" "02133"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "042" "02233" "041" "0233" "033" "051"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "051" "0232" "042" "05222" "053" "01223"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "053" "02124" "02122" "0233" "051" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02114" "02232" "0521" "053" "02221" "02231"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01222" "0232" "0224" "0232" "02131" "01223"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "043" "0232" "0521" "041" "043" "013"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01222" "05221" "0225" "02221" "02123" "0232"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "051" "01222" "0234" "02124" "043" "02221"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02132" "02124" "02124" "02111" "0121" "01222"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "053" "013" "02123" "0224" "02222" "0524"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02232" "02222" "02211" "041" "02223" "0232"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "0225" "053" "05222" "0232" "02131" "041"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "0121" "02212" "0112" "043" "042" "0224"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02221" "041" "02222" "01223" "042" "0232"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "0224" "0231" "0234" "0112" "05222" "041"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "0112" "053" "043" "02114" "0232" "0121"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01222" "02211" "02212" "02232" "02111" "01221"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "05222" "01222" "02232" "0233" "05221" "01221"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02132" "0233" "053" "0231" "02121" "0112"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "041" "02213" "051" "051" "0224"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "0112" "043" "013" "013" "02124" "051"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02124" "02232" "02133" "041" "02112" "0224"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02222" "02223" "013" "02111" "041" "0232"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "042" "0233" "02132" "0232" "013" "0521"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "041" "051" "0524" "0224" "0121" "043"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02131" "0111" "013" "0121" "0524" "0232"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "041" "0121" "0112" "051" "02233" "02131"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "0232" "05222" "02114" "042" "042" "043"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "041" "051" "0224" "051" "02113"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02123" "043" "02112" "051" "01222" "0232"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02133" "051" "02232" "051" "013" "041"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "043" "051" "042" "02124" "0233" "053"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "042" "051" "041" "0231" "0232" "0231"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02231" "05221" "02213" "02111" "0234" "0231"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "042" "02113" "0232" "02223" "0233" "0113"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02132" "051" "043" "0112" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "0521" "02221" "0112" "01222" "02233" "0233"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02123" "051" "013" "0232" "0121" "01221"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "051" "02231" "051" "02211" "02111" "05222"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "0224" "0111" "053" "0234" "05222" "031"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "041" "02232" "031" "0234" "051" "043"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "053" "01223" "0524" "051" "01221"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "05222" "0121" "0524" "013" "0224" "0232"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "053" "042" "013" "0121" "051" "0232"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "042" "041" "0121" "0234" "041" "0111"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02133" "041" "053" "053" "0521" "01222"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01221" "043" "0524" "02221" "042" "043"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02222" "0113" "051" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2775))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "05222" "02113" "033" "0224" "0222" "0521"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02131" "0224" "041" "02212" "0112" "0232"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "0224" "05221" "02122" "034" "02114" "02111"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "034" "02113" "02213" "053" "0224" "033"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "031" "02111" "0234" "0233" "031" "031"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "0233" "0233" "02132" "0222" "0224" "02233"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02122" "0112" "02132" "051" "02211" "0121"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "051" "0222" "032" "013" "0524" "033"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "0224" "013" "031" "0112" "0224" "02232"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "041" "051" "02233" "032" "0112"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "033" "0233" "0111" "031" "02211" "02132"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "0521" "0113" "0234" "053" "0523" "0112"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01223" "02121" "02121" "053" "0232" "02123"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "032" "032" "0222" "02111" "013"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "031" "031" "0232" "041" "0232" "0222"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "013" "02213" "033" "033" "02122" "0225"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "013" "043" "0225" "0231" "0111" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "032" "032" "02123" "0224" "033" "041"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02113" "042" "034" "0112" "01223" "051"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "0233" "0521" "0111" "032" "05221" "02132"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "051" "043" "032" "0233" "05221" "01221"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02112" "041" "0524" "02131" "013" "0233"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "0233" "034" "02132" "02233" "02121" "051"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02124" "05222" "032" "02113" "0222" "0521"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "0222" "02121" "013" "031" "042" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "0112" "0121" "013" "05221" "033" "0222"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "0232" "033" "02131" "02121" "051" "0234"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "051" "013" "042" "02231" "0234" "02232"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "053" "02111" "031" "02133" "043" "031"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "05222" "031" "033" "01222" "051" "02114"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "043" "051" "0232" "02121" "042" "013"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "032" "02113" "034" "051" "042" "02231"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "033" "043" "033" "053" "02232" "034"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01222" "0233" "0225" "02132" "02112" "01223"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02124" "0111" "051" "0231" "02232" "02121"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "0113" "02124" "042" "051" "034" "0222"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "031" "01221" "0231" "02212" "033" "053"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "0234" "0224" "0231" "032" "02121" "02121"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "031" "02211" "053" "02113" "02231" "033"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "013" "043" "041" "0222" "013" "0222"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "031" "051" "051" "043" "02132" "034"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02131" "0232" "02121" "0222" "05221" "02132"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "051" "0121" "02233" "02131" "013" "02231"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02231" "051" "02111" "042" "0233" "0224"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "0222" "02121" "02111" "02121" "02121" "031"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "042" "0232" "032" "0231" "031" "041"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "0233" "041" "0222" "0232" "053"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "0224" "0113" "031" "02131" "0224" "02132"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "0224" "02231" "0232" "02232" "033" "02133"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "042" "02233" "041" "0233" "033" "051"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "051" "0232" "042" "05222" "053" "01223"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "053" "02124" "02122" "0233" "051" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02114" "02232" "0521" "053" "0222" "02231"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01222" "0232" "0224" "0232" "02131" "01223"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "043" "0232" "0521" "041" "043" "013"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01222" "05221" "0225" "0222" "02123" "0232"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "051" "01222" "0234" "02124" "043" "0222"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02132" "02124" "02124" "02111" "0121" "01222"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "053" "013" "02123" "0224" "0222" "0524"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02232" "0222" "02211" "041" "0222" "0232"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "0225" "053" "05222" "0232" "02131" "041"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "0121" "02212" "0112" "043" "042" "0224"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "0222" "041" "0222" "01223" "042" "0232"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "0224" "0231" "0234" "0112" "05222" "041"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "0112" "053" "043" "02114" "0232" "0121"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01222" "02211" "02212" "02232" "02111" "01221"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "05222" "01222" "02232" "0233" "05221" "01221"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02132" "0233" "053" "0231" "02121" "0112"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "041" "02213" "051" "051" "0224"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "0112" "043" "013" "013" "02124" "051"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02124" "02232" "02133" "041" "02112" "0224"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "0222" "0222" "013" "02111" "041" "0232"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "042" "0233" "02132" "0232" "013" "0521"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "041" "051" "0524" "0224" "0121" "043"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02131" "0111" "013" "0121" "0524" "0232"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "041" "0121" "0112" "051" "02233" "02131"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "0232" "05222" "02114" "042" "042" "043"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "041" "051" "0224" "051" "02113"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02123" "043" "02112" "051" "01222" "0232"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02133" "051" "02232" "051" "013" "041"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "043" "051" "042" "02124" "0233" "053"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "042" "051" "041" "0231" "0232" "0231"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02231" "05221" "02213" "02111" "0234" "0231"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "042" "02113" "0232" "0222" "0233" "0113"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02132" "051" "043" "0112" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "0521" "0222" "0112" "01222" "02233" "0233"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02123" "051" "013" "0232" "0121" "01221"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "051" "02231" "051" "02211" "02111" "05222"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "0224" "0111" "053" "0234" "05222" "031"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "041" "02232" "031" "0234" "051" "043"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "053" "01223" "0524" "051" "01221"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "05222" "0121" "0524" "013" "0224" "0232"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "053" "042" "013" "0121" "051" "0232"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "042" "041" "0121" "0234" "041" "0111"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02133" "041" "053" "053" "0521" "01222"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01221" "043" "0524" "0222" "042" "043"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "0222" "0113" "051" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2836))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "0522" "02113" "033" "0224" "0222" "0521"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02131" "0224" "041" "02212" "0112" "0232"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "0224" "0522" "02122" "034" "02114" "02111"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "034" "02113" "02213" "053" "0224" "033"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "031" "02111" "0234" "0233" "031" "031"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "0233" "0233" "02132" "0222" "0224" "02233"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02122" "0112" "02132" "051" "02211" "0121"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "051" "0222" "032" "013" "0524" "033"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "0224" "013" "031" "0112" "0224" "02232"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "041" "051" "02233" "032" "0112"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "033" "0233" "0111" "031" "02211" "02132"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "0521" "0113" "0234" "053" "0523" "0112"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01223" "02121" "02121" "053" "0232" "02123"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "032" "032" "0222" "02111" "013"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "031" "031" "0232" "041" "0232" "0222"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "013" "02213" "033" "033" "02122" "0225"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "013" "043" "0225" "0231" "0111" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "032" "032" "02123" "0224" "033" "041"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02113" "042" "034" "0112" "01223" "051"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "0233" "0521" "0111" "032" "0522" "02132"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "051" "043" "032" "0233" "0522" "01221"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02112" "041" "0524" "02131" "013" "0233"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "0233" "034" "02132" "02233" "02121" "051"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02124" "0522" "032" "02113" "0222" "0521"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "0222" "02121" "013" "031" "042" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "0112" "0121" "013" "0522" "033" "0222"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "0232" "033" "02131" "02121" "051" "0234"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "051" "013" "042" "02231" "0234" "02232"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "053" "02111" "031" "02133" "043" "031"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "0522" "031" "033" "01222" "051" "02114"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "043" "051" "0232" "02121" "042" "013"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "032" "02113" "034" "051" "042" "02231"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "033" "043" "033" "053" "02232" "034"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01222" "0233" "0225" "02132" "02112" "01223"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02124" "0111" "051" "0231" "02232" "02121"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "0113" "02124" "042" "051" "034" "0222"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "031" "01221" "0231" "02212" "033" "053"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "0234" "0224" "0231" "032" "02121" "02121"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "031" "02211" "053" "02113" "02231" "033"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "013" "043" "041" "0222" "013" "0222"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "031" "051" "051" "043" "02132" "034"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02131" "0232" "02121" "0222" "0522" "02132"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "051" "0121" "02233" "02131" "013" "02231"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02231" "051" "02111" "042" "0233" "0224"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "0222" "02121" "02111" "02121" "02121" "031"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "042" "0232" "032" "0231" "031" "041"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "0233" "041" "0222" "0232" "053"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "0224" "0113" "031" "02131" "0224" "02132"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "0224" "02231" "0232" "02232" "033" "02133"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "042" "02233" "041" "0233" "033" "051"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "051" "0232" "042" "0522" "053" "01223"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "053" "02124" "02122" "0233" "051" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02114" "02232" "0521" "053" "0222" "02231"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01222" "0232" "0224" "0232" "02131" "01223"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "043" "0232" "0521" "041" "043" "013"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01222" "0522" "0225" "0222" "02123" "0232"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "051" "01222" "0234" "02124" "043" "0222"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02132" "02124" "02124" "02111" "0121" "01222"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "053" "013" "02123" "0224" "0222" "0524"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02232" "0222" "02211" "041" "0222" "0232"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "0225" "053" "0522" "0232" "02131" "041"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "0121" "02212" "0112" "043" "042" "0224"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "0222" "041" "0222" "01223" "042" "0232"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "0224" "0231" "0234" "0112" "0522" "041"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "0112" "053" "043" "02114" "0232" "0121"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01222" "02211" "02212" "02232" "02111" "01221"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "0522" "01222" "02232" "0233" "0522" "01221"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02132" "0233" "053" "0231" "02121" "0112"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "041" "02213" "051" "051" "0224"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "0112" "043" "013" "013" "02124" "051"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02124" "02232" "02133" "041" "02112" "0224"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "0222" "0222" "013" "02111" "041" "0232"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "042" "0233" "02132" "0232" "013" "0521"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "041" "051" "0524" "0224" "0121" "043"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02131" "0111" "013" "0121" "0524" "0232"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "041" "0121" "0112" "051" "02233" "02131"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "0232" "0522" "02114" "042" "042" "043"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "041" "051" "0224" "051" "02113"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02123" "043" "02112" "051" "01222" "0232"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02133" "051" "02232" "051" "013" "041"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "043" "051" "042" "02124" "0233" "053"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "042" "051" "041" "0231" "0232" "0231"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02231" "0522" "02213" "02111" "0234" "0231"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "042" "02113" "0232" "0222" "0233" "0113"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02132" "051" "043" "0112" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "0521" "0222" "0112" "01222" "02233" "0233"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02123" "051" "013" "0232" "0121" "01221"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "051" "02231" "051" "02211" "02111" "0522"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "0224" "0111" "053" "0234" "0522" "031"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "041" "02232" "031" "0234" "051" "043"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "053" "01223" "0524" "051" "01221"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "0522" "0121" "0524" "013" "0224" "0232"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "053" "042" "013" "0121" "051" "0232"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "042" "041" "0121" "0234" "041" "0111"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02133" "041" "053" "053" "0521" "01222"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01221" "043" "0524" "0222" "042" "043"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "0222" "0113" "051" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3188))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "0522" "02113" "033" "0224" "0222" "0521"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02131" "0224" "041" "02212" "0112" "0232"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "0224" "0522" "02122" "034" "02114" "02111"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "034" "02113" "02213" "053" "0224" "033"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "031" "02111" "0234" "0233" "031" "031"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "0233" "0233" "02132" "0222" "0224" "02233"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02122" "0112" "02132" "051" "02211" "012"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "051" "0222" "032" "013" "0524" "033"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "0224" "013" "031" "0112" "0224" "02232"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "041" "051" "02233" "032" "0112"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "033" "0233" "0111" "031" "02211" "02132"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "0521" "0113" "0234" "053" "0523" "0112"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "012" "02121" "02121" "053" "0232" "02123"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "032" "032" "0222" "02111" "013"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "031" "031" "0232" "041" "0232" "0222"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "013" "02213" "033" "033" "02122" "0225"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "013" "043" "0225" "0231" "0111" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "032" "032" "02123" "0224" "033" "041"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02113" "042" "034" "0112" "012" "051"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "0233" "0521" "0111" "032" "0522" "02132"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "051" "043" "032" "0233" "0522" "012"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02112" "041" "0524" "02131" "013" "0233"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "0233" "034" "02132" "02233" "02121" "051"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02124" "0522" "032" "02113" "0222" "0521"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "0222" "02121" "013" "031" "042" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "0112" "012" "013" "0522" "033" "0222"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "0232" "033" "02131" "02121" "051" "0234"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "051" "013" "042" "02231" "0234" "02232"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "053" "02111" "031" "02133" "043" "031"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "0522" "031" "033" "012" "051" "02114"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "043" "051" "0232" "02121" "042" "013"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "032" "02113" "034" "051" "042" "02231"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "033" "043" "033" "053" "02232" "034"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "012" "0233" "0225" "02132" "02112" "012"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02124" "0111" "051" "0231" "02232" "02121"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "0113" "02124" "042" "051" "034" "0222"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "031" "012" "0231" "02212" "033" "053"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "0234" "0224" "0231" "032" "02121" "02121"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "031" "02211" "053" "02113" "02231" "033"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "013" "043" "041" "0222" "013" "0222"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "031" "051" "051" "043" "02132" "034"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02131" "0232" "02121" "0222" "0522" "02132"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "051" "012" "02233" "02131" "013" "02231"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02231" "051" "02111" "042" "0233" "0224"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "0222" "02121" "02111" "02121" "02121" "031"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "042" "0232" "032" "0231" "031" "041"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "0233" "041" "0222" "0232" "053"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "0224" "0113" "031" "02131" "0224" "02132"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "0224" "02231" "0232" "02232" "033" "02133"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "042" "02233" "041" "0233" "033" "051"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "051" "0232" "042" "0522" "053" "012"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "053" "02124" "02122" "0233" "051" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02114" "02232" "0521" "053" "0222" "02231"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "012" "0232" "0224" "0232" "02131" "012"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "043" "0232" "0521" "041" "043" "013"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "012" "0522" "0225" "0222" "02123" "0232"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "051" "012" "0234" "02124" "043" "0222"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02132" "02124" "02124" "02111" "012" "012"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "053" "013" "02123" "0224" "0222" "0524"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02232" "0222" "02211" "041" "0222" "0232"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "0225" "053" "0522" "0232" "02131" "041"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "012" "02212" "0112" "043" "042" "0224"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "0222" "041" "0222" "012" "042" "0232"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "0224" "0231" "0234" "0112" "0522" "041"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "0112" "053" "043" "02114" "0232" "012"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "012" "02211" "02212" "02232" "02111" "012"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "0522" "012" "02232" "0233" "0522" "012"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02132" "0233" "053" "0231" "02121" "0112"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "041" "02213" "051" "051" "0224"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "0112" "043" "013" "013" "02124" "051"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02124" "02232" "02133" "041" "02112" "0224"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "0222" "0222" "013" "02111" "041" "0232"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "042" "0233" "02132" "0232" "013" "0521"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "041" "051" "0524" "0224" "012" "043"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02131" "0111" "013" "012" "0524" "0232"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "041" "012" "0112" "051" "02233" "02131"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "0232" "0522" "02114" "042" "042" "043"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "041" "051" "0224" "051" "02113"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02123" "043" "02112" "051" "012" "0232"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02133" "051" "02232" "051" "013" "041"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "043" "051" "042" "02124" "0233" "053"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "042" "051" "041" "0231" "0232" "0231"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02231" "0522" "02213" "02111" "0234" "0231"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "042" "02113" "0232" "0222" "0233" "0113"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02132" "051" "043" "0112" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "0521" "0222" "0112" "012" "02233" "0233"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02123" "051" "013" "0232" "012" "012"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "051" "02231" "051" "02211" "02111" "0522"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "0224" "0111" "053" "0234" "0522" "031"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "041" "02232" "031" "0234" "051" "043"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "053" "012" "0524" "051" "012"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "0522" "012" "0524" "013" "0224" "0232"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "053" "042" "013" "012" "051" "0232"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "042" "041" "012" "0234" "041" "0111"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02133" "041" "053" "053" "0521" "012"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "012" "043" "0524" "0222" "042" "043"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "0222" "0113" "051" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3867))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "0522" "02113" "033" "0224" "0222" "0521"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02131" "0224" "041" "02212" "011" "0232"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "0224" "0522" "02122" "034" "02114" "02111"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "034" "02113" "02213" "053" "0224" "033"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "031" "02111" "0234" "0233" "031" "031"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "0233" "0233" "02132" "0222" "0224" "02233"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02122" "011" "02132" "051" "02211" "012"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "051" "0222" "032" "013" "0524" "033"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "0224" "013" "031" "011" "0224" "02232"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "041" "051" "02233" "032" "011"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "033" "0233" "011" "031" "02211" "02132"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "0521" "011" "0234" "053" "0523" "011"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "012" "02121" "02121" "053" "0232" "02123"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "032" "032" "0222" "02111" "013"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "031" "031" "0232" "041" "0232" "0222"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "013" "02213" "033" "033" "02122" "0225"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "013" "043" "0225" "0231" "011" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "032" "032" "02123" "0224" "033" "041"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02113" "042" "034" "011" "012" "051"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "0233" "0521" "011" "032" "0522" "02132"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "051" "043" "032" "0233" "0522" "012"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02112" "041" "0524" "02131" "013" "0233"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "0233" "034" "02132" "02233" "02121" "051"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02124" "0522" "032" "02113" "0222" "0521"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "0222" "02121" "013" "031" "042" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "011" "012" "013" "0522" "033" "0222"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "0232" "033" "02131" "02121" "051" "0234"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "051" "013" "042" "02231" "0234" "02232"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "053" "02111" "031" "02133" "043" "031"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "0522" "031" "033" "012" "051" "02114"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "043" "051" "0232" "02121" "042" "013"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "032" "02113" "034" "051" "042" "02231"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "033" "043" "033" "053" "02232" "034"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "012" "0233" "0225" "02132" "02112" "012"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02124" "011" "051" "0231" "02232" "02121"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "011" "02124" "042" "051" "034" "0222"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "031" "012" "0231" "02212" "033" "053"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "0234" "0224" "0231" "032" "02121" "02121"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "031" "02211" "053" "02113" "02231" "033"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "013" "043" "041" "0222" "013" "0222"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "031" "051" "051" "043" "02132" "034"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02131" "0232" "02121" "0222" "0522" "02132"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "051" "012" "02233" "02131" "013" "02231"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02231" "051" "02111" "042" "0233" "0224"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "0222" "02121" "02111" "02121" "02121" "031"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "042" "0232" "032" "0231" "031" "041"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "0233" "041" "0222" "0232" "053"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "0224" "011" "031" "02131" "0224" "02132"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "0224" "02231" "0232" "02232" "033" "02133"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "042" "02233" "041" "0233" "033" "051"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "051" "0232" "042" "0522" "053" "012"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "053" "02124" "02122" "0233" "051" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02114" "02232" "0521" "053" "0222" "02231"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "012" "0232" "0224" "0232" "02131" "012"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "043" "0232" "0521" "041" "043" "013"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "012" "0522" "0225" "0222" "02123" "0232"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "051" "012" "0234" "02124" "043" "0222"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02132" "02124" "02124" "02111" "012" "012"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "053" "013" "02123" "0224" "0222" "0524"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02232" "0222" "02211" "041" "0222" "0232"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "0225" "053" "0522" "0232" "02131" "041"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "012" "02212" "011" "043" "042" "0224"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "0222" "041" "0222" "012" "042" "0232"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "0224" "0231" "0234" "011" "0522" "041"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "011" "053" "043" "02114" "0232" "012"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "012" "02211" "02212" "02232" "02111" "012"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "0522" "012" "02232" "0233" "0522" "012"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02132" "0233" "053" "0231" "02121" "011"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "041" "02213" "051" "051" "0224"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "011" "043" "013" "013" "02124" "051"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02124" "02232" "02133" "041" "02112" "0224"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "0222" "0222" "013" "02111" "041" "0232"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "042" "0233" "02132" "0232" "013" "0521"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "041" "051" "0524" "0224" "012" "043"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02131" "011" "013" "012" "0524" "0232"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "041" "012" "011" "051" "02233" "02131"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "0232" "0522" "02114" "042" "042" "043"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "041" "051" "0224" "051" "02113"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02123" "043" "02112" "051" "012" "0232"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02133" "051" "02232" "051" "013" "041"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "043" "051" "042" "02124" "0233" "053"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "042" "051" "041" "0231" "0232" "0231"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02231" "0522" "02213" "02111" "0234" "0231"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "042" "02113" "0232" "0222" "0233" "011"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02132" "051" "043" "011" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "0521" "0222" "011" "012" "02233" "0233"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02123" "051" "013" "0232" "012" "012"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "051" "02231" "051" "02211" "02111" "0522"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "0224" "011" "053" "0234" "0522" "031"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "041" "02232" "031" "0234" "051" "043"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "053" "012" "0524" "051" "012"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "0522" "012" "0524" "013" "0224" "0232"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "053" "042" "013" "012" "051" "0232"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "042" "041" "012" "0234" "041" "011"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02133" "041" "053" "053" "0521" "012"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "012" "043" "0524" "0222" "042" "043"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "0222" "011" "051" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4027))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "0522" "02113" "033" "0224" "0222" "0521"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02131" "0224" "04" "02212" "011" "0232"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "0224" "0522" "02122" "034" "02114" "02111"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "034" "02113" "02213" "053" "0224" "033"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "031" "02111" "0234" "0233" "031" "031"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "0233" "0233" "02132" "0222" "0224" "02233"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02122" "011" "02132" "051" "02211" "012"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "051" "0222" "032" "013" "0524" "033"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "0224" "013" "031" "011" "0224" "02232"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "04" "051" "02233" "032" "011"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "033" "0233" "011" "031" "02211" "02132"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "0521" "011" "0234" "053" "0523" "011"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "012" "02121" "02121" "053" "0232" "02123"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "032" "032" "0222" "02111" "013"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "031" "031" "0232" "04" "0232" "0222"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "013" "02213" "033" "033" "02122" "0225"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "013" "04" "0225" "0231" "011" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "032" "032" "02123" "0224" "033" "04"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02113" "04" "034" "011" "012" "051"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "0233" "0521" "011" "032" "0522" "02132"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "051" "04" "032" "0233" "0522" "012"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02112" "04" "0524" "02131" "013" "0233"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "0233" "034" "02132" "02233" "02121" "051"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02124" "0522" "032" "02113" "0222" "0521"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "0222" "02121" "013" "031" "04" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "011" "012" "013" "0522" "033" "0222"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "0232" "033" "02131" "02121" "051" "0234"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "051" "013" "04" "02231" "0234" "02232"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "053" "02111" "031" "02133" "04" "031"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "0522" "031" "033" "012" "051" "02114"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "04" "051" "0232" "02121" "04" "013"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "032" "02113" "034" "051" "04" "02231"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "033" "04" "033" "053" "02232" "034"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "012" "0233" "0225" "02132" "02112" "012"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02124" "011" "051" "0231" "02232" "02121"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "011" "02124" "04" "051" "034" "0222"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "031" "012" "0231" "02212" "033" "053"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "0234" "0224" "0231" "032" "02121" "02121"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "031" "02211" "053" "02113" "02231" "033"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "013" "04" "04" "0222" "013" "0222"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "031" "051" "051" "04" "02132" "034"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02131" "0232" "02121" "0222" "0522" "02132"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "051" "012" "02233" "02131" "013" "02231"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02231" "051" "02111" "04" "0233" "0224"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "0222" "02121" "02111" "02121" "02121" "031"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "04" "0232" "032" "0231" "031" "04"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "0233" "04" "0222" "0232" "053"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "0224" "011" "031" "02131" "0224" "02132"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "0224" "02231" "0232" "02232" "033" "02133"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "04" "02233" "04" "0233" "033" "051"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "051" "0232" "04" "0522" "053" "012"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "053" "02124" "02122" "0233" "051" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02114" "02232" "0521" "053" "0222" "02231"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "012" "0232" "0224" "0232" "02131" "012"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "04" "0232" "0521" "04" "04" "013"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "012" "0522" "0225" "0222" "02123" "0232"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "051" "012" "0234" "02124" "04" "0222"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02132" "02124" "02124" "02111" "012" "012"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "053" "013" "02123" "0224" "0222" "0524"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02232" "0222" "02211" "04" "0222" "0232"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "0225" "053" "0522" "0232" "02131" "04"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "012" "02212" "011" "04" "04" "0224"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "0222" "04" "0222" "012" "04" "0232"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "0224" "0231" "0234" "011" "0522" "04"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "011" "053" "04" "02114" "0232" "012"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "012" "02211" "02212" "02232" "02111" "012"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "0522" "012" "02232" "0233" "0522" "012"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02132" "0233" "053" "0231" "02121" "011"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "04" "02213" "051" "051" "0224"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "011" "04" "013" "013" "02124" "051"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02124" "02232" "02133" "04" "02112" "0224"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "0222" "0222" "013" "02111" "04" "0232"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "04" "0233" "02132" "0232" "013" "0521"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "04" "051" "0524" "0224" "012" "04"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02131" "011" "013" "012" "0524" "0232"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "04" "012" "011" "051" "02233" "02131"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "0232" "0522" "02114" "04" "04" "04"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "04" "051" "0224" "051" "02113"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02123" "04" "02112" "051" "012" "0232"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02133" "051" "02232" "051" "013" "04"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "04" "051" "04" "02124" "0233" "053"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "04" "051" "04" "0231" "0232" "0231"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02231" "0522" "02213" "02111" "0234" "0231"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "04" "02113" "0232" "0222" "0233" "011"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02132" "051" "04" "011" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "0521" "0222" "011" "012" "02233" "0233"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02123" "051" "013" "0232" "012" "012"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "051" "02231" "051" "02211" "02111" "0522"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "0224" "011" "053" "0234" "0522" "031"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "04" "02232" "031" "0234" "051" "04"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "053" "012" "0524" "051" "012"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "0522" "012" "0524" "013" "0224" "0232"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "053" "04" "013" "012" "051" "0232"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "04" "04" "012" "0234" "04" "011"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02133" "04" "053" "053" "0521" "012"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "012" "04" "0524" "0222" "04" "04"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "0222" "011" "051" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4522))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "0522" "02113" "033" "02" "02" "0521"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02131" "02" "04" "02212" "011" "02"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "02" "0522" "02122" "034" "02114" "02111"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "034" "02113" "02213" "053" "02" "033"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "031" "02111" "02" "02" "031" "031"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "02" "02" "02132" "02" "02" "02233"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02122" "011" "02132" "051" "02211" "012"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "051" "02" "032" "013" "0524" "033"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "02" "013" "031" "011" "02" "02232"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "04" "051" "02233" "032" "011"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "033" "02" "011" "031" "02211" "02132"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "0521" "011" "02" "053" "0523" "011"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "012" "02121" "02121" "053" "02" "02123"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "032" "032" "02" "02111" "013"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "031" "031" "02" "04" "02" "02"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "013" "02213" "033" "033" "02122" "02"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "013" "04" "02" "02" "011" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "032" "032" "02123" "02" "033" "04"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02113" "04" "034" "011" "012" "051"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "02" "0521" "011" "032" "0522" "02132"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "051" "04" "032" "02" "0522" "012"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02112" "04" "0524" "02131" "013" "02"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "02" "034" "02132" "02233" "02121" "051"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02124" "0522" "032" "02113" "02" "0521"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02" "02121" "013" "031" "04" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "011" "012" "013" "0522" "033" "02"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "02" "033" "02131" "02121" "051" "02"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "051" "013" "04" "02231" "02" "02232"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "053" "02111" "031" "02133" "04" "031"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "0522" "031" "033" "012" "051" "02114"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "04" "051" "02" "02121" "04" "013"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "032" "02113" "034" "051" "04" "02231"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "033" "04" "033" "053" "02232" "034"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "012" "02" "02" "02132" "02112" "012"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02124" "011" "051" "02" "02232" "02121"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "011" "02124" "04" "051" "034" "02"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "031" "012" "02" "02212" "033" "053"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "02" "02" "02" "032" "02121" "02121"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "031" "02211" "053" "02113" "02231" "033"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "013" "04" "04" "02" "013" "02"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "031" "051" "051" "04" "02132" "034"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02131" "02" "02121" "02" "0522" "02132"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "051" "012" "02233" "02131" "013" "02231"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02231" "051" "02111" "04" "02" "02"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02" "02121" "02111" "02121" "02121" "031"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "04" "02" "032" "02" "031" "04"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "02" "04" "02" "02" "053"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "02" "011" "031" "02131" "02" "02132"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "02" "02231" "02" "02232" "033" "02133"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "04" "02233" "04" "02" "033" "051"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "051" "02" "04" "0522" "053" "012"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "053" "02124" "02122" "02" "051" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02114" "02232" "0521" "053" "02" "02231"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "012" "02" "02" "02" "02131" "012"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "04" "02" "0521" "04" "04" "013"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "012" "0522" "02" "02" "02123" "02"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "051" "012" "02" "02124" "04" "02"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02132" "02124" "02124" "02111" "012" "012"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "053" "013" "02123" "02" "02" "0524"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02232" "02" "02211" "04" "02" "02"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "02" "053" "0522" "02" "02131" "04"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "012" "02212" "011" "04" "04" "02"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02" "04" "02" "012" "04" "02"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "02" "02" "02" "011" "0522" "04"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "011" "053" "04" "02114" "02" "012"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "012" "02211" "02212" "02232" "02111" "012"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "0522" "012" "02232" "02" "0522" "012"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02132" "02" "053" "02" "02121" "011"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "04" "02213" "051" "051" "02"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "011" "04" "013" "013" "02124" "051"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02124" "02232" "02133" "04" "02112" "02"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02" "02" "013" "02111" "04" "02"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "04" "02" "02132" "02" "013" "0521"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "04" "051" "0524" "02" "012" "04"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02131" "011" "013" "012" "0524" "02"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "04" "012" "011" "051" "02233" "02131"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "02" "0522" "02114" "04" "04" "04"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "04" "051" "02" "051" "02113"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02123" "04" "02112" "051" "012" "02"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02133" "051" "02232" "051" "013" "04"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "04" "051" "04" "02124" "02" "053"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "04" "051" "04" "02" "02" "02"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02231" "0522" "02213" "02111" "02" "02"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "04" "02113" "02" "02" "02" "011"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02132" "051" "04" "011" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "0521" "02" "011" "012" "02233" "02"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02123" "051" "013" "02" "012" "012"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "051" "02231" "051" "02211" "02111" "0522"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "02" "011" "053" "02" "0522" "031"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "04" "02232" "031" "02" "051" "04"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "053" "012" "0524" "051" "012"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "0522" "012" "0524" "013" "02" "02"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "053" "04" "013" "012" "051" "02"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "04" "04" "012" "02" "04" "011"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02133" "04" "053" "053" "0521" "012"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "012" "04" "0524" "02" "04" "04"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02" "011" "051" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4660))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "0522" "02" "033" "02" "02" "0521"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02" "02" "04" "02212" "011" "02"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "02" "0522" "02" "034" "02" "02"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "034" "02" "02213" "053" "02" "033"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "031" "02" "02" "02" "031" "031"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "02" "02" "02" "02" "02" "02233"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02" "011" "02" "051" "02211" "012"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "051" "02" "032" "013" "0524" "033"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "02" "013" "031" "011" "02" "02232"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "04" "051" "02233" "032" "011"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "033" "02" "011" "031" "02211" "02"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "0521" "011" "02" "053" "0523" "011"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "012" "02" "02" "053" "02" "02"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "032" "032" "02" "02" "013"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "031" "031" "02" "04" "02" "02"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "013" "02213" "033" "033" "02" "02"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "013" "04" "02" "02" "011" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "032" "032" "02" "02" "033" "04"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02" "04" "034" "011" "012" "051"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "02" "0521" "011" "032" "0522" "02"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "051" "04" "032" "02" "0522" "012"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02" "04" "0524" "02" "013" "02"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "02" "034" "02" "02233" "02" "051"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02" "0522" "032" "02" "02" "0521"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02" "02" "013" "031" "04" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "011" "012" "013" "0522" "033" "02"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "02" "033" "02" "02" "051" "02"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "051" "013" "04" "02231" "02" "02232"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "053" "02" "031" "02" "04" "031"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "0522" "031" "033" "012" "051" "02"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "04" "051" "02" "02" "04" "013"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "032" "02" "034" "051" "04" "02231"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "033" "04" "033" "053" "02232" "034"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "012" "02" "02" "02" "02" "012"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02" "011" "051" "02" "02232" "02"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "011" "02" "04" "051" "034" "02"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "031" "012" "02" "02212" "033" "053"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "02" "02" "02" "032" "02" "02"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "031" "02211" "053" "02" "02231" "033"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "013" "04" "04" "02" "013" "02"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "031" "051" "051" "04" "02" "034"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02" "02" "02" "02" "0522" "02"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "051" "012" "02233" "02" "013" "02231"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02231" "051" "02" "04" "02" "02"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02" "02" "02" "02" "02" "031"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "04" "02" "032" "02" "031" "04"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "02" "04" "02" "02" "053"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "02" "011" "031" "02" "02" "02"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "02" "02231" "02" "02232" "033" "02"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "04" "02233" "04" "02" "033" "051"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "051" "02" "04" "0522" "053" "012"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "053" "02" "02" "02" "051" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02" "02232" "0521" "053" "02" "02231"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "012" "02" "02" "02" "02" "012"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "04" "02" "0521" "04" "04" "013"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "012" "0522" "02" "02" "02" "02"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "051" "012" "02" "02" "04" "02"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02" "02" "02" "02" "012" "012"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "053" "013" "02" "02" "02" "0524"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02232" "02" "02211" "04" "02" "02"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "02" "053" "0522" "02" "02" "04"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "012" "02212" "011" "04" "04" "02"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02" "04" "02" "012" "04" "02"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "02" "02" "02" "011" "0522" "04"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "011" "053" "04" "02" "02" "012"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "012" "02211" "02212" "02232" "02" "012"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "0522" "012" "02232" "02" "0522" "012"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02" "02" "053" "02" "02" "011"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "04" "02213" "051" "051" "02"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "011" "04" "013" "013" "02" "051"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02" "02232" "02" "04" "02" "02"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02" "02" "013" "02" "04" "02"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "04" "02" "02" "02" "013" "0521"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "04" "051" "0524" "02" "012" "04"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02" "011" "013" "012" "0524" "02"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "04" "012" "011" "051" "02233" "02"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "02" "0522" "02" "04" "04" "04"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "04" "051" "02" "051" "02"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02" "04" "02" "051" "012" "02"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02" "051" "02232" "051" "013" "04"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "04" "051" "04" "02" "02" "053"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "04" "051" "04" "02" "02" "02"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02231" "0522" "02213" "02" "02" "02"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "04" "02" "02" "02" "02" "011"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02" "051" "04" "011" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "0521" "02" "011" "012" "02233" "02"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02" "051" "013" "02" "012" "012"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "051" "02231" "051" "02211" "02" "0522"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "02" "011" "053" "02" "0522" "031"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "04" "02232" "031" "02" "051" "04"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "053" "012" "0524" "051" "012"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "0522" "012" "0524" "013" "02" "02"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "053" "04" "013" "012" "051" "02"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "04" "04" "012" "02" "04" "011"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02" "04" "053" "053" "0521" "012"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "012" "04" "0524" "02" "04" "04"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02" "011" "051" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4864))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "0522" "02" "033" "02" "02" "0521"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02" "02" "04" "02212" "01" "02"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "02" "0522" "02" "034" "02" "02"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "034" "02" "02213" "053" "02" "033"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "031" "02" "02" "02" "031" "031"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "02" "02" "02" "02" "02" "02233"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02" "01" "02" "051" "02211" "01"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "051" "02" "032" "01" "0524" "033"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "02" "01" "031" "01" "02" "02232"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "04" "051" "02233" "032" "01"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "033" "02" "01" "031" "02211" "02"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "0521" "01" "02" "053" "0523" "01"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01" "02" "02" "053" "02" "02"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "032" "032" "02" "02" "01"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "031" "031" "02" "04" "02" "02"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "01" "02213" "033" "033" "02" "02"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "01" "04" "02" "02" "01" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "032" "032" "02" "02" "033" "04"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02" "04" "034" "01" "01" "051"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "02" "0521" "01" "032" "0522" "02"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "051" "04" "032" "02" "0522" "01"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02" "04" "0524" "02" "01" "02"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "02" "034" "02" "02233" "02" "051"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02" "0522" "032" "02" "02" "0521"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02" "02" "01" "031" "04" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "01" "01" "01" "0522" "033" "02"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "02" "033" "02" "02" "051" "02"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "051" "01" "04" "02231" "02" "02232"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "053" "02" "031" "02" "04" "031"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "0522" "031" "033" "01" "051" "02"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "04" "051" "02" "02" "04" "01"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "032" "02" "034" "051" "04" "02231"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "033" "04" "033" "053" "02232" "034"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02" "01" "051" "02" "02232" "02"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "01" "02" "04" "051" "034" "02"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "031" "01" "02" "02212" "033" "053"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "02" "02" "02" "032" "02" "02"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "031" "02211" "053" "02" "02231" "033"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "01" "04" "04" "02" "01" "02"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "031" "051" "051" "04" "02" "034"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02" "02" "02" "02" "0522" "02"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "051" "01" "02233" "02" "01" "02231"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02231" "051" "02" "04" "02" "02"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02" "02" "02" "02" "02" "031"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "04" "02" "032" "02" "031" "04"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "02" "04" "02" "02" "053"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "02" "01" "031" "02" "02" "02"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "02" "02231" "02" "02232" "033" "02"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "04" "02233" "04" "02" "033" "051"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "051" "02" "04" "0522" "053" "01"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "053" "02" "02" "02" "051" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02" "02232" "0521" "053" "02" "02231"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "04" "02" "0521" "04" "04" "01"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01" "0522" "02" "02" "02" "02"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "051" "01" "02" "02" "04" "02"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02" "02" "02" "02" "01" "01"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "053" "01" "02" "02" "02" "0524"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02232" "02" "02211" "04" "02" "02"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "02" "053" "0522" "02" "02" "04"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "01" "02212" "01" "04" "04" "02"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02" "04" "02" "01" "04" "02"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "02" "02" "02" "01" "0522" "04"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "01" "053" "04" "02" "02" "01"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01" "02211" "02212" "02232" "02" "01"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "0522" "01" "02232" "02" "0522" "01"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02" "02" "053" "02" "02" "01"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "04" "02213" "051" "051" "02"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "01" "04" "01" "01" "02" "051"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02" "02232" "02" "04" "02" "02"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02" "02" "01" "02" "04" "02"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "04" "02" "02" "02" "01" "0521"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "04" "051" "0524" "02" "01" "04"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02" "01" "01" "01" "0524" "02"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "04" "01" "01" "051" "02233" "02"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "02" "0522" "02" "04" "04" "04"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "04" "051" "02" "051" "02"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02" "04" "02" "051" "01" "02"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02" "051" "02232" "051" "01" "04"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "04" "051" "04" "02" "02" "053"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "04" "051" "04" "02" "02" "02"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02231" "0522" "02213" "02" "02" "02"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "04" "02" "02" "02" "02" "01"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02" "051" "04" "01" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "0521" "02" "01" "01" "02233" "02"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02" "051" "01" "02" "01" "01"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "051" "02231" "051" "02211" "02" "0522"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "02" "01" "053" "02" "0522" "031"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "04" "02232" "031" "02" "051" "04"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "053" "01" "0524" "051" "01"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "0522" "01" "0524" "01" "02" "02"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "053" "04" "01" "01" "051" "02"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "04" "04" "01" "02" "04" "01"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02" "04" "053" "053" "0521" "01"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01" "04" "0524" "02" "04" "04"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02" "01" "051" "01"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5547))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "0522" "02" "033" "02" "02" "0521"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02" "02" "04" "02212" "01" "02"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "02" "0522" "02" "034" "02" "02"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "034" "02" "02213" "053" "02" "033"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "031" "02" "02" "02" "031" "031"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02" "01" "02" "051" "02211" "01"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "051" "02" "032" "01" "0524" "033"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "02" "01" "031" "01" "02" "02"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "04" "051" "02" "032" "01"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "033" "02" "01" "031" "02211" "02"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "0521" "01" "02" "053" "0523" "01"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01" "02" "02" "053" "02" "02"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "032" "032" "02" "02" "01"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "031" "031" "02" "04" "02" "02"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "01" "02213" "033" "033" "02" "02"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "01" "04" "02" "02" "01" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "032" "032" "02" "02" "033" "04"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02" "04" "034" "01" "01" "051"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "02" "0521" "01" "032" "0522" "02"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "051" "04" "032" "02" "0522" "01"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02" "04" "0524" "02" "01" "02"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "02" "034" "02" "02" "02" "051"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02" "0522" "032" "02" "02" "0521"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02" "02" "01" "031" "04" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "01" "01" "01" "0522" "033" "02"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "02" "033" "02" "02" "051" "02"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "051" "01" "04" "02" "02" "02"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "053" "02" "031" "02" "04" "031"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "0522" "031" "033" "01" "051" "02"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "04" "051" "02" "02" "04" "01"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "032" "02" "034" "051" "04" "02"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "033" "04" "033" "053" "02" "034"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02" "01" "051" "02" "02" "02"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "01" "02" "04" "051" "034" "02"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "031" "01" "02" "02212" "033" "053"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "02" "02" "02" "032" "02" "02"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "031" "02211" "053" "02" "02" "033"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "01" "04" "04" "02" "01" "02"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "031" "051" "051" "04" "02" "034"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02" "02" "02" "02" "0522" "02"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "051" "01" "02" "02" "01" "02"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02" "051" "02" "04" "02" "02"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02" "02" "02" "02" "02" "031"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "04" "02" "032" "02" "031" "04"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "02" "04" "02" "02" "053"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "02" "01" "031" "02" "02" "02"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "02" "02" "02" "02" "033" "02"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "04" "02" "04" "02" "033" "051"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "051" "02" "04" "0522" "053" "01"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "053" "02" "02" "02" "051" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02" "02" "0521" "053" "02" "02"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "04" "02" "0521" "04" "04" "01"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01" "0522" "02" "02" "02" "02"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "051" "01" "02" "02" "04" "02"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02" "02" "02" "02" "01" "01"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "053" "01" "02" "02" "02" "0524"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02" "02" "02211" "04" "02" "02"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "02" "053" "0522" "02" "02" "04"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "01" "02212" "01" "04" "04" "02"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02" "04" "02" "01" "04" "02"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "02" "02" "02" "01" "0522" "04"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "01" "053" "04" "02" "02" "01"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01" "02211" "02212" "02" "02" "01"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "0522" "01" "02" "02" "0522" "01"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02" "02" "053" "02" "02" "01"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "04" "02213" "051" "051" "02"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "01" "04" "01" "01" "02" "051"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02" "02" "02" "04" "02" "02"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02" "02" "01" "02" "04" "02"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "04" "02" "02" "02" "01" "0521"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "04" "051" "0524" "02" "01" "04"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02" "01" "01" "01" "0524" "02"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "04" "01" "01" "051" "02" "02"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "02" "0522" "02" "04" "04" "04"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "04" "051" "02" "051" "02"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02" "04" "02" "051" "01" "02"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02" "051" "02" "051" "01" "04"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "04" "051" "04" "02" "02" "053"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "04" "051" "04" "02" "02" "02"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02" "0522" "02213" "02" "02" "02"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "04" "02" "02" "02" "02" "01"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02" "051" "04" "01" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "0521" "02" "01" "01" "02" "02"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02" "051" "01" "02" "01" "01"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "051" "02" "051" "02211" "02" "0522"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "02" "01" "053" "02" "0522" "031"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "04" "02" "031" "02" "051" "04"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "053" "01" "0524" "051" "01"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "0522" "01" "0524" "01" "02" "02"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "053" "04" "01" "01" "051" "02"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "04" "04" "01" "02" "04" "01"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02" "04" "053" "053" "0521" "01"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01" "04" "0524" "02" "04" "04"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02" "01" "051" "01"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5764))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "0522" "02" "03" "02" "02" "0521"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02" "02" "04" "02212" "01" "02"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "02" "0522" "02" "03" "02" "02"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "03" "02" "02213" "053" "02" "03"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "03" "02" "02" "02" "03" "03"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02" "01" "02" "051" "02211" "01"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "051" "02" "03" "01" "0524" "03"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "02" "01" "03" "01" "02" "02"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "04" "051" "02" "03" "01"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "03" "02" "01" "03" "02211" "02"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "0521" "01" "02" "053" "0523" "01"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01" "02" "02" "053" "02" "02"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "03" "03" "02" "02" "01"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "03" "03" "02" "04" "02" "02"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "01" "02213" "03" "03" "02" "02"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "01" "04" "02" "02" "01" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "03" "03" "02" "02" "03" "04"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02" "04" "03" "01" "01" "051"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "02" "0521" "01" "03" "0522" "02"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "051" "04" "03" "02" "0522" "01"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02" "04" "0524" "02" "01" "02"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "02" "03" "02" "02" "02" "051"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02" "0522" "03" "02" "02" "0521"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02" "02" "01" "03" "04" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "01" "01" "01" "0522" "03" "02"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "02" "03" "02" "02" "051" "02"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "051" "01" "04" "02" "02" "02"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "053" "02" "03" "02" "04" "03"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "0522" "03" "03" "01" "051" "02"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "04" "051" "02" "02" "04" "01"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "03" "02" "03" "051" "04" "02"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "03" "04" "03" "053" "02" "03"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02" "01" "051" "02" "02" "02"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "01" "02" "04" "051" "03" "02"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "03" "01" "02" "02212" "03" "053"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "02" "02" "02" "03" "02" "02"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "03" "02211" "053" "02" "02" "03"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "01" "04" "04" "02" "01" "02"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "03" "051" "051" "04" "02" "03"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02" "02" "02" "02" "0522" "02"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "051" "01" "02" "02" "01" "02"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02" "051" "02" "04" "02" "02"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02" "02" "02" "02" "02" "03"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "04" "02" "03" "02" "03" "04"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "02" "04" "02" "02" "053"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "02" "01" "03" "02" "02" "02"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "04" "02" "04" "02" "03" "051"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "051" "02" "04" "0522" "053" "01"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "053" "02" "02" "02" "051" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02" "02" "0521" "053" "02" "02"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "04" "02" "0521" "04" "04" "01"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01" "0522" "02" "02" "02" "02"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "051" "01" "02" "02" "04" "02"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02" "02" "02" "02" "01" "01"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "053" "01" "02" "02" "02" "0524"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02" "02" "02211" "04" "02" "02"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "02" "053" "0522" "02" "02" "04"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "01" "02212" "01" "04" "04" "02"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02" "04" "02" "01" "04" "02"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "02" "02" "02" "01" "0522" "04"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "01" "053" "04" "02" "02" "01"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01" "02211" "02212" "02" "02" "01"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "0522" "01" "02" "02" "0522" "01"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02" "02" "053" "02" "02" "01"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "04" "02213" "051" "051" "02"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "01" "04" "01" "01" "02" "051"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02" "02" "02" "04" "02" "02"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02" "02" "01" "02" "04" "02"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "04" "02" "02" "02" "01" "0521"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "04" "051" "0524" "02" "01" "04"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02" "01" "01" "01" "0524" "02"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "04" "01" "01" "051" "02" "02"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "02" "0522" "02" "04" "04" "04"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "04" "051" "02" "051" "02"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02" "04" "02" "051" "01" "02"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02" "051" "02" "051" "01" "04"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "04" "051" "04" "02" "02" "053"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "04" "051" "04" "02" "02" "02"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02" "0522" "02213" "02" "02" "02"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "04" "02" "02" "02" "02" "01"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02" "051" "04" "01" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "0521" "02" "01" "01" "02" "02"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02" "051" "01" "02" "01" "01"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "051" "02" "051" "02211" "02" "0522"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "02" "01" "053" "02" "0522" "03"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "04" "02" "03" "02" "051" "04"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "053" "01" "0524" "051" "01"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "0522" "01" "0524" "01" "02" "02"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "053" "04" "01" "01" "051" "02"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "04" "04" "01" "02" "04" "01"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02" "04" "053" "053" "0521" "01"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01" "04" "0524" "02" "04" "04"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02" "01" "051" "01"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6152))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "052" "02" "03" "02" "02" "052"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02" "02" "04" "02212" "01" "02"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "02" "052" "02" "03" "02" "02"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "03" "02" "02213" "053" "02" "03"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "03" "02" "02" "02" "03" "03"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02" "01" "02" "051" "02211" "01"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "051" "02" "03" "01" "052" "03"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "02" "01" "03" "01" "02" "02"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "04" "051" "02" "03" "01"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "03" "02" "01" "03" "02211" "02"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "052" "01" "02" "053" "052" "01"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01" "02" "02" "053" "02" "02"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "03" "03" "02" "02" "01"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "03" "03" "02" "04" "02" "02"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "01" "02213" "03" "03" "02" "02"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "01" "04" "02" "02" "01" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "03" "03" "02" "02" "03" "04"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02" "04" "03" "01" "01" "051"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "02" "052" "01" "03" "052" "02"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "051" "04" "03" "02" "052" "01"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02" "04" "052" "02" "01" "02"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "02" "03" "02" "02" "02" "051"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02" "052" "03" "02" "02" "052"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02" "02" "01" "03" "04" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "01" "01" "01" "052" "03" "02"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "02" "03" "02" "02" "051" "02"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "051" "01" "04" "02" "02" "02"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "053" "02" "03" "02" "04" "03"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "052" "03" "03" "01" "051" "02"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "04" "051" "02" "02" "04" "01"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "03" "02" "03" "051" "04" "02"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "03" "04" "03" "053" "02" "03"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02" "01" "051" "02" "02" "02"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "01" "02" "04" "051" "03" "02"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "03" "01" "02" "02212" "03" "053"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "02" "02" "02" "03" "02" "02"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "03" "02211" "053" "02" "02" "03"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "01" "04" "04" "02" "01" "02"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "03" "051" "051" "04" "02" "03"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02" "02" "02" "02" "052" "02"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "051" "01" "02" "02" "01" "02"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02" "051" "02" "04" "02" "02"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02" "02" "02" "02" "02" "03"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "04" "02" "03" "02" "03" "04"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "02" "04" "02" "02" "053"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "02" "01" "03" "02" "02" "02"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "04" "02" "04" "02" "03" "051"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "051" "02" "04" "052" "053" "01"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "053" "02" "02" "02" "051" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02" "02" "052" "053" "02" "02"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "04" "02" "052" "04" "04" "01"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01" "052" "02" "02" "02" "02"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "051" "01" "02" "02" "04" "02"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02" "02" "02" "02" "01" "01"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "053" "01" "02" "02" "02" "052"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02" "02" "02211" "04" "02" "02"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "02" "053" "052" "02" "02" "04"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "01" "02212" "01" "04" "04" "02"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02" "04" "02" "01" "04" "02"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "02" "02" "02" "01" "052" "04"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "01" "053" "04" "02" "02" "01"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01" "02211" "02212" "02" "02" "01"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "052" "01" "02" "02" "052" "01"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02" "02" "053" "02" "02" "01"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "04" "02213" "051" "051" "02"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "01" "04" "01" "01" "02" "051"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02" "02" "02" "04" "02" "02"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02" "02" "01" "02" "04" "02"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "04" "02" "02" "02" "01" "052"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "04" "051" "052" "02" "01" "04"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02" "01" "01" "01" "052" "02"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "04" "01" "01" "051" "02" "02"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "02" "052" "02" "04" "04" "04"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "04" "051" "02" "051" "02"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02" "04" "02" "051" "01" "02"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02" "051" "02" "051" "01" "04"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "04" "051" "04" "02" "02" "053"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "04" "051" "04" "02" "02" "02"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02" "052" "02213" "02" "02" "02"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "04" "02" "02" "02" "02" "01"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02" "051" "04" "01" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "052" "02" "01" "01" "02" "02"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02" "051" "01" "02" "01" "01"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "051" "02" "051" "02211" "02" "052"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "02" "01" "053" "02" "052" "03"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "04" "02" "03" "02" "051" "04"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "053" "01" "052" "051" "01"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "052" "01" "052" "01" "02" "02"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "053" "04" "01" "01" "051" "02"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "04" "04" "01" "02" "04" "01"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02" "04" "053" "053" "052" "01"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01" "04" "052" "02" "04" "04"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02" "01" "051" "01"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7175))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "05" "02" "03" "02" "02" "05"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02" "02" "04" "02212" "01" "02"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "02" "05" "02" "03" "02" "02"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "03" "02" "02213" "05" "02" "03"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "03" "02" "02" "02" "03" "03"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02" "01" "02" "05" "02211" "01"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "05" "02" "03" "01" "05" "03"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "02" "01" "03" "01" "02" "02"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "04" "05" "02" "03" "01"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "03" "02" "01" "03" "02211" "02"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "05" "01" "02" "05" "05" "01"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01" "02" "02" "05" "02" "02"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "03" "03" "02" "02" "01"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "03" "03" "02" "04" "02" "02"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "01" "02213" "03" "03" "02" "02"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "01" "04" "02" "02" "01" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "03" "03" "02" "02" "03" "04"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02" "04" "03" "01" "01" "05"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "02" "05" "01" "03" "05" "02"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "05" "04" "03" "02" "05" "01"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02" "04" "05" "02" "01" "02"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "02" "03" "02" "02" "02" "05"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02" "05" "03" "02" "02" "05"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02" "02" "01" "03" "04" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "01" "01" "01" "05" "03" "02"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "02" "03" "02" "02" "05" "02"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "05" "01" "04" "02" "02" "02"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "05" "02" "03" "02" "04" "03"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "05" "03" "03" "01" "05" "02"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "04" "05" "02" "02" "04" "01"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "03" "02" "03" "05" "04" "02"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "03" "04" "03" "05" "02" "03"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02" "01" "05" "02" "02" "02"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "01" "02" "04" "05" "03" "02"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "03" "01" "02" "02212" "03" "05"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "02" "02" "02" "03" "02" "02"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "03" "02211" "05" "02" "02" "03"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "01" "04" "04" "02" "01" "02"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "03" "05" "05" "04" "02" "03"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02" "02" "02" "02" "05" "02"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "05" "01" "02" "02" "01" "02"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02" "05" "02" "04" "02" "02"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02" "02" "02" "02" "02" "03"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "04" "02" "03" "02" "03" "04"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "02" "04" "02" "02" "05"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "02" "01" "03" "02" "02" "02"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "04" "02" "04" "02" "03" "05"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "05" "02" "04" "05" "05" "01"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "05" "02" "02" "02" "05" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02" "02" "05" "05" "02" "02"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "04" "02" "05" "04" "04" "01"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01" "05" "02" "02" "02" "02"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "05" "01" "02" "02" "04" "02"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02" "02" "02" "02" "01" "01"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "05" "01" "02" "02" "02" "05"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02" "02" "02211" "04" "02" "02"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "02" "05" "05" "02" "02" "04"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "01" "02212" "01" "04" "04" "02"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02" "04" "02" "01" "04" "02"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "02" "02" "02" "01" "05" "04"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "01" "05" "04" "02" "02" "01"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01" "02211" "02212" "02" "02" "01"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "05" "01" "02" "02" "05" "01"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02" "02" "05" "02" "02" "01"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "04" "02213" "05" "05" "02"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "01" "04" "01" "01" "02" "05"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02" "02" "02" "04" "02" "02"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02" "02" "01" "02" "04" "02"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "04" "02" "02" "02" "01" "05"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "04" "05" "05" "02" "01" "04"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02" "01" "01" "01" "05" "02"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "04" "01" "01" "05" "02" "02"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "02" "05" "02" "04" "04" "04"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "04" "05" "02" "05" "02"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02" "04" "02" "05" "01" "02"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02" "05" "02" "05" "01" "04"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "04" "05" "04" "02" "02" "05"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "04" "05" "04" "02" "02" "02"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02" "05" "02213" "02" "02" "02"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "04" "02" "02" "02" "02" "01"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02" "05" "04" "01" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "05" "02" "01" "01" "02" "02"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02" "05" "01" "02" "01" "01"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "05" "02" "05" "02211" "02" "05"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "02" "01" "05" "02" "05" "03"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "04" "02" "03" "02" "05" "04"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "05" "01" "05" "05" "01"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "05" "01" "05" "01" "02" "02"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "05" "04" "01" "01" "05" "02"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "04" "04" "01" "02" "04" "01"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02" "04" "05" "05" "05" "01"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01" "04" "05" "02" "04" "04"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02" "01" "05" "01"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7761))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "05" "02" "03" "02" "02" "05"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02" "02" "04" "02212" "01" "02"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "02" "05" "02" "03" "02" "02"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "03" "02" "02213" "05" "02" "03"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "03" "02" "02" "02" "03" "03"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02" "01" "02" "05" "02211" "01"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "05" "02" "03" "01" "05" "03"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "02" "01" "03" "01" "02" "02"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "04" "05" "02" "03" "01"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "03" "02" "01" "03" "02211" "02"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "05" "01" "02" "05" "05" "01"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01" "02" "02" "05" "02" "02"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "03" "03" "02" "02" "01"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "03" "03" "02" "04" "02" "02"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "01" "02213" "03" "03" "02" "02"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "01" "04" "02" "02" "01" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "03" "03" "02" "02" "03" "04"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02" "04" "03" "01" "01" "05"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "02" "05" "01" "03" "05" "02"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "05" "04" "03" "02" "05" "01"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02" "04" "05" "02" "01" "02"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "02" "03" "02" "02" "02" "05"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02" "05" "03" "02" "02" "05"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02" "02" "01" "03" "04" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "01" "01" "01" "05" "03" "02"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "02" "03" "02" "02" "05" "02"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "05" "01" "04" "02" "02" "02"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "05" "02" "03" "02" "04" "03"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "05" "03" "03" "01" "05" "02"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "04" "05" "02" "02" "04" "01"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "03" "02" "03" "05" "04" "02"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "03" "04" "03" "05" "02" "03"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02" "01" "05" "02" "02" "02"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "01" "02" "04" "05" "03" "02"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "03" "01" "02" "02212" "03" "05"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "02" "02" "02" "03" "02" "02"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "03" "02211" "05" "02" "02" "03"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "01" "04" "04" "02" "01" "02"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "03" "05" "05" "04" "02" "03"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02" "02" "02" "02" "05" "02"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "05" "01" "02" "02" "01" "02"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02" "05" "02" "04" "02" "02"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02" "02" "02" "02" "02" "03"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "04" "02" "03" "02" "03" "04"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "02" "04" "02" "02" "05"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "02" "01" "03" "02" "02" "02"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "04" "02" "04" "02" "03" "05"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "05" "02" "04" "05" "05" "01"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "05" "02" "02" "02" "05" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02" "02" "05" "05" "02" "02"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "04" "02" "05" "04" "04" "01"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01" "05" "02" "02" "02" "02"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "05" "01" "02" "02" "04" "02"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02" "02" "02" "02" "01" "01"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "05" "01" "02" "02" "02" "05"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02" "02" "02211" "04" "02" "02"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "02" "05" "05" "02" "02" "04"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "01" "02212" "01" "04" "04" "02"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02" "04" "02" "01" "04" "02"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "02" "02" "02" "01" "05" "04"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "01" "05" "04" "02" "02" "01"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01" "02211" "02212" "02" "02" "01"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "05" "01" "02" "02" "05" "01"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02" "02" "05" "02" "02" "01"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "04" "02213" "05" "05" "02"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "01" "04" "01" "01" "02" "05"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02" "02" "02" "04" "02" "02"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02" "02" "01" "02" "04" "02"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "04" "02" "02" "02" "01" "05"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "04" "05" "05" "02" "01" "04"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02" "01" "01" "01" "05" "02"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "04" "01" "01" "05" "02" "02"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "02" "05" "02" "04" "04" "04"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "04" "05" "02" "05" "02"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02" "04" "02" "05" "01" "02"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02" "05" "02" "05" "01" "04"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "04" "05" "04" "02" "02" "05"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "04" "05" "04" "02" "02" "02"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02" "05" "02213" "02" "02" "02"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "04" "02" "02" "02" "02" "01"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02" "05" "04" "01" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "05" "02" "01" "01" "02" "02"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02" "05" "01" "02" "01" "01"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "05" "02" "05" "02211" "02" "05"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "02" "01" "05" "02" "05" "03"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "04" "02" "03" "02" "05" "04"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "05" "01" "05" "05" "01"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "05" "01" "05" "01" "02" "02"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "05" "04" "01" "01" "05" "02"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "04" "04" "01" "02" "04" "01"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02" "04" "05" "05" "05" "01"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01" "04" "05" "02" "04" "04"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02" "01" "05" "01"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8181))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "05" "02" "03" "02" "02" "05"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02" "02" "04" "02212" "01" "02"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "02" "05" "02" "03" "02" "02"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "03" "02" "02213" "05" "02" "03"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "03" "02" "02" "02" "03" "03"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02" "01" "02" "05" "02211" "01"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "05" "02" "03" "01" "05" "03"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "02" "01" "03" "01" "02" "02"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "04" "05" "02" "03" "01"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "03" "02" "01" "03" "02211" "02"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "05" "01" "02" "05" "05" "01"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01" "02" "02" "05" "02" "02"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "03" "03" "02" "02" "01"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "03" "03" "02" "04" "02" "02"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "01" "02213" "03" "03" "02" "02"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "01" "04" "02" "02" "01" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "03" "03" "02" "02" "03" "04"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02" "04" "03" "01" "01" "05"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "02" "05" "01" "03" "05" "02"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "05" "04" "03" "02" "05" "01"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02" "04" "05" "02" "01" "02"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "02" "03" "02" "02" "02" "05"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02" "05" "03" "02" "02" "05"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02" "02" "01" "03" "04" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "01" "01" "01" "05" "03" "02"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "02" "03" "02" "02" "05" "02"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "05" "01" "04" "02" "02" "02"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "05" "02" "03" "02" "04" "03"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "05" "03" "03" "01" "05" "02"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "04" "05" "02" "02" "04" "01"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "03" "02" "03" "05" "04" "02"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "03" "04" "03" "05" "02" "03"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02" "01" "05" "02" "02" "02"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "01" "02" "04" "05" "03" "02"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "03" "01" "02" "02212" "03" "05"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "02" "02" "02" "03" "02" "02"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "03" "02211" "05" "02" "02" "03"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "01" "04" "04" "02" "01" "02"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "03" "05" "05" "04" "02" "03"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02" "02" "02" "02" "05" "02"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "05" "01" "02" "02" "01" "02"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02" "05" "02" "04" "02" "02"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02" "02" "02" "02" "02" "03"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "04" "02" "03" "02" "03" "04"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "02" "04" "02" "02" "05"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "02" "01" "03" "02" "02" "02"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "04" "02" "04" "02" "03" "05"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "05" "02" "04" "05" "05" "01"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "05" "02" "02" "02" "05" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02" "02" "05" "05" "02" "02"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "04" "02" "05" "04" "04" "01"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01" "05" "02" "02" "02" "02"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "05" "01" "02" "02" "04" "02"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02" "02" "02" "02" "01" "01"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "05" "01" "02" "02" "02" "05"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02" "02" "02211" "04" "02" "02"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "02" "05" "05" "02" "02" "04"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "01" "02212" "01" "04" "04" "02"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02" "04" "02" "01" "04" "02"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "02" "02" "02" "01" "05" "04"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "01" "05" "04" "02" "02" "01"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01" "02211" "02212" "02" "02" "01"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "05" "01" "02" "02" "05" "01"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02" "02" "05" "02" "02" "01"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "04" "02213" "05" "05" "02"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "01" "04" "01" "01" "02" "05"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02" "02" "02" "04" "02" "02"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02" "02" "01" "02" "04" "02"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "04" "02" "02" "02" "01" "05"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "04" "05" "05" "02" "01" "04"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02" "01" "01" "01" "05" "02"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "04" "01" "01" "05" "02" "02"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "02" "05" "02" "04" "04" "04"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "04" "05" "02" "05" "02"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02" "04" "02" "05" "01" "02"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02" "05" "02" "05" "01" "04"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "04" "05" "04" "02" "02" "05"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "04" "05" "04" "02" "02" "02"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02" "05" "02213" "02" "02" "02"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "04" "02" "02" "02" "02" "01"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02" "05" "04" "01" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "05" "02" "01" "01" "02" "02"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02" "05" "01" "02" "01" "01"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "05" "02" "05" "02211" "02" "05"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "02" "01" "05" "02" "05" "03"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "04" "02" "03" "02" "05" "04"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "05" "01" "05" "05" "01"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "05" "01" "05" "01" "02" "02"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "05" "04" "01" "01" "05" "02"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "04" "04" "01" "02" "04" "01"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02" "04" "05" "05" "05" "01"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01" "04" "05" "02" "04" "04"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02" "01" "05" "01"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8755))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "05" "02" "03" "02" "02" "05"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02" "02" "04" "02212" "01" "02"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "02" "05" "02" "03" "02" "02"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "03" "02" "02213" "05" "02" "03"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "03" "02" "02" "02" "03" "03"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02" "01" "02" "05" "02211" "01"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "05" "02" "03" "01" "05" "03"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "02" "01" "03" "01" "02" "02"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "04" "05" "02" "03" "01"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "03" "02" "01" "03" "02211" "02"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "05" "01" "02" "05" "05" "01"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01" "02" "02" "05" "02" "02"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "03" "03" "02" "02" "01"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "03" "03" "02" "04" "02" "02"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "01" "02213" "03" "03" "02" "02"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "01" "04" "02" "02" "01" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "03" "03" "02" "02" "03" "04"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02" "04" "03" "01" "01" "05"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "02" "05" "01" "03" "05" "02"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "05" "04" "03" "02" "05" "01"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02" "04" "05" "02" "01" "02"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "02" "03" "02" "02" "02" "05"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02" "05" "03" "02" "02" "05"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02" "02" "01" "03" "04" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "01" "01" "01" "05" "03" "02"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "02" "03" "02" "02" "05" "02"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "05" "01" "04" "02" "02" "02"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "05" "02" "03" "02" "04" "03"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "05" "03" "03" "01" "05" "02"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "04" "05" "02" "02" "04" "01"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "03" "02" "03" "05" "04" "02"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "03" "04" "03" "05" "02" "03"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02" "01" "05" "02" "02" "02"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "01" "02" "04" "05" "03" "02"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "03" "01" "02" "02212" "03" "05"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "02" "02" "02" "03" "02" "02"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "03" "02211" "05" "02" "02" "03"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "01" "04" "04" "02" "01" "02"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "03" "05" "05" "04" "02" "03"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02" "02" "02" "02" "05" "02"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "05" "01" "02" "02" "01" "02"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02" "05" "02" "04" "02" "02"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02" "02" "02" "02" "02" "03"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "04" "02" "03" "02" "03" "04"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "02" "04" "02" "02" "05"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "02" "01" "03" "02" "02" "02"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "04" "02" "04" "02" "03" "05"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "05" "02" "04" "05" "05" "01"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "05" "02" "02" "02" "05" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02" "02" "05" "05" "02" "02"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "04" "02" "05" "04" "04" "01"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01" "05" "02" "02" "02" "02"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "05" "01" "02" "02" "04" "02"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02" "02" "02" "02" "01" "01"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "05" "01" "02" "02" "02" "05"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02" "02" "02211" "04" "02" "02"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "02" "05" "05" "02" "02" "04"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "01" "02212" "01" "04" "04" "02"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02" "04" "02" "01" "04" "02"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "02" "02" "02" "01" "05" "04"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "01" "05" "04" "02" "02" "01"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01" "02211" "02212" "02" "02" "01"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "05" "01" "02" "02" "05" "01"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02" "02" "05" "02" "02" "01"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "04" "02213" "05" "05" "02"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "01" "04" "01" "01" "02" "05"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02" "02" "02" "04" "02" "02"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02" "02" "01" "02" "04" "02"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "04" "02" "02" "02" "01" "05"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "04" "05" "05" "02" "01" "04"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02" "01" "01" "01" "05" "02"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "04" "01" "01" "05" "02" "02"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "02" "05" "02" "04" "04" "04"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "04" "05" "02" "05" "02"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02" "04" "02" "05" "01" "02"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02" "05" "02" "05" "01" "04"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "04" "05" "04" "02" "02" "05"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "04" "05" "04" "02" "02" "02"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02" "05" "02213" "02" "02" "02"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "04" "02" "02" "02" "02" "01"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02" "05" "04" "01" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "05" "02" "01" "01" "02" "02"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02" "05" "01" "02" "01" "01"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "05" "02" "05" "02211" "02" "05"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "02" "01" "05" "02" "05" "03"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "04" "02" "03" "02" "05" "04"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "05" "01" "05" "05" "01"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "05" "01" "05" "01" "02" "02"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "05" "04" "01" "01" "05" "02"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "04" "04" "01" "02" "04" "01"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02" "04" "05" "05" "05" "01"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01" "04" "05" "02" "04" "04"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02" "01" "05" "01"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 9384))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "05" "02" "03" "02" "02" "05"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02" "02" "04" "02212" "01" "02"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "02" "05" "02" "03" "02" "02"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "03" "02" "02213" "05" "02" "03"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "03" "02" "02" "02" "03" "03"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02" "01" "02" "05" "02211" "01"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "05" "02" "03" "01" "05" "03"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "02" "01" "03" "01" "02" "02"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "04" "05" "02" "03" "01"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "03" "02" "01" "03" "02211" "02"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "05" "01" "02" "05" "05" "01"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01" "02" "02" "05" "02" "02"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "03" "03" "02" "02" "01"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "03" "03" "02" "04" "02" "02"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "01" "02213" "03" "03" "02" "02"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "01" "04" "02" "02" "01" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "03" "03" "02" "02" "03" "04"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02" "04" "03" "01" "01" "05"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "02" "05" "01" "03" "05" "02"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "05" "04" "03" "02" "05" "01"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02" "04" "05" "02" "01" "02"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "02" "03" "02" "02" "02" "05"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02" "05" "03" "02" "02" "05"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02" "02" "01" "03" "04" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "01" "01" "01" "05" "03" "02"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "02" "03" "02" "02" "05" "02"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "05" "01" "04" "02" "02" "02"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "05" "02" "03" "02" "04" "03"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "05" "03" "03" "01" "05" "02"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "04" "05" "02" "02" "04" "01"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "03" "02" "03" "05" "04" "02"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "03" "04" "03" "05" "02" "03"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02" "01" "05" "02" "02" "02"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "01" "02" "04" "05" "03" "02"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "03" "01" "02" "02212" "03" "05"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "02" "02" "02" "03" "02" "02"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "03" "02211" "05" "02" "02" "03"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "01" "04" "04" "02" "01" "02"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "03" "05" "05" "04" "02" "03"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02" "02" "02" "02" "05" "02"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "05" "01" "02" "02" "01" "02"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02" "05" "02" "04" "02" "02"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02" "02" "02" "02" "02" "03"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "04" "02" "03" "02" "03" "04"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "02" "04" "02" "02" "05"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "02" "01" "03" "02" "02" "02"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "04" "02" "04" "02" "03" "05"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "05" "02" "04" "05" "05" "01"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "05" "02" "02" "02" "05" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02" "02" "05" "05" "02" "02"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "04" "02" "05" "04" "04" "01"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01" "05" "02" "02" "02" "02"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "05" "01" "02" "02" "04" "02"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02" "02" "02" "02" "01" "01"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "05" "01" "02" "02" "02" "05"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02" "02" "02211" "04" "02" "02"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "02" "05" "05" "02" "02" "04"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "01" "02212" "01" "04" "04" "02"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02" "04" "02" "01" "04" "02"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "02" "02" "02" "01" "05" "04"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "01" "05" "04" "02" "02" "01"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01" "02211" "02212" "02" "02" "01"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "05" "01" "02" "02" "05" "01"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02" "02" "05" "02" "02" "01"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "04" "02213" "05" "05" "02"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "01" "04" "01" "01" "02" "05"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02" "02" "02" "04" "02" "02"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02" "02" "01" "02" "04" "02"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "04" "02" "02" "02" "01" "05"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "04" "05" "05" "02" "01" "04"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02" "01" "01" "01" "05" "02"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "04" "01" "01" "05" "02" "02"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "02" "05" "02" "04" "04" "04"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "04" "05" "02" "05" "02"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02" "04" "02" "05" "01" "02"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02" "05" "02" "05" "01" "04"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "04" "05" "04" "02" "02" "05"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "04" "05" "04" "02" "02" "02"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02" "05" "02213" "02" "02" "02"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "04" "02" "02" "02" "02" "01"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02" "05" "04" "01" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "05" "02" "01" "01" "02" "02"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02" "05" "01" "02" "01" "01"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "05" "02" "05" "02211" "02" "05"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "02" "01" "05" "02" "05" "03"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "04" "02" "03" "02" "05" "04"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "05" "01" "05" "05" "01"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "05" "01" "05" "01" "02" "02"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "05" "04" "01" "01" "05" "02"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "04" "04" "01" "02" "04" "01"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02" "04" "05" "05" "05" "01"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01" "04" "05" "02" "04" "04"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02" "01" "05" "01"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 10841))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "05" "02" "03" "02" "02" "05"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02" "02" "04" "02212" "01" "02"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "02" "05" "02" "03" "02" "02"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "03" "02" "02213" "05" "02" "03"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "03" "02" "02" "02" "03" "03"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02" "01" "02" "05" "02211" "01"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "05" "02" "03" "01" "05" "03"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "02" "01" "03" "01" "02" "02"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02213" "04" "05" "02" "03" "01"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "03" "02" "01" "03" "02211" "02"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "05" "01" "02" "05" "05" "01"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01" "02" "02" "05" "02" "02"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02211" "03" "03" "02" "02" "01"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "03" "03" "02" "04" "02" "02"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "01" "02213" "03" "03" "02" "02"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "01" "04" "02" "02" "01" "02211"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "03" "03" "02" "02" "03" "04"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02" "04" "03" "01" "01" "05"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "02" "05" "01" "03" "05" "02"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "05" "04" "03" "02" "05" "01"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02" "04" "05" "02" "01" "02"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "02" "03" "02" "02" "02" "05"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02" "05" "03" "02" "02" "05"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02" "02" "01" "03" "04" "02213"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "01" "01" "01" "05" "03" "02"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "02" "03" "02" "02" "05" "02"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "05" "01" "04" "02" "02" "02"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "05" "02" "03" "02" "04" "03"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "05" "03" "03" "01" "05" "02"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "04" "05" "02" "02" "04" "01"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "03" "02" "03" "05" "04" "02"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "03" "04" "03" "05" "02" "03"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02" "01" "05" "02" "02" "02"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "01" "02" "04" "05" "03" "02"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "03" "01" "02" "02212" "03" "05"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "02" "02" "02" "03" "02" "02"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "03" "02211" "05" "02" "02" "03"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "01" "04" "04" "02" "01" "02"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "03" "05" "05" "04" "02" "03"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02" "02" "02" "02" "05" "02"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "05" "01" "02" "02" "01" "02"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02" "05" "02" "04" "02" "02"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02" "02" "02" "02" "02" "03"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "04" "02" "03" "02" "03" "04"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02212" "02" "04" "02" "02" "05"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "02" "01" "03" "02" "02" "02"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "04" "02" "04" "02" "03" "05"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "05" "02" "04" "05" "05" "01"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "05" "02" "02" "02" "05" "02213"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02" "02" "05" "05" "02" "02"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "04" "02" "05" "04" "04" "01"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01" "05" "02" "02" "02" "02"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "05" "01" "02" "02" "04" "02"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02" "02" "02" "02" "01" "01"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "05" "01" "02" "02" "02" "05"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02" "02" "02211" "04" "02" "02"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "02" "05" "05" "02" "02" "04"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "01" "02212" "01" "04" "04" "02"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02" "04" "02" "01" "04" "02"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "02" "02" "02" "01" "05" "04"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "01" "05" "04" "02" "02" "01"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01" "02211" "02212" "02" "02" "01"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "05" "01" "02" "02" "05" "01"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02" "02" "05" "02" "02" "01"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02211" "04" "02213" "05" "05" "02"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "01" "04" "01" "01" "02" "05"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02" "02" "02" "04" "02" "02"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02" "02" "01" "02" "04" "02"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "04" "02" "02" "02" "01" "05"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "04" "05" "05" "02" "01" "04"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02" "01" "01" "01" "05" "02"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "04" "01" "01" "05" "02" "02"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "02" "05" "02" "04" "04" "04"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02212" "04" "05" "02" "05" "02"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02" "04" "02" "05" "01" "02"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02" "05" "02" "05" "01" "04"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "04" "05" "04" "02" "02" "05"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "04" "05" "04" "02" "02" "02"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02" "05" "02213" "02" "02" "02"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "04" "02" "02" "02" "02" "01"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02211" "02" "05" "04" "01" "02212"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "05" "02" "01" "01" "02" "02"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02" "05" "01" "02" "01" "01"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "05" "02" "05" "02211" "02" "05"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "02" "01" "05" "02" "05" "03"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "04" "02" "03" "02" "05" "04"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02212" "05" "01" "05" "05" "01"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "05" "01" "05" "01" "02" "02"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "05" "04" "01" "01" "05" "02"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "04" "04" "01" "02" "04" "01"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02" "04" "05" "05" "05" "01"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01" "04" "05" "02" "04" "04"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02" "01" "05" "01"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 20003))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "05" "02" "03" "02" "02" "05"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02" "02" "04" "02" "01" "02"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "02" "05" "02" "03" "02" "02"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "03" "02" "02" "05" "02" "03"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "03" "02" "02" "02" "03" "03"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02" "01" "02" "05" "02" "01"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "05" "02" "03" "01" "05" "03"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "02" "01" "03" "01" "02" "02"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02" "04" "05" "02" "03" "01"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "03" "02" "01" "03" "02" "02"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "05" "01" "02" "05" "05" "01"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01" "02" "02" "05" "02" "02"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02" "03" "03" "02" "02" "01"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "03" "03" "02" "04" "02" "02"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "01" "02" "03" "03" "02" "02"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "01" "04" "02" "02" "01" "02"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "03" "03" "02" "02" "03" "04"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02" "04" "03" "01" "01" "05"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "02" "05" "01" "03" "05" "02"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "05" "04" "03" "02" "05" "01"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02" "04" "05" "02" "01" "02"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "02" "03" "02" "02" "02" "05"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02" "05" "03" "02" "02" "05"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02" "02" "01" "03" "04" "02"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "01" "01" "01" "05" "03" "02"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "02" "03" "02" "02" "05" "02"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "05" "01" "04" "02" "02" "02"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "05" "02" "03" "02" "04" "03"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "05" "03" "03" "01" "05" "02"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "04" "05" "02" "02" "04" "01"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "03" "02" "03" "05" "04" "02"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "03" "04" "03" "05" "02" "03"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02" "01" "05" "02" "02" "02"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "01" "02" "04" "05" "03" "02"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "03" "01" "02" "02" "03" "05"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "02" "02" "02" "03" "02" "02"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "03" "02" "05" "02" "02" "03"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "01" "04" "04" "02" "01" "02"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "03" "05" "05" "04" "02" "03"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02" "02" "02" "02" "05" "02"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "05" "01" "02" "02" "01" "02"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02" "05" "02" "04" "02" "02"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02" "02" "02" "02" "02" "03"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "04" "02" "03" "02" "03" "04"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02" "02" "04" "02" "02" "05"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "02" "01" "03" "02" "02" "02"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "04" "02" "04" "02" "03" "05"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "05" "02" "04" "05" "05" "01"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "05" "02" "02" "02" "05" "02"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02" "02" "05" "05" "02" "02"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "04" "02" "05" "04" "04" "01"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01" "05" "02" "02" "02" "02"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "05" "01" "02" "02" "04" "02"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02" "02" "02" "02" "01" "01"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "05" "01" "02" "02" "02" "05"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02" "02" "02" "04" "02" "02"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "02" "05" "05" "02" "02" "04"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "01" "02" "01" "04" "04" "02"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02" "04" "02" "01" "04" "02"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "02" "02" "02" "01" "05" "04"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "01" "05" "04" "02" "02" "01"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "05" "01" "02" "02" "05" "01"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02" "02" "05" "02" "02" "01"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02" "04" "02" "05" "05" "02"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "01" "04" "01" "01" "02" "05"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02" "02" "02" "04" "02" "02"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02" "02" "01" "02" "04" "02"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "04" "02" "02" "02" "01" "05"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "04" "05" "05" "02" "01" "04"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02" "01" "01" "01" "05" "02"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "04" "01" "01" "05" "02" "02"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "02" "05" "02" "04" "04" "04"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02" "04" "05" "02" "05" "02"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02" "04" "02" "05" "01" "02"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02" "05" "02" "05" "01" "04"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "04" "05" "04" "02" "02" "05"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "04" "05" "04" "02" "02" "02"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02" "05" "02" "02" "02" "02"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "04" "02" "02" "02" "02" "01"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02" "02" "05" "04" "01" "02"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "05" "02" "01" "01" "02" "02"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02" "05" "01" "02" "01" "01"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "05" "02" "05" "02" "02" "05"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "02" "01" "05" "02" "05" "03"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "04" "02" "03" "02" "05" "04"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02" "05" "01" "05" "05" "01"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "05" "01" "05" "01" "02" "02"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "05" "04" "01" "01" "05" "02"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "04" "04" "01" "02" "04" "01"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02" "04" "05" "05" "05" "01"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01" "04" "05" "02" "04" "04"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02" "01" "05" "01"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 24546))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "05" "02" "03" "02" "02" "05"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02" "02" "04" "02" "01" "02"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "02" "05" "02" "03" "02" "02"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "03" "02" "02" "05" "02" "03"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "03" "02" "02" "02" "03" "03"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02" "01" "02" "05" "02" "01"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "05" "02" "03" "01" "05" "03"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "02" "01" "03" "01" "02" "02"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02" "04" "05" "02" "03" "01"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "03" "02" "01" "03" "02" "02"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "05" "01" "02" "05" "05" "01"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01" "02" "02" "05" "02" "02"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02" "03" "03" "02" "02" "01"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "03" "03" "02" "04" "02" "02"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "01" "02" "03" "03" "02" "02"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "01" "04" "02" "02" "01" "02"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "03" "03" "02" "02" "03" "04"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02" "04" "03" "01" "01" "05"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "02" "05" "01" "03" "05" "02"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "05" "04" "03" "02" "05" "01"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02" "04" "05" "02" "01" "02"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "02" "03" "02" "02" "02" "05"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02" "05" "03" "02" "02" "05"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02" "02" "01" "03" "04" "02"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "01" "01" "01" "05" "03" "02"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "02" "03" "02" "02" "05" "02"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "05" "01" "04" "02" "02" "02"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "05" "02" "03" "02" "04" "03"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "05" "03" "03" "01" "05" "02"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "04" "05" "02" "02" "04" "01"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "03" "02" "03" "05" "04" "02"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "03" "04" "03" "05" "02" "03"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02" "01" "05" "02" "02" "02"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "01" "02" "04" "05" "03" "02"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "03" "01" "02" "02" "03" "05"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "02" "02" "02" "03" "02" "02"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "03" "02" "05" "02" "02" "03"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "01" "04" "04" "02" "01" "02"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "03" "05" "05" "04" "02" "03"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02" "02" "02" "02" "05" "02"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "05" "01" "02" "02" "01" "02"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02" "05" "02" "04" "02" "02"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02" "02" "02" "02" "02" "03"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "04" "02" "03" "02" "03" "04"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02" "02" "04" "02" "02" "05"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "02" "01" "03" "02" "02" "02"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "04" "02" "04" "02" "03" "05"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "05" "02" "04" "05" "05" "01"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "05" "02" "02" "02" "05" "02"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02" "02" "05" "05" "02" "02"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "04" "02" "05" "04" "04" "01"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01" "05" "02" "02" "02" "02"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "05" "01" "02" "02" "04" "02"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02" "02" "02" "02" "01" "01"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "05" "01" "02" "02" "02" "05"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02" "02" "02" "04" "02" "02"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "02" "05" "05" "02" "02" "04"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "01" "02" "01" "04" "04" "02"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02" "04" "02" "01" "04" "02"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "02" "02" "02" "01" "05" "04"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "01" "05" "04" "02" "02" "01"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "05" "01" "02" "02" "05" "01"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02" "02" "05" "02" "02" "01"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02" "04" "02" "05" "05" "02"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "01" "04" "01" "01" "02" "05"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02" "02" "02" "04" "02" "02"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02" "02" "01" "02" "04" "02"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "04" "02" "02" "02" "01" "05"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "04" "05" "05" "02" "01" "04"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02" "01" "01" "01" "05" "02"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "04" "01" "01" "05" "02" "02"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "02" "05" "02" "04" "04" "04"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02" "04" "05" "02" "05" "02"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02" "04" "02" "05" "01" "02"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02" "05" "02" "05" "01" "04"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "04" "05" "04" "02" "02" "05"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "04" "05" "04" "02" "02" "02"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02" "05" "02" "02" "02" "02"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "04" "02" "02" "02" "02" "01"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02" "02" "05" "04" "01" "02"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "05" "02" "01" "01" "02" "02"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02" "05" "01" "02" "01" "01"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "05" "02" "05" "02" "02" "05"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "02" "01" "05" "02" "05" "03"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "04" "02" "03" "02" "05" "04"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02" "05" "01" "05" "05" "01"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "05" "01" "05" "01" "02" "02"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "05" "04" "01" "01" "05" "02"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "04" "04" "01" "02" "04" "01"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02" "04" "05" "05" "05" "01"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01" "04" "05" "02" "04" "04"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02" "01" "05" "01"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 30719))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "05" "02" "03" "02" "02" "05"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02" "02" "04" "02" "01" "02"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "02" "05" "02" "03" "02" "02"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "03" "02" "02" "05" "02" "03"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "03" "02" "02" "02" "03" "03"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02" "01" "02" "05" "02" "01"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "05" "02" "03" "01" "05" "03"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "02" "01" "03" "01" "02" "02"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02" "04" "05" "02" "03" "01"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "03" "02" "01" "03" "02" "02"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "05" "01" "02" "05" "05" "01"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01" "02" "02" "05" "02" "02"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02" "03" "03" "02" "02" "01"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "03" "03" "02" "04" "02" "02"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "01" "02" "03" "03" "02" "02"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "01" "04" "02" "02" "01" "02"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "03" "03" "02" "02" "03" "04"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02" "04" "03" "01" "01" "05"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "02" "05" "01" "03" "05" "02"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "05" "04" "03" "02" "05" "01"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02" "04" "05" "02" "01" "02"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "02" "03" "02" "02" "02" "05"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02" "05" "03" "02" "02" "05"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02" "02" "01" "03" "04" "02"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "01" "01" "01" "05" "03" "02"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "02" "03" "02" "02" "05" "02"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "05" "01" "04" "02" "02" "02"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "05" "02" "03" "02" "04" "03"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "05" "03" "03" "01" "05" "02"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "04" "05" "02" "02" "04" "01"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "03" "02" "03" "05" "04" "02"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "03" "04" "03" "05" "02" "03"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02" "01" "05" "02" "02" "02"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "01" "02" "04" "05" "03" "02"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "03" "01" "02" "02" "03" "05"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "02" "02" "02" "03" "02" "02"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "03" "02" "05" "02" "02" "03"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "01" "04" "04" "02" "01" "02"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "03" "05" "05" "04" "02" "03"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02" "02" "02" "02" "05" "02"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "05" "01" "02" "02" "01" "02"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02" "05" "02" "04" "02" "02"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02" "02" "02" "02" "02" "03"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "04" "02" "03" "02" "03" "04"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02" "02" "04" "02" "02" "05"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "02" "01" "03" "02" "02" "02"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "04" "02" "04" "02" "03" "05"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "05" "02" "04" "05" "05" "01"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "05" "02" "02" "02" "05" "02"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02" "02" "05" "05" "02" "02"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "04" "02" "05" "04" "04" "01"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01" "05" "02" "02" "02" "02"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "05" "01" "02" "02" "04" "02"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02" "02" "02" "02" "01" "01"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "05" "01" "02" "02" "02" "05"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02" "02" "02" "04" "02" "02"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "02" "05" "05" "02" "02" "04"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "01" "02" "01" "04" "04" "02"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02" "04" "02" "01" "04" "02"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "02" "02" "02" "01" "05" "04"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "01" "05" "04" "02" "02" "01"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "05" "01" "02" "02" "05" "01"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02" "02" "05" "02" "02" "01"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02" "04" "02" "05" "05" "02"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "01" "04" "01" "01" "02" "05"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02" "02" "02" "04" "02" "02"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02" "02" "01" "02" "04" "02"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "04" "02" "02" "02" "01" "05"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "04" "05" "05" "02" "01" "04"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02" "01" "01" "01" "05" "02"
#> TCGA.UF.A71D.01 TCGA.CQ.7067.01 TCGA.BA.4078.01 TCGA.CN.5374.01 TCGA.DQ.7590.01 TCGA.CN.5369.01
#> "04" "01" "01" "05" "02" "02"
#> TCGA.BA.5151.01 TCGA.TN.A7HJ.01 TCGA.IQ.A61E.01 TCGA.BB.7870.01 TCGA.CN.4727.01 TCGA.DQ.7595.01
#> "02" "05" "02" "04" "04" "04"
#> TCGA.BA.4076.01 TCGA.CN.5360.01 TCGA.BB.4228.01 TCGA.MZ.A7D7.01 TCGA.H7.A76A.01 TCGA.UF.A7JT.01
#> "02" "04" "05" "02" "05" "02"
#> TCGA.CN.5373.01 TCGA.CN.A6V3.01 TCGA.BB.7863.01 TCGA.DQ.7593.01 TCGA.UF.A7JJ.01 TCGA.CN.5363.01
#> "02" "04" "02" "05" "01" "02"
#> TCGA.BA.4077.01 TCGA.BB.4225.01 TCGA.BB.7872.01 TCGA.CN.A6UY.01 TCGA.MT.A7BN.01 TCGA.UF.A7JF.01
#> "02" "05" "02" "05" "01" "04"
#> TCGA.CN.4731.01 TCGA.MZ.A5BI.01 TCGA.CN.A63W.01 TCGA.H7.A6C4.01 TCGA.T2.A6X2.01 TCGA.CN.5364.01
#> "04" "05" "04" "02" "02" "05"
#> TCGA.CN.A63U.01 TCGA.BB.A6UM.01 TCGA.H7.A6C5.01 TCGA.CN.4741.01 TCGA.CV.A6JO.01 TCGA.BB.7866.01
#> "04" "05" "04" "02" "02" "02"
#> TCGA.CN.5365.01 TCGA.CN.4740.01 TCGA.BB.4224.01 TCGA.MT.A67F.01 TCGA.CN.5366.01 TCGA.QK.A6V9.01
#> "02" "05" "02" "02" "02" "02"
#> TCGA.CN.5356.01 TCGA.T2.A6WX.01 TCGA.CV.A6JZ.01 TCGA.CN.A6V1.01 TCGA.HD.A6I0.01 TCGA.UF.A71A.01
#> "04" "02" "02" "02" "02" "01"
#> TCGA.CV.7430.01 TCGA.CR.7383.01 TCGA.CN.A6V6.01 TCGA.F7.7848.01 TCGA.TN.A7HI.01 TCGA.UF.A7JC.01
#> "02" "02" "05" "04" "01" "02"
#> TCGA.D6.A6ES.01 TCGA.CV.7568.01 TCGA.BA.A6D8.01 TCGA.P3.A6T4.01 TCGA.QK.A6IF.01 TCGA.CV.A6JT.01
#> "05" "02" "01" "01" "02" "02"
#> TCGA.CV.7438.01 TCGA.RS.A6TP.01 TCGA.P3.A6SW.01 TCGA.D6.A6EN.01 TCGA.D6.A6EM.01 TCGA.UF.A7JK.01
#> "02" "05" "01" "02" "01" "01"
#> TCGA.KU.A6H7.06 TCGA.CV.7429.01 TCGA.UP.A6WW.01 TCGA.CV.7437.01 TCGA.CV.A6JD.01 TCGA.CV.A6JY.01
#> "05" "02" "05" "02" "02" "05"
#> TCGA.CV.A6JN.01 TCGA.CV.7446.01 TCGA.CV.7432.01 TCGA.CV.7434.01 TCGA.WA.A7H4.01 TCGA.KU.A6H8.01
#> "02" "01" "05" "02" "05" "03"
#> TCGA.CV.7428.01 TCGA.D6.A6EK.01 TCGA.CV.A6K0.01 TCGA.HD.7832.01 TCGA.MZ.A6I9.01 TCGA.CV.7435.01
#> "04" "02" "03" "02" "05" "04"
#> TCGA.P3.A6SX.01 TCGA.QK.A6IG.01 TCGA.HD.7831.01 TCGA.CV.A6JM.01 TCGA.CR.7404.01 TCGA.D6.A6EQ.01
#> "02" "05" "01" "05" "05" "01"
#> TCGA.QK.A6IJ.01 TCGA.P3.A6T0.01 TCGA.CV.A6JE.01 TCGA.HD.A6HZ.01 TCGA.QK.A6II.01 TCGA.P3.A6T7.01
#> "05" "01" "05" "01" "02" "02"
#> TCGA.BA.A6DD.01 TCGA.UF.A719.01 TCGA.TN.A7HL.01 TCGA.UF.A7JA.01 TCGA.CR.7368.01 TCGA.CR.7382.01
#> "05" "04" "01" "01" "05" "02"
#> TCGA.UF.A7JD.01 TCGA.UF.A7JH.01 TCGA.BA.A6DA.01 TCGA.T2.A6WZ.01 TCGA.D6.A6EO.01 TCGA.CR.7370.01
#> "04" "04" "01" "02" "04" "01"
#> TCGA.P3.A6T5.01 TCGA.D6.A74Q.01 TCGA.UF.A718.01 TCGA.CR.7369.01 TCGA.QK.A6IH.01 TCGA.CV.A6K2.01
#> "02" "04" "05" "05" "05" "01"
#> TCGA.CV.A6K1.01 TCGA.BA.A6DE.01 TCGA.WA.A7GZ.01 TCGA.CV.7433.01 TCGA.CV.7440.01 TCGA.CV.A6JU.01
#> "01" "04" "05" "02" "04" "04"
#> TCGA.CR.7376.01 TCGA.UF.A71A.06 TCGA.KU.A6H7.01 TCGA.D6.A6EP.01
#> "02" "01" "05" "01"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 63548))
#> TCGA.CN.6022.01 TCGA.CQ.5327.01 TCGA.CV.5435.11 TCGA.HD.7753.01 TCGA.CQ.5325.01 TCGA.CV.5432.01
#> "05" "02" "03" "02" "02" "05"
#> TCGA.CR.7391.01 TCGA.CV.7415.01 TCGA.CR.5247.01 TCGA.CN.6011.01 TCGA.CV.7414.01 TCGA.CV.6436.01
#> "02" "02" "04" "02" "01" "02"
#> TCGA.DQ.7592.01 TCGA.IQ.7632.01 TCGA.CV.7416.01 TCGA.CV.5432.11 TCGA.H7.7774.01 TCGA.CQ.5330.01
#> "02" "05" "02" "03" "02" "02"
#> TCGA.CV.5430.11 TCGA.CV.7427.01 TCGA.CV.5979.01 TCGA.CR.6488.01 TCGA.CQ.6221.01 TCGA.CV.5434.11
#> "03" "02" "02" "05" "02" "03"
#> TCGA.CV.5970.11 TCGA.CV.7425.01 TCGA.CV.6441.01 TCGA.IQ.7630.01 TCGA.CV.5976.11 TCGA.CV.7103.11
#> "03" "02" "02" "02" "03" "03"
#> TCGA.CV.5977.01 TCGA.CQ.5324.01 TCGA.CV.7407.01 TCGA.CV.5971.01 TCGA.CV.5970.01 TCGA.CN.6016.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.CV.6003.01 TCGA.CN.6010.01 TCGA.CN.6021.01 TCGA.CV.6433.01 TCGA.CV.5434.01 TCGA.CV.7413.01
#> "02" "01" "02" "05" "02" "01"
#> TCGA.HD.7754.01 TCGA.CN.6017.01 TCGA.CV.6003.11 TCGA.CV.7422.01 TCGA.CV.7421.01 TCGA.CV.5439.11
#> "05" "02" "03" "01" "05" "03"
#> TCGA.CV.7235.01 TCGA.BA.7269.01 TCGA.CV.5971.11 TCGA.CQ.5332.01 TCGA.CV.5439.01 TCGA.CN.6020.01
#> "02" "01" "03" "01" "02" "02"
#> TCGA.CV.7423.01 TCGA.CV.7263.01 TCGA.CV.7406.01 TCGA.CN.6023.01 TCGA.CV.5966.11 TCGA.CV.7101.01
#> "02" "04" "05" "02" "03" "01"
#> TCGA.CV.5977.11 TCGA.CR.7365.01 TCGA.CN.6012.01 TCGA.CV.6441.11 TCGA.CN.6024.01 TCGA.CV.5978.01
#> "03" "02" "01" "03" "02" "02"
#> TCGA.CX.7086.01 TCGA.CV.7424.01 TCGA.CV.7089.01 TCGA.CQ.7065.01 TCGA.IQ.7631.01 TCGA.CV.7418.01
#> "05" "01" "02" "05" "05" "01"
#> TCGA.CV.6937.01 TCGA.CN.6018.01 TCGA.CV.5966.01 TCGA.CQ.5329.01 TCGA.CV.5976.01 TCGA.CV.7411.01
#> "01" "02" "02" "05" "02" "02"
#> TCGA.CQ.5323.01 TCGA.CV.5978.11 TCGA.CV.5973.11 TCGA.BB.4217.01 TCGA.CQ.7068.01 TCGA.CN.6013.01
#> "02" "03" "03" "02" "02" "01"
#> TCGA.CV.6436.11 TCGA.CV.6433.11 TCGA.CN.6995.01 TCGA.CV.6960.01 TCGA.CQ.5334.01 TCGA.CV.7410.01
#> "03" "03" "02" "04" "02" "02"
#> TCGA.CN.6019.01 TCGA.DQ.7588.01 TCGA.CV.5979.11 TCGA.CR.6492.01 TCGA.CV.5973.01 TCGA.DQ.7591.01
#> "01" "02" "03" "03" "02" "02"
#> TCGA.CR.7389.01 TCGA.CV.7245.01 TCGA.CV.5430.01 TCGA.CV.5435.01 TCGA.CR.7374.01 TCGA.CV.5440.01
#> "01" "04" "02" "02" "01" "02"
#> TCGA.CV.6955.11 TCGA.CV.7238.11 TCGA.CV.7104.01 TCGA.CV.7100.01 TCGA.CV.7089.11 TCGA.CN.4739.01
#> "03" "03" "02" "02" "03" "04"
#> TCGA.CV.7095.01 TCGA.CV.6956.01 TCGA.CV.5431.11 TCGA.CV.7261.01 TCGA.CN.5358.01 TCGA.BA.5559.01
#> "02" "04" "03" "01" "01" "05"
#> TCGA.CR.7373.01 TCGA.CX.7082.01 TCGA.DQ.5629.01 TCGA.CV.7255.11 TCGA.CR.7379.01 TCGA.CV.7178.01
#> "02" "05" "01" "03" "05" "02"
#> TCGA.CR.5249.01 TCGA.CV.7091.01 TCGA.CV.7236.01 TCGA.CN.6998.01 TCGA.CR.7399.01 TCGA.CR.7372.01
#> "05" "04" "03" "02" "05" "01"
#> TCGA.CV.7252.01 TCGA.CV.7242.01 TCGA.CV.7103.01 TCGA.CR.6478.01 TCGA.CR.7371.01 TCGA.CR.7380.01
#> "02" "04" "05" "02" "01" "02"
#> TCGA.CV.7183.01 TCGA.CV.7250.11 TCGA.CV.7102.01 TCGA.CV.7254.01 TCGA.CR.7394.01 TCGA.CV.5443.01
#> "02" "03" "02" "02" "02" "05"
#> TCGA.CV.6955.01 TCGA.CV.5441.11 TCGA.CV.5442.11 TCGA.BA.5556.01 TCGA.CR.7386.01 TCGA.CV.7255.01
#> "02" "05" "03" "02" "02" "05"
#> TCGA.CR.6474.01 TCGA.BA.5557.01 TCGA.CR.7388.01 TCGA.CV.5436.11 TCGA.CR.7398.01 TCGA.CV.7247.01
#> "02" "02" "01" "03" "04" "02"
#> TCGA.CN.6997.01 TCGA.CN.4742.01 TCGA.CN.4738.01 TCGA.CR.7392.01 TCGA.CV.7245.11 TCGA.CR.7377.01
#> "01" "01" "01" "05" "03" "02"
#> TCGA.HD.7229.01 TCGA.CV.7235.11 TCGA.D6.6515.01 TCGA.CV.7238.01 TCGA.CR.5248.01 TCGA.CV.7097.01
#> "02" "03" "02" "02" "05" "02"
#> TCGA.CR.5250.01 TCGA.CV.7248.01 TCGA.CV.7253.01 TCGA.CN.5370.01 TCGA.CR.7367.01 TCGA.CR.7401.01
#> "05" "01" "04" "02" "02" "02"
#> TCGA.BA.5149.01 TCGA.CV.6942.01 TCGA.CV.7263.11 TCGA.CV.7177.01 TCGA.BA.5555.01 TCGA.CV.6956.11
#> "05" "02" "03" "02" "04" "03"
#> TCGA.CV.5431.01 TCGA.CR.7393.01 TCGA.CV.5444.11 TCGA.CV.5444.01 TCGA.CR.5243.01 TCGA.CR.7395.01
#> "05" "03" "03" "01" "05" "02"
#> TCGA.CV.5441.01 TCGA.CV.5442.01 TCGA.BA.5558.01 TCGA.CX.7085.01 TCGA.CV.7250.01 TCGA.CR.7390.01
#> "04" "05" "02" "02" "04" "01"
#> TCGA.CV.7178.11 TCGA.CV.7099.01 TCGA.CV.5443.11 TCGA.CR.7385.01 TCGA.CR.7364.01 TCGA.CV.7090.01
#> "03" "02" "03" "05" "04" "02"
#> TCGA.CR.7397.01 TCGA.CR.7402.01 TCGA.CV.5440.11 TCGA.CV.7180.01 TCGA.CX.7219.01 TCGA.CV.7101.11
#> "03" "04" "03" "05" "02" "03"
#> TCGA.CV.5436.01 TCGA.CV.7243.01 TCGA.BA.6871.01 TCGA.CQ.6218.01 TCGA.C9.A47Z.01 TCGA.CV.6961.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.DQ.5625.01 TCGA.CN.6992.01 TCGA.CV.6939.01 TCGA.CR.6480.01 TCGA.D6.6825.01 TCGA.C9.A480.01
#> "02" "01" "05" "02" "02" "02"
#> TCGA.CV.6962.01 TCGA.CV.6952.01 TCGA.CN.A49A.01 TCGA.CR.6487.01 TCGA.CV.6935.11 TCGA.CQ.6222.01
#> "01" "02" "04" "05" "03" "02"
#> TCGA.CV.6959.11 TCGA.BB.4227.01 TCGA.CN.A49C.01 TCGA.CN.6994.01 TCGA.CV.6938.11 TCGA.CV.6936.01
#> "03" "01" "02" "02" "03" "05"
#> TCGA.CR.6491.01 TCGA.CV.6950.01 TCGA.CR.6473.01 TCGA.CV.6952.11 TCGA.CQ.5331.01 TCGA.D6.6826.01
#> "02" "02" "02" "03" "02" "02"
#> TCGA.CV.6951.11 TCGA.CV.6935.01 TCGA.DQ.5631.01 TCGA.CV.6953.01 TCGA.CV.6945.01 TCGA.CV.6939.11
#> "03" "02" "05" "02" "02" "03"
#> TCGA.CV.A45U.01 TCGA.CN.A497.01 TCGA.D6.6823.01 TCGA.DQ.5630.01 TCGA.D6.6827.01 TCGA.CV.6943.01
#> "01" "04" "04" "02" "01" "02"
#> TCGA.CV.6954.11 TCGA.CR.6472.01 TCGA.CR.6481.01 TCGA.BA.A4IF.01 TCGA.BA.6870.01 TCGA.CV.6962.11
#> "03" "05" "05" "04" "02" "03"
#> TCGA.CR.6477.01 TCGA.CV.A45O.01 TCGA.CQ.6219.01 TCGA.CN.4733.01 TCGA.CR.6484.01 TCGA.CN.A498.01
#> "02" "02" "02" "02" "05" "02"
#> TCGA.CR.6470.01 TCGA.CV.6934.01 TCGA.CN.6989.01 TCGA.CV.6953.11 TCGA.CV.6933.01 TCGA.D6.6517.01
#> "05" "01" "02" "02" "01" "02"
#> TCGA.CQ.6220.01 TCGA.BA.A4IH.01 TCGA.HD.A4C1.01 TCGA.BA.6869.01 TCGA.CR.6493.01 TCGA.D6.6516.01
#> "02" "05" "02" "04" "02" "02"
#> TCGA.CQ.6227.01 TCGA.CV.A45P.01 TCGA.CV.A45Q.01 TCGA.CV.A45T.01 TCGA.CN.6996.01 TCGA.CV.6961.11
#> "02" "02" "02" "02" "02" "03"
#> TCGA.CV.6941.01 TCGA.BA.6873.01 TCGA.CV.6934.11 TCGA.CR.6467.01 TCGA.CV.6943.11 TCGA.CV.6954.01
#> "04" "02" "03" "02" "03" "04"
#> TCGA.BA.6868.01 TCGA.CV.6959.01 TCGA.CQ.6228.01 TCGA.CQ.6229.01 TCGA.CQ.6224.01 TCGA.CV.6951.01
#> "02" "02" "04" "02" "02" "05"
#> TCGA.CQ.6223.01 TCGA.CV.6948.01 TCGA.CV.6936.11 TCGA.DQ.5624.01 TCGA.CV.A45R.01 TCGA.CN.A499.01
#> "02" "01" "03" "02" "02" "02"
#> TCGA.CN.A49B.01 TCGA.BA.5152.01 TCGA.CV.6938.01 TCGA.CQ.5326.01 TCGA.D6.6824.01 TCGA.CV.6940.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.CQ.6225.01 TCGA.CR.6471.01 TCGA.CN.6988.01 TCGA.BA.6872.01 TCGA.CV.6933.11 TCGA.CR.6482.01
#> "04" "02" "04" "02" "03" "05"
#> TCGA.P3.A5Q5.01 TCGA.CQ.A4C6.01 TCGA.QK.A8Z8.01 TCGA.CV.A45W.01 TCGA.F7.A624.01 TCGA.F7.A623.01
#> "05" "02" "04" "05" "05" "01"
#> TCGA.F7.A622.01 TCGA.CQ.7064.01 TCGA.IQ.A61K.01 TCGA.HD.A633.01 TCGA.BA.A4IG.01 TCGA.F7.A61W.01
#> "05" "02" "02" "02" "05" "02"
#> TCGA.BA.A6DF.01 TCGA.D6.A4ZB.01 TCGA.KU.A66T.01 TCGA.HD.8224.01 TCGA.CV.A45Y.01 TCGA.BB.A5HU.01
#> "02" "02" "05" "05" "02" "02"
#> TCGA.T3.A92M.01 TCGA.CQ.A4C7.01 TCGA.P3.A5Q6.01 TCGA.CQ.A4CD.01 TCGA.BA.A6DB.01 TCGA.CV.A468.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.QK.A8Z7.01 TCGA.F7.A620.01 TCGA.BA.A8YP.01 TCGA.CQ.A4C9.01 TCGA.CQ.7072.01 TCGA.IQ.A61H.01
#> "04" "02" "05" "04" "04" "01"
#> TCGA.QK.AA3K.01 TCGA.CQ.7069.01 TCGA.CX.A4AQ.01 TCGA.CV.A464.01 TCGA.IQ.A61L.01 TCGA.QK.A8Z9.01
#> "01" "05" "02" "02" "02" "02"
#> TCGA.HD.A634.01 TCGA.4P.AA8J.01 TCGA.BB.A5HY.01 TCGA.HD.8635.01 TCGA.CN.A63T.01 TCGA.QK.A652.01
#> "05" "01" "02" "02" "04" "02"
#> TCGA.MT.A67G.01 TCGA.QK.A64Z.01 TCGA.HD.8634.01 TCGA.CQ.7063.01 TCGA.CV.A45V.01 TCGA.CV.A460.01
#> "02" "02" "02" "02" "01" "01"
#> TCGA.CV.A465.01 TCGA.CQ.A4CG.01 TCGA.F7.A50J.01 TCGA.F7.8298.01 TCGA.F7.8489.01 TCGA.P3.A5QA.01
#> "05" "01" "02" "02" "02" "05"
#> TCGA.F7.A50G.01 TCGA.CQ.A4CA.01 TCGA.T3.A92N.01 TCGA.F7.A61V.01 TCGA.CN.A63Y.01 TCGA.CQ.5333.01
#> "02" "02" "02" "04" "02" "02"
#> TCGA.P3.A5QE.01 TCGA.MT.A67D.01 TCGA.CN.A63V.01 TCGA.BA.A6DJ.01 TCGA.MT.A51W.01 TCGA.P3.A5QF.01
#> "02" "05" "05" "02" "02" "04"
#> TCGA.CQ.A4CE.01 TCGA.IQ.A61G.01 TCGA.HD.8314.01 TCGA.BB.A5HZ.01 TCGA.CN.A641.01 TCGA.IQ.A61J.01
#> "01" "02" "01" "04" "04" "02"
#> TCGA.BA.A6DG.01 TCGA.QK.AA3J.01 TCGA.CQ.A4CH.01 TCGA.BA.A4II.01 TCGA.KU.A66S.01 TCGA.CQ.A4CB.01
#> "02" "04" "02" "01" "04" "02"
#> TCGA.D6.8569.01 TCGA.IQ.A61I.01 TCGA.D6.A4Z9.01 TCGA.QK.A8ZA.01 TCGA.QK.A8ZB.01 TCGA.BA.A6DL.01
#> "02" "02" "02" "01" "05" "04"
#> TCGA.CQ.A4CI.01 TCGA.MT.A51X.01 TCGA.CV.A461.01 TCGA.CQ.7071.01 TCGA.H7.8501.01 TCGA.BB.8596.01
#> "01" "05" "04" "02" "02" "01"
#> TCGA.F7.A50I.01 TCGA.BB.8601.01 TCGA.H7.8502.01 TCGA.F7.A61S.01 TCGA.CV.A463.01 TCGA.IQ.A61O.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.CV.A45Z.01 TCGA.CV.A45X.01 TCGA.D6.8568.01 TCGA.CN.A642.01 TCGA.CN.4722.01 TCGA.IQ.A6SH.01
#> "05" "01" "02" "02" "05" "01"
#> TCGA.CN.5367.01 TCGA.P3.A6T2.01 TCGA.P3.A6T8.01 TCGA.CN.A6V7.01 TCGA.CN.A640.01 TCGA.UF.A71E.01
#> "02" "02" "05" "02" "02" "01"
#> TCGA.DQ.7589.01 TCGA.P3.A6T6.01 TCGA.CN.4725.01 TCGA.BA.5153.01 TCGA.DQ.7594.01 TCGA.HL.7533.01
#> "02" "04" "02" "05" "05" "02"
#> TCGA.T2.A6X0.01 TCGA.CN.4730.01 TCGA.CN.4723.01 TCGA.UF.A7J9.01 TCGA.UF.A7JO.01 TCGA.DQ.7596.01
#> "01" "04" "01" "01" "02" "05"
#> TCGA.UF.A7JV.01 TCGA.CN.4729.01 TCGA.IQ.A6SG.01 TCGA.BB.7864.01 TCGA.MT.A67A.01 TCGA.CN.5361.01
#> "02" "02" "02" "04" "02" "02"
#> TCGA.CN.5359.01 TCGA.BB.7861.01 TCGA.CN.4728.01 TCGA.BB.A6UO.01 TCGA.BA.4074.01 TCGA.CN.4734.01
#> "02" "02" "01" "02" "04" "02"
#> TCGA.QK.A6VB.01 TCGA.BA.4075.01 TCGA.BB.7871.01 TCGA.CN.4726.01 TCGA.CN.4735.01 TCGA.P3.A6T3.01
#> "04" "02" "02" "02" "01" "05"
#> TCGA.HD.7917.01 TCGA.BB.4223.01 TCGA.UF.A71B.01 TCGA.UF.A7JS.01 TCGA.QK.A6VC.01 TCGA.CV.7409.01
#> "04" "05" "05" "02" "01" "04"
#> TCGA.CN.4736.01 TCGA.BB.7862.01 TCGA.BA.A6DI.01 TCGA.RS.A6TO.01 TCGA.CN.4737.01 TCGA.CN.5355.01
#> "02" "01" "01" "01" "05" "02"
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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 = 1269),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1269),
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 = 1469),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1469),
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 = 1526),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1526),
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 = 1540),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1540),
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 = 1619),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1619),
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 = 1622),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1622),
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 = 2262),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2262),
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 = 2279),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2279),
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 = 2489),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2489),
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 = 2775),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2775),
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 = 2836),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2836),
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 = 3188),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3188),
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 = 3867),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3867),
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 = 4027),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4027),
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 = 4522),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4522),
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 = 4660),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4660),
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 = 4864),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4864),
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 = 5547),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5547),
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 = 5764),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5764),
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 = 6152),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 6152),
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 = 7175),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 7175),
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 = 7761),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 7761),
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 = 8181),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 8181),
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 = 8755),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 8755),
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 = 9384),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 9384),
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 = 10841),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 10841),
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 = 20003),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 20003),
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 = 24546),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 24546),
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 = 30719),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 30719),
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 = 63548),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 63548),
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 = 1269))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1469))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1526))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1540))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1619))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1622))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2262))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2279))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2489))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2775))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2836))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3188))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3867))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4027))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4522))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4660))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4864))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5547))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5764))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 6152))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 7175))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 7761))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 8181))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 8755))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 9384))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 10841))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 20003))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 24546))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 30719))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 63548))
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 , Node05 .
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 376162 rows and 500 columns, randomly sampled from 580 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 '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 0.980 0.991 0.3805 0.622 0.622
#> 3 3 0.642 0.827 0.896 0.5410 0.693 0.546
#> 4 4 0.873 0.906 0.954 0.1818 0.812 0.591
#> 5 5 0.992 0.954 0.983 0.0708 0.889 0.674
#> 6 6 0.858 0.890 0.931 0.0956 0.881 0.577
#> 7 7 0.803 0.686 0.831 0.0301 0.958 0.785
#> 8 8 0.796 0.628 0.786 0.0239 0.971 0.835
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
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.CN.6022.01 1 0.000
#> TCGA.CQ.5327.01 2 0.000
#> TCGA.CV.5435.11 1 0.000
#> TCGA.HD.7753.01 2 0.000
#> TCGA.CQ.5325.01 2 0.000
#> TCGA.CV.5432.01 1 0.000
#> TCGA.CR.7391.01 1 0.000
#> TCGA.CV.7415.01 2 0.000
#> TCGA.CR.5247.01 2 0.000
#> TCGA.CN.6011.01 2 0.000
#> TCGA.CV.7414.01 2 0.000
#> TCGA.CV.6436.01 2 0.000
#> TCGA.DQ.7592.01 2 0.000
#> TCGA.IQ.7632.01 1 0.000
#> TCGA.CV.7416.01 2 0.000
#> TCGA.CV.5432.11 1 0.000
#> TCGA.H7.7774.01 2 0.000
#> TCGA.CQ.5330.01 2 0.000
#> TCGA.CV.5430.11 1 0.000
#> TCGA.CV.7427.01 2 0.000
#> TCGA.CV.5979.01 2 0.000
#> TCGA.CR.6488.01 2 0.000
#> TCGA.CQ.6221.01 1 0.000
#> TCGA.CV.5434.11 1 0.000
#> TCGA.CV.5970.11 1 0.000
#> TCGA.CV.7425.01 2 0.000
#> TCGA.CV.6441.01 2 0.000
#> TCGA.IQ.7630.01 2 0.000
#> TCGA.CV.5976.11 1 0.000
#> TCGA.CV.7103.11 1 0.000
#> TCGA.CV.5977.01 2 0.000
#> TCGA.CQ.5324.01 2 0.000
#> TCGA.CV.7407.01 1 0.000
#> TCGA.CV.5971.01 1 0.000
#> TCGA.CV.5970.01 2 0.000
#> TCGA.CN.6016.01 2 0.000
#> TCGA.CV.6003.01 2 0.000
#> TCGA.CN.6010.01 2 0.000
#> TCGA.CN.6021.01 1 0.000
#> TCGA.CV.6433.01 2 0.000
#> TCGA.CV.5434.01 2 0.000
#> TCGA.CV.7413.01 1 0.000
#> TCGA.HD.7754.01 2 0.000
#> TCGA.CN.6017.01 1 0.000
#> TCGA.CV.6003.11 1 0.000
#> TCGA.CV.7422.01 2 0.000
#> TCGA.CV.7421.01 2 0.000
#> TCGA.CV.5439.11 1 0.000
#> TCGA.CV.7235.01 1 0.000
#> TCGA.BA.7269.01 1 0.000
#> TCGA.CV.5971.11 1 0.000
#> TCGA.CQ.5332.01 2 0.000
#> TCGA.CV.5439.01 2 0.000
#> TCGA.CN.6020.01 2 0.000
#> TCGA.CV.7423.01 2 0.000
#> TCGA.CV.7263.01 2 0.000
#> TCGA.CV.7406.01 1 0.000
#> TCGA.CN.6023.01 1 0.000
#> TCGA.CV.5966.11 1 0.000
#> TCGA.CV.7101.01 2 0.000
#> TCGA.CV.5977.11 1 0.000
#> TCGA.CR.7365.01 2 0.000
#> TCGA.CN.6012.01 1 0.000
#> TCGA.CV.6441.11 1 0.000
#> TCGA.CN.6024.01 2 0.000
#> TCGA.CV.5978.01 1 0.000
#> TCGA.CX.7086.01 2 0.000
#> TCGA.CV.7424.01 1 0.000
#> TCGA.CV.7089.01 2 0.000
#> TCGA.CQ.7065.01 2 0.000
#> TCGA.IQ.7631.01 1 0.000
#> TCGA.CV.7418.01 2 0.000
#> TCGA.CV.6937.01 1 0.000
#> TCGA.CN.6018.01 2 0.000
#> TCGA.CV.5966.01 2 0.000
#> TCGA.CQ.5329.01 2 0.000
#> TCGA.CV.5976.01 2 0.000
#> TCGA.CV.7411.01 2 0.000
#> TCGA.CQ.5323.01 2 0.000
#> TCGA.CV.5978.11 1 0.000
#> TCGA.CV.5973.11 1 0.000
#> TCGA.BB.4217.01 1 0.000
#> TCGA.CQ.7068.01 2 0.000
#> TCGA.CN.6013.01 2 0.000
#> TCGA.CV.6436.11 1 0.000
#> TCGA.CV.6433.11 1 0.000
#> TCGA.CN.6995.01 2 0.000
#> TCGA.CV.6960.01 2 0.000
#> TCGA.CQ.5334.01 2 0.000
#> TCGA.CV.7410.01 1 0.000
#> TCGA.CN.6019.01 1 0.000
#> TCGA.DQ.7588.01 2 0.000
#> TCGA.CV.5979.11 1 0.000
#> TCGA.CR.6492.01 1 0.000
#> TCGA.CV.5973.01 2 0.000
#> TCGA.DQ.7591.01 2 0.000
#> TCGA.CR.7389.01 2 0.000
#> TCGA.CV.7245.01 2 0.000
#> TCGA.CV.5430.01 1 0.000
#> TCGA.CV.5435.01 2 0.000
#> TCGA.CR.7374.01 1 0.000
#> TCGA.CV.5440.01 2 0.000
#> TCGA.CV.6955.11 2 0.751
#> TCGA.CV.7238.11 1 0.000
#> TCGA.CV.7104.01 2 0.000
#> TCGA.CV.7100.01 2 0.000
#> TCGA.CV.7089.11 1 0.000
#> TCGA.CN.4739.01 2 0.000
#> TCGA.CV.7095.01 2 0.000
#> TCGA.CV.6956.01 2 0.000
#> TCGA.CV.5431.11 1 0.000
#> TCGA.CV.7261.01 2 0.000
#> TCGA.CN.5358.01 1 0.000
#> TCGA.BA.5559.01 2 0.000
#> TCGA.CR.7373.01 2 0.000
#> TCGA.CX.7082.01 2 0.000
#> TCGA.DQ.5629.01 1 0.000
#> TCGA.CV.7255.11 1 0.000
#> TCGA.CR.7379.01 2 0.000
#> TCGA.CV.7178.01 2 0.000
#> TCGA.CR.5249.01 2 0.000
#> TCGA.CV.7091.01 2 0.000
#> TCGA.CV.7236.01 2 0.000
#> TCGA.CN.6998.01 2 0.000
#> TCGA.CR.7399.01 2 0.000
#> TCGA.CR.7372.01 2 0.000
#> TCGA.CV.7252.01 2 0.000
#> TCGA.CV.7242.01 2 0.000
#> TCGA.CV.7103.01 1 0.000
#> TCGA.CR.6478.01 2 0.000
#> TCGA.CR.7371.01 1 0.000
#> TCGA.CR.7380.01 2 0.000
#> TCGA.CV.7183.01 2 0.000
#> TCGA.CV.7250.11 1 0.000
#> TCGA.CV.7102.01 2 0.000
#> TCGA.CV.7254.01 2 1.000
#> TCGA.CR.7394.01 2 0.000
#> TCGA.CV.5443.01 2 0.000
#> TCGA.CV.6955.01 2 0.000
#> TCGA.CV.5441.11 1 0.000
#> TCGA.CV.5442.11 1 0.000
#> TCGA.BA.5556.01 2 0.000
#> TCGA.CR.7386.01 2 0.000
#> TCGA.CV.7255.01 2 0.000
#> TCGA.CR.6474.01 1 0.000
#> TCGA.BA.5557.01 2 0.000
#> TCGA.CR.7388.01 1 0.000
#> TCGA.CV.5436.11 1 0.000
#> TCGA.CR.7398.01 1 0.000
#> TCGA.CV.7247.01 1 0.000
#> TCGA.CN.6997.01 2 0.000
#> TCGA.CN.4742.01 2 0.000
#> TCGA.CN.4738.01 1 0.000
#> TCGA.CR.7392.01 1 0.000
#> TCGA.CV.7245.11 1 0.000
#> TCGA.CR.7377.01 2 0.000
#> TCGA.HD.7229.01 2 0.000
#> TCGA.CV.7235.11 1 0.000
#> TCGA.D6.6515.01 1 0.000
#> TCGA.CV.7238.01 2 0.000
#> TCGA.CR.5248.01 2 0.000
#> TCGA.CV.7097.01 2 0.000
#> TCGA.CR.5250.01 2 0.000
#> TCGA.CV.7248.01 1 0.000
#> TCGA.CV.7253.01 2 0.000
#> TCGA.CN.5370.01 2 0.000
#> TCGA.CR.7367.01 2 0.000
#> TCGA.CR.7401.01 2 0.000
#> TCGA.BA.5149.01 2 0.000
#> TCGA.CV.6942.01 2 0.000
#> TCGA.CV.7263.11 1 0.000
#> TCGA.CV.7177.01 2 0.000
#> TCGA.BA.5555.01 2 0.000
#> TCGA.CV.6956.11 1 0.000
#> TCGA.CV.5431.01 2 0.000
#> TCGA.CR.7393.01 1 0.000
#> TCGA.CV.5444.11 1 0.000
#> TCGA.CV.5444.01 2 0.000
#> TCGA.CR.5243.01 2 0.000
#> TCGA.CR.7395.01 2 0.000
#> TCGA.CV.5441.01 2 0.000
#> TCGA.CV.5442.01 2 0.000
#> TCGA.BA.5558.01 2 0.000
#> TCGA.CX.7085.01 2 0.000
#> TCGA.CV.7250.01 2 0.000
#> TCGA.CR.7390.01 2 0.000
#> TCGA.CV.7178.11 1 0.000
#> TCGA.CV.7099.01 2 0.000
#> TCGA.CV.5443.11 1 0.000
#> TCGA.CR.7385.01 2 0.000
#> TCGA.CR.7364.01 1 0.000
#> TCGA.CV.7090.01 2 1.000
#> TCGA.CR.7397.01 1 0.000
#> TCGA.CR.7402.01 2 1.000
#> TCGA.CV.5440.11 1 0.000
#> TCGA.CV.7180.01 2 0.000
#> TCGA.CX.7219.01 1 0.000
#> TCGA.CV.7101.11 1 0.000
#> TCGA.CV.5436.01 2 0.000
#> TCGA.CV.7243.01 2 0.000
#> TCGA.BA.6871.01 2 0.000
#> TCGA.CQ.6218.01 2 0.000
#> TCGA.C9.A47Z.01 2 0.000
#> TCGA.CV.6961.01 1 0.000
#> TCGA.DQ.5625.01 2 0.000
#> TCGA.CN.6992.01 1 0.000
#> TCGA.CV.6939.01 2 0.000
#> TCGA.CR.6480.01 2 0.000
#> TCGA.D6.6825.01 2 0.000
#> TCGA.C9.A480.01 2 0.000
#> TCGA.CV.6962.01 2 0.498
#> TCGA.CV.6952.01 2 0.000
#> TCGA.CN.A49A.01 1 0.000
#> TCGA.CR.6487.01 2 0.000
#> TCGA.CV.6935.11 1 0.000
#> TCGA.CQ.6222.01 2 0.000
#> TCGA.CV.6959.11 1 0.000
#> TCGA.BB.4227.01 1 0.000
#> TCGA.CN.A49C.01 2 0.000
#> TCGA.CN.6994.01 2 0.000
#> TCGA.CV.6938.11 1 0.000
#> TCGA.CV.6936.01 2 0.000
#> TCGA.CR.6491.01 2 0.000
#> TCGA.CV.6950.01 2 0.000
#> TCGA.CR.6473.01 2 0.000
#> TCGA.CV.6952.11 1 0.000
#> TCGA.CQ.5331.01 2 0.000
#> TCGA.D6.6826.01 2 0.000
#> TCGA.CV.6951.11 1 0.000
#> TCGA.CV.6935.01 2 0.000
#> TCGA.DQ.5631.01 2 0.000
#> TCGA.CV.6953.01 2 0.000
#> TCGA.CV.6945.01 1 0.000
#> TCGA.CV.6939.11 1 0.000
#> TCGA.CV.A45U.01 1 0.000
#> TCGA.CN.A497.01 2 0.000
#> TCGA.D6.6823.01 2 0.000
#> TCGA.DQ.5630.01 2 0.000
#> TCGA.D6.6827.01 1 0.000
#> TCGA.CV.6943.01 2 0.000
#> TCGA.CV.6954.11 1 0.000
#> TCGA.CR.6472.01 2 0.000
#> TCGA.CR.6481.01 2 0.000
#> TCGA.BA.A4IF.01 1 0.000
#> TCGA.BA.6870.01 2 0.498
#> TCGA.CV.6962.11 1 0.000
#> TCGA.CR.6477.01 1 0.000
#> TCGA.CV.A45O.01 2 0.000
#> TCGA.CQ.6219.01 2 0.000
#> TCGA.CN.4733.01 1 0.000
#> TCGA.CR.6484.01 2 0.747
#> TCGA.CN.A498.01 2 0.000
#> TCGA.CR.6470.01 2 0.000
#> TCGA.CV.6934.01 2 0.000
#> TCGA.CN.6989.01 1 0.000
#> TCGA.CV.6953.11 1 0.000
#> TCGA.CV.6933.01 2 0.000
#> TCGA.D6.6517.01 2 0.000
#> TCGA.CQ.6220.01 2 0.000
#> TCGA.BA.A4IH.01 1 0.000
#> TCGA.HD.A4C1.01 2 0.000
#> TCGA.BA.6869.01 2 0.000
#> TCGA.CR.6493.01 2 0.000
#> TCGA.D6.6516.01 2 0.000
#> TCGA.CQ.6227.01 2 0.000
#> TCGA.CV.A45P.01 2 0.000
#> TCGA.CV.A45Q.01 2 0.000
#> TCGA.CV.A45T.01 2 0.000
#> TCGA.CN.6996.01 2 0.000
#> TCGA.CV.6961.11 1 0.000
#> TCGA.CV.6941.01 2 0.000
#> TCGA.BA.6873.01 2 0.000
#> TCGA.CV.6934.11 1 0.000
#> TCGA.CR.6467.01 2 0.000
#> TCGA.CV.6943.11 1 0.000
#> TCGA.CV.6954.01 2 0.000
#> TCGA.BA.6868.01 2 0.000
#> TCGA.CV.6959.01 2 0.000
#> TCGA.CQ.6228.01 2 0.000
#> TCGA.CQ.6229.01 2 0.000
#> TCGA.CQ.6224.01 2 0.000
#> TCGA.CV.6951.01 2 0.000
#> TCGA.CQ.6223.01 2 0.000
#> TCGA.CV.6948.01 1 0.000
#> TCGA.CV.6936.11 1 0.000
#> TCGA.DQ.5624.01 2 0.000
#> TCGA.CV.A45R.01 2 0.000
#> TCGA.CN.A499.01 2 0.000
#> TCGA.CN.A49B.01 2 0.000
#> TCGA.BA.5152.01 2 0.000
#> TCGA.CV.6938.01 2 0.000
#> TCGA.CQ.5326.01 2 1.000
#> TCGA.D6.6824.01 1 0.000
#> TCGA.CV.6940.01 2 0.000
#> TCGA.CQ.6225.01 2 0.000
#> TCGA.CR.6471.01 2 0.000
#> TCGA.CN.6988.01 2 0.000
#> TCGA.BA.6872.01 2 0.000
#> TCGA.CV.6933.11 1 0.000
#> TCGA.CR.6482.01 2 0.000
#> TCGA.P3.A5Q5.01 2 0.000
#> TCGA.CQ.A4C6.01 2 0.000
#> TCGA.QK.A8Z8.01 2 0.000
#> TCGA.CV.A45W.01 1 0.747
#> TCGA.F7.A624.01 2 0.000
#> TCGA.F7.A623.01 1 0.000
#> TCGA.F7.A622.01 2 0.000
#> TCGA.CQ.7064.01 2 0.000
#> TCGA.IQ.A61K.01 2 0.000
#> TCGA.HD.A633.01 2 0.000
#> TCGA.BA.A4IG.01 2 0.000
#> TCGA.F7.A61W.01 1 0.000
#> TCGA.BA.A6DF.01 2 0.000
#> TCGA.D6.A4ZB.01 2 0.000
#> TCGA.KU.A66T.01 2 0.000
#> TCGA.HD.8224.01 2 0.000
#> TCGA.CV.A45Y.01 2 0.000
#> TCGA.BB.A5HU.01 1 1.000
#> TCGA.T3.A92M.01 1 0.000
#> TCGA.CQ.A4C7.01 2 0.000
#> TCGA.P3.A5Q6.01 2 0.000
#> TCGA.CQ.A4CD.01 2 0.000
#> TCGA.BA.A6DB.01 1 0.000
#> TCGA.CV.A468.01 1 0.000
#> TCGA.QK.A8Z7.01 2 0.000
#> TCGA.F7.A620.01 2 0.000
#> TCGA.BA.A8YP.01 2 0.000
#> TCGA.CQ.A4C9.01 2 0.000
#> TCGA.CQ.7072.01 2 0.000
#> TCGA.IQ.A61H.01 1 0.000
#> TCGA.QK.AA3K.01 1 0.000
#> TCGA.CQ.7069.01 1 0.000
#> TCGA.CX.A4AQ.01 2 0.000
#> TCGA.CV.A464.01 1 0.000
#> TCGA.IQ.A61L.01 2 0.000
#> TCGA.QK.A8Z9.01 2 0.000
#> TCGA.HD.A634.01 2 0.000
#> TCGA.4P.AA8J.01 1 0.000
#> TCGA.BB.A5HY.01 2 0.000
#> TCGA.HD.8635.01 2 0.000
#> TCGA.CN.A63T.01 2 0.000
#> TCGA.QK.A652.01 2 0.000
#> TCGA.MT.A67G.01 2 0.000
#> TCGA.QK.A64Z.01 2 0.000
#> TCGA.HD.8634.01 2 0.000
#> TCGA.CQ.7063.01 2 0.000
#> TCGA.CV.A45V.01 2 0.000
#> TCGA.CV.A460.01 2 1.000
#> TCGA.CV.A465.01 2 0.000
#> TCGA.CQ.A4CG.01 2 0.000
#> TCGA.F7.A50J.01 2 0.000
#> TCGA.F7.8298.01 2 0.000
#> TCGA.F7.8489.01 2 0.000
#> TCGA.P3.A5QA.01 2 0.000
#> TCGA.F7.A50G.01 2 0.000
#> TCGA.CQ.A4CA.01 2 0.000
#> TCGA.T3.A92N.01 2 0.000
#> TCGA.F7.A61V.01 2 0.000
#> TCGA.CN.A63Y.01 1 0.000
#> TCGA.CQ.5333.01 2 0.000
#> TCGA.P3.A5QE.01 1 0.000
#> TCGA.MT.A67D.01 2 0.000
#> TCGA.CN.A63V.01 2 0.000
#> TCGA.BA.A6DJ.01 2 0.000
#> TCGA.MT.A51W.01 1 0.000
#> TCGA.P3.A5QF.01 2 0.000
#> TCGA.CQ.A4CE.01 2 0.000
#> TCGA.IQ.A61G.01 2 0.000
#> TCGA.HD.8314.01 2 0.000
#> TCGA.BB.A5HZ.01 2 0.000
#> TCGA.CN.A641.01 2 0.000
#> TCGA.IQ.A61J.01 2 0.000
#> TCGA.BA.A6DG.01 1 0.751
#> TCGA.QK.AA3J.01 2 0.000
#> TCGA.CQ.A4CH.01 1 0.000
#> TCGA.BA.A4II.01 1 0.000
#> TCGA.KU.A66S.01 2 0.000
#> TCGA.CQ.A4CB.01 2 0.000
#> TCGA.D6.8569.01 2 0.000
#> TCGA.IQ.A61I.01 2 0.000
#> TCGA.D6.A4Z9.01 2 0.000
#> TCGA.QK.A8ZA.01 2 0.000
#> TCGA.QK.A8ZB.01 1 0.000
#> TCGA.BA.A6DL.01 2 0.000
#> TCGA.CQ.A4CI.01 2 0.000
#> TCGA.MT.A51X.01 2 0.000
#> TCGA.CV.A461.01 2 0.000
#> TCGA.CQ.7071.01 2 0.000
#> TCGA.H7.8501.01 2 0.000
#> TCGA.BB.8596.01 1 0.000
#> TCGA.F7.A50I.01 2 0.000
#> TCGA.BB.8601.01 2 0.000
#> TCGA.H7.8502.01 2 0.000
#> TCGA.F7.A61S.01 2 0.000
#> TCGA.CV.A463.01 2 0.000
#> TCGA.IQ.A61O.01 1 0.000
#> TCGA.CV.A45Z.01 2 0.000
#> TCGA.CV.A45X.01 2 0.000
#> TCGA.D6.8568.01 2 0.000
#> TCGA.CN.A642.01 2 0.000
#> TCGA.CN.4722.01 2 0.000
#> TCGA.IQ.A6SH.01 2 1.000
#> TCGA.CN.5367.01 2 0.000
#> TCGA.P3.A6T2.01 2 0.000
#> TCGA.P3.A6T8.01 1 0.000
#> TCGA.CN.A6V7.01 2 0.000
#> TCGA.CN.A640.01 2 0.000
#> TCGA.UF.A71E.01 2 0.000
#> TCGA.DQ.7589.01 1 0.000
#> TCGA.P3.A6T6.01 2 0.000
#> TCGA.CN.4725.01 2 0.000
#> TCGA.BA.5153.01 2 0.000
#> TCGA.DQ.7594.01 2 0.000
#> TCGA.HL.7533.01 2 0.000
#> TCGA.T2.A6X0.01 2 0.000
#> TCGA.CN.4730.01 2 0.000
#> TCGA.CN.4723.01 2 0.000
#> TCGA.UF.A7J9.01 1 0.000
#> TCGA.UF.A7JO.01 2 0.000
#> TCGA.DQ.7596.01 2 0.000
#> TCGA.UF.A7JV.01 2 0.000
#> TCGA.CN.4729.01 2 0.000
#> TCGA.IQ.A6SG.01 1 0.000
#> TCGA.BB.7864.01 2 0.000
#> TCGA.MT.A67A.01 2 0.000
#> TCGA.CN.5361.01 2 0.000
#> TCGA.CN.5359.01 1 0.000
#> TCGA.BB.7861.01 1 0.000
#> TCGA.CN.4728.01 1 0.000
#> TCGA.BB.A6UO.01 2 0.000
#> TCGA.BA.4074.01 2 0.000
#> TCGA.CN.4734.01 2 0.000
#> TCGA.QK.A6VB.01 2 0.000
#> TCGA.BA.4075.01 2 0.000
#> TCGA.BB.7871.01 1 0.000
#> TCGA.CN.4726.01 2 0.000
#> TCGA.CN.4735.01 1 0.000
#> TCGA.P3.A6T3.01 2 0.000
#> TCGA.HD.7917.01 2 0.000
#> TCGA.BB.4223.01 2 0.000
#> TCGA.UF.A71B.01 2 0.000
#> TCGA.UF.A7JS.01 2 0.000
#> TCGA.QK.A6VC.01 1 0.000
#> TCGA.CV.7409.01 2 0.000
#> TCGA.CN.4736.01 2 1.000
#> TCGA.BB.7862.01 1 0.000
#> TCGA.BA.A6DI.01 1 0.000
#> TCGA.RS.A6TO.01 2 0.000
#> TCGA.CN.4737.01 2 0.502
#> TCGA.CN.5355.01 2 0.000
#> TCGA.UF.A71D.01 2 0.000
#> TCGA.CQ.7067.01 2 0.000
#> TCGA.BA.4078.01 2 0.000
#> TCGA.CN.5374.01 2 0.000
#> TCGA.DQ.7590.01 2 0.000
#> TCGA.CN.5369.01 1 0.000
#> TCGA.BA.5151.01 2 0.000
#> TCGA.TN.A7HJ.01 2 0.000
#> TCGA.IQ.A61E.01 2 0.000
#> TCGA.BB.7870.01 2 0.000
#> TCGA.CN.4727.01 1 0.000
#> TCGA.DQ.7595.01 1 0.000
#> TCGA.BA.4076.01 1 0.000
#> TCGA.CN.5360.01 1 0.253
#> TCGA.BB.4228.01 2 0.000
#> TCGA.MZ.A7D7.01 1 0.000
#> TCGA.H7.A76A.01 1 0.000
#> TCGA.UF.A7JT.01 2 0.000
#> TCGA.CN.5373.01 2 0.000
#> TCGA.CN.A6V3.01 2 0.000
#> TCGA.BB.7863.01 2 0.000
#> TCGA.DQ.7593.01 2 0.000
#> TCGA.UF.A7JJ.01 1 0.000
#> TCGA.CN.5363.01 2 0.000
#> TCGA.BA.4077.01 2 0.000
#> TCGA.BB.4225.01 2 0.000
#> TCGA.BB.7872.01 2 0.000
#> TCGA.CN.A6UY.01 2 0.000
#> TCGA.MT.A7BN.01 2 0.498
#> TCGA.UF.A7JF.01 2 0.000
#> TCGA.CN.4731.01 2 0.000
#> TCGA.MZ.A5BI.01 2 1.000
#> TCGA.CN.A63W.01 1 0.000
#> TCGA.H7.A6C4.01 2 0.000
#> TCGA.T2.A6X2.01 2 0.000
#> TCGA.CN.5364.01 2 0.000
#> TCGA.CN.A63U.01 2 0.000
#> TCGA.BB.A6UM.01 2 0.000
#> TCGA.H7.A6C5.01 2 0.000
#> TCGA.CN.4741.01 2 0.000
#> TCGA.CV.A6JO.01 2 0.000
#> TCGA.BB.7866.01 2 0.000
#> TCGA.CN.5365.01 2 0.000
#> TCGA.CN.4740.01 2 0.000
#> TCGA.BB.4224.01 2 0.000
#> TCGA.MT.A67F.01 2 0.000
#> TCGA.CN.5366.01 2 0.000
#> TCGA.QK.A6V9.01 2 0.000
#> TCGA.CN.5356.01 2 0.000
#> TCGA.T2.A6WX.01 2 0.000
#> TCGA.CV.A6JZ.01 2 0.000
#> TCGA.CN.A6V1.01 1 0.000
#> TCGA.HD.A6I0.01 2 0.000
#> TCGA.UF.A71A.01 1 0.000
#> TCGA.CV.7430.01 2 1.000
#> TCGA.CR.7383.01 2 0.000
#> TCGA.CN.A6V6.01 2 0.000
#> TCGA.F7.7848.01 2 0.000
#> TCGA.TN.A7HI.01 2 0.000
#> TCGA.UF.A7JC.01 2 0.000
#> TCGA.D6.A6ES.01 2 0.000
#> TCGA.CV.7568.01 1 0.000
#> TCGA.BA.A6D8.01 2 0.000
#> TCGA.P3.A6T4.01 1 0.000
#> TCGA.QK.A6IF.01 2 1.000
#> TCGA.CV.A6JT.01 2 0.000
#> TCGA.CV.7438.01 2 0.000
#> TCGA.RS.A6TP.01 2 0.000
#> TCGA.P3.A6SW.01 2 0.000
#> TCGA.D6.A6EN.01 2 0.000
#> TCGA.D6.A6EM.01 2 0.000
#> TCGA.UF.A7JK.01 2 0.000
#> TCGA.KU.A6H7.06 2 0.000
#> TCGA.CV.7429.01 1 0.000
#> TCGA.UP.A6WW.01 2 0.000
#> TCGA.CV.7437.01 2 0.000
#> TCGA.CV.A6JD.01 2 0.000
#> TCGA.CV.A6JY.01 2 0.000
#> TCGA.CV.A6JN.01 2 0.000
#> TCGA.CV.7446.01 1 0.000
#> TCGA.CV.7432.01 2 0.000
#> TCGA.CV.7434.01 2 0.000
#> TCGA.WA.A7H4.01 1 0.000
#> TCGA.KU.A6H8.01 1 0.000
#> TCGA.CV.7428.01 2 0.000
#> TCGA.D6.A6EK.01 2 0.000
#> TCGA.CV.A6K0.01 1 0.000
#> TCGA.HD.7832.01 2 0.000
#> TCGA.MZ.A6I9.01 2 0.000
#> TCGA.CV.7435.01 2 0.000
#> TCGA.P3.A6SX.01 2 0.000
#> TCGA.QK.A6IG.01 2 0.000
#> TCGA.HD.7831.01 1 0.000
#> TCGA.CV.A6JM.01 2 0.000
#> TCGA.CR.7404.01 2 0.000
#> TCGA.D6.A6EQ.01 2 0.000
#> TCGA.QK.A6IJ.01 2 0.000
#> TCGA.P3.A6T0.01 2 0.000
#> TCGA.CV.A6JE.01 2 0.000
#> TCGA.HD.A6HZ.01 2 0.000
#> TCGA.QK.A6II.01 2 0.000
#> TCGA.P3.A6T7.01 2 0.000
#> TCGA.BA.A6DD.01 2 1.000
#> TCGA.UF.A719.01 2 0.000
#> TCGA.TN.A7HL.01 2 0.000
#> TCGA.UF.A7JA.01 1 0.000
#> TCGA.CR.7368.01 2 0.000
#> TCGA.CR.7382.01 1 0.000
#> TCGA.UF.A7JD.01 2 0.000
#> TCGA.UF.A7JH.01 2 0.000
#> TCGA.BA.A6DA.01 2 0.000
#> TCGA.T2.A6WZ.01 2 0.000
#> TCGA.D6.A6EO.01 2 0.000
#> TCGA.CR.7370.01 1 0.000
#> TCGA.P3.A6T5.01 2 0.000
#> TCGA.D6.A74Q.01 2 0.000
#> TCGA.UF.A718.01 2 0.000
#> TCGA.CR.7369.01 2 0.000
#> TCGA.QK.A6IH.01 2 0.000
#> TCGA.CV.A6K2.01 2 1.000
#> TCGA.CV.A6K1.01 2 0.000
#> TCGA.BA.A6DE.01 2 0.000
#> TCGA.WA.A7GZ.01 1 0.000
#> TCGA.CV.7433.01 1 0.000
#> TCGA.CV.7440.01 2 0.000
#> TCGA.CV.A6JU.01 2 0.000
#> TCGA.CR.7376.01 1 0.000
#> TCGA.UF.A71A.06 1 0.000
#> TCGA.KU.A6H7.01 2 0.000
#> TCGA.D6.A6EP.01 1 0.000
get_classes(res, k = 3)
#> class p
#> TCGA.CN.6022.01 1 0.000
#> TCGA.CQ.5327.01 2 0.000
#> TCGA.CV.5435.11 3 0.000
#> TCGA.HD.7753.01 2 0.751
#> TCGA.CQ.5325.01 2 0.000
#> TCGA.CV.5432.01 1 0.000
#> TCGA.CR.7391.01 3 0.000
#> TCGA.CV.7415.01 1 0.000
#> TCGA.CR.5247.01 2 0.000
#> TCGA.CN.6011.01 1 1.000
#> TCGA.CV.7414.01 2 1.000
#> TCGA.CV.6436.01 2 0.000
#> TCGA.DQ.7592.01 2 1.000
#> TCGA.IQ.7632.01 2 0.502
#> TCGA.CV.7416.01 2 0.000
#> TCGA.CV.5432.11 3 0.000
#> TCGA.H7.7774.01 2 0.000
#> TCGA.CQ.5330.01 2 0.000
#> TCGA.CV.5430.11 3 0.000
#> TCGA.CV.7427.01 2 0.000
#> TCGA.CV.5979.01 2 0.000
#> TCGA.CR.6488.01 2 0.000
#> TCGA.CQ.6221.01 1 0.000
#> TCGA.CV.5434.11 3 0.000
#> TCGA.CV.5970.11 3 0.000
#> TCGA.CV.7425.01 2 0.000
#> TCGA.CV.6441.01 2 0.000
#> TCGA.IQ.7630.01 2 0.000
#> TCGA.CV.5976.11 3 0.000
#> TCGA.CV.7103.11 3 0.000
#> TCGA.CV.5977.01 2 0.000
#> TCGA.CQ.5324.01 2 0.000
#> TCGA.CV.7407.01 1 0.000
#> TCGA.CV.5971.01 3 0.000
#> TCGA.CV.5970.01 2 0.000
#> TCGA.CN.6016.01 2 0.000
#> TCGA.CV.6003.01 2 0.000
#> TCGA.CN.6010.01 1 0.000
#> TCGA.CN.6021.01 1 0.000
#> TCGA.CV.6433.01 1 0.000
#> TCGA.CV.5434.01 1 1.000
#> TCGA.CV.7413.01 2 0.000
#> TCGA.HD.7754.01 1 0.000
#> TCGA.CN.6017.01 3 0.000
#> TCGA.CV.6003.11 3 0.000
#> TCGA.CV.7422.01 1 0.000
#> TCGA.CV.7421.01 2 0.000
#> TCGA.CV.5439.11 3 0.000
#> TCGA.CV.7235.01 1 0.000
#> TCGA.BA.7269.01 1 0.000
#> TCGA.CV.5971.11 3 0.000
#> TCGA.CQ.5332.01 1 0.000
#> TCGA.CV.5439.01 1 0.000
#> TCGA.CN.6020.01 2 0.000
#> TCGA.CV.7423.01 2 0.000
#> TCGA.CV.7263.01 2 0.000
#> TCGA.CV.7406.01 1 0.000
#> TCGA.CN.6023.01 1 0.000
#> TCGA.CV.5966.11 3 0.000
#> TCGA.CV.7101.01 2 1.000
#> TCGA.CV.5977.11 3 0.000
#> TCGA.CR.7365.01 2 0.000
#> TCGA.CN.6012.01 1 0.000
#> TCGA.CV.6441.11 3 0.000
#> TCGA.CN.6024.01 1 0.502
#> TCGA.CV.5978.01 1 0.000
#> TCGA.CX.7086.01 2 0.000
#> TCGA.CV.7424.01 1 0.000
#> TCGA.CV.7089.01 2 0.000
#> TCGA.CQ.7065.01 2 0.000
#> TCGA.IQ.7631.01 1 0.000
#> TCGA.CV.7418.01 1 0.000
#> TCGA.CV.6937.01 1 0.000
#> TCGA.CN.6018.01 2 0.000
#> TCGA.CV.5966.01 2 0.000
#> TCGA.CQ.5329.01 2 0.000
#> TCGA.CV.5976.01 2 0.000
#> TCGA.CV.7411.01 2 0.000
#> TCGA.CQ.5323.01 1 0.000
#> TCGA.CV.5978.11 3 0.000
#> TCGA.CV.5973.11 3 0.000
#> TCGA.BB.4217.01 1 0.000
#> TCGA.CQ.7068.01 2 0.000
#> TCGA.CN.6013.01 2 0.000
#> TCGA.CV.6436.11 3 0.000
#> TCGA.CV.6433.11 3 0.000
#> TCGA.CN.6995.01 2 0.000
#> TCGA.CV.6960.01 2 0.000
#> TCGA.CQ.5334.01 2 0.000
#> TCGA.CV.7410.01 3 0.000
#> TCGA.CN.6019.01 1 0.498
#> TCGA.DQ.7588.01 1 1.000
#> TCGA.CV.5979.11 3 0.000
#> TCGA.CR.6492.01 3 0.000
#> TCGA.CV.5973.01 2 0.000
#> TCGA.DQ.7591.01 1 0.000
#> TCGA.CR.7389.01 1 0.000
#> TCGA.CV.7245.01 2 0.000
#> TCGA.CV.5430.01 1 0.000
#> TCGA.CV.5435.01 2 0.000
#> TCGA.CR.7374.01 1 0.000
#> TCGA.CV.5440.01 1 0.000
#> TCGA.CV.6955.11 2 0.000
#> TCGA.CV.7238.11 3 0.000
#> TCGA.CV.7104.01 2 0.000
#> TCGA.CV.7100.01 1 0.000
#> TCGA.CV.7089.11 3 0.000
#> TCGA.CN.4739.01 2 0.000
#> TCGA.CV.7095.01 2 0.000
#> TCGA.CV.6956.01 2 0.000
#> TCGA.CV.5431.11 3 0.000
#> TCGA.CV.7261.01 1 0.000
#> TCGA.CN.5358.01 3 0.000
#> TCGA.BA.5559.01 1 0.000
#> TCGA.CR.7373.01 2 0.000
#> TCGA.CX.7082.01 1 1.000
#> TCGA.DQ.5629.01 1 0.000
#> TCGA.CV.7255.11 3 0.000
#> TCGA.CR.7379.01 2 0.000
#> TCGA.CV.7178.01 2 0.000
#> TCGA.CR.5249.01 1 0.000
#> TCGA.CV.7091.01 2 0.000
#> TCGA.CV.7236.01 2 0.000
#> TCGA.CN.6998.01 2 0.000
#> TCGA.CR.7399.01 1 0.000
#> TCGA.CR.7372.01 2 0.000
#> TCGA.CV.7252.01 2 0.000
#> TCGA.CV.7242.01 2 0.000
#> TCGA.CV.7103.01 1 0.000
#> TCGA.CR.6478.01 1 1.000
#> TCGA.CR.7371.01 1 0.000
#> TCGA.CR.7380.01 2 0.000
#> TCGA.CV.7183.01 2 0.000
#> TCGA.CV.7250.11 3 0.000
#> TCGA.CV.7102.01 2 0.000
#> TCGA.CV.7254.01 1 0.000
#> TCGA.CR.7394.01 2 0.000
#> TCGA.CV.5443.01 1 0.000
#> TCGA.CV.6955.01 2 0.000
#> TCGA.CV.5441.11 3 0.000
#> TCGA.CV.5442.11 3 0.000
#> TCGA.BA.5556.01 2 0.000
#> TCGA.CR.7386.01 2 0.000
#> TCGA.CV.7255.01 2 0.000
#> TCGA.CR.6474.01 1 0.000
#> TCGA.BA.5557.01 2 0.000
#> TCGA.CR.7388.01 1 0.000
#> TCGA.CV.5436.11 3 0.000
#> TCGA.CR.7398.01 1 0.000
#> TCGA.CV.7247.01 1 0.000
#> TCGA.CN.6997.01 1 0.000
#> TCGA.CN.4742.01 2 0.000
#> TCGA.CN.4738.01 3 0.000
#> TCGA.CR.7392.01 1 1.000
#> TCGA.CV.7245.11 3 0.000
#> TCGA.CR.7377.01 2 0.000
#> TCGA.HD.7229.01 2 0.000
#> TCGA.CV.7235.11 3 0.000
#> TCGA.D6.6515.01 2 0.000
#> TCGA.CV.7238.01 2 0.000
#> TCGA.CR.5248.01 1 0.000
#> TCGA.CV.7097.01 2 0.000
#> TCGA.CR.5250.01 1 0.000
#> TCGA.CV.7248.01 1 0.000
#> TCGA.CV.7253.01 2 0.000
#> TCGA.CN.5370.01 2 0.000
#> TCGA.CR.7367.01 2 0.000
#> TCGA.CR.7401.01 2 0.000
#> TCGA.BA.5149.01 2 0.000
#> TCGA.CV.6942.01 2 0.000
#> TCGA.CV.7263.11 3 0.000
#> TCGA.CV.7177.01 1 1.000
#> TCGA.BA.5555.01 2 1.000
#> TCGA.CV.6956.11 3 0.000
#> TCGA.CV.5431.01 1 0.000
#> TCGA.CR.7393.01 3 0.000
#> TCGA.CV.5444.11 3 0.000
#> TCGA.CV.5444.01 2 0.000
#> TCGA.CR.5243.01 1 0.000
#> TCGA.CR.7395.01 2 0.000
#> TCGA.CV.5441.01 2 0.000
#> TCGA.CV.5442.01 2 0.000
#> TCGA.BA.5558.01 2 0.000
#> TCGA.CX.7085.01 2 0.000
#> TCGA.CV.7250.01 2 0.000
#> TCGA.CR.7390.01 1 0.000
#> TCGA.CV.7178.11 3 0.000
#> TCGA.CV.7099.01 2 0.000
#> TCGA.CV.5443.11 3 0.000
#> TCGA.CR.7385.01 1 0.000
#> TCGA.CR.7364.01 1 0.000
#> TCGA.CV.7090.01 2 1.000
#> TCGA.CR.7397.01 3 0.000
#> TCGA.CR.7402.01 2 1.000
#> TCGA.CV.5440.11 3 0.000
#> TCGA.CV.7180.01 2 0.000
#> TCGA.CX.7219.01 1 0.000
#> TCGA.CV.7101.11 3 0.000
#> TCGA.CV.5436.01 2 0.000
#> TCGA.CV.7243.01 2 0.000
#> TCGA.BA.6871.01 1 0.000
#> TCGA.CQ.6218.01 2 0.000
#> TCGA.C9.A47Z.01 2 0.000
#> TCGA.CV.6961.01 1 0.000
#> TCGA.DQ.5625.01 2 0.000
#> TCGA.CN.6992.01 1 0.000
#> TCGA.CV.6939.01 1 0.000
#> TCGA.CR.6480.01 1 0.000
#> TCGA.D6.6825.01 2 0.000
#> TCGA.C9.A480.01 2 0.000
#> TCGA.CV.6962.01 1 0.000
#> TCGA.CV.6952.01 2 0.000
#> TCGA.CN.A49A.01 1 0.000
#> TCGA.CR.6487.01 2 0.000
#> TCGA.CV.6935.11 3 0.000
#> TCGA.CQ.6222.01 2 0.000
#> TCGA.CV.6959.11 3 0.000
#> TCGA.BB.4227.01 1 0.000
#> TCGA.CN.A49C.01 1 1.000
#> TCGA.CN.6994.01 2 1.000
#> TCGA.CV.6938.11 3 0.000
#> TCGA.CV.6936.01 2 0.000
#> TCGA.CR.6491.01 2 0.000
#> TCGA.CV.6950.01 2 0.000
#> TCGA.CR.6473.01 1 0.751
#> TCGA.CV.6952.11 3 0.000
#> TCGA.CQ.5331.01 2 0.000
#> TCGA.D6.6826.01 2 0.000
#> TCGA.CV.6951.11 3 0.000
#> TCGA.CV.6935.01 1 0.000
#> TCGA.DQ.5631.01 2 0.000
#> TCGA.CV.6953.01 2 0.000
#> TCGA.CV.6945.01 1 0.000
#> TCGA.CV.6939.11 3 0.000
#> TCGA.CV.A45U.01 1 0.000
#> TCGA.CN.A497.01 1 1.000
#> TCGA.D6.6823.01 2 0.000
#> TCGA.DQ.5630.01 2 0.000
#> TCGA.D6.6827.01 1 0.000
#> TCGA.CV.6943.01 2 0.000
#> TCGA.CV.6954.11 3 0.000
#> TCGA.CR.6472.01 1 0.000
#> TCGA.CR.6481.01 1 0.000
#> TCGA.BA.A4IF.01 1 0.000
#> TCGA.BA.6870.01 1 0.000
#> TCGA.CV.6962.11 3 0.000
#> TCGA.CR.6477.01 1 0.000
#> TCGA.CV.A45O.01 2 0.000
#> TCGA.CQ.6219.01 2 0.000
#> TCGA.CN.4733.01 3 0.000
#> TCGA.CR.6484.01 2 0.000
#> TCGA.CN.A498.01 1 1.000
#> TCGA.CR.6470.01 1 0.000
#> TCGA.CV.6934.01 2 0.000
#> TCGA.CN.6989.01 1 0.000
#> TCGA.CV.6953.11 3 0.000
#> TCGA.CV.6933.01 1 1.000
#> TCGA.D6.6517.01 2 0.000
#> TCGA.CQ.6220.01 2 0.000
#> TCGA.BA.A4IH.01 1 0.000
#> TCGA.HD.A4C1.01 2 0.000
#> TCGA.BA.6869.01 2 0.000
#> TCGA.CR.6493.01 2 0.000
#> TCGA.D6.6516.01 2 0.000
#> TCGA.CQ.6227.01 2 0.000
#> TCGA.CV.A45P.01 2 0.000
#> TCGA.CV.A45Q.01 2 0.000
#> TCGA.CV.A45T.01 2 0.000
#> TCGA.CN.6996.01 2 0.000
#> TCGA.CV.6961.11 3 0.000
#> TCGA.CV.6941.01 2 0.000
#> TCGA.BA.6873.01 2 0.000
#> TCGA.CV.6934.11 3 0.000
#> TCGA.CR.6467.01 1 1.000
#> TCGA.CV.6943.11 3 0.000
#> TCGA.CV.6954.01 2 0.000
#> TCGA.BA.6868.01 1 0.751
#> TCGA.CV.6959.01 2 0.000
#> TCGA.CQ.6228.01 2 0.000
#> TCGA.CQ.6229.01 2 0.000
#> TCGA.CQ.6224.01 2 0.000
#> TCGA.CV.6951.01 1 0.000
#> TCGA.CQ.6223.01 2 0.000
#> TCGA.CV.6948.01 1 0.000
#> TCGA.CV.6936.11 3 0.000
#> TCGA.DQ.5624.01 1 1.000
#> TCGA.CV.A45R.01 2 0.000
#> TCGA.CN.A499.01 1 0.000
#> TCGA.CN.A49B.01 1 0.000
#> TCGA.BA.5152.01 2 0.000
#> TCGA.CV.6938.01 2 0.000
#> TCGA.CQ.5326.01 1 0.000
#> TCGA.D6.6824.01 3 0.000
#> TCGA.CV.6940.01 2 0.000
#> TCGA.CQ.6225.01 2 0.000
#> TCGA.CR.6471.01 2 0.000
#> TCGA.CN.6988.01 2 0.000
#> TCGA.BA.6872.01 2 0.000
#> TCGA.CV.6933.11 3 0.000
#> TCGA.CR.6482.01 1 0.000
#> TCGA.P3.A5Q5.01 1 0.000
#> TCGA.CQ.A4C6.01 2 0.000
#> TCGA.QK.A8Z8.01 2 0.000
#> TCGA.CV.A45W.01 1 0.000
#> TCGA.F7.A624.01 2 0.000
#> TCGA.F7.A623.01 1 0.000
#> TCGA.F7.A622.01 2 0.000
#> TCGA.CQ.7064.01 2 0.000
#> TCGA.IQ.A61K.01 2 0.000
#> TCGA.HD.A633.01 2 0.000
#> TCGA.BA.A4IG.01 1 0.000
#> TCGA.F7.A61W.01 1 0.747
#> TCGA.BA.A6DF.01 2 0.000
#> TCGA.D6.A4ZB.01 2 0.000
#> TCGA.KU.A66T.01 2 0.000
#> TCGA.HD.8224.01 2 1.000
#> TCGA.CV.A45Y.01 2 0.000
#> TCGA.BB.A5HU.01 2 0.000
#> TCGA.T3.A92M.01 1 0.000
#> TCGA.CQ.A4C7.01 2 0.000
#> TCGA.P3.A5Q6.01 1 1.000
#> TCGA.CQ.A4CD.01 2 0.000
#> TCGA.BA.A6DB.01 3 0.000
#> TCGA.CV.A468.01 3 0.000
#> TCGA.QK.A8Z7.01 2 1.000
#> TCGA.F7.A620.01 2 0.000
#> TCGA.BA.A8YP.01 2 1.000
#> TCGA.CQ.A4C9.01 2 0.000
#> TCGA.CQ.7072.01 2 0.000
#> TCGA.IQ.A61H.01 1 0.000
#> TCGA.QK.AA3K.01 1 0.000
#> TCGA.CQ.7069.01 1 0.502
#> TCGA.CX.A4AQ.01 1 0.000
#> TCGA.CV.A464.01 2 0.000
#> TCGA.IQ.A61L.01 2 0.000
#> TCGA.QK.A8Z9.01 2 0.000
#> TCGA.HD.A634.01 1 0.000
#> TCGA.4P.AA8J.01 1 0.000
#> TCGA.BB.A5HY.01 2 0.000
#> TCGA.HD.8635.01 2 0.000
#> TCGA.CN.A63T.01 2 0.000
#> TCGA.QK.A652.01 2 0.000
#> TCGA.MT.A67G.01 1 0.000
#> TCGA.QK.A64Z.01 2 0.000
#> TCGA.HD.8634.01 2 0.000
#> TCGA.CQ.7063.01 2 0.000
#> TCGA.CV.A45V.01 2 0.000
#> TCGA.CV.A460.01 1 0.000
#> TCGA.CV.A465.01 2 0.000
#> TCGA.CQ.A4CG.01 2 0.000
#> TCGA.F7.A50J.01 2 0.000
#> TCGA.F7.8298.01 2 0.000
#> TCGA.F7.8489.01 2 0.000
#> TCGA.P3.A5QA.01 2 0.000
#> TCGA.F7.A50G.01 2 0.000
#> TCGA.CQ.A4CA.01 1 1.000
#> TCGA.T3.A92N.01 1 0.751
#> TCGA.F7.A61V.01 2 0.000
#> TCGA.CN.A63Y.01 1 0.000
#> TCGA.CQ.5333.01 2 0.000
#> TCGA.P3.A5QE.01 1 0.000
#> TCGA.MT.A67D.01 2 0.000
#> TCGA.CN.A63V.01 2 0.000
#> TCGA.BA.A6DJ.01 2 0.000
#> TCGA.MT.A51W.01 1 0.000
#> TCGA.P3.A5QF.01 1 0.000
#> TCGA.CQ.A4CE.01 2 0.000
#> TCGA.IQ.A61G.01 1 0.000
#> TCGA.HD.8314.01 1 0.000
#> TCGA.BB.A5HZ.01 2 0.000
#> TCGA.CN.A641.01 2 0.000
#> TCGA.IQ.A61J.01 2 0.000
#> TCGA.BA.A6DG.01 2 0.000
#> TCGA.QK.AA3J.01 1 1.000
#> TCGA.CQ.A4CH.01 3 0.000
#> TCGA.BA.A4II.01 1 0.000
#> TCGA.KU.A66S.01 2 0.502
#> TCGA.CQ.A4CB.01 2 0.000
#> TCGA.D6.8569.01 2 0.000
#> TCGA.IQ.A61I.01 1 1.000
#> TCGA.D6.A4Z9.01 2 0.000
#> TCGA.QK.A8ZA.01 2 0.751
#> TCGA.QK.A8ZB.01 1 0.000
#> TCGA.BA.A6DL.01 2 0.000
#> TCGA.CQ.A4CI.01 1 0.000
#> TCGA.MT.A51X.01 2 0.000
#> TCGA.CV.A461.01 2 0.000
#> TCGA.CQ.7071.01 2 0.000
#> TCGA.H7.8501.01 2 0.000
#> TCGA.BB.8596.01 1 1.000
#> TCGA.F7.A50I.01 1 1.000
#> TCGA.BB.8601.01 1 0.000
#> TCGA.H7.8502.01 1 1.000
#> TCGA.F7.A61S.01 2 0.000
#> TCGA.CV.A463.01 2 0.000
#> TCGA.IQ.A61O.01 2 0.000
#> TCGA.CV.A45Z.01 1 1.000
#> TCGA.CV.A45X.01 1 1.000
#> TCGA.D6.8568.01 2 0.000
#> TCGA.CN.A642.01 2 0.000
#> TCGA.CN.4722.01 2 0.000
#> TCGA.IQ.A6SH.01 1 0.000
#> TCGA.CN.5367.01 2 0.000
#> TCGA.P3.A6T2.01 2 0.000
#> TCGA.P3.A6T8.01 1 0.000
#> TCGA.CN.A6V7.01 1 0.000
#> TCGA.CN.A640.01 2 0.000
#> TCGA.UF.A71E.01 2 1.000
#> TCGA.DQ.7589.01 1 0.000
#> TCGA.P3.A6T6.01 2 0.000
#> TCGA.CN.4725.01 2 0.000
#> TCGA.BA.5153.01 1 0.000
#> TCGA.DQ.7594.01 1 0.000
#> TCGA.HL.7533.01 1 0.000
#> TCGA.T2.A6X0.01 1 0.000
#> TCGA.CN.4730.01 2 0.000
#> TCGA.CN.4723.01 1 1.000
#> TCGA.UF.A7J9.01 1 0.000
#> TCGA.UF.A7JO.01 2 0.000
#> TCGA.DQ.7596.01 1 0.000
#> TCGA.UF.A7JV.01 2 0.000
#> TCGA.CN.4729.01 2 0.000
#> TCGA.IQ.A6SG.01 1 0.000
#> TCGA.BB.7864.01 2 0.000
#> TCGA.MT.A67A.01 2 0.000
#> TCGA.CN.5361.01 2 0.000
#> TCGA.CN.5359.01 1 0.502
#> TCGA.BB.7861.01 1 0.000
#> TCGA.CN.4728.01 1 0.000
#> TCGA.BB.A6UO.01 2 0.000
#> TCGA.BA.4074.01 2 0.000
#> TCGA.CN.4734.01 2 0.000
#> TCGA.QK.A6VB.01 2 0.000
#> TCGA.BA.4075.01 2 0.000
#> TCGA.BB.7871.01 1 0.000
#> TCGA.CN.4726.01 2 0.000
#> TCGA.CN.4735.01 1 0.000
#> TCGA.P3.A6T3.01 2 0.000
#> TCGA.HD.7917.01 2 0.000
#> TCGA.BB.4223.01 1 0.249
#> TCGA.UF.A71B.01 2 0.000
#> TCGA.UF.A7JS.01 2 0.000
#> TCGA.QK.A6VC.01 1 0.000
#> TCGA.CV.7409.01 2 0.000
#> TCGA.CN.4736.01 2 0.000
#> TCGA.BB.7862.01 1 0.000
#> TCGA.BA.A6DI.01 2 0.751
#> TCGA.RS.A6TO.01 2 0.000
#> TCGA.CN.4737.01 2 0.000
#> TCGA.CN.5355.01 2 0.000
#> TCGA.UF.A71D.01 2 0.000
#> TCGA.CQ.7067.01 2 0.000
#> TCGA.BA.4078.01 1 0.000
#> TCGA.CN.5374.01 1 0.000
#> TCGA.DQ.7590.01 1 0.000
#> TCGA.CN.5369.01 2 0.000
#> TCGA.BA.5151.01 2 0.000
#> TCGA.TN.A7HJ.01 2 0.000
#> TCGA.IQ.A61E.01 2 0.000
#> TCGA.BB.7870.01 2 0.000
#> TCGA.CN.4727.01 2 0.000
#> TCGA.DQ.7595.01 1 0.000
#> TCGA.BA.4076.01 1 0.000
#> TCGA.CN.5360.01 1 1.000
#> TCGA.BB.4228.01 1 0.000
#> TCGA.MZ.A7D7.01 1 0.000
#> TCGA.H7.A76A.01 1 0.000
#> TCGA.UF.A7JT.01 2 0.000
#> TCGA.CN.5373.01 2 0.000
#> TCGA.CN.A6V3.01 2 0.000
#> TCGA.BB.7863.01 2 0.000
#> TCGA.DQ.7593.01 1 0.000
#> TCGA.UF.A7JJ.01 2 0.000
#> TCGA.CN.5363.01 2 0.000
#> TCGA.BA.4077.01 1 0.000
#> TCGA.BB.4225.01 2 1.000
#> TCGA.BB.7872.01 2 0.000
#> TCGA.CN.A6UY.01 1 0.000
#> TCGA.MT.A7BN.01 2 1.000
#> TCGA.UF.A7JF.01 2 0.000
#> TCGA.CN.4731.01 2 0.000
#> TCGA.MZ.A5BI.01 1 0.000
#> TCGA.CN.A63W.01 1 0.498
#> TCGA.H7.A6C4.01 2 0.000
#> TCGA.T2.A6X2.01 2 0.000
#> TCGA.CN.5364.01 2 0.000
#> TCGA.CN.A63U.01 2 0.000
#> TCGA.BB.A6UM.01 1 0.000
#> TCGA.H7.A6C5.01 2 0.000
#> TCGA.CN.4741.01 1 0.000
#> TCGA.CV.A6JO.01 2 0.000
#> TCGA.BB.7866.01 1 1.000
#> TCGA.CN.5365.01 2 0.000
#> TCGA.CN.4740.01 2 0.000
#> TCGA.BB.4224.01 2 0.000
#> TCGA.MT.A67F.01 2 0.000
#> TCGA.CN.5366.01 2 0.000
#> TCGA.QK.A6V9.01 1 0.000
#> TCGA.CN.5356.01 2 0.000
#> TCGA.T2.A6WX.01 2 0.000
#> TCGA.CV.A6JZ.01 2 0.000
#> TCGA.CN.A6V1.01 1 0.000
#> TCGA.HD.A6I0.01 2 0.000
#> TCGA.UF.A71A.01 1 0.000
#> TCGA.CV.7430.01 1 0.000
#> TCGA.CR.7383.01 1 1.000
#> TCGA.CN.A6V6.01 1 1.000
#> TCGA.F7.7848.01 2 0.000
#> TCGA.TN.A7HI.01 2 1.000
#> TCGA.UF.A7JC.01 1 0.751
#> TCGA.D6.A6ES.01 2 0.000
#> TCGA.CV.7568.01 1 0.000
#> TCGA.BA.A6D8.01 2 1.000
#> TCGA.P3.A6T4.01 1 0.000
#> TCGA.QK.A6IF.01 1 0.000
#> TCGA.CV.A6JT.01 2 0.000
#> TCGA.CV.7438.01 2 0.000
#> TCGA.RS.A6TP.01 2 1.000
#> TCGA.P3.A6SW.01 2 0.000
#> TCGA.D6.A6EN.01 2 0.000
#> TCGA.D6.A6EM.01 2 0.000
#> TCGA.UF.A7JK.01 2 0.000
#> TCGA.KU.A6H7.06 1 0.000
#> TCGA.CV.7429.01 1 0.000
#> TCGA.UP.A6WW.01 1 0.000
#> TCGA.CV.7437.01 2 1.000
#> TCGA.CV.A6JD.01 2 0.000
#> TCGA.CV.A6JY.01 1 1.000
#> TCGA.CV.A6JN.01 2 0.000
#> TCGA.CV.7446.01 1 0.000
#> TCGA.CV.7432.01 2 0.000
#> TCGA.CV.7434.01 2 0.000
#> TCGA.WA.A7H4.01 3 0.000
#> TCGA.KU.A6H8.01 3 0.000
#> TCGA.CV.7428.01 2 0.000
#> TCGA.D6.A6EK.01 2 0.000
#> TCGA.CV.A6K0.01 3 0.000
#> TCGA.HD.7832.01 2 0.000
#> TCGA.MZ.A6I9.01 1 1.000
#> TCGA.CV.7435.01 1 1.000
#> TCGA.P3.A6SX.01 1 0.000
#> TCGA.QK.A6IG.01 2 0.000
#> TCGA.HD.7831.01 2 1.000
#> TCGA.CV.A6JM.01 1 0.000
#> TCGA.CR.7404.01 2 0.000
#> TCGA.D6.A6EQ.01 2 0.000
#> TCGA.QK.A6IJ.01 2 0.000
#> TCGA.P3.A6T0.01 2 0.000
#> TCGA.CV.A6JE.01 2 0.000
#> TCGA.HD.A6HZ.01 2 1.000
#> TCGA.QK.A6II.01 2 0.000
#> TCGA.P3.A6T7.01 2 0.000
#> TCGA.BA.A6DD.01 2 0.253
#> TCGA.UF.A719.01 2 0.000
#> TCGA.TN.A7HL.01 1 0.000
#> TCGA.UF.A7JA.01 1 0.000
#> TCGA.CR.7368.01 2 0.000
#> TCGA.CR.7382.01 2 1.000
#> TCGA.UF.A7JD.01 2 0.000
#> TCGA.UF.A7JH.01 2 0.000
#> TCGA.BA.A6DA.01 2 1.000
#> TCGA.T2.A6WZ.01 2 0.000
#> TCGA.D6.A6EO.01 2 0.000
#> TCGA.CR.7370.01 1 0.000
#> TCGA.P3.A6T5.01 2 0.000
#> TCGA.D6.A74Q.01 2 0.000
#> TCGA.UF.A718.01 2 0.000
#> TCGA.CR.7369.01 2 0.000
#> TCGA.QK.A6IH.01 2 0.000
#> TCGA.CV.A6K2.01 2 0.000
#> TCGA.CV.A6K1.01 1 0.000
#> TCGA.BA.A6DE.01 2 0.000
#> TCGA.WA.A7GZ.01 1 0.000
#> TCGA.CV.7433.01 1 0.000
#> TCGA.CV.7440.01 2 0.000
#> TCGA.CV.A6JU.01 2 0.000
#> TCGA.CR.7376.01 3 0.000
#> TCGA.UF.A71A.06 1 0.000
#> TCGA.KU.A6H7.01 1 0.000
#> TCGA.D6.A6EP.01 1 0.000
get_classes(res, k = 4)
#> class p
#> TCGA.CN.6022.01 1 0.253
#> TCGA.CQ.5327.01 2 0.000
#> TCGA.CV.5435.11 3 0.000
#> TCGA.HD.7753.01 2 0.000
#> TCGA.CQ.5325.01 2 0.000
#> TCGA.CV.5432.01 1 0.000
#> TCGA.CR.7391.01 2 0.000
#> TCGA.CV.7415.01 2 0.000
#> TCGA.CR.5247.01 4 0.000
#> TCGA.CN.6011.01 2 0.000
#> TCGA.CV.7414.01 1 0.000
#> TCGA.CV.6436.01 2 0.000
#> TCGA.DQ.7592.01 2 0.000
#> TCGA.IQ.7632.01 1 0.751
#> TCGA.CV.7416.01 2 0.000
#> TCGA.CV.5432.11 3 0.000
#> TCGA.H7.7774.01 2 0.000
#> TCGA.CQ.5330.01 2 0.000
#> TCGA.CV.5430.11 3 0.000
#> TCGA.CV.7427.01 2 0.000
#> TCGA.CV.5979.01 2 0.000
#> TCGA.CR.6488.01 1 1.000
#> TCGA.CQ.6221.01 2 0.000
#> TCGA.CV.5434.11 3 0.000
#> TCGA.CV.5970.11 3 0.000
#> TCGA.CV.7425.01 2 0.000
#> TCGA.CV.6441.01 2 0.000
#> TCGA.IQ.7630.01 2 0.000
#> TCGA.CV.5976.11 3 0.000
#> TCGA.CV.7103.11 3 0.000
#> TCGA.CV.5977.01 2 0.000
#> TCGA.CQ.5324.01 2 0.000
#> TCGA.CV.7407.01 2 0.000
#> TCGA.CV.5971.01 3 1.000
#> TCGA.CV.5970.01 2 0.000
#> TCGA.CN.6016.01 3 0.000
#> TCGA.CV.6003.01 2 0.000
#> TCGA.CN.6010.01 2 0.249
#> TCGA.CN.6021.01 2 1.000
#> TCGA.CV.6433.01 1 0.000
#> TCGA.CV.5434.01 2 0.249
#> TCGA.CV.7413.01 2 0.000
#> TCGA.HD.7754.01 1 0.000
#> TCGA.CN.6017.01 2 0.000
#> TCGA.CV.6003.11 3 0.000
#> TCGA.CV.7422.01 1 0.249
#> TCGA.CV.7421.01 1 0.000
#> TCGA.CV.5439.11 3 0.000
#> TCGA.CV.7235.01 2 0.000
#> TCGA.BA.7269.01 1 1.000
#> TCGA.CV.5971.11 3 0.000
#> TCGA.CQ.5332.01 1 1.000
#> TCGA.CV.5439.01 2 0.000
#> TCGA.CN.6020.01 2 0.000
#> TCGA.CV.7423.01 2 0.000
#> TCGA.CV.7263.01 4 0.000
#> TCGA.CV.7406.01 1 0.000
#> TCGA.CN.6023.01 2 0.000
#> TCGA.CV.5966.11 3 0.000
#> TCGA.CV.7101.01 1 0.000
#> TCGA.CV.5977.11 3 0.000
#> TCGA.CR.7365.01 2 0.000
#> TCGA.CN.6012.01 1 0.000
#> TCGA.CV.6441.11 3 0.000
#> TCGA.CN.6024.01 2 0.000
#> TCGA.CV.5978.01 2 0.000
#> TCGA.CX.7086.01 4 0.000
#> TCGA.CV.7424.01 1 0.000
#> TCGA.CV.7089.01 3 0.000
#> TCGA.CQ.7065.01 1 1.000
#> TCGA.IQ.7631.01 1 0.000
#> TCGA.CV.7418.01 1 1.000
#> TCGA.CV.6937.01 3 0.502
#> TCGA.CN.6018.01 2 0.000
#> TCGA.CV.5966.01 2 0.000
#> TCGA.CQ.5329.01 2 1.000
#> TCGA.CV.5976.01 2 0.000
#> TCGA.CV.7411.01 2 0.000
#> TCGA.CQ.5323.01 2 0.249
#> TCGA.CV.5978.11 3 0.000
#> TCGA.CV.5973.11 3 0.000
#> TCGA.BB.4217.01 2 0.000
#> TCGA.CQ.7068.01 2 0.000
#> TCGA.CN.6013.01 1 0.000
#> TCGA.CV.6436.11 3 0.000
#> TCGA.CV.6433.11 3 0.000
#> TCGA.CN.6995.01 2 0.000
#> TCGA.CV.6960.01 4 0.000
#> TCGA.CQ.5334.01 2 0.000
#> TCGA.CV.7410.01 2 0.000
#> TCGA.CN.6019.01 3 0.000
#> TCGA.DQ.7588.01 2 0.502
#> TCGA.CV.5979.11 3 0.000
#> TCGA.CR.6492.01 3 0.000
#> TCGA.CV.5973.01 2 0.000
#> TCGA.DQ.7591.01 2 0.751
#> TCGA.CR.7389.01 1 0.502
#> TCGA.CV.7245.01 4 0.000
#> TCGA.CV.5430.01 2 1.000
#> TCGA.CV.5435.01 2 1.000
#> TCGA.CR.7374.01 1 0.000
#> TCGA.CV.5440.01 1 0.249
#> TCGA.CV.6955.11 3 0.000
#> TCGA.CV.7238.11 3 0.000
#> TCGA.CV.7104.01 2 0.000
#> TCGA.CV.7100.01 1 0.498
#> TCGA.CV.7089.11 3 0.000
#> TCGA.CN.4739.01 4 0.000
#> TCGA.CV.7095.01 2 0.000
#> TCGA.CV.6956.01 4 0.000
#> TCGA.CV.5431.11 3 0.000
#> TCGA.CV.7261.01 2 0.751
#> TCGA.CN.5358.01 2 0.751
#> TCGA.BA.5559.01 1 0.000
#> TCGA.CR.7373.01 2 0.000
#> TCGA.CX.7082.01 1 0.000
#> TCGA.DQ.5629.01 1 0.000
#> TCGA.CV.7255.11 3 0.000
#> TCGA.CR.7379.01 1 1.000
#> TCGA.CV.7178.01 1 1.000
#> TCGA.CR.5249.01 1 0.000
#> TCGA.CV.7091.01 4 0.000
#> TCGA.CV.7236.01 2 1.000
#> TCGA.CN.6998.01 2 0.000
#> TCGA.CR.7399.01 1 0.000
#> TCGA.CR.7372.01 1 1.000
#> TCGA.CV.7252.01 2 0.000
#> TCGA.CV.7242.01 4 0.000
#> TCGA.CV.7103.01 1 0.000
#> TCGA.CR.6478.01 2 0.000
#> TCGA.CR.7371.01 1 0.000
#> TCGA.CR.7380.01 2 0.000
#> TCGA.CV.7183.01 2 0.000
#> TCGA.CV.7250.11 3 0.000
#> TCGA.CV.7102.01 2 0.000
#> TCGA.CV.7254.01 2 0.000
#> TCGA.CR.7394.01 2 0.000
#> TCGA.CV.5443.01 1 0.000
#> TCGA.CV.6955.01 2 0.000
#> TCGA.CV.5441.11 3 1.000
#> TCGA.CV.5442.11 3 0.000
#> TCGA.BA.5556.01 2 0.000
#> TCGA.CR.7386.01 2 0.000
#> TCGA.CV.7255.01 2 1.000
#> TCGA.CR.6474.01 2 0.000
#> TCGA.BA.5557.01 2 0.000
#> TCGA.CR.7388.01 1 0.000
#> TCGA.CV.5436.11 3 0.000
#> TCGA.CR.7398.01 4 0.000
#> TCGA.CV.7247.01 2 0.000
#> TCGA.CN.6997.01 1 0.000
#> TCGA.CN.4742.01 2 1.000
#> TCGA.CN.4738.01 1 0.000
#> TCGA.CR.7392.01 2 1.000
#> TCGA.CV.7245.11 3 0.000
#> TCGA.CR.7377.01 2 0.000
#> TCGA.HD.7229.01 2 0.000
#> TCGA.CV.7235.11 3 0.000
#> TCGA.D6.6515.01 2 0.000
#> TCGA.CV.7238.01 2 0.000
#> TCGA.CR.5248.01 1 0.000
#> TCGA.CV.7097.01 2 0.000
#> TCGA.CR.5250.01 1 0.000
#> TCGA.CV.7248.01 1 0.502
#> TCGA.CV.7253.01 4 0.000
#> TCGA.CN.5370.01 2 0.000
#> TCGA.CR.7367.01 2 0.000
#> TCGA.CR.7401.01 2 0.000
#> TCGA.BA.5149.01 1 1.000
#> TCGA.CV.6942.01 2 0.000
#> TCGA.CV.7263.11 3 0.000
#> TCGA.CV.7177.01 2 0.000
#> TCGA.BA.5555.01 4 0.000
#> TCGA.CV.6956.11 3 0.000
#> TCGA.CV.5431.01 1 0.000
#> TCGA.CR.7393.01 3 0.000
#> TCGA.CV.5444.11 3 0.000
#> TCGA.CV.5444.01 3 1.000
#> TCGA.CR.5243.01 1 0.000
#> TCGA.CR.7395.01 2 0.000
#> TCGA.CV.5441.01 4 0.000
#> TCGA.CV.5442.01 1 0.000
#> TCGA.BA.5558.01 2 0.000
#> TCGA.CX.7085.01 2 0.000
#> TCGA.CV.7250.01 4 0.000
#> TCGA.CR.7390.01 1 0.000
#> TCGA.CV.7178.11 3 0.000
#> TCGA.CV.7099.01 2 0.000
#> TCGA.CV.5443.11 3 0.000
#> TCGA.CR.7385.01 1 0.000
#> TCGA.CR.7364.01 4 0.000
#> TCGA.CV.7090.01 2 0.000
#> TCGA.CR.7397.01 3 0.000
#> TCGA.CR.7402.01 4 0.000
#> TCGA.CV.5440.11 3 0.000
#> TCGA.CV.7180.01 1 1.000
#> TCGA.CX.7219.01 2 0.000
#> TCGA.CV.7101.11 3 0.000
#> TCGA.CV.5436.01 1 1.000
#> TCGA.CV.7243.01 2 0.000
#> TCGA.BA.6871.01 1 0.000
#> TCGA.CQ.6218.01 2 0.000
#> TCGA.C9.A47Z.01 2 0.000
#> TCGA.CV.6961.01 2 0.249
#> TCGA.DQ.5625.01 2 0.000
#> TCGA.CN.6992.01 1 0.000
#> TCGA.CV.6939.01 1 0.000
#> TCGA.CR.6480.01 2 0.000
#> TCGA.D6.6825.01 2 0.000
#> TCGA.C9.A480.01 2 0.000
#> TCGA.CV.6962.01 1 0.000
#> TCGA.CV.6952.01 2 0.000
#> TCGA.CN.A49A.01 4 0.000
#> TCGA.CR.6487.01 1 0.000
#> TCGA.CV.6935.11 3 0.000
#> TCGA.CQ.6222.01 2 0.000
#> TCGA.CV.6959.11 3 0.000
#> TCGA.BB.4227.01 2 0.000
#> TCGA.CN.A49C.01 2 0.000
#> TCGA.CN.6994.01 2 0.000
#> TCGA.CV.6938.11 3 0.000
#> TCGA.CV.6936.01 1 0.751
#> TCGA.CR.6491.01 2 0.000
#> TCGA.CV.6950.01 2 0.000
#> TCGA.CR.6473.01 2 1.000
#> TCGA.CV.6952.11 3 0.000
#> TCGA.CQ.5331.01 2 0.000
#> TCGA.D6.6826.01 2 0.000
#> TCGA.CV.6951.11 3 0.000
#> TCGA.CV.6935.01 2 0.000
#> TCGA.DQ.5631.01 1 0.751
#> TCGA.CV.6953.01 2 0.000
#> TCGA.CV.6945.01 2 0.000
#> TCGA.CV.6939.11 3 0.000
#> TCGA.CV.A45U.01 1 0.249
#> TCGA.CN.A497.01 4 0.000
#> TCGA.D6.6823.01 4 0.000
#> TCGA.DQ.5630.01 2 0.000
#> TCGA.D6.6827.01 3 0.498
#> TCGA.CV.6943.01 2 0.000
#> TCGA.CV.6954.11 3 0.000
#> TCGA.CR.6472.01 1 0.000
#> TCGA.CR.6481.01 1 0.000
#> TCGA.BA.A4IF.01 4 0.000
#> TCGA.BA.6870.01 2 0.000
#> TCGA.CV.6962.11 3 0.000
#> TCGA.CR.6477.01 2 0.000
#> TCGA.CV.A45O.01 2 0.000
#> TCGA.CQ.6219.01 2 0.000
#> TCGA.CN.4733.01 2 0.000
#> TCGA.CR.6484.01 1 0.249
#> TCGA.CN.A498.01 2 0.000
#> TCGA.CR.6470.01 1 0.000
#> TCGA.CV.6934.01 1 1.000
#> TCGA.CN.6989.01 2 1.000
#> TCGA.CV.6953.11 2 0.000
#> TCGA.CV.6933.01 1 0.000
#> TCGA.D6.6517.01 2 0.000
#> TCGA.CQ.6220.01 2 0.000
#> TCGA.BA.A4IH.01 1 0.000
#> TCGA.HD.A4C1.01 2 0.000
#> TCGA.BA.6869.01 4 0.000
#> TCGA.CR.6493.01 2 0.000
#> TCGA.D6.6516.01 2 0.000
#> TCGA.CQ.6227.01 2 0.000
#> TCGA.CV.A45P.01 2 0.000
#> TCGA.CV.A45Q.01 2 0.000
#> TCGA.CV.A45T.01 2 0.000
#> TCGA.CN.6996.01 2 0.000
#> TCGA.CV.6961.11 3 0.000
#> TCGA.CV.6941.01 4 0.000
#> TCGA.BA.6873.01 2 0.000
#> TCGA.CV.6934.11 3 0.000
#> TCGA.CR.6467.01 1 1.000
#> TCGA.CV.6943.11 3 0.000
#> TCGA.CV.6954.01 4 0.000
#> TCGA.BA.6868.01 2 0.000
#> TCGA.CV.6959.01 2 0.000
#> TCGA.CQ.6228.01 4 0.000
#> TCGA.CQ.6229.01 2 0.000
#> TCGA.CQ.6224.01 2 0.498
#> TCGA.CV.6951.01 1 0.751
#> TCGA.CQ.6223.01 2 0.000
#> TCGA.CV.6948.01 1 0.000
#> TCGA.CV.6936.11 3 0.000
#> TCGA.DQ.5624.01 2 0.000
#> TCGA.CV.A45R.01 2 0.000
#> TCGA.CN.A499.01 2 0.000
#> TCGA.CN.A49B.01 2 0.000
#> TCGA.BA.5152.01 2 0.000
#> TCGA.CV.6938.01 2 0.000
#> TCGA.CQ.5326.01 2 0.000
#> TCGA.D6.6824.01 3 0.000
#> TCGA.CV.6940.01 2 0.000
#> TCGA.CQ.6225.01 4 0.000
#> TCGA.CR.6471.01 2 0.000
#> TCGA.CN.6988.01 4 0.000
#> TCGA.BA.6872.01 2 0.000
#> TCGA.CV.6933.11 3 0.000
#> TCGA.CR.6482.01 1 0.000
#> TCGA.P3.A5Q5.01 1 0.000
#> TCGA.CQ.A4C6.01 2 0.000
#> TCGA.QK.A8Z8.01 4 0.000
#> TCGA.CV.A45W.01 1 0.000
#> TCGA.F7.A624.01 1 1.000
#> TCGA.F7.A623.01 1 0.000
#> TCGA.F7.A622.01 1 1.000
#> TCGA.CQ.7064.01 2 0.000
#> TCGA.IQ.A61K.01 2 0.000
#> TCGA.HD.A633.01 2 0.000
#> TCGA.BA.A4IG.01 1 0.000
#> TCGA.F7.A61W.01 2 0.000
#> TCGA.BA.A6DF.01 2 0.000
#> TCGA.D6.A4ZB.01 2 0.000
#> TCGA.KU.A66T.01 1 0.000
#> TCGA.HD.8224.01 1 0.000
#> TCGA.CV.A45Y.01 2 0.000
#> TCGA.BB.A5HU.01 2 0.000
#> TCGA.T3.A92M.01 1 0.000
#> TCGA.CQ.A4C7.01 2 0.000
#> TCGA.P3.A5Q6.01 2 0.000
#> TCGA.CQ.A4CD.01 2 0.000
#> TCGA.BA.A6DB.01 3 0.000
#> TCGA.CV.A468.01 3 0.000
#> TCGA.QK.A8Z7.01 4 0.000
#> TCGA.F7.A620.01 2 0.000
#> TCGA.BA.A8YP.01 1 0.000
#> TCGA.CQ.A4C9.01 4 0.000
#> TCGA.CQ.7072.01 4 0.000
#> TCGA.IQ.A61H.01 2 0.000
#> TCGA.QK.AA3K.01 1 0.751
#> TCGA.CQ.7069.01 2 1.000
#> TCGA.CX.A4AQ.01 2 1.000
#> TCGA.CV.A464.01 3 0.000
#> TCGA.IQ.A61L.01 2 0.000
#> TCGA.QK.A8Z9.01 2 0.000
#> TCGA.HD.A634.01 1 0.000
#> TCGA.4P.AA8J.01 2 0.498
#> TCGA.BB.A5HY.01 2 0.000
#> TCGA.HD.8635.01 2 0.000
#> TCGA.CN.A63T.01 4 0.000
#> TCGA.QK.A652.01 2 0.000
#> TCGA.MT.A67G.01 2 0.000
#> TCGA.QK.A64Z.01 2 0.000
#> TCGA.HD.8634.01 2 0.000
#> TCGA.CQ.7063.01 2 0.000
#> TCGA.CV.A45V.01 1 1.000
#> TCGA.CV.A460.01 2 1.000
#> TCGA.CV.A465.01 1 1.000
#> TCGA.CQ.A4CG.01 2 0.000
#> TCGA.F7.A50J.01 2 0.000
#> TCGA.F7.8298.01 2 0.000
#> TCGA.F7.8489.01 2 0.000
#> TCGA.P3.A5QA.01 2 1.000
#> TCGA.F7.A50G.01 2 0.000
#> TCGA.CQ.A4CA.01 2 0.000
#> TCGA.T3.A92N.01 2 0.000
#> TCGA.F7.A61V.01 4 0.000
#> TCGA.CN.A63Y.01 1 0.000
#> TCGA.CQ.5333.01 2 0.000
#> TCGA.P3.A5QE.01 1 0.000
#> TCGA.MT.A67D.01 1 0.253
#> TCGA.CN.A63V.01 1 1.000
#> TCGA.BA.A6DJ.01 2 0.000
#> TCGA.MT.A51W.01 2 0.000
#> TCGA.P3.A5QF.01 4 0.000
#> TCGA.CQ.A4CE.01 1 1.000
#> TCGA.IQ.A61G.01 2 0.000
#> TCGA.HD.8314.01 1 0.000
#> TCGA.BB.A5HZ.01 4 0.000
#> TCGA.CN.A641.01 4 0.000
#> TCGA.IQ.A61J.01 2 0.000
#> TCGA.BA.A6DG.01 2 0.000
#> TCGA.QK.AA3J.01 4 0.000
#> TCGA.CQ.A4CH.01 2 0.000
#> TCGA.BA.A4II.01 2 0.000
#> TCGA.KU.A66S.01 4 0.000
#> TCGA.CQ.A4CB.01 2 0.000
#> TCGA.D6.8569.01 2 0.000
#> TCGA.IQ.A61I.01 2 0.000
#> TCGA.D6.A4Z9.01 2 0.000
#> TCGA.QK.A8ZA.01 1 0.000
#> TCGA.QK.A8ZB.01 1 0.000
#> TCGA.BA.A6DL.01 4 0.000
#> TCGA.CQ.A4CI.01 1 0.000
#> TCGA.MT.A51X.01 1 1.000
#> TCGA.CV.A461.01 4 0.000
#> TCGA.CQ.7071.01 2 0.000
#> TCGA.H7.8501.01 2 0.000
#> TCGA.BB.8596.01 1 0.502
#> TCGA.F7.A50I.01 2 0.000
#> TCGA.BB.8601.01 2 0.000
#> TCGA.H7.8502.01 2 0.000
#> TCGA.F7.A61S.01 2 0.000
#> TCGA.CV.A463.01 2 0.000
#> TCGA.IQ.A61O.01 2 1.000
#> TCGA.CV.A45Z.01 1 0.000
#> TCGA.CV.A45X.01 2 0.502
#> TCGA.D6.8568.01 2 0.000
#> TCGA.CN.A642.01 2 0.000
#> TCGA.CN.4722.01 2 1.000
#> TCGA.IQ.A6SH.01 1 0.751
#> TCGA.CN.5367.01 2 0.000
#> TCGA.P3.A6T2.01 2 0.000
#> TCGA.P3.A6T8.01 1 1.000
#> TCGA.CN.A6V7.01 2 0.000
#> TCGA.CN.A640.01 2 0.000
#> TCGA.UF.A71E.01 1 0.000
#> TCGA.DQ.7589.01 2 0.000
#> TCGA.P3.A6T6.01 4 0.000
#> TCGA.CN.4725.01 2 0.000
#> TCGA.BA.5153.01 1 0.000
#> TCGA.DQ.7594.01 1 0.000
#> TCGA.HL.7533.01 2 0.502
#> TCGA.T2.A6X0.01 1 0.000
#> TCGA.CN.4730.01 4 0.000
#> TCGA.CN.4723.01 1 0.000
#> TCGA.UF.A7J9.01 1 0.000
#> TCGA.UF.A7JO.01 2 0.000
#> TCGA.DQ.7596.01 1 0.000
#> TCGA.UF.A7JV.01 2 0.000
#> TCGA.CN.4729.01 2 0.000
#> TCGA.IQ.A6SG.01 2 0.000
#> TCGA.BB.7864.01 4 0.000
#> TCGA.MT.A67A.01 2 0.000
#> TCGA.CN.5361.01 2 0.000
#> TCGA.CN.5359.01 2 0.000
#> TCGA.BB.7861.01 1 0.000
#> TCGA.CN.4728.01 3 0.498
#> TCGA.BB.A6UO.01 2 0.000
#> TCGA.BA.4074.01 4 0.000
#> TCGA.CN.4734.01 2 0.000
#> TCGA.QK.A6VB.01 4 0.000
#> TCGA.BA.4075.01 2 0.000
#> TCGA.BB.7871.01 2 0.000
#> TCGA.CN.4726.01 2 0.000
#> TCGA.CN.4735.01 1 0.000
#> TCGA.P3.A6T3.01 2 1.000
#> TCGA.HD.7917.01 4 0.000
#> TCGA.BB.4223.01 1 0.000
#> TCGA.UF.A71B.01 1 0.000
#> TCGA.UF.A7JS.01 2 0.000
#> TCGA.QK.A6VC.01 1 0.000
#> TCGA.CV.7409.01 4 0.000
#> TCGA.CN.4736.01 2 0.000
#> TCGA.BB.7862.01 1 0.000
#> TCGA.BA.A6DI.01 1 1.000
#> TCGA.RS.A6TO.01 1 1.000
#> TCGA.CN.4737.01 4 0.000
#> TCGA.CN.5355.01 2 0.000
#> TCGA.UF.A71D.01 4 0.000
#> TCGA.CQ.7067.01 2 0.249
#> TCGA.BA.4078.01 1 0.000
#> TCGA.CN.5374.01 1 0.000
#> TCGA.DQ.7590.01 1 1.000
#> TCGA.CN.5369.01 2 0.000
#> TCGA.BA.5151.01 2 0.000
#> TCGA.TN.A7HJ.01 1 1.000
#> TCGA.IQ.A61E.01 2 0.000
#> TCGA.BB.7870.01 4 0.000
#> TCGA.CN.4727.01 4 0.000
#> TCGA.DQ.7595.01 4 0.000
#> TCGA.BA.4076.01 2 0.000
#> TCGA.CN.5360.01 4 0.000
#> TCGA.BB.4228.01 1 0.000
#> TCGA.MZ.A7D7.01 2 1.000
#> TCGA.H7.A76A.01 1 0.000
#> TCGA.UF.A7JT.01 2 0.000
#> TCGA.CN.5373.01 2 0.000
#> TCGA.CN.A6V3.01 4 0.000
#> TCGA.BB.7863.01 2 0.000
#> TCGA.DQ.7593.01 1 0.000
#> TCGA.UF.A7JJ.01 1 1.000
#> TCGA.CN.5363.01 2 0.000
#> TCGA.BA.4077.01 2 0.000
#> TCGA.BB.4225.01 1 0.000
#> TCGA.BB.7872.01 2 0.000
#> TCGA.CN.A6UY.01 1 1.000
#> TCGA.MT.A7BN.01 1 0.000
#> TCGA.UF.A7JF.01 4 0.000
#> TCGA.CN.4731.01 4 0.000
#> TCGA.MZ.A5BI.01 1 0.000
#> TCGA.CN.A63W.01 4 0.000
#> TCGA.H7.A6C4.01 2 0.000
#> TCGA.T2.A6X2.01 2 0.000
#> TCGA.CN.5364.01 1 0.000
#> TCGA.CN.A63U.01 4 0.000
#> TCGA.BB.A6UM.01 1 0.000
#> TCGA.H7.A6C5.01 4 0.000
#> TCGA.CN.4741.01 2 0.000
#> TCGA.CV.A6JO.01 2 0.000
#> TCGA.BB.7866.01 2 0.498
#> TCGA.CN.5365.01 2 0.000
#> TCGA.CN.4740.01 1 0.498
#> TCGA.BB.4224.01 2 0.000
#> TCGA.MT.A67F.01 2 0.000
#> TCGA.CN.5366.01 2 0.000
#> TCGA.QK.A6V9.01 2 0.000
#> TCGA.CN.5356.01 4 0.000
#> TCGA.T2.A6WX.01 2 0.000
#> TCGA.CV.A6JZ.01 2 0.000
#> TCGA.CN.A6V1.01 2 0.498
#> TCGA.HD.A6I0.01 2 0.000
#> TCGA.UF.A71A.01 1 0.000
#> TCGA.CV.7430.01 2 0.751
#> TCGA.CR.7383.01 2 0.000
#> TCGA.CN.A6V6.01 1 0.000
#> TCGA.F7.7848.01 4 0.000
#> TCGA.TN.A7HI.01 1 0.000
#> TCGA.UF.A7JC.01 2 0.000
#> TCGA.D6.A6ES.01 1 1.000
#> TCGA.CV.7568.01 2 0.000
#> TCGA.BA.A6D8.01 1 0.000
#> TCGA.P3.A6T4.01 1 0.000
#> TCGA.QK.A6IF.01 1 0.000
#> TCGA.CV.A6JT.01 2 0.000
#> TCGA.CV.7438.01 2 0.000
#> TCGA.RS.A6TP.01 1 0.000
#> TCGA.P3.A6SW.01 1 1.000
#> TCGA.D6.A6EN.01 2 0.000
#> TCGA.D6.A6EM.01 1 0.502
#> TCGA.UF.A7JK.01 2 0.249
#> TCGA.KU.A6H7.06 1 0.000
#> TCGA.CV.7429.01 2 0.000
#> TCGA.UP.A6WW.01 1 0.249
#> TCGA.CV.7437.01 2 0.000
#> TCGA.CV.A6JD.01 2 0.000
#> TCGA.CV.A6JY.01 1 0.000
#> TCGA.CV.A6JN.01 2 0.000
#> TCGA.CV.7446.01 1 0.000
#> TCGA.CV.7432.01 2 0.000
#> TCGA.CV.7434.01 2 0.000
#> TCGA.WA.A7H4.01 1 0.751
#> TCGA.KU.A6H8.01 3 0.000
#> TCGA.CV.7428.01 4 0.000
#> TCGA.D6.A6EK.01 1 1.000
#> TCGA.CV.A6K0.01 3 0.000
#> TCGA.HD.7832.01 2 0.000
#> TCGA.MZ.A6I9.01 1 0.000
#> TCGA.CV.7435.01 4 0.000
#> TCGA.P3.A6SX.01 2 0.000
#> TCGA.QK.A6IG.01 2 1.000
#> TCGA.HD.7831.01 3 0.000
#> TCGA.CV.A6JM.01 1 0.502
#> TCGA.CR.7404.01 1 0.000
#> TCGA.D6.A6EQ.01 2 1.000
#> TCGA.QK.A6IJ.01 1 0.502
#> TCGA.P3.A6T0.01 2 0.253
#> TCGA.CV.A6JE.01 1 1.000
#> TCGA.HD.A6HZ.01 1 0.000
#> TCGA.QK.A6II.01 2 0.000
#> TCGA.P3.A6T7.01 2 0.000
#> TCGA.BA.A6DD.01 1 0.502
#> TCGA.UF.A719.01 4 0.000
#> TCGA.TN.A7HL.01 1 0.000
#> TCGA.UF.A7JA.01 1 0.253
#> TCGA.CR.7368.01 1 0.000
#> TCGA.CR.7382.01 2 0.000
#> TCGA.UF.A7JD.01 4 0.000
#> TCGA.UF.A7JH.01 4 0.000
#> TCGA.BA.A6DA.01 2 0.502
#> TCGA.T2.A6WZ.01 2 0.000
#> TCGA.D6.A6EO.01 4 0.000
#> TCGA.CR.7370.01 1 0.000
#> TCGA.P3.A6T5.01 2 0.000
#> TCGA.D6.A74Q.01 4 0.000
#> TCGA.UF.A718.01 1 1.000
#> TCGA.CR.7369.01 1 0.000
#> TCGA.QK.A6IH.01 1 1.000
#> TCGA.CV.A6K2.01 2 1.000
#> TCGA.CV.A6K1.01 1 0.000
#> TCGA.BA.A6DE.01 4 0.000
#> TCGA.WA.A7GZ.01 1 0.751
#> TCGA.CV.7433.01 2 0.000
#> TCGA.CV.7440.01 4 0.000
#> TCGA.CV.A6JU.01 4 0.000
#> TCGA.CR.7376.01 2 0.000
#> TCGA.UF.A71A.06 1 0.000
#> TCGA.KU.A6H7.01 1 0.000
#> TCGA.D6.A6EP.01 1 0.000
get_classes(res, k = 5)
#> class p
#> TCGA.CN.6022.01 5 0.751
#> TCGA.CQ.5327.01 2 0.000
#> TCGA.CV.5435.11 3 0.000
#> TCGA.HD.7753.01 2 0.000
#> TCGA.CQ.5325.01 2 0.000
#> TCGA.CV.5432.01 5 1.000
#> TCGA.CR.7391.01 2 0.000
#> TCGA.CV.7415.01 2 0.000
#> TCGA.CR.5247.01 4 0.000
#> TCGA.CN.6011.01 2 0.000
#> TCGA.CV.7414.01 1 0.000
#> TCGA.CV.6436.01 2 0.000
#> TCGA.DQ.7592.01 2 0.000
#> TCGA.IQ.7632.01 5 0.000
#> TCGA.CV.7416.01 2 0.000
#> TCGA.CV.5432.11 3 0.000
#> TCGA.H7.7774.01 2 0.000
#> TCGA.CQ.5330.01 2 0.000
#> TCGA.CV.5430.11 3 0.000
#> TCGA.CV.7427.01 2 0.000
#> TCGA.CV.5979.01 2 0.000
#> TCGA.CR.6488.01 5 0.502
#> TCGA.CQ.6221.01 2 0.000
#> TCGA.CV.5434.11 3 0.000
#> TCGA.CV.5970.11 3 0.000
#> TCGA.CV.7425.01 2 0.000
#> TCGA.CV.6441.01 2 0.000
#> TCGA.IQ.7630.01 2 0.000
#> TCGA.CV.5976.11 3 0.000
#> TCGA.CV.7103.11 3 0.000
#> TCGA.CV.5977.01 2 0.000
#> TCGA.CQ.5324.01 2 0.000
#> TCGA.CV.7407.01 2 0.000
#> TCGA.CV.5971.01 2 0.000
#> TCGA.CV.5970.01 2 0.000
#> TCGA.CN.6016.01 2 1.000
#> TCGA.CV.6003.01 2 0.000
#> TCGA.CN.6010.01 1 1.000
#> TCGA.CN.6021.01 2 1.000
#> TCGA.CV.6433.01 5 0.000
#> TCGA.CV.5434.01 2 1.000
#> TCGA.CV.7413.01 1 0.747
#> TCGA.HD.7754.01 5 0.000
#> TCGA.CN.6017.01 2 0.000
#> TCGA.CV.6003.11 3 0.000
#> TCGA.CV.7422.01 1 0.000
#> TCGA.CV.7421.01 5 0.000
#> TCGA.CV.5439.11 3 0.000
#> TCGA.CV.7235.01 2 0.000
#> TCGA.BA.7269.01 1 0.000
#> TCGA.CV.5971.11 3 0.000
#> TCGA.CQ.5332.01 1 1.000
#> TCGA.CV.5439.01 2 0.000
#> TCGA.CN.6020.01 2 0.000
#> TCGA.CV.7423.01 2 0.000
#> TCGA.CV.7263.01 4 0.000
#> TCGA.CV.7406.01 5 0.000
#> TCGA.CN.6023.01 2 0.000
#> TCGA.CV.5966.11 3 0.000
#> TCGA.CV.7101.01 1 0.000
#> TCGA.CV.5977.11 3 0.000
#> TCGA.CR.7365.01 2 0.000
#> TCGA.CN.6012.01 1 0.000
#> TCGA.CV.6441.11 3 0.000
#> TCGA.CN.6024.01 2 0.253
#> TCGA.CV.5978.01 2 0.000
#> TCGA.CX.7086.01 5 0.000
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#> TCGA.CV.A6JD.01 2 0.000
#> TCGA.CV.A6JY.01 5 0.000
#> TCGA.CV.A6JN.01 2 0.000
#> TCGA.CV.7446.01 1 0.000
#> TCGA.CV.7432.01 5 0.502
#> TCGA.CV.7434.01 2 0.000
#> TCGA.WA.A7H4.01 5 0.000
#> TCGA.KU.A6H8.01 3 0.000
#> TCGA.CV.7428.01 4 0.000
#> TCGA.D6.A6EK.01 2 0.747
#> TCGA.CV.A6K0.01 3 0.000
#> TCGA.HD.7832.01 2 0.000
#> TCGA.MZ.A6I9.01 5 0.000
#> TCGA.CV.7435.01 4 0.000
#> TCGA.P3.A6SX.01 2 0.747
#> TCGA.QK.A6IG.01 5 0.000
#> TCGA.HD.7831.01 1 1.000
#> TCGA.CV.A6JM.01 5 1.000
#> TCGA.CR.7404.01 5 0.000
#> TCGA.D6.A6EQ.01 1 0.000
#> TCGA.QK.A6IJ.01 5 0.000
#> TCGA.P3.A6T0.01 1 1.000
#> TCGA.CV.A6JE.01 5 0.000
#> TCGA.HD.A6HZ.01 1 0.000
#> TCGA.QK.A6II.01 2 0.000
#> TCGA.P3.A6T7.01 2 0.000
#> TCGA.BA.A6DD.01 5 0.000
#> TCGA.UF.A719.01 4 0.000
#> TCGA.TN.A7HL.01 1 0.747
#> TCGA.UF.A7JA.01 1 0.000
#> TCGA.CR.7368.01 5 0.000
#> TCGA.CR.7382.01 2 0.000
#> TCGA.UF.A7JD.01 4 0.000
#> TCGA.UF.A7JH.01 4 0.000
#> TCGA.BA.A6DA.01 1 1.000
#> TCGA.T2.A6WZ.01 2 0.000
#> TCGA.D6.A6EO.01 4 0.000
#> TCGA.CR.7370.01 1 0.000
#> TCGA.P3.A6T5.01 2 0.000
#> TCGA.D6.A74Q.01 4 0.000
#> TCGA.UF.A718.01 5 0.000
#> TCGA.CR.7369.01 5 0.000
#> TCGA.QK.A6IH.01 5 0.000
#> TCGA.CV.A6K2.01 1 0.498
#> TCGA.CV.A6K1.01 1 0.249
#> TCGA.BA.A6DE.01 4 0.000
#> TCGA.WA.A7GZ.01 5 0.000
#> TCGA.CV.7433.01 2 0.000
#> TCGA.CV.7440.01 4 0.000
#> TCGA.CV.A6JU.01 4 0.000
#> TCGA.CR.7376.01 2 0.000
#> TCGA.UF.A71A.06 1 0.000
#> TCGA.KU.A6H7.01 5 0.000
#> TCGA.D6.A6EP.01 1 0.000
get_classes(res, k = 6)
#> class p
#> TCGA.CN.6022.01 1 0.000
#> TCGA.CQ.5327.01 6 0.747
#> TCGA.CV.5435.11 3 0.000
#> TCGA.HD.7753.01 2 0.000
#> TCGA.CQ.5325.01 6 0.000
#> TCGA.CV.5432.01 1 0.000
#> TCGA.CR.7391.01 6 0.502
#> TCGA.CV.7415.01 2 0.000
#> TCGA.CR.5247.01 4 0.000
#> TCGA.CN.6011.01 2 0.000
#> TCGA.CV.7414.01 1 0.000
#> TCGA.CV.6436.01 2 0.000
#> TCGA.DQ.7592.01 2 0.000
#> TCGA.IQ.7632.01 6 0.751
#> TCGA.CV.7416.01 6 0.751
#> TCGA.CV.5432.11 3 0.000
#> TCGA.H7.7774.01 2 0.249
#> TCGA.CQ.5330.01 2 0.000
#> TCGA.CV.5430.11 3 0.000
#> TCGA.CV.7427.01 2 0.000
#> TCGA.CV.5979.01 2 0.000
#> TCGA.CR.6488.01 6 0.747
#> TCGA.CQ.6221.01 2 0.249
#> TCGA.CV.5434.11 3 0.000
#> TCGA.CV.5970.11 3 0.000
#> TCGA.CV.7425.01 2 0.000
#> TCGA.CV.6441.01 2 0.000
#> TCGA.IQ.7630.01 2 0.000
#> TCGA.CV.5976.11 3 0.000
#> TCGA.CV.7103.11 3 0.000
#> TCGA.CV.5977.01 2 0.000
#> TCGA.CQ.5324.01 2 0.000
#> TCGA.CV.7407.01 2 0.000
#> TCGA.CV.5971.01 2 0.502
#> TCGA.CV.5970.01 2 0.751
#> TCGA.CN.6016.01 3 0.249
#> TCGA.CV.6003.01 2 0.000
#> TCGA.CN.6010.01 1 0.000
#> TCGA.CN.6021.01 1 0.000
#> TCGA.CV.6433.01 5 0.000
#> TCGA.CV.5434.01 1 0.502
#> TCGA.CV.7413.01 6 0.000
#> TCGA.HD.7754.01 5 0.000
#> TCGA.CN.6017.01 6 0.000
#> TCGA.CV.6003.11 3 0.000
#> TCGA.CV.7422.01 1 0.000
#> TCGA.CV.7421.01 1 0.502
#> TCGA.CV.5439.11 3 0.000
#> TCGA.CV.7235.01 2 0.498
#> TCGA.BA.7269.01 1 0.000
#> TCGA.CV.5971.11 3 0.000
#> TCGA.CQ.5332.01 1 0.000
#> TCGA.CV.5439.01 2 0.249
#> TCGA.CN.6020.01 2 0.000
#> TCGA.CV.7423.01 2 0.000
#> TCGA.CV.7263.01 4 0.000
#> TCGA.CV.7406.01 5 0.000
#> TCGA.CN.6023.01 2 0.249
#> TCGA.CV.5966.11 3 0.000
#> TCGA.CV.7101.01 1 0.000
#> TCGA.CV.5977.11 3 0.000
#> TCGA.CR.7365.01 2 0.000
#> TCGA.CN.6012.01 1 0.000
#> TCGA.CV.6441.11 3 0.000
#> TCGA.CN.6024.01 2 0.000
#> TCGA.CV.5978.01 2 0.000
#> TCGA.CX.7086.01 5 0.747
#> TCGA.CV.7424.01 1 0.000
#> TCGA.CV.7089.01 3 0.000
#> TCGA.CQ.7065.01 2 0.249
#> TCGA.IQ.7631.01 6 0.249
#> TCGA.CV.7418.01 1 0.000
#> TCGA.CV.6937.01 1 0.000
#> TCGA.CN.6018.01 6 0.000
#> TCGA.CV.5966.01 6 0.751
#> TCGA.CQ.5329.01 2 1.000
#> TCGA.CV.5976.01 2 0.000
#> TCGA.CV.7411.01 6 0.000
#> TCGA.CQ.5323.01 5 0.000
#> TCGA.CV.5978.11 3 0.000
#> TCGA.CV.5973.11 3 0.000
#> TCGA.BB.4217.01 6 0.000
#> TCGA.CQ.7068.01 2 0.000
#> TCGA.CN.6013.01 6 0.253
#> TCGA.CV.6436.11 3 0.000
#> TCGA.CV.6433.11 3 0.000
#> TCGA.CN.6995.01 6 0.498
#> TCGA.CV.6960.01 4 0.000
#> TCGA.CQ.5334.01 2 0.249
#> TCGA.CV.7410.01 6 0.000
#> TCGA.CN.6019.01 1 0.000
#> TCGA.DQ.7588.01 2 0.249
#> TCGA.CV.5979.11 3 0.000
#> TCGA.CR.6492.01 3 0.000
#> TCGA.CV.5973.01 2 0.751
#> TCGA.DQ.7591.01 5 0.000
#> TCGA.CR.7389.01 1 0.000
#> TCGA.CV.7245.01 4 0.000
#> TCGA.CV.5430.01 2 1.000
#> TCGA.CV.5435.01 2 0.000
#> TCGA.CR.7374.01 1 0.000
#> TCGA.CV.5440.01 2 0.502
#> TCGA.CV.6955.11 3 0.000
#> TCGA.CV.7238.11 3 0.000
#> TCGA.CV.7104.01 6 0.751
#> TCGA.CV.7100.01 2 0.000
#> TCGA.CV.7089.11 3 0.000
#> TCGA.CN.4739.01 4 0.000
#> TCGA.CV.7095.01 6 0.000
#> TCGA.CV.6956.01 4 0.000
#> TCGA.CV.5431.11 3 0.000
#> TCGA.CV.7261.01 1 0.000
#> TCGA.CN.5358.01 6 0.000
#> TCGA.BA.5559.01 5 0.000
#> TCGA.CR.7373.01 2 0.502
#> TCGA.CX.7082.01 1 0.000
#> TCGA.DQ.5629.01 1 0.000
#> TCGA.CV.7255.11 3 0.000
#> TCGA.CR.7379.01 1 0.000
#> TCGA.CV.7178.01 6 0.000
#> TCGA.CR.5249.01 5 0.000
#> TCGA.CV.7091.01 4 0.000
#> TCGA.CV.7236.01 6 0.000
#> TCGA.CN.6998.01 2 0.000
#> TCGA.CR.7399.01 6 0.249
#> TCGA.CR.7372.01 1 0.751
#> TCGA.CV.7252.01 6 1.000
#> TCGA.CV.7242.01 4 0.000
#> TCGA.CV.7103.01 5 0.747
#> TCGA.CR.6478.01 6 0.502
#> TCGA.CR.7371.01 1 0.000
#> TCGA.CR.7380.01 2 0.000
#> TCGA.CV.7183.01 2 0.000
#> TCGA.CV.7250.11 3 0.000
#> TCGA.CV.7102.01 2 0.000
#> TCGA.CV.7254.01 6 0.751
#> TCGA.CR.7394.01 6 0.000
#> TCGA.CV.5443.01 5 0.000
#> TCGA.CV.6955.01 2 0.000
#> TCGA.CV.5441.11 6 0.502
#> TCGA.CV.5442.11 3 0.000
#> TCGA.BA.5556.01 6 0.751
#> TCGA.CR.7386.01 6 0.498
#> TCGA.CV.7255.01 6 0.000
#> TCGA.CR.6474.01 2 0.000
#> TCGA.BA.5557.01 6 0.000
#> TCGA.CR.7388.01 1 0.000
#> TCGA.CV.5436.11 3 0.000
#> TCGA.CR.7398.01 4 0.000
#> TCGA.CV.7247.01 2 0.000
#> TCGA.CN.6997.01 1 0.000
#> TCGA.CN.4742.01 1 1.000
#> TCGA.CN.4738.01 2 0.000
#> TCGA.CR.7392.01 6 0.000
#> TCGA.CV.7245.11 3 0.000
#> TCGA.CR.7377.01 6 0.751
#> TCGA.HD.7229.01 2 0.000
#> TCGA.CV.7235.11 3 0.000
#> TCGA.D6.6515.01 6 1.000
#> TCGA.CV.7238.01 6 0.000
#> TCGA.CR.5248.01 5 0.000
#> TCGA.CV.7097.01 2 0.000
#> TCGA.CR.5250.01 5 0.000
#> TCGA.CV.7248.01 1 0.000
#> TCGA.CV.7253.01 4 0.000
#> TCGA.CN.5370.01 6 0.498
#> TCGA.CR.7367.01 6 0.000
#> TCGA.CR.7401.01 2 0.000
#> TCGA.BA.5149.01 2 1.000
#> TCGA.CV.6942.01 6 0.000
#> TCGA.CV.7263.11 3 0.000
#> TCGA.CV.7177.01 2 0.000
#> TCGA.BA.5555.01 4 0.000
#> TCGA.CV.6956.11 3 0.000
#> TCGA.CV.5431.01 1 0.751
#> TCGA.CR.7393.01 3 0.000
#> TCGA.CV.5444.11 3 0.000
#> TCGA.CV.5444.01 1 0.253
#> TCGA.CR.5243.01 5 0.000
#> TCGA.CR.7395.01 6 0.249
#> TCGA.CV.5441.01 4 0.000
#> TCGA.CV.5442.01 5 0.000
#> TCGA.BA.5558.01 2 0.502
#> TCGA.CX.7085.01 6 0.000
#> TCGA.CV.7250.01 4 0.000
#> TCGA.CR.7390.01 1 0.000
#> TCGA.CV.7178.11 3 0.000
#> TCGA.CV.7099.01 2 0.000
#> TCGA.CV.5443.11 3 0.000
#> TCGA.CR.7385.01 5 0.000
#> TCGA.CR.7364.01 4 0.000
#> TCGA.CV.7090.01 6 0.249
#> TCGA.CR.7397.01 3 0.751
#> TCGA.CR.7402.01 4 0.000
#> TCGA.CV.5440.11 3 0.000
#> TCGA.CV.7180.01 2 1.000
#> TCGA.CX.7219.01 6 0.498
#> TCGA.CV.7101.11 3 0.000
#> TCGA.CV.5436.01 1 0.498
#> TCGA.CV.7243.01 2 0.000
#> TCGA.BA.6871.01 1 0.000
#> TCGA.CQ.6218.01 2 0.502
#> TCGA.C9.A47Z.01 6 0.000
#> TCGA.CV.6961.01 5 0.000
#> TCGA.DQ.5625.01 2 0.249
#> TCGA.CN.6992.01 1 0.000
#> TCGA.CV.6939.01 5 0.000
#> TCGA.CR.6480.01 5 0.000
#> TCGA.D6.6825.01 2 0.000
#> TCGA.C9.A480.01 2 0.502
#> TCGA.CV.6962.01 1 0.000
#> TCGA.CV.6952.01 2 0.000
#> TCGA.CN.A49A.01 4 0.000
#> TCGA.CR.6487.01 5 0.000
#> TCGA.CV.6935.11 3 0.000
#> TCGA.CQ.6222.01 2 0.000
#> TCGA.CV.6959.11 3 0.000
#> TCGA.BB.4227.01 1 0.000
#> TCGA.CN.A49C.01 5 0.000
#> TCGA.CN.6994.01 2 0.000
#> TCGA.CV.6938.11 3 0.000
#> TCGA.CV.6936.01 5 0.498
#> TCGA.CR.6491.01 2 0.000
#> TCGA.CV.6950.01 2 0.000
#> TCGA.CR.6473.01 5 0.000
#> TCGA.CV.6952.11 3 0.000
#> TCGA.CQ.5331.01 6 0.000
#> TCGA.D6.6826.01 2 0.000
#> TCGA.CV.6951.11 3 0.000
#> TCGA.CV.6935.01 2 0.000
#> TCGA.DQ.5631.01 2 0.249
#> TCGA.CV.6953.01 6 0.000
#> TCGA.CV.6945.01 1 0.751
#> TCGA.CV.6939.11 3 0.000
#> TCGA.CV.A45U.01 1 0.000
#> TCGA.CN.A497.01 4 0.000
#> TCGA.D6.6823.01 4 0.000
#> TCGA.DQ.5630.01 2 0.751
#> TCGA.D6.6827.01 1 0.000
#> TCGA.CV.6943.01 2 0.249
#> TCGA.CV.6954.11 3 0.000
#> TCGA.CR.6472.01 5 0.000
#> TCGA.CR.6481.01 5 0.000
#> TCGA.BA.A4IF.01 4 0.000
#> TCGA.BA.6870.01 6 0.000
#> TCGA.CV.6962.11 3 0.000
#> TCGA.CR.6477.01 6 0.000
#> TCGA.CV.A45O.01 2 0.502
#> TCGA.CQ.6219.01 2 0.000
#> TCGA.CN.4733.01 6 0.000
#> TCGA.CR.6484.01 5 0.249
#> TCGA.CN.A498.01 2 1.000
#> TCGA.CR.6470.01 5 0.000
#> TCGA.CV.6934.01 1 0.000
#> TCGA.CN.6989.01 2 0.502
#> TCGA.CV.6953.11 6 0.000
#> TCGA.CV.6933.01 1 0.000
#> TCGA.D6.6517.01 2 0.502
#> TCGA.CQ.6220.01 2 0.000
#> TCGA.BA.A4IH.01 5 0.000
#> TCGA.HD.A4C1.01 2 0.751
#> TCGA.BA.6869.01 4 0.000
#> TCGA.CR.6493.01 2 0.000
#> TCGA.D6.6516.01 2 0.000
#> TCGA.CQ.6227.01 2 0.000
#> TCGA.CV.A45P.01 6 0.000
#> TCGA.CV.A45Q.01 2 0.000
#> TCGA.CV.A45T.01 6 0.000
#> TCGA.CN.6996.01 2 0.000
#> TCGA.CV.6961.11 3 0.000
#> TCGA.CV.6941.01 4 0.000
#> TCGA.BA.6873.01 2 0.249
#> TCGA.CV.6934.11 3 0.000
#> TCGA.CR.6467.01 5 0.000
#> TCGA.CV.6943.11 3 0.000
#> TCGA.CV.6954.01 4 0.000
#> TCGA.BA.6868.01 2 0.000
#> TCGA.CV.6959.01 2 0.000
#> TCGA.CQ.6228.01 4 0.000
#> TCGA.CQ.6229.01 2 0.000
#> TCGA.CQ.6224.01 2 0.000
#> TCGA.CV.6951.01 1 0.000
#> TCGA.CQ.6223.01 2 0.751
#> TCGA.CV.6948.01 1 0.000
#> TCGA.CV.6936.11 3 0.000
#> TCGA.DQ.5624.01 2 0.502
#> TCGA.CV.A45R.01 2 0.000
#> TCGA.CN.A499.01 2 0.000
#> TCGA.CN.A49B.01 2 0.000
#> TCGA.BA.5152.01 6 0.000
#> TCGA.CV.6938.01 2 0.249
#> TCGA.CQ.5326.01 2 0.000
#> TCGA.D6.6824.01 3 0.000
#> TCGA.CV.6940.01 2 0.000
#> TCGA.CQ.6225.01 4 0.000
#> TCGA.CR.6471.01 2 0.249
#> TCGA.CN.6988.01 4 0.000
#> TCGA.BA.6872.01 2 0.000
#> TCGA.CV.6933.11 3 0.000
#> TCGA.CR.6482.01 5 0.000
#> TCGA.P3.A5Q5.01 5 0.000
#> TCGA.CQ.A4C6.01 2 0.000
#> TCGA.QK.A8Z8.01 4 0.000
#> TCGA.CV.A45W.01 1 1.000
#> TCGA.F7.A624.01 2 0.249
#> TCGA.F7.A623.01 1 0.000
#> TCGA.F7.A622.01 2 0.000
#> TCGA.CQ.7064.01 6 1.000
#> TCGA.IQ.A61K.01 2 0.000
#> TCGA.HD.A633.01 2 0.000
#> TCGA.BA.A4IG.01 5 0.000
#> TCGA.F7.A61W.01 1 0.249
#> TCGA.BA.A6DF.01 6 0.751
#> TCGA.D6.A4ZB.01 6 0.249
#> TCGA.KU.A66T.01 1 0.000
#> TCGA.HD.8224.01 5 0.000
#> TCGA.CV.A45Y.01 6 0.000
#> TCGA.BB.A5HU.01 2 0.000
#> TCGA.T3.A92M.01 1 0.000
#> TCGA.CQ.A4C7.01 2 0.000
#> TCGA.P3.A5Q6.01 2 0.000
#> TCGA.CQ.A4CD.01 2 0.000
#> TCGA.BA.A6DB.01 3 0.000
#> TCGA.CV.A468.01 1 0.000
#> TCGA.QK.A8Z7.01 4 0.000
#> TCGA.F7.A620.01 6 0.751
#> TCGA.BA.A8YP.01 1 0.000
#> TCGA.CQ.A4C9.01 4 0.000
#> TCGA.CQ.7072.01 4 0.000
#> TCGA.IQ.A61H.01 1 0.000
#> TCGA.QK.AA3K.01 5 0.000
#> TCGA.CQ.7069.01 6 0.502
#> TCGA.CX.A4AQ.01 2 1.000
#> TCGA.CV.A464.01 2 0.000
#> TCGA.IQ.A61L.01 2 0.000
#> TCGA.QK.A8Z9.01 2 0.000
#> TCGA.HD.A634.01 5 0.000
#> TCGA.4P.AA8J.01 1 0.000
#> TCGA.BB.A5HY.01 2 0.000
#> TCGA.HD.8635.01 2 0.000
#> TCGA.CN.A63T.01 4 0.000
#> TCGA.QK.A652.01 2 0.000
#> TCGA.MT.A67G.01 6 0.502
#> TCGA.QK.A64Z.01 2 0.000
#> TCGA.HD.8634.01 2 0.000
#> TCGA.CQ.7063.01 2 0.249
#> TCGA.CV.A45V.01 6 0.502
#> TCGA.CV.A460.01 1 0.000
#> TCGA.CV.A465.01 1 1.000
#> TCGA.CQ.A4CG.01 1 0.000
#> TCGA.F7.A50J.01 6 0.000
#> TCGA.F7.8298.01 2 0.000
#> TCGA.F7.8489.01 6 0.000
#> TCGA.P3.A5QA.01 2 0.000
#> TCGA.F7.A50G.01 2 0.000
#> TCGA.CQ.A4CA.01 2 0.249
#> TCGA.T3.A92N.01 2 0.000
#> TCGA.F7.A61V.01 4 0.000
#> TCGA.CN.A63Y.01 5 0.000
#> TCGA.CQ.5333.01 2 0.000
#> TCGA.P3.A5QE.01 1 0.000
#> TCGA.MT.A67D.01 5 0.751
#> TCGA.CN.A63V.01 5 1.000
#> TCGA.BA.A6DJ.01 2 0.000
#> TCGA.MT.A51W.01 2 0.502
#> TCGA.P3.A5QF.01 4 0.000
#> TCGA.CQ.A4CE.01 6 1.000
#> TCGA.IQ.A61G.01 2 0.000
#> TCGA.HD.8314.01 5 0.000
#> TCGA.BB.A5HZ.01 4 0.000
#> TCGA.CN.A641.01 4 0.000
#> TCGA.IQ.A61J.01 2 0.000
#> TCGA.BA.A6DG.01 2 0.000
#> TCGA.QK.AA3J.01 4 0.000
#> TCGA.CQ.A4CH.01 6 0.000
#> TCGA.BA.A4II.01 6 0.000
#> TCGA.KU.A66S.01 4 0.000
#> TCGA.CQ.A4CB.01 2 0.000
#> TCGA.D6.8569.01 2 0.000
#> TCGA.IQ.A61I.01 5 0.000
#> TCGA.D6.A4Z9.01 2 0.249
#> TCGA.QK.A8ZA.01 1 0.000
#> TCGA.QK.A8ZB.01 1 0.000
#> TCGA.BA.A6DL.01 4 0.000
#> TCGA.CQ.A4CI.01 1 0.000
#> TCGA.MT.A51X.01 5 0.498
#> TCGA.CV.A461.01 4 0.000
#> TCGA.CQ.7071.01 6 1.000
#> TCGA.H7.8501.01 2 0.000
#> TCGA.BB.8596.01 2 0.000
#> TCGA.F7.A50I.01 6 0.000
#> TCGA.BB.8601.01 2 0.000
#> TCGA.H7.8502.01 2 0.000
#> TCGA.F7.A61S.01 2 0.502
#> TCGA.CV.A463.01 2 0.249
#> TCGA.IQ.A61O.01 2 1.000
#> TCGA.CV.A45Z.01 5 1.000
#> TCGA.CV.A45X.01 6 0.000
#> TCGA.D6.8568.01 2 0.249
#> TCGA.CN.A642.01 2 0.249
#> TCGA.CN.4722.01 6 0.000
#> TCGA.IQ.A6SH.01 2 0.000
#> TCGA.CN.5367.01 2 0.249
#> TCGA.P3.A6T2.01 2 0.000
#> TCGA.P3.A6T8.01 1 1.000
#> TCGA.CN.A6V7.01 5 0.000
#> TCGA.CN.A640.01 6 0.000
#> TCGA.UF.A71E.01 1 0.000
#> TCGA.DQ.7589.01 2 0.000
#> TCGA.P3.A6T6.01 4 0.000
#> TCGA.CN.4725.01 2 0.000
#> TCGA.BA.5153.01 5 0.000
#> TCGA.DQ.7594.01 5 0.000
#> TCGA.HL.7533.01 5 0.000
#> TCGA.T2.A6X0.01 5 0.000
#> TCGA.CN.4730.01 4 0.000
#> TCGA.CN.4723.01 1 0.000
#> TCGA.UF.A7J9.01 1 0.000
#> TCGA.UF.A7JO.01 6 0.000
#> TCGA.DQ.7596.01 5 0.000
#> TCGA.UF.A7JV.01 6 0.000
#> TCGA.CN.4729.01 6 0.000
#> TCGA.IQ.A6SG.01 2 0.000
#> TCGA.BB.7864.01 4 0.000
#> TCGA.MT.A67A.01 6 0.000
#> TCGA.CN.5361.01 2 0.000
#> TCGA.CN.5359.01 6 0.751
#> TCGA.BB.7861.01 5 0.000
#> TCGA.CN.4728.01 1 0.000
#> TCGA.BB.A6UO.01 2 0.000
#> TCGA.BA.4074.01 4 0.000
#> TCGA.CN.4734.01 2 0.000
#> TCGA.QK.A6VB.01 4 0.000
#> TCGA.BA.4075.01 2 0.000
#> TCGA.BB.7871.01 2 0.751
#> TCGA.CN.4726.01 2 0.000
#> TCGA.CN.4735.01 1 0.000
#> TCGA.P3.A6T3.01 6 0.502
#> TCGA.HD.7917.01 4 0.000
#> TCGA.BB.4223.01 5 0.000
#> TCGA.UF.A71B.01 1 0.000
#> TCGA.UF.A7JS.01 2 0.249
#> TCGA.QK.A6VC.01 1 0.000
#> TCGA.CV.7409.01 4 0.000
#> TCGA.CN.4736.01 6 0.498
#> TCGA.BB.7862.01 1 0.000
#> TCGA.BA.A6DI.01 1 0.000
#> TCGA.RS.A6TO.01 1 0.000
#> TCGA.CN.4737.01 5 0.747
#> TCGA.CN.5355.01 2 0.000
#> TCGA.UF.A71D.01 4 0.000
#> TCGA.CQ.7067.01 6 0.000
#> TCGA.BA.4078.01 1 0.000
#> TCGA.CN.5374.01 5 0.000
#> TCGA.DQ.7590.01 1 0.502
#> TCGA.CN.5369.01 6 0.000
#> TCGA.BA.5151.01 2 0.249
#> TCGA.TN.A7HJ.01 2 1.000
#> TCGA.IQ.A61E.01 2 0.751
#> TCGA.BB.7870.01 4 0.000
#> TCGA.CN.4727.01 4 0.000
#> TCGA.DQ.7595.01 4 0.000
#> TCGA.BA.4076.01 2 0.000
#> TCGA.CN.5360.01 4 0.000
#> TCGA.BB.4228.01 5 0.000
#> TCGA.MZ.A7D7.01 1 0.000
#> TCGA.H7.A76A.01 5 0.000
#> TCGA.UF.A7JT.01 6 0.000
#> TCGA.CN.5373.01 2 0.249
#> TCGA.CN.A6V3.01 4 0.000
#> TCGA.BB.7863.01 2 1.000
#> TCGA.DQ.7593.01 5 0.000
#> TCGA.UF.A7JJ.01 6 0.000
#> TCGA.CN.5363.01 2 0.249
#> TCGA.BA.4077.01 5 0.000
#> TCGA.BB.4225.01 5 0.000
#> TCGA.BB.7872.01 2 0.000
#> TCGA.CN.A6UY.01 5 0.000
#> TCGA.MT.A7BN.01 5 0.000
#> TCGA.UF.A7JF.01 4 0.000
#> TCGA.CN.4731.01 4 0.000
#> TCGA.MZ.A5BI.01 5 0.000
#> TCGA.CN.A63W.01 4 0.000
#> TCGA.H7.A6C4.01 6 0.000
#> TCGA.T2.A6X2.01 2 0.000
#> TCGA.CN.5364.01 6 1.000
#> TCGA.CN.A63U.01 4 0.000
#> TCGA.BB.A6UM.01 5 0.000
#> TCGA.H7.A6C5.01 4 0.000
#> TCGA.CN.4741.01 5 0.000
#> TCGA.CV.A6JO.01 2 0.000
#> TCGA.BB.7866.01 5 0.000
#> TCGA.CN.5365.01 2 0.000
#> TCGA.CN.4740.01 5 1.000
#> TCGA.BB.4224.01 2 0.000
#> TCGA.MT.A67F.01 2 0.502
#> TCGA.CN.5366.01 2 0.000
#> TCGA.QK.A6V9.01 5 0.000
#> TCGA.CN.5356.01 4 0.000
#> TCGA.T2.A6WX.01 6 0.000
#> TCGA.CV.A6JZ.01 6 0.000
#> TCGA.CN.A6V1.01 5 0.000
#> TCGA.HD.A6I0.01 2 0.000
#> TCGA.UF.A71A.01 1 0.000
#> TCGA.CV.7430.01 1 0.000
#> TCGA.CR.7383.01 6 0.502
#> TCGA.CN.A6V6.01 5 0.000
#> TCGA.F7.7848.01 4 0.000
#> TCGA.TN.A7HI.01 1 0.000
#> TCGA.UF.A7JC.01 2 0.000
#> TCGA.D6.A6ES.01 6 0.751
#> TCGA.CV.7568.01 2 0.751
#> TCGA.BA.A6D8.01 1 0.000
#> TCGA.P3.A6T4.01 1 0.000
#> TCGA.QK.A6IF.01 5 0.000
#> TCGA.CV.A6JT.01 2 0.000
#> TCGA.CV.7438.01 2 1.000
#> TCGA.RS.A6TP.01 5 0.000
#> TCGA.P3.A6SW.01 5 0.000
#> TCGA.D6.A6EN.01 2 0.498
#> TCGA.D6.A6EM.01 6 0.000
#> TCGA.UF.A7JK.01 1 0.000
#> TCGA.KU.A6H7.06 5 0.000
#> TCGA.CV.7429.01 2 0.000
#> TCGA.UP.A6WW.01 5 0.000
#> TCGA.CV.7437.01 2 0.000
#> TCGA.CV.A6JD.01 2 0.249
#> TCGA.CV.A6JY.01 1 0.751
#> TCGA.CV.A6JN.01 2 0.000
#> TCGA.CV.7446.01 1 0.000
#> TCGA.CV.7432.01 2 0.000
#> TCGA.CV.7434.01 2 0.000
#> TCGA.WA.A7H4.01 6 1.000
#> TCGA.KU.A6H8.01 3 0.000
#> TCGA.CV.7428.01 4 0.000
#> TCGA.D6.A6EK.01 6 0.000
#> TCGA.CV.A6K0.01 3 0.000
#> TCGA.HD.7832.01 2 0.000
#> TCGA.MZ.A6I9.01 5 0.000
#> TCGA.CV.7435.01 4 0.000
#> TCGA.P3.A6SX.01 2 0.000
#> TCGA.QK.A6IG.01 2 0.253
#> TCGA.HD.7831.01 1 0.502
#> TCGA.CV.A6JM.01 1 0.000
#> TCGA.CR.7404.01 5 0.000
#> TCGA.D6.A6EQ.01 2 0.498
#> TCGA.QK.A6IJ.01 6 1.000
#> TCGA.P3.A6T0.01 1 0.502
#> TCGA.CV.A6JE.01 5 1.000
#> TCGA.HD.A6HZ.01 1 0.000
#> TCGA.QK.A6II.01 2 0.249
#> TCGA.P3.A6T7.01 2 0.000
#> TCGA.BA.A6DD.01 6 1.000
#> TCGA.UF.A719.01 4 0.000
#> TCGA.TN.A7HL.01 5 0.000
#> TCGA.UF.A7JA.01 1 0.000
#> TCGA.CR.7368.01 5 0.000
#> TCGA.CR.7382.01 2 0.000
#> TCGA.UF.A7JD.01 4 0.000
#> TCGA.UF.A7JH.01 4 0.000
#> TCGA.BA.A6DA.01 6 0.000
#> TCGA.T2.A6WZ.01 2 0.000
#> TCGA.D6.A6EO.01 4 0.000
#> TCGA.CR.7370.01 1 0.000
#> TCGA.P3.A6T5.01 6 1.000
#> TCGA.D6.A74Q.01 4 0.000
#> TCGA.UF.A718.01 2 0.498
#> TCGA.CR.7369.01 5 0.000
#> TCGA.QK.A6IH.01 6 0.751
#> TCGA.CV.A6K2.01 6 0.249
#> TCGA.CV.A6K1.01 1 0.000
#> TCGA.BA.A6DE.01 4 0.000
#> TCGA.WA.A7GZ.01 1 0.000
#> TCGA.CV.7433.01 6 0.747
#> TCGA.CV.7440.01 4 0.000
#> TCGA.CV.A6JU.01 4 0.000
#> TCGA.CR.7376.01 6 0.253
#> TCGA.UF.A71A.06 1 0.000
#> TCGA.KU.A6H7.01 5 0.000
#> TCGA.D6.A6EP.01 1 0.000
get_classes(res, k = 7)
#> class p
#> TCGA.CN.6022.01 1 0.000
#> TCGA.CQ.5327.01 6 0.498
#> TCGA.CV.5435.11 3 0.000
#> TCGA.HD.7753.01 2 0.000
#> TCGA.CQ.5325.01 7 0.000
#> TCGA.CV.5432.01 1 0.000
#> TCGA.CR.7391.01 7 0.000
#> TCGA.CV.7415.01 2 0.502
#> TCGA.CR.5247.01 4 0.000
#> TCGA.CN.6011.01 2 0.000
#> TCGA.CV.7414.01 1 0.000
#> TCGA.CV.6436.01 6 0.000
#> TCGA.DQ.7592.01 2 0.000
#> TCGA.IQ.7632.01 7 0.502
#> TCGA.CV.7416.01 2 0.751
#> TCGA.CV.5432.11 3 0.000
#> TCGA.H7.7774.01 6 1.000
#> TCGA.CQ.5330.01 2 0.000
#> TCGA.CV.5430.11 3 0.000
#> TCGA.CV.7427.01 6 0.502
#> TCGA.CV.5979.01 2 0.000
#> TCGA.CR.6488.01 6 1.000
#> TCGA.CQ.6221.01 6 0.751
#> TCGA.CV.5434.11 3 0.000
#> TCGA.CV.5970.11 3 0.000
#> TCGA.CV.7425.01 6 1.000
#> TCGA.CV.6441.01 2 0.000
#> TCGA.IQ.7630.01 2 1.000
#> TCGA.CV.5976.11 3 0.000
#> TCGA.CV.7103.11 3 0.000
#> TCGA.CV.5977.01 2 0.000
#> TCGA.CQ.5324.01 2 0.000
#> TCGA.CV.7407.01 6 0.253
#> TCGA.CV.5971.01 7 0.000
#> TCGA.CV.5970.01 6 0.502
#> TCGA.CN.6016.01 6 0.000
#> TCGA.CV.6003.01 2 1.000
#> TCGA.CN.6010.01 6 0.751
#> TCGA.CN.6021.01 6 1.000
#> TCGA.CV.6433.01 5 0.000
#> TCGA.CV.5434.01 2 0.751
#> TCGA.CV.7413.01 6 0.498
#> TCGA.HD.7754.01 5 0.000
#> TCGA.CN.6017.01 7 0.000
#> TCGA.CV.6003.11 3 0.000
#> TCGA.CV.7422.01 6 0.253
#> TCGA.CV.7421.01 1 0.000
#> TCGA.CV.5439.11 3 0.000
#> TCGA.CV.7235.01 2 1.000
#> TCGA.BA.7269.01 1 0.000
#> TCGA.CV.5971.11 3 0.000
#> TCGA.CQ.5332.01 1 0.000
#> TCGA.CV.5439.01 2 0.000
#> TCGA.CN.6020.01 6 0.000
#> TCGA.CV.7423.01 2 0.000
#> TCGA.CV.7263.01 4 0.000
#> TCGA.CV.7406.01 5 0.000
#> TCGA.CN.6023.01 6 0.502
#> TCGA.CV.5966.11 3 0.000
#> TCGA.CV.7101.01 1 0.000
#> TCGA.CV.5977.11 3 0.000
#> TCGA.CR.7365.01 2 0.000
#> TCGA.CN.6012.01 1 0.000
#> TCGA.CV.6441.11 3 0.000
#> TCGA.CN.6024.01 2 0.253
#> TCGA.CV.5978.01 6 0.502
#> TCGA.CX.7086.01 1 0.751
#> TCGA.CV.7424.01 1 0.000
#> TCGA.CV.7089.01 6 0.502
#> TCGA.CQ.7065.01 1 1.000
#> TCGA.IQ.7631.01 1 1.000
#> TCGA.CV.7418.01 1 0.000
#> TCGA.CV.6937.01 1 0.498
#> TCGA.CN.6018.01 6 0.000
#> TCGA.CV.5966.01 6 0.000
#> TCGA.CQ.5329.01 2 1.000
#> TCGA.CV.5976.01 2 0.000
#> TCGA.CV.7411.01 6 0.000
#> TCGA.CQ.5323.01 5 0.000
#> TCGA.CV.5978.11 3 0.000
#> TCGA.CV.5973.11 3 0.000
#> TCGA.BB.4217.01 7 0.000
#> TCGA.CQ.7068.01 2 0.751
#> TCGA.CN.6013.01 1 1.000
#> TCGA.CV.6436.11 3 0.000
#> TCGA.CV.6433.11 3 0.000
#> TCGA.CN.6995.01 6 0.000
#> TCGA.CV.6960.01 4 0.000
#> TCGA.CQ.5334.01 6 0.000
#> TCGA.CV.7410.01 7 0.000
#> TCGA.CN.6019.01 7 0.751
#> TCGA.DQ.7588.01 2 0.751
#> TCGA.CV.5979.11 3 0.000
#> TCGA.CR.6492.01 7 0.000
#> TCGA.CV.5973.01 2 0.000
#> TCGA.DQ.7591.01 5 0.000
#> TCGA.CR.7389.01 1 0.000
#> TCGA.CV.7245.01 4 0.000
#> TCGA.CV.5430.01 2 0.249
#> TCGA.CV.5435.01 2 0.000
#> TCGA.CR.7374.01 1 0.000
#> TCGA.CV.5440.01 1 0.000
#> TCGA.CV.6955.11 6 1.000
#> TCGA.CV.7238.11 3 0.000
#> TCGA.CV.7104.01 6 0.000
#> TCGA.CV.7100.01 2 0.000
#> TCGA.CV.7089.11 3 0.000
#> TCGA.CN.4739.01 4 0.000
#> TCGA.CV.7095.01 6 0.000
#> TCGA.CV.6956.01 4 0.000
#> TCGA.CV.5431.11 3 0.000
#> TCGA.CV.7261.01 1 0.253
#> TCGA.CN.5358.01 7 0.000
#> TCGA.BA.5559.01 5 0.000
#> TCGA.CR.7373.01 6 1.000
#> TCGA.CX.7082.01 1 0.000
#> TCGA.DQ.5629.01 1 0.000
#> TCGA.CV.7255.11 3 0.000
#> TCGA.CR.7379.01 1 0.000
#> TCGA.CV.7178.01 6 0.751
#> TCGA.CR.5249.01 5 0.000
#> TCGA.CV.7091.01 4 0.000
#> TCGA.CV.7236.01 7 0.000
#> TCGA.CN.6998.01 2 0.502
#> TCGA.CR.7399.01 2 0.000
#> TCGA.CR.7372.01 1 0.498
#> TCGA.CV.7252.01 2 0.747
#> TCGA.CV.7242.01 4 0.000
#> TCGA.CV.7103.01 1 0.000
#> TCGA.CR.6478.01 6 0.000
#> TCGA.CR.7371.01 7 0.502
#> TCGA.CR.7380.01 2 0.000
#> TCGA.CV.7183.01 2 0.000
#> TCGA.CV.7250.11 3 0.000
#> TCGA.CV.7102.01 6 1.000
#> TCGA.CV.7254.01 6 0.000
#> TCGA.CR.7394.01 7 0.000
#> TCGA.CV.5443.01 5 0.000
#> TCGA.CV.6955.01 6 1.000
#> TCGA.CV.5441.11 7 0.000
#> TCGA.CV.5442.11 3 0.000
#> TCGA.BA.5556.01 6 0.000
#> TCGA.CR.7386.01 6 0.498
#> TCGA.CV.7255.01 1 0.502
#> TCGA.CR.6474.01 7 0.000
#> TCGA.BA.5557.01 7 0.751
#> TCGA.CR.7388.01 7 0.751
#> TCGA.CV.5436.11 3 0.000
#> TCGA.CR.7398.01 4 0.000
#> TCGA.CV.7247.01 2 0.000
#> TCGA.CN.6997.01 1 0.000
#> TCGA.CN.4742.01 1 0.498
#> TCGA.CN.4738.01 7 0.000
#> TCGA.CR.7392.01 7 0.000
#> TCGA.CV.7245.11 3 0.000
#> TCGA.CR.7377.01 7 0.000
#> TCGA.HD.7229.01 6 1.000
#> TCGA.CV.7235.11 3 0.000
#> TCGA.D6.6515.01 6 0.000
#> TCGA.CV.7238.01 7 0.000
#> TCGA.CR.5248.01 5 0.000
#> TCGA.CV.7097.01 6 0.751
#> TCGA.CR.5250.01 5 0.000
#> TCGA.CV.7248.01 6 0.000
#> TCGA.CV.7253.01 4 0.000
#> TCGA.CN.5370.01 6 0.000
#> TCGA.CR.7367.01 6 0.000
#> TCGA.CR.7401.01 6 0.751
#> TCGA.BA.5149.01 2 1.000
#> TCGA.CV.6942.01 6 0.000
#> TCGA.CV.7263.11 3 0.000
#> TCGA.CV.7177.01 6 1.000
#> TCGA.BA.5555.01 4 0.000
#> TCGA.CV.6956.11 3 0.000
#> TCGA.CV.5431.01 7 1.000
#> TCGA.CR.7393.01 3 0.000
#> TCGA.CV.5444.11 3 0.000
#> TCGA.CV.5444.01 7 0.000
#> TCGA.CR.5243.01 5 0.000
#> TCGA.CR.7395.01 6 0.000
#> TCGA.CV.5441.01 4 0.000
#> TCGA.CV.5442.01 5 0.000
#> TCGA.BA.5558.01 6 1.000
#> TCGA.CX.7085.01 7 0.000
#> TCGA.CV.7250.01 4 0.000
#> TCGA.CR.7390.01 1 0.000
#> TCGA.CV.7178.11 3 0.000
#> TCGA.CV.7099.01 2 0.253
#> TCGA.CV.5443.11 3 0.000
#> TCGA.CR.7385.01 5 0.000
#> TCGA.CR.7364.01 4 0.000
#> TCGA.CV.7090.01 6 0.000
#> TCGA.CR.7397.01 7 0.000
#> TCGA.CR.7402.01 4 0.000
#> TCGA.CV.5440.11 3 0.000
#> TCGA.CV.7180.01 1 1.000
#> TCGA.CX.7219.01 6 0.000
#> TCGA.CV.7101.11 3 0.000
#> TCGA.CV.5436.01 2 1.000
#> TCGA.CV.7243.01 2 0.253
#> TCGA.BA.6871.01 2 0.751
#> TCGA.CQ.6218.01 6 0.502
#> TCGA.C9.A47Z.01 2 0.000
#> TCGA.CV.6961.01 5 0.000
#> TCGA.DQ.5625.01 6 0.000
#> TCGA.CN.6992.01 1 0.000
#> TCGA.CV.6939.01 5 0.000
#> TCGA.CR.6480.01 5 0.000
#> TCGA.D6.6825.01 6 0.000
#> TCGA.C9.A480.01 6 0.253
#> TCGA.CV.6962.01 1 0.000
#> TCGA.CV.6952.01 2 1.000
#> TCGA.CN.A49A.01 4 0.000
#> TCGA.CR.6487.01 5 0.000
#> TCGA.CV.6935.11 3 0.000
#> TCGA.CQ.6222.01 6 0.000
#> TCGA.CV.6959.11 3 0.000
#> TCGA.BB.4227.01 1 0.000
#> TCGA.CN.A49C.01 5 0.000
#> TCGA.CN.6994.01 2 0.000
#> TCGA.CV.6938.11 3 0.000
#> TCGA.CV.6936.01 1 0.498
#> TCGA.CR.6491.01 2 0.000
#> TCGA.CV.6950.01 2 0.000
#> TCGA.CR.6473.01 5 0.000
#> TCGA.CV.6952.11 3 0.000
#> TCGA.CQ.5331.01 6 0.000
#> TCGA.D6.6826.01 6 1.000
#> TCGA.CV.6951.11 3 0.000
#> TCGA.CV.6935.01 2 0.253
#> TCGA.DQ.5631.01 2 0.502
#> TCGA.CV.6953.01 6 0.000
#> TCGA.CV.6945.01 6 0.751
#> TCGA.CV.6939.11 3 0.000
#> TCGA.CV.A45U.01 1 0.000
#> TCGA.CN.A497.01 4 0.000
#> TCGA.D6.6823.01 4 0.000
#> TCGA.DQ.5630.01 6 0.000
#> TCGA.D6.6827.01 6 0.751
#> TCGA.CV.6943.01 7 0.249
#> TCGA.CV.6954.11 3 0.000
#> TCGA.CR.6472.01 5 0.000
#> TCGA.CR.6481.01 5 0.000
#> TCGA.BA.A4IF.01 4 0.000
#> TCGA.BA.6870.01 6 0.000
#> TCGA.CV.6962.11 3 0.000
#> TCGA.CR.6477.01 6 0.000
#> TCGA.CV.A45O.01 6 0.000
#> TCGA.CQ.6219.01 6 0.000
#> TCGA.CN.4733.01 7 0.000
#> TCGA.CR.6484.01 1 0.249
#> TCGA.CN.A498.01 6 1.000
#> TCGA.CR.6470.01 5 0.000
#> TCGA.CV.6934.01 6 1.000
#> TCGA.CN.6989.01 6 1.000
#> TCGA.CV.6953.11 7 0.000
#> TCGA.CV.6933.01 1 0.000
#> TCGA.D6.6517.01 6 0.751
#> TCGA.CQ.6220.01 2 0.000
#> TCGA.BA.A4IH.01 5 0.000
#> TCGA.HD.A4C1.01 6 1.000
#> TCGA.BA.6869.01 4 0.000
#> TCGA.CR.6493.01 2 0.000
#> TCGA.D6.6516.01 2 0.502
#> TCGA.CQ.6227.01 2 0.000
#> TCGA.CV.A45P.01 6 0.000
#> TCGA.CV.A45Q.01 2 1.000
#> TCGA.CV.A45T.01 7 0.000
#> TCGA.CN.6996.01 6 1.000
#> TCGA.CV.6961.11 3 0.000
#> TCGA.CV.6941.01 4 0.000
#> TCGA.BA.6873.01 2 1.000
#> TCGA.CV.6934.11 3 0.000
#> TCGA.CR.6467.01 5 0.000
#> TCGA.CV.6943.11 3 0.000
#> TCGA.CV.6954.01 4 0.000
#> TCGA.BA.6868.01 2 0.000
#> TCGA.CV.6959.01 2 0.000
#> TCGA.CQ.6228.01 4 0.000
#> TCGA.CQ.6229.01 6 1.000
#> TCGA.CQ.6224.01 2 0.253
#> TCGA.CV.6951.01 1 0.000
#> TCGA.CQ.6223.01 6 1.000
#> TCGA.CV.6948.01 1 0.000
#> TCGA.CV.6936.11 3 0.000
#> TCGA.DQ.5624.01 6 0.000
#> TCGA.CV.A45R.01 2 0.000
#> TCGA.CN.A499.01 5 0.000
#> TCGA.CN.A49B.01 2 1.000
#> TCGA.BA.5152.01 6 0.502
#> TCGA.CV.6938.01 6 0.000
#> TCGA.CQ.5326.01 6 0.253
#> TCGA.D6.6824.01 3 0.000
#> TCGA.CV.6940.01 2 0.000
#> TCGA.CQ.6225.01 4 0.000
#> TCGA.CR.6471.01 6 0.253
#> TCGA.CN.6988.01 4 0.000
#> TCGA.BA.6872.01 2 0.000
#> TCGA.CV.6933.11 3 0.000
#> TCGA.CR.6482.01 5 0.000
#> TCGA.P3.A5Q5.01 5 0.000
#> TCGA.CQ.A4C6.01 2 1.000
#> TCGA.QK.A8Z8.01 4 0.000
#> TCGA.CV.A45W.01 1 0.000
#> TCGA.F7.A624.01 2 0.249
#> TCGA.F7.A623.01 1 0.249
#> TCGA.F7.A622.01 2 0.498
#> TCGA.CQ.7064.01 6 0.747
#> TCGA.IQ.A61K.01 2 0.000
#> TCGA.HD.A633.01 2 0.000
#> TCGA.BA.A4IG.01 5 0.000
#> TCGA.F7.A61W.01 2 0.000
#> TCGA.BA.A6DF.01 2 0.498
#> TCGA.D6.A4ZB.01 6 0.000
#> TCGA.KU.A66T.01 1 0.000
#> TCGA.HD.8224.01 1 0.000
#> TCGA.CV.A45Y.01 7 0.000
#> TCGA.BB.A5HU.01 2 1.000
#> TCGA.T3.A92M.01 1 0.000
#> TCGA.CQ.A4C7.01 2 0.000
#> TCGA.P3.A5Q6.01 2 0.000
#> TCGA.CQ.A4CD.01 2 1.000
#> TCGA.BA.A6DB.01 7 0.000
#> TCGA.CV.A468.01 7 0.000
#> TCGA.QK.A8Z7.01 4 0.000
#> TCGA.F7.A620.01 6 0.000
#> TCGA.BA.A8YP.01 1 0.000
#> TCGA.CQ.A4C9.01 4 0.000
#> TCGA.CQ.7072.01 4 0.000
#> TCGA.IQ.A61H.01 6 0.000
#> TCGA.QK.AA3K.01 5 0.000
#> TCGA.CQ.7069.01 2 1.000
#> TCGA.CX.A4AQ.01 2 0.000
#> TCGA.CV.A464.01 6 0.249
#> TCGA.IQ.A61L.01 2 0.000
#> TCGA.QK.A8Z9.01 2 0.000
#> TCGA.HD.A634.01 5 0.000
#> TCGA.4P.AA8J.01 7 0.000
#> TCGA.BB.A5HY.01 2 0.502
#> TCGA.HD.8635.01 2 1.000
#> TCGA.CN.A63T.01 4 0.000
#> TCGA.QK.A652.01 6 0.000
#> TCGA.MT.A67G.01 5 0.000
#> TCGA.QK.A64Z.01 6 0.000
#> TCGA.HD.8634.01 6 0.253
#> TCGA.CQ.7063.01 6 0.751
#> TCGA.CV.A45V.01 1 0.000
#> TCGA.CV.A460.01 2 0.249
#> TCGA.CV.A465.01 1 0.249
#> TCGA.CQ.A4CG.01 1 1.000
#> TCGA.F7.A50J.01 6 0.751
#> TCGA.F7.8298.01 6 0.751
#> TCGA.F7.8489.01 6 0.000
#> TCGA.P3.A5QA.01 2 0.502
#> TCGA.F7.A50G.01 2 0.000
#> TCGA.CQ.A4CA.01 7 0.000
#> TCGA.T3.A92N.01 2 0.000
#> TCGA.F7.A61V.01 4 0.000
#> TCGA.CN.A63Y.01 5 0.000
#> TCGA.CQ.5333.01 6 0.000
#> TCGA.P3.A5QE.01 6 0.751
#> TCGA.MT.A67D.01 5 1.000
#> TCGA.CN.A63V.01 1 1.000
#> TCGA.BA.A6DJ.01 2 1.000
#> TCGA.MT.A51W.01 6 0.000
#> TCGA.P3.A5QF.01 4 0.000
#> TCGA.CQ.A4CE.01 1 0.000
#> TCGA.IQ.A61G.01 2 0.000
#> TCGA.HD.8314.01 5 0.000
#> TCGA.BB.A5HZ.01 4 0.000
#> TCGA.CN.A641.01 4 0.000
#> TCGA.IQ.A61J.01 2 0.751
#> TCGA.BA.A6DG.01 7 0.000
#> TCGA.QK.AA3J.01 4 0.000
#> TCGA.CQ.A4CH.01 7 0.000
#> TCGA.BA.A4II.01 7 0.502
#> TCGA.KU.A66S.01 4 0.000
#> TCGA.CQ.A4CB.01 6 0.253
#> TCGA.D6.8569.01 2 0.000
#> TCGA.IQ.A61I.01 5 0.000
#> TCGA.D6.A4Z9.01 6 1.000
#> TCGA.QK.A8ZA.01 1 0.000
#> TCGA.QK.A8ZB.01 1 0.751
#> TCGA.BA.A6DL.01 4 0.000
#> TCGA.CQ.A4CI.01 1 0.000
#> TCGA.MT.A51X.01 1 1.000
#> TCGA.CV.A461.01 4 0.000
#> TCGA.CQ.7071.01 6 0.253
#> TCGA.H7.8501.01 2 1.000
#> TCGA.BB.8596.01 7 0.751
#> TCGA.F7.A50I.01 6 0.000
#> TCGA.BB.8601.01 2 0.000
#> TCGA.H7.8502.01 2 0.000
#> TCGA.F7.A61S.01 6 0.502
#> TCGA.CV.A463.01 2 1.000
#> TCGA.IQ.A61O.01 1 1.000
#> TCGA.CV.A45Z.01 5 1.000
#> TCGA.CV.A45X.01 1 0.249
#> TCGA.D6.8568.01 2 0.000
#> TCGA.CN.A642.01 2 0.502
#> TCGA.CN.4722.01 6 1.000
#> TCGA.IQ.A6SH.01 1 0.498
#> TCGA.CN.5367.01 6 0.000
#> TCGA.P3.A6T2.01 2 0.000
#> TCGA.P3.A6T8.01 1 0.253
#> TCGA.CN.A6V7.01 5 0.000
#> TCGA.CN.A640.01 7 0.000
#> TCGA.UF.A71E.01 1 0.000
#> TCGA.DQ.7589.01 2 1.000
#> TCGA.P3.A6T6.01 4 0.000
#> TCGA.CN.4725.01 2 0.000
#> TCGA.BA.5153.01 5 0.000
#> TCGA.DQ.7594.01 5 0.000
#> TCGA.HL.7533.01 5 0.000
#> TCGA.T2.A6X0.01 5 0.000
#> TCGA.CN.4730.01 4 0.000
#> TCGA.CN.4723.01 6 0.249
#> TCGA.UF.A7J9.01 1 0.000
#> TCGA.UF.A7JO.01 6 0.000
#> TCGA.DQ.7596.01 5 0.000
#> TCGA.UF.A7JV.01 6 0.000
#> TCGA.CN.4729.01 6 0.000
#> TCGA.IQ.A6SG.01 2 0.000
#> TCGA.BB.7864.01 4 0.000
#> TCGA.MT.A67A.01 2 0.747
#> TCGA.CN.5361.01 2 0.502
#> TCGA.CN.5359.01 6 0.000
#> TCGA.BB.7861.01 5 0.000
#> TCGA.CN.4728.01 7 0.000
#> TCGA.BB.A6UO.01 2 0.502
#> TCGA.BA.4074.01 4 0.000
#> TCGA.CN.4734.01 2 1.000
#> TCGA.QK.A6VB.01 4 0.000
#> TCGA.BA.4075.01 2 0.253
#> TCGA.BB.7871.01 6 0.502
#> TCGA.CN.4726.01 2 0.000
#> TCGA.CN.4735.01 1 0.000
#> TCGA.P3.A6T3.01 2 1.000
#> TCGA.HD.7917.01 4 0.000
#> TCGA.BB.4223.01 5 0.000
#> TCGA.UF.A71B.01 1 0.000
#> TCGA.UF.A7JS.01 2 0.498
#> TCGA.QK.A6VC.01 7 0.502
#> TCGA.CV.7409.01 4 0.000
#> TCGA.CN.4736.01 6 0.000
#> TCGA.BB.7862.01 1 0.000
#> TCGA.BA.A6DI.01 7 0.000
#> TCGA.RS.A6TO.01 1 0.249
#> TCGA.CN.4737.01 5 1.000
#> TCGA.CN.5355.01 7 0.498
#> TCGA.UF.A71D.01 4 0.000
#> TCGA.CQ.7067.01 6 0.000
#> TCGA.BA.4078.01 1 0.000
#> TCGA.CN.5374.01 5 0.000
#> TCGA.DQ.7590.01 5 0.000
#> TCGA.CN.5369.01 7 0.000
#> TCGA.BA.5151.01 6 0.000
#> TCGA.TN.A7HJ.01 2 0.000
#> TCGA.IQ.A61E.01 6 0.000
#> TCGA.BB.7870.01 4 0.000
#> TCGA.CN.4727.01 4 0.000
#> TCGA.DQ.7595.01 4 0.000
#> TCGA.BA.4076.01 2 0.000
#> TCGA.CN.5360.01 4 0.000
#> TCGA.BB.4228.01 5 0.000
#> TCGA.MZ.A7D7.01 2 0.253
#> TCGA.H7.A76A.01 5 0.000
#> TCGA.UF.A7JT.01 6 0.000
#> TCGA.CN.5373.01 6 0.000
#> TCGA.CN.A6V3.01 4 0.000
#> TCGA.BB.7863.01 6 1.000
#> TCGA.DQ.7593.01 5 0.000
#> TCGA.UF.A7JJ.01 7 0.000
#> TCGA.CN.5363.01 6 0.000
#> TCGA.BA.4077.01 5 0.000
#> TCGA.BB.4225.01 5 0.000
#> TCGA.BB.7872.01 6 0.502
#> TCGA.CN.A6UY.01 5 0.000
#> TCGA.MT.A7BN.01 5 0.000
#> TCGA.UF.A7JF.01 4 0.000
#> TCGA.CN.4731.01 4 0.000
#> TCGA.MZ.A5BI.01 5 0.000
#> TCGA.CN.A63W.01 4 0.000
#> TCGA.H7.A6C4.01 6 0.000
#> TCGA.T2.A6X2.01 6 1.000
#> TCGA.CN.5364.01 2 1.000
#> TCGA.CN.A63U.01 4 0.000
#> TCGA.BB.A6UM.01 5 0.000
#> TCGA.H7.A6C5.01 4 0.000
#> TCGA.CN.4741.01 5 0.000
#> TCGA.CV.A6JO.01 6 0.498
#> TCGA.BB.7866.01 5 0.000
#> TCGA.CN.5365.01 2 1.000
#> TCGA.CN.4740.01 1 0.751
#> TCGA.BB.4224.01 2 0.000
#> TCGA.MT.A67F.01 6 0.000
#> TCGA.CN.5366.01 6 0.502
#> TCGA.QK.A6V9.01 5 0.000
#> TCGA.CN.5356.01 4 0.000
#> TCGA.T2.A6WX.01 6 1.000
#> TCGA.CV.A6JZ.01 6 0.000
#> TCGA.CN.A6V1.01 5 0.000
#> TCGA.HD.A6I0.01 2 0.000
#> TCGA.UF.A71A.01 1 0.000
#> TCGA.CV.7430.01 2 1.000
#> TCGA.CR.7383.01 6 0.000
#> TCGA.CN.A6V6.01 5 0.000
#> TCGA.F7.7848.01 4 0.000
#> TCGA.TN.A7HI.01 1 0.000
#> TCGA.UF.A7JC.01 2 0.000
#> TCGA.D6.A6ES.01 1 1.000
#> TCGA.CV.7568.01 6 0.000
#> TCGA.BA.A6D8.01 1 0.000
#> TCGA.P3.A6T4.01 1 0.751
#> TCGA.QK.A6IF.01 5 0.000
#> TCGA.CV.A6JT.01 2 0.253
#> TCGA.CV.7438.01 6 0.000
#> TCGA.RS.A6TP.01 5 0.000
#> TCGA.P3.A6SW.01 5 0.000
#> TCGA.D6.A6EN.01 2 0.249
#> TCGA.D6.A6EM.01 7 1.000
#> TCGA.UF.A7JK.01 1 0.000
#> TCGA.KU.A6H7.06 5 0.000
#> TCGA.CV.7429.01 6 0.000
#> TCGA.UP.A6WW.01 5 0.000
#> TCGA.CV.7437.01 2 0.000
#> TCGA.CV.A6JD.01 6 0.751
#> TCGA.CV.A6JY.01 1 0.000
#> TCGA.CV.A6JN.01 2 0.000
#> TCGA.CV.7446.01 1 0.000
#> TCGA.CV.7432.01 2 0.000
#> TCGA.CV.7434.01 2 0.502
#> TCGA.WA.A7H4.01 7 0.000
#> TCGA.KU.A6H8.01 3 0.000
#> TCGA.CV.7428.01 4 0.000
#> TCGA.D6.A6EK.01 7 0.249
#> TCGA.CV.A6K0.01 7 1.000
#> TCGA.HD.7832.01 2 0.000
#> TCGA.MZ.A6I9.01 5 0.000
#> TCGA.CV.7435.01 4 0.000
#> TCGA.P3.A6SX.01 2 0.000
#> TCGA.QK.A6IG.01 2 0.249
#> TCGA.HD.7831.01 7 0.000
#> TCGA.CV.A6JM.01 1 0.000
#> TCGA.CR.7404.01 5 0.000
#> TCGA.D6.A6EQ.01 2 1.000
#> TCGA.QK.A6IJ.01 1 0.249
#> TCGA.P3.A6T0.01 2 0.751
#> TCGA.CV.A6JE.01 1 0.000
#> TCGA.HD.A6HZ.01 1 0.498
#> TCGA.QK.A6II.01 6 0.000
#> TCGA.P3.A6T7.01 6 0.000
#> TCGA.BA.A6DD.01 7 0.000
#> TCGA.UF.A719.01 4 0.000
#> TCGA.TN.A7HL.01 5 0.000
#> TCGA.UF.A7JA.01 7 0.751
#> TCGA.CR.7368.01 5 0.000
#> TCGA.CR.7382.01 7 0.000
#> TCGA.UF.A7JD.01 4 0.000
#> TCGA.UF.A7JH.01 4 0.000
#> TCGA.BA.A6DA.01 6 0.751
#> TCGA.T2.A6WZ.01 2 0.747
#> TCGA.D6.A6EO.01 4 0.000
#> TCGA.CR.7370.01 1 0.000
#> TCGA.P3.A6T5.01 2 0.249
#> TCGA.D6.A74Q.01 4 0.000
#> TCGA.UF.A718.01 7 0.000
#> TCGA.CR.7369.01 5 0.000
#> TCGA.QK.A6IH.01 1 0.751
#> TCGA.CV.A6K2.01 6 1.000
#> TCGA.CV.A6K1.01 1 0.000
#> TCGA.BA.A6DE.01 4 0.000
#> TCGA.WA.A7GZ.01 1 0.000
#> TCGA.CV.7433.01 6 0.000
#> TCGA.CV.7440.01 4 0.000
#> TCGA.CV.A6JU.01 4 0.000
#> TCGA.CR.7376.01 7 0.000
#> TCGA.UF.A71A.06 1 0.000
#> TCGA.KU.A6H7.01 5 0.000
#> TCGA.D6.A6EP.01 1 0.253
get_classes(res, k = 8)
#> class p
#> TCGA.CN.6022.01 7 1.000
#> TCGA.CQ.5327.01 6 0.000
#> TCGA.CV.5435.11 3 0.000
#> TCGA.HD.7753.01 2 0.249
#> TCGA.CQ.5325.01 7 0.000
#> TCGA.CV.5432.01 1 0.000
#> TCGA.CR.7391.01 7 0.000
#> TCGA.CV.7415.01 6 0.249
#> TCGA.CR.5247.01 4 0.000
#> TCGA.CN.6011.01 6 0.000
#> TCGA.CV.7414.01 1 0.000
#> TCGA.CV.6436.01 6 0.000
#> TCGA.DQ.7592.01 2 1.000
#> TCGA.IQ.7632.01 7 0.000
#> TCGA.CV.7416.01 2 1.000
#> TCGA.CV.5432.11 3 0.000
#> TCGA.H7.7774.01 6 0.000
#> TCGA.CQ.5330.01 6 0.000
#> TCGA.CV.5430.11 3 0.000
#> TCGA.CV.7427.01 6 0.000
#> TCGA.CV.5979.01 2 0.000
#> TCGA.CR.6488.01 7 0.000
#> TCGA.CQ.6221.01 6 0.000
#> TCGA.CV.5434.11 3 0.000
#> TCGA.CV.5970.11 3 0.000
#> TCGA.CV.7425.01 6 0.000
#> TCGA.CV.6441.01 2 0.000
#> TCGA.IQ.7630.01 6 0.000
#> TCGA.CV.5976.11 3 0.000
#> TCGA.CV.7103.11 3 0.000
#> TCGA.CV.5977.01 6 0.000
#> TCGA.CQ.5324.01 2 0.000
#> TCGA.CV.7407.01 6 0.000
#> TCGA.CV.5971.01 7 0.000
#> TCGA.CV.5970.01 6 0.000
#> TCGA.CN.6016.01 6 1.000
#> TCGA.CV.6003.01 6 0.000
#> TCGA.CN.6010.01 1 0.000
#> TCGA.CN.6021.01 6 0.249
#> TCGA.CV.6433.01 5 0.000
#> TCGA.CV.5434.01 6 0.000
#> TCGA.CV.7413.01 7 0.000
#> TCGA.HD.7754.01 5 0.000
#> TCGA.CN.6017.01 7 0.000
#> TCGA.CV.6003.11 3 0.000
#> TCGA.CV.7422.01 6 1.000
#> TCGA.CV.7421.01 1 0.498
#> TCGA.CV.5439.11 3 0.000
#> TCGA.CV.7235.01 6 0.000
#> TCGA.BA.7269.01 1 0.000
#> TCGA.CV.5971.11 3 0.000
#> TCGA.CQ.5332.01 1 0.000
#> TCGA.CV.5439.01 6 0.000
#> TCGA.CN.6020.01 2 0.000
#> TCGA.CV.7423.01 2 0.000
#> TCGA.CV.7263.01 4 0.000
#> TCGA.CV.7406.01 5 0.000
#> TCGA.CN.6023.01 6 0.000
#> TCGA.CV.5966.11 3 0.000
#> TCGA.CV.7101.01 1 0.000
#> TCGA.CV.5977.11 3 0.000
#> TCGA.CR.7365.01 6 0.000
#> TCGA.CN.6012.01 1 0.000
#> TCGA.CV.6441.11 3 0.000
#> TCGA.CN.6024.01 6 0.000
#> TCGA.CV.5978.01 6 0.000
#> TCGA.CX.7086.01 1 0.249
#> TCGA.CV.7424.01 1 0.000
#> TCGA.CV.7089.01 6 0.000
#> TCGA.CQ.7065.01 1 1.000
#> TCGA.IQ.7631.01 7 1.000
#> TCGA.CV.7418.01 1 0.000
#> TCGA.CV.6937.01 1 0.498
#> TCGA.CN.6018.01 6 0.000
#> TCGA.CV.5966.01 6 0.000
#> TCGA.CQ.5329.01 7 0.249
#> TCGA.CV.5976.01 6 0.502
#> TCGA.CV.7411.01 6 0.000
#> TCGA.CQ.5323.01 5 0.000
#> TCGA.CV.5978.11 3 0.000
#> TCGA.CV.5973.11 3 0.000
#> TCGA.BB.4217.01 7 0.000
#> TCGA.CQ.7068.01 6 0.000
#> TCGA.CN.6013.01 1 0.249
#> TCGA.CV.6436.11 3 0.000
#> TCGA.CV.6433.11 3 0.000
#> TCGA.CN.6995.01 6 0.000
#> TCGA.CV.6960.01 4 0.000
#> TCGA.CQ.5334.01 6 0.502
#> TCGA.CV.7410.01 7 0.000
#> TCGA.CN.6019.01 7 0.000
#> TCGA.DQ.7588.01 2 0.000
#> TCGA.CV.5979.11 3 0.000
#> TCGA.CR.6492.01 7 0.000
#> TCGA.CV.5973.01 2 0.000
#> TCGA.DQ.7591.01 5 0.000
#> TCGA.CR.7389.01 1 0.000
#> TCGA.CV.7245.01 4 0.000
#> TCGA.CV.5430.01 6 0.502
#> TCGA.CV.5435.01 2 0.000
#> TCGA.CR.7374.01 1 0.000
#> TCGA.CV.5440.01 1 0.000
#> TCGA.CV.6955.11 6 0.000
#> TCGA.CV.7238.11 3 0.000
#> TCGA.CV.7104.01 6 0.000
#> TCGA.CV.7100.01 2 0.000
#> TCGA.CV.7089.11 3 0.000
#> TCGA.CN.4739.01 4 0.000
#> TCGA.CV.7095.01 2 0.751
#> TCGA.CV.6956.01 4 0.000
#> TCGA.CV.5431.11 3 0.000
#> TCGA.CV.7261.01 1 0.000
#> TCGA.CN.5358.01 7 0.000
#> TCGA.BA.5559.01 5 0.000
#> TCGA.CR.7373.01 6 0.000
#> TCGA.CX.7082.01 1 0.000
#> TCGA.DQ.5629.01 1 0.000
#> TCGA.CV.7255.11 3 0.000
#> TCGA.CR.7379.01 1 1.000
#> TCGA.CV.7178.01 1 0.751
#> TCGA.CR.5249.01 5 0.000
#> TCGA.CV.7091.01 4 0.000
#> TCGA.CV.7236.01 7 0.000
#> TCGA.CN.6998.01 6 0.000
#> TCGA.CR.7399.01 2 0.000
#> TCGA.CR.7372.01 1 0.000
#> TCGA.CV.7252.01 6 0.502
#> TCGA.CV.7242.01 4 0.000
#> TCGA.CV.7103.01 1 0.000
#> TCGA.CR.6478.01 6 0.000
#> TCGA.CR.7371.01 7 0.249
#> TCGA.CR.7380.01 6 0.000
#> TCGA.CV.7183.01 2 0.000
#> TCGA.CV.7250.11 3 0.000
#> TCGA.CV.7102.01 6 0.249
#> TCGA.CV.7254.01 6 0.000
#> TCGA.CR.7394.01 7 0.000
#> TCGA.CV.5443.01 5 0.000
#> TCGA.CV.6955.01 6 0.000
#> TCGA.CV.5441.11 7 0.000
#> TCGA.CV.5442.11 3 0.000
#> TCGA.BA.5556.01 6 0.000
#> TCGA.CR.7386.01 7 0.000
#> TCGA.CV.7255.01 1 1.000
#> TCGA.CR.6474.01 7 0.000
#> TCGA.BA.5557.01 7 0.000
#> TCGA.CR.7388.01 7 0.498
#> TCGA.CV.5436.11 3 0.000
#> TCGA.CR.7398.01 4 0.000
#> TCGA.CV.7247.01 2 0.000
#> TCGA.CN.6997.01 1 0.000
#> TCGA.CN.4742.01 7 0.000
#> TCGA.CN.4738.01 7 0.000
#> TCGA.CR.7392.01 7 0.000
#> TCGA.CV.7245.11 3 0.000
#> TCGA.CR.7377.01 7 0.000
#> TCGA.HD.7229.01 6 0.000
#> TCGA.CV.7235.11 3 0.000
#> TCGA.D6.6515.01 7 0.000
#> TCGA.CV.7238.01 7 0.000
#> TCGA.CR.5248.01 5 0.000
#> TCGA.CV.7097.01 6 0.000
#> TCGA.CR.5250.01 5 0.000
#> TCGA.CV.7248.01 1 0.000
#> TCGA.CV.7253.01 4 0.000
#> TCGA.CN.5370.01 6 0.000
#> TCGA.CR.7367.01 6 1.000
#> TCGA.CR.7401.01 6 0.000
#> TCGA.BA.5149.01 7 1.000
#> TCGA.CV.6942.01 6 0.000
#> TCGA.CV.7263.11 3 0.000
#> TCGA.CV.7177.01 6 0.000
#> TCGA.BA.5555.01 4 0.000
#> TCGA.CV.6956.11 3 0.000
#> TCGA.CV.5431.01 7 0.000
#> TCGA.CR.7393.01 3 0.000
#> TCGA.CV.5444.11 3 0.000
#> TCGA.CV.5444.01 7 0.000
#> TCGA.CR.5243.01 5 0.000
#> TCGA.CR.7395.01 6 0.000
#> TCGA.CV.5441.01 4 0.000
#> TCGA.CV.5442.01 5 0.000
#> TCGA.BA.5558.01 6 0.000
#> TCGA.CX.7085.01 7 0.000
#> TCGA.CV.7250.01 4 0.000
#> TCGA.CR.7390.01 1 0.000
#> TCGA.CV.7178.11 3 0.000
#> TCGA.CV.7099.01 6 0.000
#> TCGA.CV.5443.11 3 0.000
#> TCGA.CR.7385.01 5 0.000
#> TCGA.CR.7364.01 4 0.000
#> TCGA.CV.7090.01 6 0.000
#> TCGA.CR.7397.01 7 0.000
#> TCGA.CR.7402.01 4 0.000
#> TCGA.CV.5440.11 3 0.751
#> TCGA.CV.7180.01 7 0.000
#> TCGA.CX.7219.01 2 1.000
#> TCGA.CV.7101.11 3 0.000
#> TCGA.CV.5436.01 2 0.000
#> TCGA.CV.7243.01 2 0.000
#> TCGA.BA.6871.01 6 1.000
#> TCGA.CQ.6218.01 6 0.000
#> TCGA.C9.A47Z.01 6 0.747
#> TCGA.CV.6961.01 5 0.000
#> TCGA.DQ.5625.01 6 0.000
#> TCGA.CN.6992.01 1 0.000
#> TCGA.CV.6939.01 5 0.000
#> TCGA.CR.6480.01 5 0.000
#> TCGA.D6.6825.01 6 0.000
#> TCGA.C9.A480.01 6 0.000
#> TCGA.CV.6962.01 1 0.000
#> TCGA.CV.6952.01 6 0.000
#> TCGA.CN.A49A.01 4 0.000
#> TCGA.CR.6487.01 5 0.000
#> TCGA.CV.6935.11 3 0.000
#> TCGA.CQ.6222.01 6 0.000
#> TCGA.CV.6959.11 3 0.000
#> TCGA.BB.4227.01 6 0.000
#> TCGA.CN.A49C.01 5 0.000
#> TCGA.CN.6994.01 6 0.249
#> TCGA.CV.6938.11 3 0.000
#> TCGA.CV.6936.01 1 1.000
#> TCGA.CR.6491.01 6 0.000
#> TCGA.CV.6950.01 2 0.000
#> TCGA.CR.6473.01 5 0.000
#> TCGA.CV.6952.11 3 0.000
#> TCGA.CQ.5331.01 6 1.000
#> TCGA.D6.6826.01 6 0.000
#> TCGA.CV.6951.11 3 0.000
#> TCGA.CV.6935.01 6 0.000
#> TCGA.DQ.5631.01 1 1.000
#> TCGA.CV.6953.01 6 0.000
#> TCGA.CV.6945.01 6 0.000
#> TCGA.CV.6939.11 3 0.000
#> TCGA.CV.A45U.01 1 0.000
#> TCGA.CN.A497.01 4 0.000
#> TCGA.D6.6823.01 4 0.000
#> TCGA.DQ.5630.01 6 0.000
#> TCGA.D6.6827.01 7 0.000
#> TCGA.CV.6943.01 7 0.000
#> TCGA.CV.6954.11 3 0.000
#> TCGA.CR.6472.01 5 0.000
#> TCGA.CR.6481.01 5 0.000
#> TCGA.BA.A4IF.01 4 0.000
#> TCGA.BA.6870.01 6 0.000
#> TCGA.CV.6962.11 3 0.000
#> TCGA.CR.6477.01 6 0.000
#> TCGA.CV.A45O.01 6 0.000
#> TCGA.CQ.6219.01 6 0.000
#> TCGA.CN.4733.01 7 0.000
#> TCGA.CR.6484.01 7 0.498
#> TCGA.CN.A498.01 6 0.000
#> TCGA.CR.6470.01 5 0.000
#> TCGA.CV.6934.01 7 0.498
#> TCGA.CN.6989.01 6 0.000
#> TCGA.CV.6953.11 7 0.000
#> TCGA.CV.6933.01 1 0.000
#> TCGA.D6.6517.01 6 0.000
#> TCGA.CQ.6220.01 2 0.000
#> TCGA.BA.A4IH.01 5 0.000
#> TCGA.HD.A4C1.01 6 0.000
#> TCGA.BA.6869.01 4 0.000
#> TCGA.CR.6493.01 2 0.000
#> TCGA.D6.6516.01 6 0.249
#> TCGA.CQ.6227.01 7 1.000
#> TCGA.CV.A45P.01 6 0.502
#> TCGA.CV.A45Q.01 6 0.000
#> TCGA.CV.A45T.01 7 0.000
#> TCGA.CN.6996.01 6 0.000
#> TCGA.CV.6961.11 3 0.000
#> TCGA.CV.6941.01 4 0.000
#> TCGA.BA.6873.01 6 0.000
#> TCGA.CV.6934.11 3 0.000
#> TCGA.CR.6467.01 5 0.000
#> TCGA.CV.6943.11 3 0.000
#> TCGA.CV.6954.01 4 0.000
#> TCGA.BA.6868.01 6 0.502
#> TCGA.CV.6959.01 2 0.000
#> TCGA.CQ.6228.01 4 0.000
#> TCGA.CQ.6229.01 6 0.249
#> TCGA.CQ.6224.01 2 0.249
#> TCGA.CV.6951.01 1 0.000
#> TCGA.CQ.6223.01 6 0.000
#> TCGA.CV.6948.01 1 0.000
#> TCGA.CV.6936.11 3 0.000
#> TCGA.DQ.5624.01 6 0.000
#> TCGA.CV.A45R.01 2 0.000
#> TCGA.CN.A499.01 5 0.000
#> TCGA.CN.A49B.01 6 0.000
#> TCGA.BA.5152.01 6 0.000
#> TCGA.CV.6938.01 6 0.000
#> TCGA.CQ.5326.01 6 0.000
#> TCGA.D6.6824.01 3 0.000
#> TCGA.CV.6940.01 6 0.249
#> TCGA.CQ.6225.01 4 0.000
#> TCGA.CR.6471.01 6 0.000
#> TCGA.CN.6988.01 4 0.000
#> TCGA.BA.6872.01 6 0.000
#> TCGA.CV.6933.11 3 0.000
#> TCGA.CR.6482.01 5 0.000
#> TCGA.P3.A5Q5.01 5 0.000
#> TCGA.CQ.A4C6.01 6 0.000
#> TCGA.QK.A8Z8.01 4 0.000
#> TCGA.CV.A45W.01 1 0.000
#> TCGA.F7.A624.01 7 1.000
#> TCGA.F7.A623.01 1 0.000
#> TCGA.F7.A622.01 2 0.747
#> TCGA.CQ.7064.01 6 0.253
#> TCGA.IQ.A61K.01 2 0.000
#> TCGA.HD.A633.01 2 0.000
#> TCGA.BA.A4IG.01 5 0.000
#> TCGA.F7.A61W.01 6 0.000
#> TCGA.BA.A6DF.01 2 0.249
#> TCGA.D6.A4ZB.01 6 0.000
#> TCGA.KU.A66T.01 1 0.000
#> TCGA.HD.8224.01 1 0.751
#> TCGA.CV.A45Y.01 6 0.000
#> TCGA.BB.A5HU.01 2 0.249
#> TCGA.T3.A92M.01 7 0.000
#> TCGA.CQ.A4C7.01 2 0.000
#> TCGA.P3.A5Q6.01 2 0.000
#> TCGA.CQ.A4CD.01 6 0.000
#> TCGA.BA.A6DB.01 7 0.000
#> TCGA.CV.A468.01 7 0.000
#> TCGA.QK.A8Z7.01 4 0.000
#> TCGA.F7.A620.01 7 0.000
#> TCGA.BA.A8YP.01 1 0.000
#> TCGA.CQ.A4C9.01 4 0.000
#> TCGA.CQ.7072.01 4 0.000
#> TCGA.IQ.A61H.01 1 0.249
#> TCGA.QK.AA3K.01 5 0.000
#> TCGA.CQ.7069.01 2 0.498
#> TCGA.CX.A4AQ.01 6 0.000
#> TCGA.CV.A464.01 2 1.000
#> TCGA.IQ.A61L.01 2 0.000
#> TCGA.QK.A8Z9.01 2 0.000
#> TCGA.HD.A634.01 5 0.000
#> TCGA.4P.AA8J.01 7 0.000
#> TCGA.BB.A5HY.01 2 0.000
#> TCGA.HD.8635.01 6 0.249
#> TCGA.CN.A63T.01 4 0.000
#> TCGA.QK.A652.01 6 0.000
#> TCGA.MT.A67G.01 5 0.000
#> TCGA.QK.A64Z.01 6 0.000
#> TCGA.HD.8634.01 6 0.000
#> TCGA.CQ.7063.01 6 0.000
#> TCGA.CV.A45V.01 1 1.000
#> TCGA.CV.A460.01 6 0.751
#> TCGA.CV.A465.01 7 0.498
#> TCGA.CQ.A4CG.01 6 1.000
#> TCGA.F7.A50J.01 7 0.000
#> TCGA.F7.8298.01 6 0.000
#> TCGA.F7.8489.01 6 0.000
#> TCGA.P3.A5QA.01 2 1.000
#> TCGA.F7.A50G.01 6 1.000
#> TCGA.CQ.A4CA.01 7 0.000
#> TCGA.T3.A92N.01 6 0.000
#> TCGA.F7.A61V.01 4 0.000
#> TCGA.CN.A63Y.01 5 0.000
#> TCGA.CQ.5333.01 6 0.000
#> TCGA.P3.A5QE.01 6 0.751
#> TCGA.MT.A67D.01 1 1.000
#> TCGA.CN.A63V.01 7 0.000
#> TCGA.BA.A6DJ.01 6 0.000
#> TCGA.MT.A51W.01 6 0.502
#> TCGA.P3.A5QF.01 4 0.000
#> TCGA.CQ.A4CE.01 7 1.000
#> TCGA.IQ.A61G.01 6 0.000
#> TCGA.HD.8314.01 5 0.000
#> TCGA.BB.A5HZ.01 4 0.000
#> TCGA.CN.A641.01 4 0.000
#> TCGA.IQ.A61J.01 2 0.249
#> TCGA.BA.A6DG.01 7 0.000
#> TCGA.QK.AA3J.01 4 0.000
#> TCGA.CQ.A4CH.01 7 0.000
#> TCGA.BA.A4II.01 7 0.000
#> TCGA.KU.A66S.01 4 0.000
#> TCGA.CQ.A4CB.01 6 0.000
#> TCGA.D6.8569.01 6 0.000
#> TCGA.IQ.A61I.01 5 0.000
#> TCGA.D6.A4Z9.01 6 0.000
#> TCGA.QK.A8ZA.01 1 0.000
#> TCGA.QK.A8ZB.01 7 0.000
#> TCGA.BA.A6DL.01 4 0.000
#> TCGA.CQ.A4CI.01 1 0.000
#> TCGA.MT.A51X.01 7 1.000
#> TCGA.CV.A461.01 4 0.000
#> TCGA.CQ.7071.01 6 0.000
#> TCGA.H7.8501.01 6 0.000
#> TCGA.BB.8596.01 7 0.000
#> TCGA.F7.A50I.01 7 0.000
#> TCGA.BB.8601.01 6 0.000
#> TCGA.H7.8502.01 6 0.000
#> TCGA.F7.A61S.01 6 0.000
#> TCGA.CV.A463.01 6 0.000
#> TCGA.IQ.A61O.01 7 0.498
#> TCGA.CV.A45Z.01 1 0.747
#> TCGA.CV.A45X.01 6 0.502
#> TCGA.D6.8568.01 2 0.000
#> TCGA.CN.A642.01 6 0.000
#> TCGA.CN.4722.01 7 0.000
#> TCGA.IQ.A6SH.01 2 0.000
#> TCGA.CN.5367.01 6 0.000
#> TCGA.P3.A6T2.01 6 0.249
#> TCGA.P3.A6T8.01 7 1.000
#> TCGA.CN.A6V7.01 5 0.000
#> TCGA.CN.A640.01 7 0.000
#> TCGA.UF.A71E.01 1 0.000
#> TCGA.DQ.7589.01 6 0.000
#> TCGA.P3.A6T6.01 4 0.000
#> TCGA.CN.4725.01 2 0.000
#> TCGA.BA.5153.01 5 0.000
#> TCGA.DQ.7594.01 5 0.000
#> TCGA.HL.7533.01 5 0.000
#> TCGA.T2.A6X0.01 5 0.000
#> TCGA.CN.4730.01 4 0.000
#> TCGA.CN.4723.01 1 0.502
#> TCGA.UF.A7J9.01 1 0.000
#> TCGA.UF.A7JO.01 6 0.000
#> TCGA.DQ.7596.01 5 0.000
#> TCGA.UF.A7JV.01 2 0.498
#> TCGA.CN.4729.01 7 1.000
#> TCGA.IQ.A6SG.01 2 0.000
#> TCGA.BB.7864.01 4 0.000
#> TCGA.MT.A67A.01 6 0.000
#> TCGA.CN.5361.01 2 0.249
#> TCGA.CN.5359.01 6 0.000
#> TCGA.BB.7861.01 5 0.000
#> TCGA.CN.4728.01 7 0.000
#> TCGA.BB.A6UO.01 2 0.249
#> TCGA.BA.4074.01 4 0.000
#> TCGA.CN.4734.01 6 0.000
#> TCGA.QK.A6VB.01 4 0.000
#> TCGA.BA.4075.01 2 0.000
#> TCGA.BB.7871.01 6 0.000
#> TCGA.CN.4726.01 2 0.000
#> TCGA.CN.4735.01 1 0.000
#> TCGA.P3.A6T3.01 1 1.000
#> TCGA.HD.7917.01 4 0.000
#> TCGA.BB.4223.01 5 0.000
#> TCGA.UF.A71B.01 1 0.000
#> TCGA.UF.A7JS.01 6 0.253
#> TCGA.QK.A6VC.01 7 0.000
#> TCGA.CV.7409.01 4 0.000
#> TCGA.CN.4736.01 6 0.000
#> TCGA.BB.7862.01 1 0.000
#> TCGA.BA.A6DI.01 7 0.000
#> TCGA.RS.A6TO.01 1 0.000
#> TCGA.CN.4737.01 1 1.000
#> TCGA.CN.5355.01 7 0.000
#> TCGA.UF.A71D.01 4 0.000
#> TCGA.CQ.7067.01 6 0.498
#> TCGA.BA.4078.01 1 0.000
#> TCGA.CN.5374.01 5 0.000
#> TCGA.DQ.7590.01 6 0.000
#> TCGA.CN.5369.01 7 0.000
#> TCGA.BA.5151.01 6 0.000
#> TCGA.TN.A7HJ.01 7 0.000
#> TCGA.IQ.A61E.01 6 0.000
#> TCGA.BB.7870.01 4 0.000
#> TCGA.CN.4727.01 4 0.000
#> TCGA.DQ.7595.01 4 0.000
#> TCGA.BA.4076.01 6 0.000
#> TCGA.CN.5360.01 4 0.000
#> TCGA.BB.4228.01 5 0.000
#> TCGA.MZ.A7D7.01 6 1.000
#> TCGA.H7.A76A.01 5 0.000
#> TCGA.UF.A7JT.01 6 0.000
#> TCGA.CN.5373.01 6 0.000
#> TCGA.CN.A6V3.01 4 0.000
#> TCGA.BB.7863.01 6 0.000
#> TCGA.DQ.7593.01 5 0.000
#> TCGA.UF.A7JJ.01 7 0.000
#> TCGA.CN.5363.01 6 0.000
#> TCGA.BA.4077.01 5 0.000
#> TCGA.BB.4225.01 5 0.000
#> TCGA.BB.7872.01 6 0.000
#> TCGA.CN.A6UY.01 5 0.000
#> TCGA.MT.A7BN.01 5 0.000
#> TCGA.UF.A7JF.01 4 0.000
#> TCGA.CN.4731.01 4 0.000
#> TCGA.MZ.A5BI.01 5 0.000
#> TCGA.CN.A63W.01 4 0.000
#> TCGA.H7.A6C4.01 6 0.000
#> TCGA.T2.A6X2.01 6 0.000
#> TCGA.CN.5364.01 1 0.751
#> TCGA.CN.A63U.01 4 0.000
#> TCGA.BB.A6UM.01 5 0.000
#> TCGA.H7.A6C5.01 4 0.000
#> TCGA.CN.4741.01 5 0.000
#> TCGA.CV.A6JO.01 7 0.000
#> TCGA.BB.7866.01 5 0.000
#> TCGA.CN.5365.01 6 0.000
#> TCGA.CN.4740.01 1 0.502
#> TCGA.BB.4224.01 2 0.000
#> TCGA.MT.A67F.01 6 0.000
#> TCGA.CN.5366.01 6 1.000
#> TCGA.QK.A6V9.01 5 0.000
#> TCGA.CN.5356.01 4 0.000
#> TCGA.T2.A6WX.01 7 0.000
#> TCGA.CV.A6JZ.01 6 0.000
#> TCGA.CN.A6V1.01 5 0.000
#> TCGA.HD.A6I0.01 2 0.751
#> TCGA.UF.A71A.01 1 0.000
#> TCGA.CV.7430.01 1 0.000
#> TCGA.CR.7383.01 6 0.000
#> TCGA.CN.A6V6.01 5 0.000
#> TCGA.F7.7848.01 4 0.000
#> TCGA.TN.A7HI.01 1 0.000
#> TCGA.UF.A7JC.01 2 0.249
#> TCGA.D6.A6ES.01 7 1.000
#> TCGA.CV.7568.01 6 0.000
#> TCGA.BA.A6D8.01 1 0.000
#> TCGA.P3.A6T4.01 7 0.249
#> TCGA.QK.A6IF.01 5 0.000
#> TCGA.CV.A6JT.01 2 0.000
#> TCGA.CV.7438.01 6 0.000
#> TCGA.RS.A6TP.01 5 0.000
#> TCGA.P3.A6SW.01 5 0.000
#> TCGA.D6.A6EN.01 2 0.253
#> TCGA.D6.A6EM.01 7 0.000
#> TCGA.UF.A7JK.01 2 1.000
#> TCGA.KU.A6H7.06 5 0.000
#> TCGA.CV.7429.01 6 0.000
#> TCGA.UP.A6WW.01 5 0.000
#> TCGA.CV.7437.01 6 0.249
#> TCGA.CV.A6JD.01 6 0.000
#> TCGA.CV.A6JY.01 7 1.000
#> TCGA.CV.A6JN.01 2 0.000
#> TCGA.CV.7446.01 1 0.000
#> TCGA.CV.7432.01 2 0.000
#> TCGA.CV.7434.01 6 0.000
#> TCGA.WA.A7H4.01 7 0.000
#> TCGA.KU.A6H8.01 7 0.249
#> TCGA.CV.7428.01 4 0.000
#> TCGA.D6.A6EK.01 7 0.000
#> TCGA.CV.A6K0.01 7 0.000
#> TCGA.HD.7832.01 2 1.000
#> TCGA.MZ.A6I9.01 5 0.000
#> TCGA.CV.7435.01 4 0.000
#> TCGA.P3.A6SX.01 2 0.000
#> TCGA.QK.A6IG.01 7 1.000
#> TCGA.HD.7831.01 7 0.000
#> TCGA.CV.A6JM.01 1 0.000
#> TCGA.CR.7404.01 5 0.000
#> TCGA.D6.A6EQ.01 2 0.498
#> TCGA.QK.A6IJ.01 7 1.000
#> TCGA.P3.A6T0.01 2 0.498
#> TCGA.CV.A6JE.01 1 1.000
#> TCGA.HD.A6HZ.01 1 0.000
#> TCGA.QK.A6II.01 6 0.249
#> TCGA.P3.A6T7.01 6 0.000
#> TCGA.BA.A6DD.01 7 0.000
#> TCGA.UF.A719.01 4 0.000
#> TCGA.TN.A7HL.01 5 0.000
#> TCGA.UF.A7JA.01 7 0.000
#> TCGA.CR.7368.01 5 0.000
#> TCGA.CR.7382.01 7 0.000
#> TCGA.UF.A7JD.01 4 0.000
#> TCGA.UF.A7JH.01 4 0.000
#> TCGA.BA.A6DA.01 7 0.000
#> TCGA.T2.A6WZ.01 2 0.000
#> TCGA.D6.A6EO.01 4 0.000
#> TCGA.CR.7370.01 1 0.000
#> TCGA.P3.A6T5.01 6 0.502
#> TCGA.D6.A74Q.01 4 0.000
#> TCGA.UF.A718.01 7 0.249
#> TCGA.CR.7369.01 5 0.000
#> TCGA.QK.A6IH.01 1 1.000
#> TCGA.CV.A6K2.01 7 0.000
#> TCGA.CV.A6K1.01 7 0.498
#> TCGA.BA.A6DE.01 4 0.000
#> TCGA.WA.A7GZ.01 1 1.000
#> TCGA.CV.7433.01 7 0.000
#> TCGA.CV.7440.01 4 0.000
#> TCGA.CV.A6JU.01 4 0.000
#> TCGA.CR.7376.01 7 0.000
#> TCGA.UF.A71A.06 1 0.000
#> TCGA.KU.A6H7.01 5 0.000
#> TCGA.D6.A6EP.01 1 0.000
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-leaf , Node021 , Node022 , Node023 , Node031-leaf , Node032-leaf , Node033 , Node034-leaf , Node041-leaf , Node042-leaf , Node043 , Node051 , Node052 , Node053-leaf .
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 90 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 0.4572 0.543 0.543
#> 3 3 1.000 0.980 0.992 0.4426 0.753 0.562
#> 4 4 0.834 0.812 0.916 0.1114 0.882 0.672
#> 5 5 0.773 0.618 0.827 0.0591 0.928 0.741
#> 6 6 0.810 0.709 0.842 0.0284 0.924 0.689
#> 7 7 0.788 0.728 0.831 0.0160 0.972 0.862
#> 8 8 0.769 0.663 0.809 0.0190 0.987 0.930
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.CV.7414.01 1 0 1 1 0
#> TCGA.CN.6010.01 1 0 1 1 0
#> TCGA.CV.7413.01 2 0 1 0 1
#> TCGA.CV.7422.01 2 0 1 0 1
#> TCGA.BA.7269.01 2 0 1 0 1
#> TCGA.CQ.5332.01 1 0 1 1 0
#> TCGA.CV.7101.01 1 0 1 1 0
#> TCGA.CN.6012.01 1 0 1 1 0
#> TCGA.CV.7424.01 1 0 1 1 0
#> TCGA.CV.7418.01 1 0 1 1 0
#> TCGA.CV.6937.01 2 0 1 0 1
#> TCGA.CN.6013.01 2 0 1 0 1
#> TCGA.CN.6019.01 2 0 1 0 1
#> TCGA.CR.7389.01 2 0 1 0 1
#> TCGA.CR.7374.01 1 0 1 1 0
#> TCGA.CV.7261.01 1 0 1 1 0
#> TCGA.CN.5358.01 2 0 1 0 1
#> TCGA.DQ.5629.01 1 0 1 1 0
#> TCGA.CR.7372.01 2 0 1 0 1
#> TCGA.CR.7371.01 2 0 1 0 1
#> TCGA.CR.7388.01 2 0 1 0 1
#> TCGA.CN.6997.01 1 0 1 1 0
#> TCGA.CN.4742.01 2 0 1 0 1
#> TCGA.CN.4738.01 2 0 1 0 1
#> TCGA.CV.7248.01 2 0 1 0 1
#> TCGA.CV.5444.01 2 0 1 0 1
#> TCGA.CR.7390.01 2 0 1 0 1
#> TCGA.CV.5436.01 2 0 1 0 1
#> TCGA.CV.6961.01 2 0 1 0 1
#> TCGA.CN.6992.01 1 0 1 1 0
#> TCGA.CV.6962.01 1 0 1 1 0
#> TCGA.BB.4227.01 2 0 1 0 1
#> TCGA.CV.A45U.01 2 0 1 0 1
#> TCGA.D6.6827.01 1 0 1 1 0
#> TCGA.CV.6934.01 2 0 1 0 1
#> TCGA.CV.6933.01 1 0 1 1 0
#> TCGA.CV.6948.01 1 0 1 1 0
#> TCGA.F7.A623.01 2 0 1 0 1
#> TCGA.T3.A92M.01 2 0 1 0 1
#> TCGA.CV.A468.01 2 0 1 0 1
#> TCGA.IQ.A61H.01 2 0 1 0 1
#> TCGA.QK.AA3K.01 2 0 1 0 1
#> TCGA.4P.AA8J.01 2 0 1 0 1
#> TCGA.CV.A45V.01 2 0 1 0 1
#> TCGA.CV.A460.01 2 0 1 0 1
#> TCGA.CQ.A4CG.01 2 0 1 0 1
#> TCGA.CQ.A4CE.01 2 0 1 0 1
#> TCGA.HD.8314.01 1 0 1 1 0
#> TCGA.BA.A4II.01 2 0 1 0 1
#> TCGA.QK.A8ZA.01 1 0 1 1 0
#> TCGA.CQ.A4CI.01 1 0 1 1 0
#> TCGA.BB.8596.01 2 0 1 0 1
#> TCGA.F7.A50I.01 2 0 1 0 1
#> TCGA.IQ.A61O.01 2 0 1 0 1
#> TCGA.CV.A45X.01 2 0 1 0 1
#> TCGA.IQ.A6SH.01 2 0 1 0 1
#> TCGA.UF.A71E.01 1 0 1 1 0
#> TCGA.T2.A6X0.01 1 0 1 1 0
#> TCGA.CN.4723.01 2 0 1 0 1
#> TCGA.UF.A7J9.01 1 0 1 1 0
#> TCGA.CN.4728.01 2 0 1 0 1
#> TCGA.CN.4735.01 1 0 1 1 0
#> TCGA.QK.A6VC.01 2 0 1 0 1
#> TCGA.BB.7862.01 1 0 1 1 0
#> TCGA.BA.A6DI.01 2 0 1 0 1
#> TCGA.RS.A6TO.01 2 0 1 0 1
#> TCGA.CQ.7067.01 2 0 1 0 1
#> TCGA.BA.4078.01 1 0 1 1 0
#> TCGA.UF.A7JJ.01 2 0 1 0 1
#> TCGA.MT.A7BN.01 2 0 1 0 1
#> TCGA.UF.A71A.01 1 0 1 1 0
#> TCGA.TN.A7HI.01 1 0 1 1 0
#> TCGA.BA.A6D8.01 1 0 1 1 0
#> TCGA.P3.A6T4.01 2 0 1 0 1
#> TCGA.P3.A6SW.01 2 0 1 0 1
#> TCGA.D6.A6EM.01 2 0 1 0 1
#> TCGA.UF.A7JK.01 2 0 1 0 1
#> TCGA.CV.7446.01 1 0 1 1 0
#> TCGA.HD.7831.01 2 0 1 0 1
#> TCGA.D6.A6EQ.01 2 0 1 0 1
#> TCGA.P3.A6T0.01 2 0 1 0 1
#> TCGA.HD.A6HZ.01 2 0 1 0 1
#> TCGA.TN.A7HL.01 2 0 1 0 1
#> TCGA.UF.A7JA.01 2 0 1 0 1
#> TCGA.BA.A6DA.01 2 0 1 0 1
#> TCGA.CR.7370.01 1 0 1 1 0
#> TCGA.CV.A6K2.01 2 0 1 0 1
#> TCGA.CV.A6K1.01 2 0 1 0 1
#> TCGA.UF.A71A.06 1 0 1 1 0
#> TCGA.D6.A6EP.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CV.7414.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CN.6010.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CV.7413.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.CV.7422.01 3 0.0000 0.967 0 0.00 1.00
#> TCGA.BA.7269.01 3 0.0000 0.967 0 0.00 1.00
#> TCGA.CQ.5332.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CV.7101.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CN.6012.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CV.7424.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CV.7418.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CV.6937.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.CN.6013.01 3 0.0000 0.967 0 0.00 1.00
#> TCGA.CN.6019.01 3 0.0000 0.967 0 0.00 1.00
#> TCGA.CR.7389.01 3 0.0000 0.967 0 0.00 1.00
#> TCGA.CR.7374.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CV.7261.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CN.5358.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.DQ.5629.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CR.7372.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.CR.7371.01 3 0.0000 0.967 0 0.00 1.00
#> TCGA.CR.7388.01 3 0.0000 0.967 0 0.00 1.00
#> TCGA.CN.6997.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CN.4742.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.CN.4738.01 3 0.5706 0.545 0 0.32 0.68
#> TCGA.CV.7248.01 3 0.0000 0.967 0 0.00 1.00
#> TCGA.CV.5444.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.CR.7390.01 3 0.0000 0.967 0 0.00 1.00
#> TCGA.CV.5436.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.CV.6961.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.CN.6992.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CV.6962.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.BB.4227.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.CV.A45U.01 3 0.0000 0.967 0 0.00 1.00
#> TCGA.D6.6827.01 3 0.0000 0.967 0 0.00 1.00
#> TCGA.CV.6934.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.CV.6933.01 3 0.0000 0.967 0 0.00 1.00
#> TCGA.CV.6948.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.F7.A623.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.T3.A92M.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.CV.A468.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.IQ.A61H.01 3 0.0000 0.967 0 0.00 1.00
#> TCGA.QK.AA3K.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.4P.AA8J.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.CV.A45V.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.CV.A460.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.CQ.A4CG.01 3 0.0000 0.967 0 0.00 1.00
#> TCGA.CQ.A4CE.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.HD.8314.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.BA.A4II.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.QK.A8ZA.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CQ.A4CI.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.BB.8596.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.F7.A50I.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.IQ.A61O.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.CV.A45X.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.IQ.A6SH.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.UF.A71E.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.T2.A6X0.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CN.4723.01 3 0.0892 0.949 0 0.02 0.98
#> TCGA.UF.A7J9.01 3 0.0000 0.967 0 0.00 1.00
#> TCGA.CN.4728.01 3 0.0000 0.967 0 0.00 1.00
#> TCGA.CN.4735.01 3 0.0000 0.967 0 0.00 1.00
#> TCGA.QK.A6VC.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.BB.7862.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.BA.A6DI.01 3 0.0000 0.967 0 0.00 1.00
#> TCGA.RS.A6TO.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.CQ.7067.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.BA.4078.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.UF.A7JJ.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.MT.A7BN.01 3 0.0000 0.967 0 0.00 1.00
#> TCGA.UF.A71A.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.TN.A7HI.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.BA.A6D8.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.P3.A6T4.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.P3.A6SW.01 3 0.0000 0.967 0 0.00 1.00
#> TCGA.D6.A6EM.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.UF.A7JK.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.CV.7446.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.HD.7831.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.D6.A6EQ.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.P3.A6T0.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.HD.A6HZ.01 3 0.6045 0.413 0 0.38 0.62
#> TCGA.TN.A7HL.01 3 0.0000 0.967 0 0.00 1.00
#> TCGA.UF.A7JA.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.BA.A6DA.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.CR.7370.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CV.A6K2.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.CV.A6K1.01 2 0.0000 1.000 0 1.00 0.00
#> TCGA.UF.A71A.06 1 0.0000 1.000 1 0.00 0.00
#> TCGA.D6.A6EP.01 3 0.0000 0.967 0 0.00 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.CV.7414.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.CN.6010.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.CV.7413.01 2 0.000 0.8358 0 1.00 0.00 0.00
#> TCGA.CV.7422.01 3 0.000 0.9415 0 0.00 1.00 0.00
#> TCGA.BA.7269.01 3 0.380 0.7959 0 0.00 0.78 0.22
#> TCGA.CQ.5332.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.CV.7101.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.CN.6012.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.CV.7424.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.CV.7418.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.CV.6937.01 2 0.000 0.8358 0 1.00 0.00 0.00
#> TCGA.CN.6013.01 4 0.479 0.1201 0 0.00 0.38 0.62
#> TCGA.CN.6019.01 3 0.000 0.9415 0 0.00 1.00 0.00
#> TCGA.CR.7389.01 3 0.361 0.8126 0 0.00 0.80 0.20
#> TCGA.CR.7374.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.CV.7261.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.CN.5358.01 2 0.000 0.8358 0 1.00 0.00 0.00
#> TCGA.DQ.5629.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.CR.7372.01 4 0.499 0.1916 0 0.48 0.00 0.52
#> TCGA.CR.7371.01 3 0.000 0.9415 0 0.00 1.00 0.00
#> TCGA.CR.7388.01 3 0.000 0.9415 0 0.00 1.00 0.00
#> TCGA.CN.6997.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.CN.4742.01 2 0.000 0.8358 0 1.00 0.00 0.00
#> TCGA.CN.4738.01 2 0.441 0.4529 0 0.70 0.30 0.00
#> TCGA.CV.7248.01 3 0.000 0.9415 0 0.00 1.00 0.00
#> TCGA.CV.5444.01 2 0.380 0.6575 0 0.78 0.00 0.22
#> TCGA.CR.7390.01 3 0.398 0.7737 0 0.00 0.76 0.24
#> TCGA.CV.5436.01 4 0.000 0.7006 0 0.00 0.00 1.00
#> TCGA.CV.6961.01 4 0.380 0.6570 0 0.22 0.00 0.78
#> TCGA.CN.6992.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.CV.6962.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.BB.4227.01 4 0.380 0.6982 0 0.22 0.00 0.78
#> TCGA.CV.A45U.01 3 0.292 0.8573 0 0.00 0.86 0.14
#> TCGA.D6.6827.01 3 0.000 0.9415 0 0.00 1.00 0.00
#> TCGA.CV.6934.01 2 0.340 0.7075 0 0.82 0.00 0.18
#> TCGA.CV.6933.01 3 0.000 0.9415 0 0.00 1.00 0.00
#> TCGA.CV.6948.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.F7.A623.01 2 0.491 0.2693 0 0.58 0.00 0.42
#> TCGA.T3.A92M.01 2 0.121 0.8189 0 0.96 0.00 0.04
#> TCGA.CV.A468.01 2 0.000 0.8358 0 1.00 0.00 0.00
#> TCGA.IQ.A61H.01 3 0.000 0.9415 0 0.00 1.00 0.00
#> TCGA.QK.AA3K.01 2 0.000 0.8358 0 1.00 0.00 0.00
#> TCGA.4P.AA8J.01 2 0.000 0.8358 0 1.00 0.00 0.00
#> TCGA.CV.A45V.01 2 0.498 -0.0293 0 0.54 0.00 0.46
#> TCGA.CV.A460.01 2 0.164 0.8084 0 0.94 0.00 0.06
#> TCGA.CQ.A4CG.01 4 0.000 0.7006 0 0.00 0.00 1.00
#> TCGA.CQ.A4CE.01 2 0.265 0.7672 0 0.88 0.00 0.12
#> TCGA.HD.8314.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.BA.A4II.01 2 0.000 0.8358 0 1.00 0.00 0.00
#> TCGA.QK.A8ZA.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.CQ.A4CI.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.BB.8596.01 2 0.000 0.8358 0 1.00 0.00 0.00
#> TCGA.F7.A50I.01 2 0.361 0.6848 0 0.80 0.00 0.20
#> TCGA.IQ.A61O.01 2 0.000 0.8358 0 1.00 0.00 0.00
#> TCGA.CV.A45X.01 2 0.000 0.8358 0 1.00 0.00 0.00
#> TCGA.IQ.A6SH.01 4 0.441 0.6356 0 0.30 0.00 0.70
#> TCGA.UF.A71E.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.T2.A6X0.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.CN.4723.01 4 0.121 0.6921 0 0.00 0.04 0.96
#> TCGA.UF.A7J9.01 3 0.000 0.9415 0 0.00 1.00 0.00
#> TCGA.CN.4728.01 3 0.164 0.8874 0 0.06 0.94 0.00
#> TCGA.CN.4735.01 3 0.000 0.9415 0 0.00 1.00 0.00
#> TCGA.QK.A6VC.01 2 0.000 0.8358 0 1.00 0.00 0.00
#> TCGA.BB.7862.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.BA.A6DI.01 3 0.000 0.9415 0 0.00 1.00 0.00
#> TCGA.RS.A6TO.01 2 0.452 0.3971 0 0.68 0.00 0.32
#> TCGA.CQ.7067.01 4 0.491 0.3897 0 0.42 0.00 0.58
#> TCGA.BA.4078.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.UF.A7JJ.01 2 0.000 0.8358 0 1.00 0.00 0.00
#> TCGA.MT.A7BN.01 3 0.000 0.9415 0 0.00 1.00 0.00
#> TCGA.UF.A71A.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.TN.A7HI.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.BA.A6D8.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.P3.A6T4.01 2 0.479 0.2920 0 0.62 0.00 0.38
#> TCGA.P3.A6SW.01 3 0.566 0.7015 0 0.12 0.72 0.16
#> TCGA.D6.A6EM.01 2 0.234 0.7827 0 0.90 0.00 0.10
#> TCGA.UF.A7JK.01 4 0.000 0.7006 0 0.00 0.00 1.00
#> TCGA.CV.7446.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.HD.7831.01 2 0.000 0.8358 0 1.00 0.00 0.00
#> TCGA.D6.A6EQ.01 4 0.413 0.6779 0 0.26 0.00 0.74
#> TCGA.P3.A6T0.01 4 0.361 0.7039 0 0.20 0.00 0.80
#> TCGA.HD.A6HZ.01 2 0.722 -0.0900 0 0.44 0.14 0.42
#> TCGA.TN.A7HL.01 3 0.000 0.9415 0 0.00 1.00 0.00
#> TCGA.UF.A7JA.01 2 0.000 0.8358 0 1.00 0.00 0.00
#> TCGA.BA.A6DA.01 2 0.380 0.6575 0 0.78 0.00 0.22
#> TCGA.CR.7370.01 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.CV.A6K2.01 2 0.000 0.8358 0 1.00 0.00 0.00
#> TCGA.CV.A6K1.01 4 0.428 0.6601 0 0.28 0.00 0.72
#> TCGA.UF.A71A.06 1 0.000 1.0000 1 0.00 0.00 0.00
#> TCGA.D6.A6EP.01 3 0.000 0.9415 0 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.CV.7414.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.CN.6010.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.CV.7413.01 2 0.3561 0.454259 0 0.74 0.00 0.26 0.00
#> TCGA.CV.7422.01 3 0.0609 0.726926 0 0.00 0.98 0.00 0.02
#> TCGA.BA.7269.01 5 0.3424 0.287803 0 0.00 0.24 0.00 0.76
#> TCGA.CQ.5332.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.CV.7101.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.CN.6012.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.CV.7424.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.CV.7418.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.CV.6937.01 2 0.1732 0.624519 0 0.92 0.00 0.00 0.08
#> TCGA.CN.6013.01 5 0.5414 0.468898 0 0.00 0.20 0.14 0.66
#> TCGA.CN.6019.01 3 0.0000 0.731842 0 0.00 1.00 0.00 0.00
#> TCGA.CR.7389.01 5 0.3983 0.303747 0 0.00 0.34 0.00 0.66
#> TCGA.CR.7374.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.CV.7261.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.CN.5358.01 2 0.0000 0.629552 0 1.00 0.00 0.00 0.00
#> TCGA.DQ.5629.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.CR.7372.01 4 0.4876 0.571241 0 0.22 0.00 0.70 0.08
#> TCGA.CR.7371.01 3 0.0000 0.731842 0 0.00 1.00 0.00 0.00
#> TCGA.CR.7388.01 3 0.0609 0.726926 0 0.00 0.98 0.00 0.02
#> TCGA.CN.6997.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.CN.4742.01 2 0.3561 0.454259 0 0.74 0.00 0.26 0.00
#> TCGA.CN.4738.01 2 0.6697 -0.143635 0 0.38 0.38 0.00 0.24
#> TCGA.CV.7248.01 3 0.0000 0.731842 0 0.00 1.00 0.00 0.00
#> TCGA.CV.5444.01 4 0.5646 0.178789 0 0.40 0.00 0.52 0.08
#> TCGA.CR.7390.01 5 0.3999 0.342775 0 0.00 0.24 0.02 0.74
#> TCGA.CV.5436.01 4 0.4182 -0.208748 0 0.00 0.00 0.60 0.40
#> TCGA.CV.6961.01 5 0.6459 -0.000637 0 0.18 0.00 0.40 0.42
#> TCGA.CN.6992.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.CV.6962.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.BB.4227.01 4 0.0000 0.606151 0 0.00 0.00 1.00 0.00
#> TCGA.CV.A45U.01 5 0.3895 0.244194 0 0.00 0.32 0.00 0.68
#> TCGA.D6.6827.01 3 0.3796 0.548289 0 0.00 0.70 0.00 0.30
#> TCGA.CV.6934.01 2 0.5892 0.387950 0 0.60 0.00 0.18 0.22
#> TCGA.CV.6933.01 3 0.3109 0.623949 0 0.00 0.80 0.00 0.20
#> TCGA.CV.6948.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.F7.A623.01 2 0.6638 0.133193 0 0.44 0.00 0.24 0.32
#> TCGA.T3.A92M.01 2 0.3697 0.580989 0 0.82 0.00 0.08 0.10
#> TCGA.CV.A468.01 2 0.0000 0.629552 0 1.00 0.00 0.00 0.00
#> TCGA.IQ.A61H.01 3 0.0000 0.731842 0 0.00 1.00 0.00 0.00
#> TCGA.QK.AA3K.01 2 0.3109 0.530218 0 0.80 0.00 0.20 0.00
#> TCGA.4P.AA8J.01 2 0.2732 0.566236 0 0.84 0.00 0.16 0.00
#> TCGA.CV.A45V.01 4 0.5425 0.413510 0 0.32 0.00 0.60 0.08
#> TCGA.CV.A460.01 2 0.6777 0.358342 0 0.58 0.10 0.08 0.24
#> TCGA.CQ.A4CG.01 5 0.4262 0.292653 0 0.00 0.00 0.44 0.56
#> TCGA.CQ.A4CE.01 2 0.5013 0.448608 0 0.68 0.00 0.24 0.08
#> TCGA.HD.8314.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.BA.A4II.01 2 0.1732 0.624519 0 0.92 0.00 0.00 0.08
#> TCGA.QK.A8ZA.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.CQ.A4CI.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.BB.8596.01 2 0.5555 0.369523 0 0.64 0.14 0.00 0.22
#> TCGA.F7.A50I.01 2 0.5498 0.270561 0 0.58 0.00 0.34 0.08
#> TCGA.IQ.A61O.01 2 0.3561 0.454259 0 0.74 0.00 0.26 0.00
#> TCGA.CV.A45X.01 2 0.4126 0.221201 0 0.62 0.00 0.38 0.00
#> TCGA.IQ.A6SH.01 4 0.2331 0.675852 0 0.08 0.00 0.90 0.02
#> TCGA.UF.A71E.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.T2.A6X0.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.CN.4723.01 5 0.4613 0.314223 0 0.00 0.02 0.36 0.62
#> TCGA.UF.A7J9.01 3 0.2516 0.663898 0 0.00 0.86 0.00 0.14
#> TCGA.CN.4728.01 3 0.6532 0.020757 0 0.28 0.48 0.00 0.24
#> TCGA.CN.4735.01 3 0.3796 0.548289 0 0.00 0.70 0.00 0.30
#> TCGA.QK.A6VC.01 2 0.0000 0.629552 0 1.00 0.00 0.00 0.00
#> TCGA.BB.7862.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.BA.A6DI.01 3 0.1043 0.715874 0 0.00 0.96 0.00 0.04
#> TCGA.RS.A6TO.01 4 0.4302 0.124929 0 0.48 0.00 0.52 0.00
#> TCGA.CQ.7067.01 4 0.4373 0.625620 0 0.16 0.00 0.76 0.08
#> TCGA.BA.4078.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.UF.A7JJ.01 2 0.1732 0.610613 0 0.92 0.00 0.08 0.00
#> TCGA.MT.A7BN.01 3 0.2873 0.631194 0 0.02 0.86 0.00 0.12
#> TCGA.UF.A71A.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.TN.A7HI.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.BA.A6D8.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.P3.A6T4.01 4 0.5341 0.455617 0 0.30 0.00 0.62 0.08
#> TCGA.P3.A6SW.01 3 0.7265 -0.198560 0 0.28 0.36 0.02 0.34
#> TCGA.D6.A6EM.01 2 0.4170 0.532512 0 0.78 0.00 0.14 0.08
#> TCGA.UF.A7JK.01 4 0.0609 0.584522 0 0.00 0.00 0.98 0.02
#> TCGA.CV.7446.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.HD.7831.01 2 0.3561 0.454259 0 0.74 0.00 0.26 0.00
#> TCGA.D6.A6EQ.01 4 0.1732 0.670832 0 0.08 0.00 0.92 0.00
#> TCGA.P3.A6T0.01 4 0.0000 0.606151 0 0.00 0.00 1.00 0.00
#> TCGA.HD.A6HZ.01 5 0.8332 0.191451 0 0.28 0.24 0.14 0.34
#> TCGA.TN.A7HL.01 3 0.3922 0.537365 0 0.04 0.78 0.00 0.18
#> TCGA.UF.A7JA.01 2 0.1043 0.628155 0 0.96 0.00 0.00 0.04
#> TCGA.BA.A6DA.01 2 0.5558 0.213839 0 0.56 0.00 0.36 0.08
#> TCGA.CR.7370.01 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.CV.A6K2.01 2 0.2929 0.550086 0 0.82 0.00 0.18 0.00
#> TCGA.CV.A6K1.01 4 0.2331 0.675852 0 0.08 0.00 0.90 0.02
#> TCGA.UF.A71A.06 1 0.0000 1.000000 1 0.00 0.00 0.00 0.00
#> TCGA.D6.A6EP.01 3 0.3796 0.548289 0 0.00 0.70 0.00 0.30
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.CV.7414.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.6010.01 1 0.0547 0.9839 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.CV.7413.01 2 0.0937 0.7887 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.CV.7422.01 3 0.0937 0.7563 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.BA.7269.01 6 0.1092 0.8064 0.00 0.00 0.02 0.00 0.02 0.96
#> TCGA.CQ.5332.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7101.01 1 0.0547 0.9839 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.CN.6012.01 1 0.0547 0.9839 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.CV.7424.01 1 0.0547 0.9839 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.CV.7418.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6937.01 2 0.3409 0.5325 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.CN.6013.01 5 0.3499 0.4104 0.00 0.00 0.00 0.00 0.68 0.32
#> TCGA.CN.6019.01 3 0.0000 0.7731 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CR.7389.01 5 0.4566 0.5631 0.00 0.00 0.16 0.00 0.70 0.14
#> TCGA.CR.7374.01 1 0.0547 0.9839 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.CV.7261.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.5358.01 2 0.0000 0.7928 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.5629.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7372.01 4 0.4328 0.6595 0.00 0.10 0.00 0.72 0.18 0.00
#> TCGA.CR.7371.01 3 0.0000 0.7731 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CR.7388.01 3 0.0547 0.7668 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.CN.6997.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4742.01 2 0.0937 0.7887 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.CN.4738.01 5 0.3982 0.6574 0.00 0.06 0.20 0.00 0.74 0.00
#> TCGA.CV.7248.01 3 0.0000 0.7731 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.5444.01 4 0.5520 0.5780 0.00 0.20 0.00 0.56 0.24 0.00
#> TCGA.CR.7390.01 6 0.1807 0.8127 0.00 0.00 0.02 0.00 0.06 0.92
#> TCGA.CV.5436.01 4 0.4247 0.3643 0.00 0.00 0.00 0.70 0.06 0.24
#> TCGA.CV.6961.01 5 0.5991 -0.0319 0.00 0.04 0.00 0.36 0.50 0.10
#> TCGA.CN.6992.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6962.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BB.4227.01 4 0.0937 0.6439 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.CV.A45U.01 6 0.5029 0.5152 0.00 0.00 0.26 0.00 0.12 0.62
#> TCGA.D6.6827.01 3 0.6168 0.3507 0.00 0.00 0.52 0.04 0.14 0.30
#> TCGA.CV.6934.01 5 0.4377 0.5466 0.00 0.16 0.00 0.12 0.72 0.00
#> TCGA.CV.6933.01 3 0.2048 0.6985 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.CV.6948.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F7.A623.01 5 0.4377 0.5070 0.00 0.12 0.00 0.16 0.72 0.00
#> TCGA.T3.A92M.01 2 0.5523 0.1694 0.00 0.50 0.00 0.14 0.36 0.00
#> TCGA.CV.A468.01 2 0.2048 0.7472 0.00 0.88 0.00 0.00 0.12 0.00
#> TCGA.IQ.A61H.01 3 0.0000 0.7731 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.QK.AA3K.01 2 0.0937 0.7887 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.4P.AA8J.01 2 0.0547 0.7944 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.CV.A45V.01 4 0.5259 0.6047 0.00 0.16 0.00 0.60 0.24 0.00
#> TCGA.CV.A460.01 5 0.3688 0.6569 0.00 0.14 0.02 0.04 0.80 0.00
#> TCGA.CQ.A4CG.01 6 0.3351 0.7354 0.00 0.00 0.00 0.16 0.04 0.80
#> TCGA.CQ.A4CE.01 4 0.6088 0.3547 0.00 0.28 0.00 0.38 0.34 0.00
#> TCGA.HD.8314.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A4II.01 2 0.2941 0.6574 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.QK.A8ZA.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.A4CI.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BB.8596.01 5 0.4200 0.6617 0.00 0.14 0.12 0.00 0.74 0.00
#> TCGA.F7.A50I.01 4 0.6047 0.3761 0.00 0.26 0.00 0.40 0.34 0.00
#> TCGA.IQ.A61O.01 2 0.0937 0.7887 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.CV.A45X.01 2 0.3578 0.3006 0.00 0.66 0.00 0.34 0.00 0.00
#> TCGA.IQ.A6SH.01 4 0.1865 0.6676 0.00 0.04 0.00 0.92 0.04 0.00
#> TCGA.UF.A71E.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.T2.A6X0.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4723.01 5 0.5523 0.2427 0.00 0.00 0.00 0.14 0.50 0.36
#> TCGA.UF.A7J9.01 3 0.1267 0.7466 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.CN.4728.01 5 0.3821 0.6483 0.00 0.04 0.22 0.00 0.74 0.00
#> TCGA.CN.4735.01 3 0.6224 0.3102 0.00 0.00 0.50 0.04 0.14 0.32
#> TCGA.QK.A6VC.01 2 0.0937 0.7838 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.BB.7862.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A6DI.01 3 0.2793 0.6145 0.00 0.00 0.80 0.00 0.20 0.00
#> TCGA.RS.A6TO.01 4 0.3797 0.2915 0.00 0.42 0.00 0.58 0.00 0.00
#> TCGA.CQ.7067.01 4 0.4328 0.6595 0.00 0.10 0.00 0.72 0.18 0.00
#> TCGA.BA.4078.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A7JJ.01 2 0.0000 0.7928 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.MT.A7BN.01 3 0.3578 0.3755 0.00 0.00 0.66 0.00 0.34 0.00
#> TCGA.UF.A71A.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TN.A7HI.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A6D8.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P3.A6T4.01 4 0.5490 0.5722 0.00 0.18 0.00 0.56 0.26 0.00
#> TCGA.P3.A6SW.01 5 0.3163 0.6841 0.00 0.04 0.14 0.00 0.82 0.00
#> TCGA.D6.A6EM.01 2 0.5888 -0.0743 0.00 0.40 0.00 0.20 0.40 0.00
#> TCGA.UF.A7JK.01 4 0.0937 0.6007 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.CV.7446.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HD.7831.01 2 0.0937 0.7887 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.D6.A6EQ.01 4 0.1865 0.6676 0.00 0.04 0.00 0.92 0.04 0.00
#> TCGA.P3.A6T0.01 4 0.0937 0.6439 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.HD.A6HZ.01 5 0.3420 0.6794 0.00 0.06 0.04 0.06 0.84 0.00
#> TCGA.TN.A7HL.01 5 0.3851 0.1212 0.00 0.00 0.46 0.00 0.54 0.00
#> TCGA.UF.A7JA.01 2 0.2631 0.7017 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.BA.A6DA.01 4 0.6088 0.3547 0.00 0.28 0.00 0.38 0.34 0.00
#> TCGA.CR.7370.01 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A6K2.01 2 0.0547 0.7944 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.CV.A6K1.01 4 0.2190 0.6762 0.00 0.06 0.00 0.90 0.04 0.00
#> TCGA.UF.A71A.06 1 0.0000 0.9964 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D6.A6EP.01 3 0.6168 0.3507 0.00 0.00 0.52 0.04 0.14 0.30
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.CV.7414.01 1 0.1006 0.9547 0.96 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.CN.6010.01 1 0.1664 0.9427 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.CV.7413.01 2 0.0504 0.8408 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.CV.7422.01 3 0.1166 0.8317 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.BA.7269.01 6 0.2722 0.7491 0.00 0.00 0.00 0.00 0.04 0.84 0.12
#> TCGA.CQ.5332.01 1 0.0000 0.9653 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7101.01 1 0.1928 0.9327 0.90 0.00 0.00 0.00 0.00 0.02 0.08
#> TCGA.CN.6012.01 1 0.1928 0.9327 0.90 0.00 0.00 0.00 0.00 0.02 0.08
#> TCGA.CV.7424.01 1 0.1664 0.9427 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.CV.7418.01 1 0.0000 0.9653 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6937.01 2 0.4905 0.6170 0.00 0.68 0.00 0.06 0.16 0.00 0.10
#> TCGA.CN.6013.01 5 0.4813 0.3894 0.00 0.00 0.02 0.10 0.64 0.24 0.00
#> TCGA.CN.6019.01 3 0.0000 0.8701 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7389.01 5 0.4671 0.4516 0.00 0.00 0.14 0.00 0.68 0.16 0.02
#> TCGA.CR.7374.01 1 0.2722 0.8885 0.84 0.00 0.00 0.00 0.00 0.04 0.12
#> TCGA.CV.7261.01 1 0.1664 0.9427 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.CN.5358.01 2 0.0000 0.8477 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.5629.01 1 0.1166 0.9507 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.CR.7372.01 4 0.2912 0.7265 0.00 0.14 0.00 0.82 0.04 0.00 0.00
#> TCGA.CR.7371.01 3 0.0000 0.8701 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7388.01 3 0.1433 0.8117 0.00 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.CN.6997.01 1 0.0000 0.9653 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4742.01 2 0.0504 0.8408 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.CN.4738.01 5 0.3680 0.6021 0.00 0.06 0.14 0.00 0.78 0.00 0.02
#> TCGA.CV.7248.01 3 0.0000 0.8701 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5444.01 4 0.4500 0.6936 0.00 0.22 0.00 0.68 0.08 0.00 0.02
#> TCGA.CR.7390.01 6 0.3061 0.7677 0.00 0.00 0.02 0.00 0.08 0.84 0.06
#> TCGA.CV.5436.01 4 0.3745 0.4171 0.00 0.00 0.00 0.70 0.04 0.26 0.00
#> TCGA.CV.6961.01 4 0.5747 0.3298 0.00 0.02 0.00 0.56 0.28 0.04 0.10
#> TCGA.CN.6992.01 1 0.2512 0.9052 0.86 0.00 0.00 0.00 0.00 0.04 0.10
#> TCGA.CV.6962.01 1 0.0000 0.9653 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BB.4227.01 4 0.4357 0.4845 0.00 0.02 0.00 0.76 0.10 0.08 0.04
#> TCGA.CV.A45U.01 6 0.6760 0.4357 0.00 0.00 0.18 0.02 0.20 0.48 0.12
#> TCGA.D6.6827.01 7 0.3294 0.8909 0.00 0.00 0.34 0.00 0.00 0.00 0.66
#> TCGA.CV.6934.01 5 0.5223 0.1751 0.00 0.10 0.00 0.36 0.52 0.00 0.02
#> TCGA.CV.6933.01 3 0.1363 0.8070 0.00 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.CV.6948.01 1 0.0000 0.9653 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F7.A623.01 5 0.5716 0.0211 0.00 0.02 0.00 0.42 0.44 0.02 0.10
#> TCGA.T3.A92M.01 2 0.6732 -0.1696 0.00 0.34 0.00 0.28 0.28 0.00 0.10
#> TCGA.CV.A468.01 2 0.2081 0.7699 0.00 0.86 0.00 0.00 0.14 0.00 0.00
#> TCGA.IQ.A61H.01 3 0.0000 0.8701 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QK.AA3K.01 2 0.0000 0.8477 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4P.AA8J.01 2 0.0000 0.8477 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A45V.01 4 0.3370 0.7244 0.00 0.16 0.00 0.78 0.06 0.00 0.00
#> TCGA.CV.A460.01 5 0.3965 0.5881 0.00 0.10 0.00 0.12 0.76 0.00 0.02
#> TCGA.CQ.A4CG.01 6 0.1006 0.7220 0.00 0.00 0.00 0.02 0.02 0.96 0.00
#> TCGA.CQ.A4CE.01 4 0.5165 0.6199 0.00 0.28 0.00 0.58 0.12 0.00 0.02
#> TCGA.HD.8314.01 1 0.0000 0.9653 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A4II.01 2 0.3863 0.6825 0.00 0.74 0.00 0.04 0.20 0.00 0.02
#> TCGA.QK.A8ZA.01 1 0.0000 0.9653 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.A4CI.01 1 0.0000 0.9653 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BB.8596.01 5 0.4001 0.5401 0.00 0.18 0.06 0.00 0.74 0.00 0.02
#> TCGA.F7.A50I.01 4 0.4813 0.6726 0.00 0.24 0.00 0.64 0.10 0.00 0.02
#> TCGA.IQ.A61O.01 2 0.0504 0.8408 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.CV.A45X.01 2 0.2945 0.5004 0.00 0.74 0.00 0.26 0.00 0.00 0.00
#> TCGA.IQ.A6SH.01 4 0.2081 0.7236 0.00 0.14 0.00 0.86 0.00 0.00 0.00
#> TCGA.UF.A71E.01 1 0.0000 0.9653 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.T2.A6X0.01 1 0.0000 0.9653 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4723.01 5 0.6471 -0.0148 0.00 0.00 0.00 0.30 0.32 0.32 0.06
#> TCGA.UF.A7J9.01 3 0.1664 0.7743 0.00 0.00 0.92 0.00 0.02 0.00 0.06
#> TCGA.CN.4728.01 5 0.2906 0.5963 0.00 0.02 0.18 0.00 0.80 0.00 0.00
#> TCGA.CN.4735.01 7 0.4718 0.8785 0.00 0.00 0.32 0.00 0.02 0.06 0.60
#> TCGA.QK.A6VC.01 2 0.0863 0.8341 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.BB.7862.01 1 0.0000 0.9653 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A6DI.01 3 0.3417 0.5189 0.00 0.00 0.72 0.00 0.26 0.00 0.02
#> TCGA.RS.A6TO.01 4 0.3525 0.3439 0.00 0.44 0.00 0.56 0.00 0.00 0.00
#> TCGA.CQ.7067.01 4 0.3396 0.7273 0.00 0.14 0.00 0.80 0.04 0.00 0.02
#> TCGA.BA.4078.01 1 0.0000 0.9653 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A7JJ.01 2 0.0000 0.8477 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MT.A7BN.01 5 0.3985 0.0923 0.00 0.00 0.46 0.00 0.52 0.00 0.02
#> TCGA.UF.A71A.01 1 0.0000 0.9653 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TN.A7HI.01 1 0.0000 0.9653 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A6D8.01 1 0.1166 0.9507 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.P3.A6T4.01 4 0.5046 0.6756 0.00 0.18 0.00 0.66 0.06 0.00 0.10
#> TCGA.P3.A6SW.01 5 0.2829 0.6132 0.00 0.00 0.08 0.08 0.84 0.00 0.00
#> TCGA.D6.A6EM.01 4 0.5829 0.3404 0.00 0.38 0.00 0.40 0.20 0.00 0.02
#> TCGA.UF.A7JK.01 4 0.4100 0.4578 0.00 0.00 0.00 0.76 0.10 0.10 0.04
#> TCGA.CV.7446.01 1 0.2278 0.9152 0.88 0.00 0.00 0.00 0.00 0.04 0.08
#> TCGA.HD.7831.01 2 0.0504 0.8408 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.D6.A6EQ.01 4 0.2569 0.7209 0.00 0.14 0.00 0.84 0.02 0.00 0.00
#> TCGA.P3.A6T0.01 4 0.4357 0.4845 0.00 0.02 0.00 0.76 0.10 0.08 0.04
#> TCGA.HD.A6HZ.01 5 0.2569 0.5891 0.00 0.00 0.00 0.14 0.84 0.02 0.00
#> TCGA.TN.A7HL.01 5 0.3417 0.5004 0.00 0.00 0.26 0.00 0.72 0.00 0.02
#> TCGA.UF.A7JA.01 2 0.3396 0.7383 0.00 0.80 0.00 0.04 0.14 0.00 0.02
#> TCGA.BA.A6DA.01 4 0.4813 0.6726 0.00 0.24 0.00 0.64 0.10 0.00 0.02
#> TCGA.CR.7370.01 1 0.0863 0.9562 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.CV.A6K2.01 2 0.0000 0.8477 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A6K1.01 4 0.2569 0.7196 0.00 0.14 0.00 0.84 0.00 0.02 0.00
#> TCGA.UF.A71A.06 1 0.0000 0.9653 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D6.A6EP.01 7 0.3841 0.8649 0.00 0.00 0.28 0.00 0.00 0.04 0.68
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.CV.7414.01 1 0.2265 0.8706 0.88 0.00 0.00 0.00 0.02 0.00 0.02 0.08
#> TCGA.CN.6010.01 1 0.3291 0.7751 0.70 0.00 0.00 0.00 0.02 0.00 0.00 0.28
#> TCGA.CV.7413.01 2 0.0471 0.8101 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.CV.7422.01 3 0.0471 0.8292 0.00 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.BA.7269.01 6 0.1341 0.6956 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.CQ.5332.01 1 0.0000 0.9005 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7101.01 1 0.3594 0.7570 0.68 0.00 0.00 0.00 0.04 0.00 0.00 0.28
#> TCGA.CN.6012.01 1 0.3594 0.7570 0.68 0.00 0.00 0.00 0.04 0.00 0.00 0.28
#> TCGA.CV.7424.01 1 0.3291 0.7751 0.70 0.00 0.00 0.00 0.02 0.00 0.00 0.28
#> TCGA.CV.7418.01 1 0.0471 0.8997 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.CV.6937.01 2 0.5277 0.3609 0.00 0.56 0.00 0.20 0.20 0.00 0.04 0.00
#> TCGA.CN.6013.01 5 0.4870 0.5031 0.00 0.00 0.00 0.12 0.62 0.22 0.04 0.00
#> TCGA.CN.6019.01 3 0.0000 0.8349 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7389.01 5 0.5273 0.5478 0.00 0.00 0.10 0.06 0.66 0.12 0.06 0.00
#> TCGA.CR.7374.01 1 0.4933 0.5825 0.54 0.00 0.02 0.00 0.06 0.00 0.02 0.36
#> TCGA.CV.7261.01 1 0.2267 0.8542 0.82 0.00 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.CN.5358.01 2 0.0000 0.8088 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.5629.01 1 0.1947 0.8693 0.86 0.00 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.CR.7372.01 4 0.3397 0.6080 0.00 0.06 0.00 0.80 0.10 0.00 0.04 0.00
#> TCGA.CR.7371.01 3 0.0000 0.8349 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7388.01 3 0.0471 0.8292 0.00 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.CN.6997.01 1 0.0471 0.8996 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.CN.4742.01 2 0.0471 0.8101 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.CN.4738.01 5 0.3337 0.5695 0.00 0.02 0.16 0.00 0.78 0.00 0.04 0.00
#> TCGA.CV.7248.01 3 0.0000 0.8349 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5444.01 4 0.3909 0.5608 0.00 0.12 0.00 0.70 0.18 0.00 0.00 0.00
#> TCGA.CR.7390.01 6 0.0471 0.7233 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.CV.5436.01 4 0.4406 0.3373 0.00 0.00 0.00 0.64 0.02 0.26 0.08 0.00
#> TCGA.CV.6961.01 4 0.5242 -0.0525 0.00 0.02 0.00 0.50 0.38 0.04 0.06 0.00
#> TCGA.CN.6992.01 1 0.2856 0.8325 0.78 0.00 0.00 0.00 0.00 0.00 0.02 0.20
#> TCGA.CV.6962.01 1 0.0000 0.9005 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BB.4227.01 4 0.3237 0.3315 0.00 0.00 0.00 0.60 0.00 0.00 0.40 0.00
#> TCGA.CV.A45U.01 6 0.6675 0.2608 0.00 0.00 0.20 0.02 0.22 0.46 0.04 0.06
#> TCGA.D6.6827.01 8 0.4953 0.8323 0.00 0.00 0.16 0.00 0.00 0.02 0.24 0.58
#> TCGA.CV.6934.01 5 0.4199 0.3776 0.00 0.08 0.00 0.32 0.60 0.00 0.00 0.00
#> TCGA.CV.6933.01 3 0.3397 0.6243 0.00 0.00 0.80 0.00 0.06 0.10 0.04 0.00
#> TCGA.CV.6948.01 1 0.0000 0.9005 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F7.A623.01 5 0.4407 0.1336 0.00 0.02 0.00 0.46 0.48 0.00 0.04 0.00
#> TCGA.T3.A92M.01 2 0.5838 -0.0910 0.00 0.38 0.00 0.30 0.28 0.00 0.04 0.00
#> TCGA.CV.A468.01 2 0.1765 0.7540 0.00 0.88 0.00 0.00 0.12 0.00 0.00 0.00
#> TCGA.IQ.A61H.01 3 0.0000 0.8349 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QK.AA3K.01 2 0.0471 0.8101 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.4P.AA8J.01 2 0.0000 0.8088 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A45V.01 4 0.3589 0.5772 0.00 0.10 0.00 0.74 0.16 0.00 0.00 0.00
#> TCGA.CV.A460.01 5 0.2994 0.6382 0.00 0.06 0.00 0.14 0.80 0.00 0.00 0.00
#> TCGA.CQ.A4CG.01 6 0.1275 0.6986 0.00 0.00 0.00 0.00 0.00 0.94 0.02 0.04
#> TCGA.CQ.A4CE.01 4 0.4342 0.5193 0.00 0.18 0.00 0.64 0.18 0.00 0.00 0.00
#> TCGA.HD.8314.01 1 0.0808 0.8982 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.BA.A4II.01 2 0.3873 0.6255 0.00 0.72 0.00 0.06 0.20 0.00 0.02 0.00
#> TCGA.QK.A8ZA.01 1 0.0000 0.9005 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.A4CI.01 1 0.0000 0.9005 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BB.8596.01 5 0.4096 0.5555 0.00 0.16 0.04 0.02 0.74 0.00 0.04 0.00
#> TCGA.F7.A50I.01 4 0.4458 0.4994 0.00 0.18 0.00 0.62 0.20 0.00 0.00 0.00
#> TCGA.IQ.A61O.01 2 0.0471 0.8101 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.CV.A45X.01 2 0.2267 0.6743 0.00 0.82 0.00 0.18 0.00 0.00 0.00 0.00
#> TCGA.IQ.A6SH.01 4 0.2132 0.5944 0.00 0.04 0.00 0.88 0.00 0.00 0.08 0.00
#> TCGA.UF.A71E.01 1 0.0000 0.9005 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.T2.A6X0.01 1 0.0808 0.8982 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.CN.4723.01 5 0.6124 0.2541 0.00 0.00 0.00 0.30 0.38 0.24 0.08 0.00
#> TCGA.UF.A7J9.01 3 0.2020 0.7460 0.00 0.00 0.90 0.00 0.06 0.02 0.02 0.00
#> TCGA.CN.4728.01 5 0.2569 0.5921 0.00 0.02 0.16 0.00 0.82 0.00 0.00 0.00
#> TCGA.CN.4735.01 8 0.6174 0.8109 0.00 0.00 0.18 0.00 0.02 0.08 0.24 0.48
#> TCGA.QK.A6VC.01 2 0.0808 0.7966 0.00 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.BB.7862.01 1 0.0000 0.9005 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A6DI.01 3 0.3293 0.6015 0.00 0.00 0.74 0.00 0.22 0.00 0.04 0.00
#> TCGA.RS.A6TO.01 2 0.4224 -0.0269 0.00 0.48 0.00 0.46 0.00 0.00 0.06 0.00
#> TCGA.CQ.7067.01 4 0.2623 0.6057 0.00 0.06 0.00 0.84 0.10 0.00 0.00 0.00
#> TCGA.BA.4078.01 1 0.0000 0.9005 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A7JJ.01 2 0.0000 0.8088 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MT.A7BN.01 3 0.4370 0.2756 0.00 0.00 0.52 0.00 0.40 0.00 0.08 0.00
#> TCGA.UF.A71A.01 1 0.0000 0.9005 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TN.A7HI.01 1 0.0000 0.9005 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A6D8.01 1 0.2406 0.8443 0.80 0.00 0.00 0.00 0.00 0.00 0.00 0.20
#> TCGA.P3.A6T4.01 4 0.4061 0.5499 0.00 0.14 0.00 0.72 0.12 0.00 0.02 0.00
#> TCGA.P3.A6SW.01 5 0.2807 0.6654 0.00 0.02 0.04 0.10 0.84 0.00 0.00 0.00
#> TCGA.D6.A6EM.01 4 0.5138 0.1833 0.00 0.24 0.00 0.44 0.32 0.00 0.00 0.00
#> TCGA.UF.A7JK.01 4 0.3570 0.3473 0.00 0.00 0.00 0.62 0.00 0.02 0.36 0.00
#> TCGA.CV.7446.01 1 0.2569 0.8489 0.82 0.00 0.00 0.00 0.00 0.00 0.02 0.16
#> TCGA.HD.7831.01 2 0.0471 0.8101 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.D6.A6EQ.01 4 0.2547 0.5795 0.00 0.04 0.00 0.84 0.00 0.00 0.12 0.00
#> TCGA.P3.A6T0.01 4 0.3618 0.3331 0.00 0.00 0.00 0.60 0.00 0.02 0.38 0.00
#> TCGA.HD.A6HZ.01 5 0.2856 0.6120 0.00 0.02 0.00 0.20 0.78 0.00 0.00 0.00
#> TCGA.TN.A7HL.01 5 0.3083 0.3182 0.00 0.00 0.34 0.00 0.66 0.00 0.00 0.00
#> TCGA.UF.A7JA.01 2 0.3744 0.6483 0.00 0.74 0.00 0.06 0.18 0.00 0.02 0.00
#> TCGA.BA.A6DA.01 4 0.4458 0.4994 0.00 0.18 0.00 0.62 0.20 0.00 0.00 0.00
#> TCGA.CR.7370.01 1 0.1091 0.8936 0.94 0.00 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.CV.A6K2.01 2 0.0471 0.8101 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.CV.A6K1.01 4 0.2132 0.5950 0.00 0.04 0.00 0.88 0.00 0.00 0.08 0.00
#> TCGA.UF.A71A.06 1 0.0000 0.9005 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D6.A6EP.01 8 0.5677 0.7901 0.00 0.00 0.12 0.00 0.02 0.04 0.34 0.48
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 , Node0121 , Node0122 , Node0211 , Node0212 , Node0213 , Node0221 , Node0222 , Node0223 , Node0224 , Node0225-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0511 , Node0512 , Node0521-leaf , Node0522 , Node0523-leaf , Node0524-leaf .
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 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 0.997 0.999 0.5135 0.487 0.487
#> 3 3 1.000 1.000 1.000 0.1935 0.900 0.795
#> 4 4 0.833 0.820 0.916 0.1735 0.823 0.569
#> 5 5 0.817 0.764 0.909 0.0175 0.943 0.802
#> 6 6 0.847 0.692 0.887 0.0420 0.991 0.967
#> 7 7 0.787 0.687 0.850 0.0361 0.926 0.726
#> 8 8 0.843 0.551 0.822 0.0267 0.977 0.893
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.CV.7414.01 2 0.000 0.997 0.00 1.00
#> TCGA.CN.6010.01 2 0.000 0.997 0.00 1.00
#> TCGA.CQ.5332.01 2 0.000 0.997 0.00 1.00
#> TCGA.CV.7101.01 2 0.000 0.997 0.00 1.00
#> TCGA.CN.6012.01 1 0.000 1.000 1.00 0.00
#> TCGA.CV.7424.01 1 0.000 1.000 1.00 0.00
#> TCGA.CV.7418.01 2 0.242 0.958 0.04 0.96
#> TCGA.CR.7374.01 1 0.000 1.000 1.00 0.00
#> TCGA.CV.7261.01 2 0.000 0.997 0.00 1.00
#> TCGA.DQ.5629.01 1 0.000 1.000 1.00 0.00
#> TCGA.CN.6997.01 2 0.000 0.997 0.00 1.00
#> TCGA.CN.6992.01 1 0.000 1.000 1.00 0.00
#> TCGA.CV.6962.01 1 0.000 1.000 1.00 0.00
#> TCGA.CV.6948.01 1 0.000 1.000 1.00 0.00
#> TCGA.HD.8314.01 2 0.000 0.997 0.00 1.00
#> TCGA.QK.A8ZA.01 2 0.000 0.997 0.00 1.00
#> TCGA.CQ.A4CI.01 2 0.000 0.997 0.00 1.00
#> TCGA.UF.A71E.01 2 0.000 0.997 0.00 1.00
#> TCGA.T2.A6X0.01 2 0.000 0.997 0.00 1.00
#> TCGA.BB.7862.01 1 0.000 1.000 1.00 0.00
#> TCGA.BA.4078.01 2 0.000 0.997 0.00 1.00
#> TCGA.UF.A71A.01 1 0.000 1.000 1.00 0.00
#> TCGA.TN.A7HI.01 2 0.000 0.997 0.00 1.00
#> TCGA.BA.A6D8.01 2 0.000 0.997 0.00 1.00
#> TCGA.CV.7446.01 1 0.000 1.000 1.00 0.00
#> TCGA.CR.7370.01 1 0.000 1.000 1.00 0.00
#> TCGA.UF.A71A.06 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.CV.7414.01 2 0 1 0 1 0
#> TCGA.CN.6010.01 2 0 1 0 1 0
#> TCGA.CQ.5332.01 2 0 1 0 1 0
#> TCGA.CV.7101.01 2 0 1 0 1 0
#> TCGA.CN.6012.01 1 0 1 1 0 0
#> TCGA.CV.7424.01 3 0 1 0 0 1
#> TCGA.CV.7418.01 2 0 1 0 1 0
#> TCGA.CR.7374.01 1 0 1 1 0 0
#> TCGA.CV.7261.01 2 0 1 0 1 0
#> TCGA.DQ.5629.01 1 0 1 1 0 0
#> TCGA.CN.6997.01 2 0 1 0 1 0
#> TCGA.CN.6992.01 1 0 1 1 0 0
#> TCGA.CV.6962.01 3 0 1 0 0 1
#> TCGA.CV.6948.01 3 0 1 0 0 1
#> TCGA.HD.8314.01 2 0 1 0 1 0
#> TCGA.QK.A8ZA.01 2 0 1 0 1 0
#> TCGA.CQ.A4CI.01 2 0 1 0 1 0
#> TCGA.UF.A71E.01 2 0 1 0 1 0
#> TCGA.T2.A6X0.01 2 0 1 0 1 0
#> TCGA.BB.7862.01 1 0 1 1 0 0
#> TCGA.BA.4078.01 2 0 1 0 1 0
#> TCGA.UF.A71A.01 3 0 1 0 0 1
#> TCGA.TN.A7HI.01 2 0 1 0 1 0
#> TCGA.BA.A6D8.01 2 0 1 0 1 0
#> TCGA.CV.7446.01 1 0 1 1 0 0
#> TCGA.CR.7370.01 1 0 1 1 0 0
#> TCGA.UF.A71A.06 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.CV.7414.01 2 0.0000 0.937 0.0 1.00 0.00 0.00
#> TCGA.CN.6010.01 2 0.0000 0.937 0.0 1.00 0.00 0.00
#> TCGA.CQ.5332.01 2 0.4977 -0.265 0.0 0.54 0.00 0.46
#> TCGA.CV.7101.01 2 0.0000 0.937 0.0 1.00 0.00 0.00
#> TCGA.CN.6012.01 4 0.5062 0.399 0.3 0.00 0.02 0.68
#> TCGA.CV.7424.01 3 0.1637 0.953 0.0 0.00 0.94 0.06
#> TCGA.CV.7418.01 4 0.3400 0.705 0.0 0.18 0.00 0.82
#> TCGA.CR.7374.01 1 0.0000 1.000 1.0 0.00 0.00 0.00
#> TCGA.CV.7261.01 4 0.3975 0.686 0.0 0.24 0.00 0.76
#> TCGA.DQ.5629.01 1 0.0000 1.000 1.0 0.00 0.00 0.00
#> TCGA.CN.6997.01 4 0.4790 0.465 0.0 0.38 0.00 0.62
#> TCGA.CN.6992.01 1 0.0000 1.000 1.0 0.00 0.00 0.00
#> TCGA.CV.6962.01 3 0.0707 0.981 0.0 0.00 0.98 0.02
#> TCGA.CV.6948.01 3 0.0707 0.981 0.0 0.00 0.98 0.02
#> TCGA.HD.8314.01 2 0.0000 0.937 0.0 1.00 0.00 0.00
#> TCGA.QK.A8ZA.01 2 0.0000 0.937 0.0 1.00 0.00 0.00
#> TCGA.CQ.A4CI.01 2 0.0000 0.937 0.0 1.00 0.00 0.00
#> TCGA.UF.A71E.01 2 0.0000 0.937 0.0 1.00 0.00 0.00
#> TCGA.T2.A6X0.01 2 0.0000 0.937 0.0 1.00 0.00 0.00
#> TCGA.BB.7862.01 4 0.2345 0.577 0.1 0.00 0.00 0.90
#> TCGA.BA.4078.01 4 0.4994 0.330 0.0 0.48 0.00 0.52
#> TCGA.UF.A71A.01 3 0.0000 0.978 0.0 0.00 1.00 0.00
#> TCGA.TN.A7HI.01 2 0.0000 0.937 0.0 1.00 0.00 0.00
#> TCGA.BA.A6D8.01 2 0.0000 0.937 0.0 1.00 0.00 0.00
#> TCGA.CV.7446.01 1 0.0000 1.000 1.0 0.00 0.00 0.00
#> TCGA.CR.7370.01 1 0.0000 1.000 1.0 0.00 0.00 0.00
#> TCGA.UF.A71A.06 3 0.0000 0.978 0.0 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.CV.7414.01 2 0.0000 0.922 0.00 1.00 0.00 0.00 0.00
#> TCGA.CN.6010.01 2 0.0000 0.922 0.00 1.00 0.00 0.00 0.00
#> TCGA.CQ.5332.01 2 0.4872 0.537 0.00 0.72 0.00 0.12 0.16
#> TCGA.CV.7101.01 2 0.0000 0.922 0.00 1.00 0.00 0.00 0.00
#> TCGA.CN.6012.01 4 0.5692 0.314 0.26 0.00 0.02 0.64 0.08
#> TCGA.CV.7424.01 3 0.2929 0.791 0.00 0.00 0.82 0.18 0.00
#> TCGA.CV.7418.01 4 0.6502 0.428 0.00 0.26 0.02 0.56 0.16
#> TCGA.CR.7374.01 1 0.0609 0.976 0.98 0.00 0.00 0.02 0.00
#> TCGA.CV.7261.01 4 0.6133 0.398 0.00 0.30 0.00 0.54 0.16
#> TCGA.DQ.5629.01 1 0.0000 0.994 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.6997.01 5 0.2280 0.000 0.00 0.12 0.00 0.00 0.88
#> TCGA.CN.6992.01 1 0.0000 0.994 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6962.01 3 0.1043 0.908 0.00 0.00 0.96 0.04 0.00
#> TCGA.CV.6948.01 3 0.1648 0.904 0.00 0.00 0.94 0.04 0.02
#> TCGA.HD.8314.01 2 0.0000 0.922 0.00 1.00 0.00 0.00 0.00
#> TCGA.QK.A8ZA.01 2 0.0000 0.922 0.00 1.00 0.00 0.00 0.00
#> TCGA.CQ.A4CI.01 2 0.0000 0.922 0.00 1.00 0.00 0.00 0.00
#> TCGA.UF.A71E.01 2 0.0000 0.922 0.00 1.00 0.00 0.00 0.00
#> TCGA.T2.A6X0.01 2 0.0000 0.922 0.00 1.00 0.00 0.00 0.00
#> TCGA.BB.7862.01 4 0.1732 0.276 0.00 0.00 0.00 0.92 0.08
#> TCGA.BA.4078.01 2 0.5297 0.100 0.00 0.58 0.00 0.36 0.06
#> TCGA.UF.A71A.01 3 0.1043 0.903 0.00 0.00 0.96 0.00 0.04
#> TCGA.TN.A7HI.01 2 0.0000 0.922 0.00 1.00 0.00 0.00 0.00
#> TCGA.BA.A6D8.01 2 0.0000 0.922 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.7446.01 1 0.0000 0.994 1.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7370.01 1 0.0000 0.994 1.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A71A.06 3 0.1043 0.903 0.00 0.00 0.96 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.CV.7414.01 2 0.1267 0.8363 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.CN.6010.01 2 0.0000 0.8817 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.5332.01 2 0.6423 -0.0883 0.00 0.48 0.00 0.30 0.18 0.04
#> TCGA.CV.7101.01 2 0.0000 0.8817 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.6012.01 4 0.3258 0.4583 0.10 0.02 0.00 0.84 0.00 0.04
#> TCGA.CV.7424.01 3 0.5174 0.5487 0.02 0.00 0.56 0.38 0.02 0.02
#> TCGA.CV.7418.01 4 0.5184 0.6672 0.00 0.20 0.00 0.66 0.12 0.02
#> TCGA.CR.7374.01 1 0.0547 0.9782 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.CV.7261.01 4 0.3829 0.6994 0.00 0.18 0.00 0.76 0.06 0.00
#> TCGA.DQ.5629.01 1 0.0000 0.9946 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.6997.01 5 0.0547 0.0000 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.CN.6992.01 1 0.0000 0.9946 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6962.01 3 0.3873 0.7457 0.00 0.00 0.78 0.16 0.02 0.04
#> TCGA.CV.6948.01 3 0.4475 0.7077 0.00 0.00 0.70 0.20 0.00 0.10
#> TCGA.HD.8314.01 2 0.0000 0.8817 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QK.A8ZA.01 2 0.0000 0.8817 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.A4CI.01 2 0.0000 0.8817 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A71E.01 2 0.0000 0.8817 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.T2.A6X0.01 2 0.0000 0.8817 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BB.7862.01 6 0.2260 0.0000 0.00 0.00 0.00 0.14 0.00 0.86
#> TCGA.BA.4078.01 2 0.6053 -0.2603 0.00 0.44 0.00 0.42 0.04 0.10
#> TCGA.UF.A71A.01 3 0.0937 0.7378 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.TN.A7HI.01 2 0.0000 0.8817 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A6D8.01 2 0.0000 0.8817 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7446.01 1 0.0000 0.9946 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7370.01 1 0.0000 0.9946 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A71A.06 3 0.0937 0.7378 0.00 0.00 0.96 0.00 0.00 0.04
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.CV.7414.01 2 0.334 0.759 0.00 0.82 0.04 0.10 0.00 0.04 0.00
#> TCGA.CN.6010.01 2 0.000 0.977 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.5332.01 4 0.704 0.304 0.00 0.26 0.10 0.46 0.10 0.08 0.00
#> TCGA.CV.7101.01 2 0.000 0.977 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.6012.01 4 0.583 0.195 0.06 0.00 0.14 0.64 0.00 0.08 0.08
#> TCGA.CV.7424.01 7 0.613 0.336 0.00 0.00 0.26 0.16 0.00 0.08 0.50
#> TCGA.CV.7418.01 4 0.539 0.354 0.00 0.08 0.12 0.68 0.00 0.08 0.04
#> TCGA.CR.7374.01 1 0.151 0.933 0.94 0.00 0.02 0.02 0.00 0.02 0.00
#> TCGA.CV.7261.01 4 0.425 0.436 0.00 0.10 0.02 0.78 0.02 0.06 0.02
#> TCGA.DQ.5629.01 1 0.000 0.984 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.6997.01 5 0.000 0.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CN.6992.01 1 0.000 0.984 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6962.01 7 0.000 0.571 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CV.6948.01 7 0.452 0.411 0.00 0.00 0.34 0.04 0.00 0.02 0.60
#> TCGA.HD.8314.01 2 0.000 0.977 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QK.A8ZA.01 2 0.000 0.977 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.A4CI.01 2 0.000 0.977 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A71E.01 2 0.000 0.977 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.T2.A6X0.01 2 0.000 0.977 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BB.7862.01 6 0.143 0.000 0.00 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.BA.4078.01 4 0.432 0.343 0.00 0.38 0.02 0.58 0.00 0.02 0.00
#> TCGA.UF.A71A.01 7 0.346 0.581 0.00 0.00 0.40 0.00 0.00 0.00 0.60
#> TCGA.TN.A7HI.01 2 0.000 0.977 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A6D8.01 2 0.000 0.977 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7446.01 1 0.000 0.984 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7370.01 1 0.000 0.984 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A71A.06 7 0.346 0.581 0.00 0.00 0.40 0.00 0.00 0.00 0.60
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.CV.7414.01 2 0.5758 0.2694 0.00 0.56 0.20 0.16 0.04 0.00 0.00 0.04
#> TCGA.CN.6010.01 2 0.0941 0.9158 0.00 0.96 0.02 0.02 0.00 0.00 0.00 0.00
#> TCGA.CQ.5332.01 4 0.6055 0.3129 0.00 0.22 0.20 0.50 0.04 0.00 0.00 0.04
#> TCGA.CV.7101.01 2 0.0000 0.9300 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.6012.01 3 0.5264 0.0000 0.02 0.00 0.48 0.40 0.00 0.04 0.00 0.06
#> TCGA.CV.7424.01 7 0.6135 0.1016 0.00 0.00 0.36 0.04 0.00 0.02 0.36 0.22
#> TCGA.CV.7418.01 4 0.4087 0.0536 0.00 0.06 0.04 0.78 0.02 0.08 0.00 0.02
#> TCGA.CR.7374.01 1 0.3178 0.8064 0.80 0.00 0.14 0.02 0.00 0.00 0.00 0.04
#> TCGA.CV.7261.01 4 0.5371 -0.2153 0.00 0.08 0.22 0.62 0.04 0.02 0.00 0.02
#> TCGA.DQ.5629.01 1 0.1091 0.9183 0.94 0.00 0.06 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.6997.01 5 0.0471 0.0000 0.00 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.CN.6992.01 1 0.0000 0.9384 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6962.01 7 0.4747 0.2422 0.00 0.00 0.16 0.00 0.00 0.00 0.54 0.30
#> TCGA.CV.6948.01 8 0.2534 0.0000 0.00 0.00 0.00 0.00 0.00 0.00 0.22 0.78
#> TCGA.HD.8314.01 2 0.0000 0.9300 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QK.A8ZA.01 2 0.0471 0.9285 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.CQ.A4CI.01 2 0.0471 0.9198 0.00 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A71E.01 2 0.0471 0.9285 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.T2.A6X0.01 2 0.0000 0.9300 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BB.7862.01 6 0.0000 0.0000 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BA.4078.01 4 0.6501 0.2377 0.00 0.26 0.18 0.46 0.04 0.04 0.00 0.02
#> TCGA.UF.A71A.01 7 0.0000 0.4993 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.TN.A7HI.01 2 0.0000 0.9300 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A6D8.01 2 0.0471 0.9285 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.CV.7446.01 1 0.0000 0.9384 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7370.01 1 0.0000 0.9384 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A71A.06 7 0.0000 0.4993 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: Node01. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0121 , Node0122 , Node0211 , Node0212 , Node0213 , Node0221 , Node0222 , Node0223 , Node0224 , Node0225-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0511 , Node0512 , Node0521-leaf , Node0522 , Node0523-leaf , Node0524-leaf .
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 38 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 1.000 1.000 0.4628 0.538 0.538
#> 3 3 0.738 0.946 0.914 0.4144 0.778 0.587
#> 4 4 0.773 0.658 0.755 0.1282 0.972 0.910
#> 5 5 0.730 0.762 0.791 0.0531 0.954 0.848
#> 6 6 0.697 0.520 0.714 0.0440 0.871 0.543
#> 7 7 0.711 0.481 0.646 0.0294 0.856 0.399
#> 8 8 0.721 0.538 0.612 0.0300 0.885 0.430
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.CV.7413.01 1 0 1 1 0
#> TCGA.CV.6937.01 2 0 1 0 1
#> TCGA.CN.5358.01 2 0 1 0 1
#> TCGA.CR.7372.01 2 0 1 0 1
#> TCGA.CN.4742.01 1 0 1 1 0
#> TCGA.CV.5444.01 2 0 1 0 1
#> TCGA.CV.5436.01 2 0 1 0 1
#> TCGA.CV.6961.01 2 0 1 0 1
#> TCGA.BB.4227.01 2 0 1 0 1
#> TCGA.CV.6934.01 1 0 1 1 0
#> TCGA.F7.A623.01 2 0 1 0 1
#> TCGA.T3.A92M.01 2 0 1 0 1
#> TCGA.CV.A468.01 2 0 1 0 1
#> TCGA.QK.AA3K.01 2 0 1 0 1
#> TCGA.4P.AA8J.01 2 0 1 0 1
#> TCGA.CV.A45V.01 1 0 1 1 0
#> TCGA.CV.A460.01 2 0 1 0 1
#> TCGA.CQ.A4CE.01 1 0 1 1 0
#> TCGA.BA.A4II.01 2 0 1 0 1
#> TCGA.BB.8596.01 1 0 1 1 0
#> TCGA.F7.A50I.01 2 0 1 0 1
#> TCGA.IQ.A61O.01 2 0 1 0 1
#> TCGA.CV.A45X.01 2 0 1 0 1
#> TCGA.IQ.A6SH.01 2 0 1 0 1
#> TCGA.QK.A6VC.01 1 0 1 1 0
#> TCGA.RS.A6TO.01 1 0 1 1 0
#> TCGA.CQ.7067.01 1 0 1 1 0
#> TCGA.UF.A7JJ.01 2 0 1 0 1
#> TCGA.P3.A6T4.01 2 0 1 0 1
#> TCGA.D6.A6EM.01 1 0 1 1 0
#> TCGA.UF.A7JK.01 2 0 1 0 1
#> TCGA.HD.7831.01 2 0 1 0 1
#> TCGA.D6.A6EQ.01 2 0 1 0 1
#> TCGA.P3.A6T0.01 1 0 1 1 0
#> TCGA.UF.A7JA.01 1 0 1 1 0
#> TCGA.BA.A6DA.01 1 0 1 1 0
#> TCGA.CV.A6K2.01 2 0 1 0 1
#> TCGA.CV.A6K1.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CV.7413.01 1 0.2066 0.957 0.94 0.06 0.00
#> TCGA.CV.6937.01 2 0.4002 0.968 0.00 0.84 0.16
#> TCGA.CN.5358.01 2 0.4002 0.968 0.00 0.84 0.16
#> TCGA.CR.7372.01 3 0.0000 0.958 0.00 0.00 1.00
#> TCGA.CN.4742.01 1 0.0892 0.961 0.98 0.02 0.00
#> TCGA.CV.5444.01 3 0.0000 0.958 0.00 0.00 1.00
#> TCGA.CV.5436.01 3 0.0000 0.958 0.00 0.00 1.00
#> TCGA.CV.6961.01 2 0.4002 0.968 0.00 0.84 0.16
#> TCGA.BB.4227.01 3 0.2066 0.942 0.00 0.06 0.94
#> TCGA.CV.6934.01 1 0.0000 0.961 1.00 0.00 0.00
#> TCGA.F7.A623.01 2 0.4002 0.968 0.00 0.84 0.16
#> TCGA.T3.A92M.01 2 0.4002 0.968 0.00 0.84 0.16
#> TCGA.CV.A468.01 2 0.4002 0.968 0.00 0.84 0.16
#> TCGA.QK.AA3K.01 2 0.4002 0.968 0.00 0.84 0.16
#> TCGA.4P.AA8J.01 2 0.4002 0.968 0.00 0.84 0.16
#> TCGA.CV.A45V.01 1 0.0000 0.961 1.00 0.00 0.00
#> TCGA.CV.A460.01 2 0.5560 0.802 0.00 0.70 0.30
#> TCGA.CQ.A4CE.01 1 0.0000 0.961 1.00 0.00 0.00
#> TCGA.BA.A4II.01 2 0.4002 0.968 0.00 0.84 0.16
#> TCGA.BB.8596.01 1 0.4002 0.924 0.84 0.16 0.00
#> TCGA.F7.A50I.01 3 0.0000 0.958 0.00 0.00 1.00
#> TCGA.IQ.A61O.01 3 0.2537 0.923 0.00 0.08 0.92
#> TCGA.CV.A45X.01 3 0.2537 0.923 0.00 0.08 0.92
#> TCGA.IQ.A6SH.01 3 0.2066 0.942 0.00 0.06 0.94
#> TCGA.QK.A6VC.01 1 0.4002 0.924 0.84 0.16 0.00
#> TCGA.RS.A6TO.01 1 0.0892 0.961 0.98 0.02 0.00
#> TCGA.CQ.7067.01 1 0.0000 0.961 1.00 0.00 0.00
#> TCGA.UF.A7JJ.01 2 0.5706 0.769 0.00 0.68 0.32
#> TCGA.P3.A6T4.01 2 0.4002 0.968 0.00 0.84 0.16
#> TCGA.D6.A6EM.01 1 0.0000 0.961 1.00 0.00 0.00
#> TCGA.UF.A7JK.01 3 0.0892 0.937 0.02 0.00 0.98
#> TCGA.HD.7831.01 2 0.4002 0.968 0.00 0.84 0.16
#> TCGA.D6.A6EQ.01 3 0.0000 0.958 0.00 0.00 1.00
#> TCGA.P3.A6T0.01 1 0.2066 0.957 0.94 0.06 0.00
#> TCGA.UF.A7JA.01 1 0.4002 0.924 0.84 0.16 0.00
#> TCGA.BA.A6DA.01 1 0.2537 0.947 0.92 0.08 0.00
#> TCGA.CV.A6K2.01 3 0.0000 0.958 0.00 0.00 1.00
#> TCGA.CV.A6K1.01 3 0.2066 0.942 0.00 0.06 0.94
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.CV.7413.01 1 0.317 0.874 0.84 0.00 0.00 0.16
#> TCGA.CV.6937.01 2 0.000 0.914 0.00 1.00 0.00 0.00
#> TCGA.CN.5358.01 2 0.201 0.897 0.00 0.92 0.00 0.08
#> TCGA.CR.7372.01 3 0.164 0.548 0.00 0.00 0.94 0.06
#> TCGA.CN.4742.01 1 0.234 0.881 0.90 0.00 0.00 0.10
#> TCGA.CV.5444.01 3 0.000 0.576 0.00 0.00 1.00 0.00
#> TCGA.CV.5436.01 3 0.164 0.548 0.00 0.00 0.94 0.06
#> TCGA.CV.6961.01 2 0.000 0.914 0.00 1.00 0.00 0.00
#> TCGA.BB.4227.01 3 0.559 -0.680 0.00 0.02 0.52 0.46
#> TCGA.CV.6934.01 1 0.000 0.880 1.00 0.00 0.00 0.00
#> TCGA.F7.A623.01 2 0.000 0.914 0.00 1.00 0.00 0.00
#> TCGA.T3.A92M.01 2 0.000 0.914 0.00 1.00 0.00 0.00
#> TCGA.CV.A468.01 2 0.201 0.897 0.00 0.92 0.00 0.08
#> TCGA.QK.AA3K.01 2 0.000 0.914 0.00 1.00 0.00 0.00
#> TCGA.4P.AA8J.01 2 0.000 0.914 0.00 1.00 0.00 0.00
#> TCGA.CV.A45V.01 1 0.000 0.880 1.00 0.00 0.00 0.00
#> TCGA.CV.A460.01 2 0.657 0.437 0.00 0.58 0.10 0.32
#> TCGA.CQ.A4CE.01 1 0.000 0.880 1.00 0.00 0.00 0.00
#> TCGA.BA.A4II.01 2 0.201 0.897 0.00 0.92 0.00 0.08
#> TCGA.BB.8596.01 1 0.479 0.785 0.62 0.00 0.00 0.38
#> TCGA.F7.A50I.01 3 0.201 0.511 0.00 0.00 0.92 0.08
#> TCGA.IQ.A61O.01 4 0.549 0.880 0.00 0.02 0.40 0.58
#> TCGA.CV.A45X.01 4 0.557 0.876 0.00 0.02 0.44 0.54
#> TCGA.IQ.A6SH.01 3 0.561 -0.734 0.00 0.02 0.50 0.48
#> TCGA.QK.A6VC.01 1 0.479 0.785 0.62 0.00 0.00 0.38
#> TCGA.RS.A6TO.01 1 0.265 0.878 0.88 0.00 0.00 0.12
#> TCGA.CQ.7067.01 1 0.000 0.880 1.00 0.00 0.00 0.00
#> TCGA.UF.A7JJ.01 2 0.586 0.655 0.00 0.70 0.12 0.18
#> TCGA.P3.A6T4.01 2 0.000 0.914 0.00 1.00 0.00 0.00
#> TCGA.D6.A6EM.01 1 0.000 0.880 1.00 0.00 0.00 0.00
#> TCGA.UF.A7JK.01 3 0.000 0.576 0.00 0.00 1.00 0.00
#> TCGA.HD.7831.01 2 0.292 0.866 0.00 0.86 0.00 0.14
#> TCGA.D6.A6EQ.01 3 0.000 0.576 0.00 0.00 1.00 0.00
#> TCGA.P3.A6T0.01 1 0.317 0.874 0.84 0.00 0.00 0.16
#> TCGA.UF.A7JA.01 1 0.479 0.785 0.62 0.00 0.00 0.38
#> TCGA.BA.A6DA.01 1 0.361 0.826 0.80 0.00 0.00 0.20
#> TCGA.CV.A6K2.01 3 0.452 -0.132 0.00 0.00 0.68 0.32
#> TCGA.CV.A6K1.01 3 0.559 -0.680 0.00 0.02 0.52 0.46
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CV.7413.01 5 0.4126 0.744 0.38 0.00 0.00 0.00 0.62
#> TCGA.CV.6937.01 2 0.1648 0.828 0.04 0.94 0.00 0.02 0.00
#> TCGA.CN.5358.01 2 0.3274 0.803 0.22 0.78 0.00 0.00 0.00
#> TCGA.CR.7372.01 3 0.4637 0.783 0.10 0.00 0.74 0.16 0.00
#> TCGA.CN.4742.01 5 0.3424 0.769 0.24 0.00 0.00 0.00 0.76
#> TCGA.CV.5444.01 3 0.4398 0.819 0.04 0.00 0.72 0.24 0.00
#> TCGA.CV.5436.01 3 0.3922 0.839 0.04 0.00 0.78 0.18 0.00
#> TCGA.CV.6961.01 2 0.2012 0.822 0.06 0.92 0.00 0.02 0.00
#> TCGA.BB.4227.01 4 0.2675 0.825 0.04 0.04 0.02 0.90 0.00
#> TCGA.CV.6934.01 5 0.0000 0.783 0.00 0.00 0.00 0.00 1.00
#> TCGA.F7.A623.01 2 0.2012 0.822 0.06 0.92 0.00 0.02 0.00
#> TCGA.T3.A92M.01 2 0.0000 0.840 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.A468.01 2 0.3274 0.803 0.22 0.78 0.00 0.00 0.00
#> TCGA.QK.AA3K.01 2 0.0000 0.840 0.00 1.00 0.00 0.00 0.00
#> TCGA.4P.AA8J.01 2 0.0000 0.840 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.A45V.01 5 0.1043 0.777 0.04 0.00 0.00 0.00 0.96
#> TCGA.CV.A460.01 2 0.7160 0.539 0.26 0.52 0.06 0.16 0.00
#> TCGA.CQ.A4CE.01 5 0.0000 0.783 0.00 0.00 0.00 0.00 1.00
#> TCGA.BA.A4II.01 2 0.3109 0.809 0.20 0.80 0.00 0.00 0.00
#> TCGA.BB.8596.01 5 0.7120 0.646 0.34 0.00 0.16 0.04 0.46
#> TCGA.F7.A50I.01 3 0.5927 0.570 0.12 0.00 0.54 0.34 0.00
#> TCGA.IQ.A61O.01 4 0.3977 0.780 0.10 0.06 0.02 0.82 0.00
#> TCGA.CV.A45X.01 4 0.2438 0.828 0.04 0.06 0.00 0.90 0.00
#> TCGA.IQ.A6SH.01 4 0.1410 0.839 0.00 0.06 0.00 0.94 0.00
#> TCGA.QK.A6VC.01 5 0.7120 0.646 0.34 0.00 0.16 0.04 0.46
#> TCGA.RS.A6TO.01 5 0.3895 0.752 0.32 0.00 0.00 0.00 0.68
#> TCGA.CQ.7067.01 5 0.0000 0.783 0.00 0.00 0.00 0.00 1.00
#> TCGA.UF.A7JJ.01 2 0.6905 0.585 0.24 0.56 0.06 0.14 0.00
#> TCGA.P3.A6T4.01 2 0.0609 0.836 0.00 0.98 0.00 0.02 0.00
#> TCGA.D6.A6EM.01 5 0.0000 0.783 0.00 0.00 0.00 0.00 1.00
#> TCGA.UF.A7JK.01 3 0.4263 0.818 0.06 0.00 0.76 0.18 0.00
#> TCGA.HD.7831.01 2 0.4132 0.778 0.26 0.72 0.02 0.00 0.00
#> TCGA.D6.A6EQ.01 3 0.3852 0.834 0.02 0.00 0.76 0.22 0.00
#> TCGA.P3.A6T0.01 5 0.4126 0.744 0.38 0.00 0.00 0.00 0.62
#> TCGA.UF.A7JA.01 5 0.7120 0.646 0.34 0.00 0.16 0.04 0.46
#> TCGA.BA.A6DA.01 5 0.3513 0.734 0.18 0.00 0.02 0.00 0.80
#> TCGA.CV.A6K2.01 4 0.4132 0.475 0.02 0.00 0.26 0.72 0.00
#> TCGA.CV.A6K1.01 4 0.3348 0.793 0.02 0.04 0.08 0.86 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.CV.7413.01 5 0.0547 0.52117 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.CV.6937.01 2 0.1807 0.72966 0.06 0.92 0.00 0.00 0.00 0.02
#> TCGA.CN.5358.01 2 0.3578 0.37564 0.00 0.66 0.00 0.00 0.00 0.34
#> TCGA.CR.7372.01 3 0.4377 0.58443 0.12 0.00 0.72 0.00 0.00 0.16
#> TCGA.CN.4742.01 5 0.0547 0.54299 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.CV.5444.01 3 0.3163 0.69512 0.00 0.00 0.82 0.04 0.00 0.14
#> TCGA.CV.5436.01 3 0.3679 0.69349 0.04 0.00 0.76 0.00 0.00 0.20
#> TCGA.CV.6961.01 2 0.2512 0.71185 0.06 0.88 0.00 0.00 0.00 0.06
#> TCGA.BB.4227.01 4 0.6373 0.41711 0.08 0.00 0.16 0.56 0.00 0.20
#> TCGA.CV.6934.01 5 0.5235 0.61896 0.10 0.00 0.00 0.38 0.52 0.00
#> TCGA.F7.A623.01 2 0.2512 0.71185 0.06 0.88 0.00 0.00 0.00 0.06
#> TCGA.T3.A92M.01 2 0.1267 0.73921 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.CV.A468.01 2 0.3578 0.37564 0.00 0.66 0.00 0.00 0.00 0.34
#> TCGA.QK.AA3K.01 2 0.1267 0.73921 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.4P.AA8J.01 2 0.1267 0.73921 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.CV.A45V.01 5 0.5248 0.62059 0.04 0.00 0.00 0.34 0.58 0.04
#> TCGA.CV.A460.01 6 0.4348 0.36791 0.00 0.32 0.00 0.04 0.00 0.64
#> TCGA.CQ.A4CE.01 5 0.5235 0.61896 0.10 0.00 0.00 0.38 0.52 0.00
#> TCGA.BA.A4II.01 2 0.3499 0.41590 0.00 0.68 0.00 0.00 0.00 0.32
#> TCGA.BB.8596.01 1 0.3309 1.00000 0.72 0.00 0.00 0.00 0.28 0.00
#> TCGA.F7.A50I.01 3 0.4552 0.55879 0.00 0.00 0.64 0.06 0.00 0.30
#> TCGA.IQ.A61O.01 6 0.6616 -0.45562 0.08 0.00 0.12 0.36 0.00 0.44
#> TCGA.CV.A45X.01 4 0.5354 0.47350 0.00 0.00 0.16 0.58 0.00 0.26
#> TCGA.IQ.A6SH.01 4 0.5419 0.46983 0.00 0.00 0.20 0.58 0.00 0.22
#> TCGA.QK.A6VC.01 1 0.3309 1.00000 0.72 0.00 0.00 0.00 0.28 0.00
#> TCGA.RS.A6TO.01 5 0.0000 0.53769 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CQ.7067.01 5 0.5949 0.61060 0.10 0.00 0.00 0.34 0.52 0.04
#> TCGA.UF.A7JJ.01 6 0.4576 0.26812 0.00 0.40 0.04 0.00 0.00 0.56
#> TCGA.P3.A6T4.01 2 0.0547 0.74319 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.D6.A6EM.01 5 0.5235 0.61896 0.10 0.00 0.00 0.38 0.52 0.00
#> TCGA.UF.A7JK.01 3 0.0937 0.68453 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.HD.7831.01 6 0.4310 0.00701 0.02 0.44 0.00 0.00 0.00 0.54
#> TCGA.D6.A6EQ.01 3 0.1092 0.70481 0.00 0.00 0.96 0.02 0.00 0.02
#> TCGA.P3.A6T0.01 5 0.1092 0.51935 0.02 0.00 0.00 0.00 0.96 0.02
#> TCGA.UF.A7JA.01 1 0.3309 1.00000 0.72 0.00 0.00 0.00 0.28 0.00
#> TCGA.BA.A6DA.01 4 0.6103 -0.62219 0.32 0.00 0.00 0.38 0.30 0.00
#> TCGA.CV.A6K2.01 3 0.5938 0.05484 0.00 0.00 0.46 0.26 0.00 0.28
#> TCGA.CV.A6K1.01 4 0.6305 0.34977 0.00 0.02 0.22 0.46 0.00 0.30
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.CV.7413.01 1 0.5252 0.5037 0.42 0.00 0.42 0.00 0.16 0.00 0.00
#> TCGA.CV.6937.01 7 0.3459 0.9090 0.00 0.40 0.00 0.00 0.00 0.00 0.60
#> TCGA.CN.5358.01 2 0.0000 0.4412 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7372.01 6 0.5243 0.4493 0.00 0.00 0.18 0.04 0.02 0.66 0.10
#> TCGA.CN.4742.01 1 0.5560 0.3273 0.42 0.00 0.30 0.00 0.28 0.00 0.00
#> TCGA.CV.5444.01 6 0.4714 0.6129 0.00 0.00 0.28 0.12 0.00 0.60 0.00
#> TCGA.CV.5436.01 6 0.4663 0.6383 0.00 0.00 0.20 0.04 0.02 0.70 0.04
#> TCGA.CV.6961.01 7 0.3358 0.9557 0.00 0.36 0.00 0.00 0.00 0.00 0.64
#> TCGA.BB.4227.01 4 0.3833 0.6020 0.00 0.00 0.04 0.78 0.12 0.00 0.06
#> TCGA.CV.6934.01 5 0.2945 0.9137 0.26 0.00 0.00 0.00 0.74 0.00 0.00
#> TCGA.F7.A623.01 7 0.3358 0.9557 0.00 0.36 0.00 0.00 0.00 0.00 0.64
#> TCGA.T3.A92M.01 2 0.6494 -0.4137 0.00 0.46 0.06 0.06 0.08 0.00 0.34
#> TCGA.CV.A468.01 2 0.0000 0.4412 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QK.AA3K.01 2 0.6654 -0.3853 0.00 0.46 0.06 0.08 0.08 0.00 0.32
#> TCGA.4P.AA8J.01 2 0.6654 -0.3853 0.00 0.46 0.06 0.08 0.08 0.00 0.32
#> TCGA.CV.A45V.01 5 0.4248 0.8593 0.26 0.00 0.00 0.00 0.66 0.00 0.08
#> TCGA.CV.A460.01 2 0.4422 0.3542 0.00 0.72 0.08 0.16 0.00 0.00 0.04
#> TCGA.CQ.A4CE.01 5 0.2945 0.9137 0.26 0.00 0.00 0.00 0.74 0.00 0.00
#> TCGA.BA.A4II.01 2 0.0000 0.4412 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BB.8596.01 1 0.0000 0.5024 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F7.A50I.01 6 0.6677 0.3894 0.00 0.12 0.28 0.20 0.00 0.40 0.00
#> TCGA.IQ.A61O.01 4 0.6360 0.4093 0.00 0.08 0.18 0.58 0.02 0.02 0.12
#> TCGA.CV.A45X.01 4 0.0863 0.6610 0.00 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.IQ.A6SH.01 4 0.0000 0.6629 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.QK.A6VC.01 1 0.0000 0.5024 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RS.A6TO.01 1 0.5252 0.5037 0.42 0.00 0.42 0.00 0.16 0.00 0.00
#> TCGA.CQ.7067.01 5 0.3887 0.8952 0.26 0.00 0.00 0.00 0.70 0.02 0.02
#> TCGA.UF.A7JJ.01 2 0.3765 0.3867 0.00 0.78 0.10 0.10 0.00 0.00 0.02
#> TCGA.P3.A6T4.01 2 0.5606 -0.5074 0.00 0.48 0.06 0.00 0.08 0.00 0.38
#> TCGA.D6.A6EM.01 5 0.2945 0.9137 0.26 0.00 0.00 0.00 0.74 0.00 0.00
#> TCGA.UF.A7JK.01 6 0.1860 0.6128 0.00 0.00 0.00 0.04 0.02 0.92 0.02
#> TCGA.HD.7831.01 2 0.2569 0.4040 0.00 0.84 0.00 0.00 0.00 0.02 0.14
#> TCGA.D6.A6EQ.01 6 0.4121 0.6325 0.00 0.00 0.20 0.10 0.00 0.70 0.00
#> TCGA.P3.A6T0.01 1 0.6333 0.4918 0.42 0.00 0.36 0.00 0.16 0.02 0.04
#> TCGA.UF.A7JA.01 1 0.0000 0.5024 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A6DA.01 5 0.3909 0.6941 0.40 0.00 0.00 0.00 0.58 0.00 0.02
#> TCGA.CV.A6K2.01 4 0.5402 -0.0351 0.00 0.00 0.24 0.48 0.00 0.28 0.00
#> TCGA.CV.A6K1.01 4 0.3991 0.5170 0.00 0.00 0.22 0.72 0.00 0.04 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.CV.7413.01 8 0.6645 -0.58972 0.08 0.00 0.06 0.00 0.36 0.00 0.14 0.36
#> TCGA.CV.6937.01 7 0.5103 0.85718 0.00 0.34 0.00 0.00 0.00 0.00 0.44 0.22
#> TCGA.CN.5358.01 2 0.0000 0.68550 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7372.01 3 0.2406 0.21744 0.00 0.00 0.80 0.00 0.00 0.20 0.00 0.00
#> TCGA.CN.4742.01 5 0.6002 0.46193 0.06 0.00 0.08 0.00 0.54 0.00 0.08 0.24
#> TCGA.CV.5444.01 6 0.1091 0.63021 0.00 0.00 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.CV.5436.01 6 0.4106 0.30849 0.00 0.00 0.30 0.00 0.00 0.64 0.04 0.02
#> TCGA.CV.6961.01 7 0.4921 0.90688 0.00 0.26 0.00 0.00 0.00 0.00 0.52 0.22
#> TCGA.BB.4227.01 4 0.3675 0.54769 0.14 0.00 0.00 0.76 0.00 0.00 0.08 0.02
#> TCGA.CV.6934.01 5 0.0000 0.67804 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.F7.A623.01 7 0.4983 0.91979 0.00 0.28 0.00 0.00 0.00 0.00 0.50 0.22
#> TCGA.T3.A92M.01 8 0.3737 0.44371 0.00 0.48 0.00 0.02 0.00 0.00 0.00 0.50
#> TCGA.CV.A468.01 2 0.0000 0.68550 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QK.AA3K.01 8 0.3737 0.44371 0.00 0.48 0.00 0.02 0.00 0.00 0.00 0.50
#> TCGA.4P.AA8J.01 8 0.3737 0.44371 0.00 0.48 0.00 0.02 0.00 0.00 0.00 0.50
#> TCGA.CV.A45V.01 5 0.1741 0.66727 0.00 0.00 0.02 0.00 0.92 0.00 0.04 0.02
#> TCGA.CV.A460.01 2 0.5504 0.57872 0.00 0.66 0.04 0.14 0.00 0.06 0.06 0.04
#> TCGA.CQ.A4CE.01 5 0.0000 0.67804 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BA.A4II.01 2 0.0000 0.68550 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BB.8596.01 1 0.2114 0.99226 0.84 0.00 0.00 0.00 0.16 0.00 0.00 0.00
#> TCGA.F7.A50I.01 6 0.3263 0.55770 0.00 0.10 0.00 0.12 0.00 0.78 0.00 0.00
#> TCGA.IQ.A61O.01 3 0.3737 0.00656 0.00 0.00 0.50 0.48 0.00 0.00 0.00 0.02
#> TCGA.CV.A45X.01 4 0.0471 0.68045 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.IQ.A6SH.01 4 0.0471 0.68045 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.QK.A6VC.01 1 0.2114 0.99226 0.84 0.00 0.00 0.00 0.16 0.00 0.00 0.00
#> TCGA.RS.A6TO.01 5 0.6484 0.36634 0.06 0.00 0.06 0.00 0.38 0.00 0.14 0.36
#> TCGA.CQ.7067.01 5 0.1091 0.67085 0.00 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.UF.A7JJ.01 2 0.4337 0.62039 0.00 0.72 0.02 0.12 0.00 0.12 0.02 0.00
#> TCGA.P3.A6T4.01 8 0.3737 0.44371 0.00 0.48 0.00 0.02 0.00 0.00 0.00 0.50
#> TCGA.D6.A6EM.01 5 0.0471 0.67473 0.00 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.UF.A7JK.01 6 0.5306 0.22816 0.02 0.00 0.26 0.00 0.00 0.58 0.10 0.04
#> TCGA.HD.7831.01 2 0.3637 0.53702 0.00 0.70 0.26 0.00 0.00 0.00 0.02 0.02
#> TCGA.D6.A6EQ.01 6 0.1408 0.60280 0.00 0.00 0.02 0.00 0.00 0.94 0.02 0.02
#> TCGA.P3.A6T0.01 5 0.6933 0.33750 0.08 0.00 0.08 0.00 0.36 0.00 0.18 0.30
#> TCGA.UF.A7JA.01 1 0.2569 0.98447 0.82 0.00 0.02 0.00 0.16 0.00 0.00 0.00
#> TCGA.BA.A6DA.01 5 0.4041 0.28583 0.22 0.00 0.04 0.00 0.70 0.00 0.04 0.00
#> TCGA.CV.A6K2.01 6 0.3514 0.29544 0.00 0.00 0.00 0.34 0.00 0.64 0.00 0.02
#> TCGA.CV.A6K1.01 4 0.4756 0.25237 0.00 0.00 0.00 0.56 0.00 0.34 0.06 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: Node012. Child nodes: Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node02111-leaf , Node02112-leaf , Node02113-leaf , Node02114-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02124-leaf , Node02131-leaf , Node02132 , Node02133-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02231-leaf , Node02232-leaf , Node02233-leaf , Node02241-leaf , Node02242-leaf , Node02243-leaf , Node02321-leaf , Node02322-leaf , Node02323-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf , Node05114-leaf , Node05121 , Node05122-leaf , Node05123-leaf , Node05221-leaf , Node05222-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0121"]
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 13 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 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 1.000 1.000 0.4621 0.538 0.538
#> 3 3 0.808 0.959 0.982 0.5299 0.654 0.413
#> 4 4 0.897 0.971 0.988 0.0884 0.910 0.708
#> 5 5 1.000 0.971 0.982 0.0953 0.897 0.579
#> 6 6 0.872 0.861 0.909 0.0403 1.000 1.000
#> 7 7 0.846 0.569 0.797 0.0228 0.974 0.833
#> 8 8 0.833 0.590 0.855 0.0274 0.910 0.364
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
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.CV.7413.01 2 0 1 0 1
#> TCGA.CN.4742.01 2 0 1 0 1
#> TCGA.CV.6934.01 1 0 1 1 0
#> TCGA.CV.A45V.01 1 0 1 1 0
#> TCGA.CQ.A4CE.01 1 0 1 1 0
#> TCGA.BB.8596.01 1 0 1 1 0
#> TCGA.QK.A6VC.01 1 0 1 1 0
#> TCGA.RS.A6TO.01 2 0 1 0 1
#> TCGA.CQ.7067.01 1 0 1 1 0
#> TCGA.D6.A6EM.01 1 0 1 1 0
#> TCGA.P3.A6T0.01 2 0 1 0 1
#> TCGA.UF.A7JA.01 1 0 1 1 0
#> TCGA.BA.A6DA.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CV.7413.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.CN.4742.01 3 0.334 0.855 0.00 0.12 0.88
#> TCGA.CV.6934.01 1 0.334 0.866 0.88 0.00 0.12
#> TCGA.CV.A45V.01 3 0.000 0.967 0.00 0.00 1.00
#> TCGA.CQ.A4CE.01 3 0.000 0.967 0.00 0.00 1.00
#> TCGA.BB.8596.01 3 0.000 0.967 0.00 0.00 1.00
#> TCGA.QK.A6VC.01 3 0.000 0.967 0.00 0.00 1.00
#> TCGA.RS.A6TO.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.CQ.7067.01 1 0.000 0.968 1.00 0.00 0.00
#> TCGA.D6.A6EM.01 1 0.000 0.968 1.00 0.00 0.00
#> TCGA.P3.A6T0.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.UF.A7JA.01 1 0.000 0.968 1.00 0.00 0.00
#> TCGA.BA.A6DA.01 1 0.000 0.968 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.CV.7413.01 4 0.000 1.000 0.00 0 0.00 1
#> TCGA.CN.4742.01 4 0.000 1.000 0.00 0 0.00 1
#> TCGA.CV.6934.01 1 0.317 0.803 0.84 0 0.16 0
#> TCGA.CV.A45V.01 3 0.000 1.000 0.00 0 1.00 0
#> TCGA.CQ.A4CE.01 3 0.000 1.000 0.00 0 1.00 0
#> TCGA.BB.8596.01 3 0.000 1.000 0.00 0 1.00 0
#> TCGA.QK.A6VC.01 3 0.000 1.000 0.00 0 1.00 0
#> TCGA.RS.A6TO.01 2 0.000 1.000 0.00 1 0.00 0
#> TCGA.CQ.7067.01 1 0.000 0.954 1.00 0 0.00 0
#> TCGA.D6.A6EM.01 1 0.000 0.954 1.00 0 0.00 0
#> TCGA.P3.A6T0.01 2 0.000 1.000 0.00 1 0.00 0
#> TCGA.UF.A7JA.01 1 0.000 0.954 1.00 0 0.00 0
#> TCGA.BA.A6DA.01 1 0.000 0.954 1.00 0 0.00 0
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CV.7413.01 4 0.0609 0.986 0.00 0 0.00 0.98 0.02
#> TCGA.CN.4742.01 4 0.0000 0.986 0.00 0 0.00 1.00 0.00
#> TCGA.CV.6934.01 5 0.1732 0.884 0.08 0 0.00 0.00 0.92
#> TCGA.CV.A45V.01 3 0.0000 0.943 0.00 0 1.00 0.00 0.00
#> TCGA.CQ.A4CE.01 3 0.1410 0.971 0.00 0 0.94 0.00 0.06
#> TCGA.BB.8596.01 5 0.0609 0.884 0.00 0 0.02 0.00 0.98
#> TCGA.QK.A6VC.01 3 0.1410 0.971 0.00 0 0.94 0.00 0.06
#> TCGA.RS.A6TO.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CQ.7067.01 1 0.0000 1.000 1.00 0 0.00 0.00 0.00
#> TCGA.D6.A6EM.01 1 0.0000 1.000 1.00 0 0.00 0.00 0.00
#> TCGA.P3.A6T0.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.UF.A7JA.01 1 0.0000 1.000 1.00 0 0.00 0.00 0.00
#> TCGA.BA.A6DA.01 1 0.0000 1.000 1.00 0 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.CV.7413.01 6 0.0547 0.986 0.0 0.00 0.00 0.02 0.00 0.98
#> TCGA.CN.4742.01 6 0.0000 0.986 0.0 0.00 0.00 0.00 0.00 1.00
#> TCGA.CV.6934.01 5 0.0000 1.000 0.0 0.00 0.00 0.00 1.00 0.00
#> TCGA.CV.A45V.01 3 0.3647 0.799 0.0 0.00 0.64 0.36 0.00 0.00
#> TCGA.CQ.A4CE.01 3 0.4926 0.779 0.0 0.00 0.64 0.24 0.12 0.00
#> TCGA.BB.8596.01 5 0.0000 1.000 0.0 0.00 0.00 0.00 1.00 0.00
#> TCGA.QK.A6VC.01 3 0.0000 0.699 0.0 0.00 1.00 0.00 0.00 0.00
#> TCGA.RS.A6TO.01 2 0.1556 0.942 0.0 0.92 0.00 0.08 0.00 0.00
#> TCGA.CQ.7067.01 1 0.3756 0.621 0.6 0.00 0.00 0.40 0.00 0.00
#> TCGA.D6.A6EM.01 1 0.0000 0.833 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.P3.A6T0.01 2 0.0000 0.942 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A7JA.01 1 0.2793 0.770 0.8 0.00 0.00 0.20 0.00 0.00
#> TCGA.BA.A6DA.01 1 0.0000 0.833 1.0 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.CV.7413.01 6 0.000 0.8575 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CN.4742.01 6 0.275 0.8575 0.00 0.16 0.00 0.00 0.00 0.82 0.02
#> TCGA.CV.6934.01 5 0.000 1.0000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.A45V.01 7 0.341 0.0000 0.00 0.00 0.38 0.00 0.00 0.00 0.62
#> TCGA.CQ.A4CE.01 3 0.639 -0.5674 0.00 0.12 0.40 0.00 0.12 0.00 0.36
#> TCGA.BB.8596.01 5 0.000 1.0000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.QK.A6VC.01 3 0.000 0.0034 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RS.A6TO.01 4 0.384 0.7899 0.00 0.16 0.00 0.74 0.00 0.00 0.10
#> TCGA.CQ.7067.01 1 0.356 0.5259 0.52 0.48 0.00 0.00 0.00 0.00 0.00
#> TCGA.D6.A6EM.01 1 0.000 0.7573 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P3.A6T0.01 4 0.000 0.7899 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.UF.A7JA.01 1 0.445 0.6264 0.64 0.10 0.00 0.00 0.00 0.00 0.26
#> TCGA.BA.A6DA.01 1 0.000 0.7573 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.CV.7413.01 6 0.0000 0.715 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CN.4742.01 6 0.4069 0.715 0.00 0.18 0.00 0.00 0.00 0.68 0.00 0.14
#> TCGA.CV.6934.01 5 0.0808 0.957 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.CV.A45V.01 7 0.2114 0.519 0.00 0.00 0.16 0.00 0.00 0.00 0.84 0.00
#> TCGA.CQ.A4CE.01 7 0.6101 0.529 0.00 0.04 0.18 0.00 0.26 0.00 0.48 0.04
#> TCGA.BB.8596.01 5 0.0000 0.957 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.QK.A6VC.01 3 0.0000 0.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RS.A6TO.01 4 0.3744 0.772 0.00 0.02 0.00 0.74 0.00 0.00 0.06 0.18
#> TCGA.CQ.7067.01 2 0.3551 0.000 0.22 0.72 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.D6.A6EM.01 1 0.1563 0.866 0.90 0.00 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.P3.A6T0.01 4 0.0000 0.772 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A7JA.01 8 0.3142 0.000 0.36 0.00 0.00 0.00 0.00 0.00 0.00 0.64
#> TCGA.BA.A6DA.01 1 0.0000 0.866 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: Node012. Child nodes: Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node02111-leaf , Node02112-leaf , Node02113-leaf , Node02114-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02124-leaf , Node02131-leaf , Node02132 , Node02133-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02231-leaf , Node02232-leaf , Node02233-leaf , Node02241-leaf , Node02242-leaf , Node02243-leaf , Node02321-leaf , Node02322-leaf , Node02323-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf , Node05114-leaf , Node05121 , Node05122-leaf , Node05123-leaf , Node05221-leaf , Node05222-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0122"]
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 '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 0.955 0.978 0.4897 0.500 0.500
#> 3 3 1.000 1.000 1.000 0.3825 0.663 0.420
#> 4 4 0.700 0.785 0.836 0.1041 0.793 0.451
#> 5 5 0.814 0.802 0.900 0.0571 0.980 0.910
#> 6 6 0.885 0.828 0.917 0.0459 0.943 0.738
#> 7 7 0.838 0.784 0.875 0.0298 0.960 0.769
#> 8 8 0.794 0.698 0.862 0.0218 0.980 0.864
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.CV.6937.01 2 0.000 0.995 0.00 1.00
#> TCGA.CN.5358.01 2 0.000 0.995 0.00 1.00
#> TCGA.CR.7372.01 1 0.000 0.945 1.00 0.00
#> TCGA.CV.5444.01 1 0.795 0.716 0.76 0.24
#> TCGA.CV.5436.01 2 0.141 0.981 0.02 0.98
#> TCGA.CV.6961.01 2 0.000 0.995 0.00 1.00
#> TCGA.BB.4227.01 1 0.000 0.945 1.00 0.00
#> TCGA.F7.A623.01 2 0.000 0.995 0.00 1.00
#> TCGA.T3.A92M.01 2 0.000 0.995 0.00 1.00
#> TCGA.CV.A468.01 2 0.000 0.995 0.00 1.00
#> TCGA.QK.AA3K.01 2 0.000 0.995 0.00 1.00
#> TCGA.4P.AA8J.01 2 0.000 0.995 0.00 1.00
#> TCGA.CV.A460.01 2 0.141 0.981 0.02 0.98
#> TCGA.BA.A4II.01 2 0.000 0.995 0.00 1.00
#> TCGA.F7.A50I.01 2 0.141 0.981 0.02 0.98
#> TCGA.IQ.A61O.01 1 0.000 0.945 1.00 0.00
#> TCGA.CV.A45X.01 1 0.000 0.945 1.00 0.00
#> TCGA.IQ.A6SH.01 1 0.000 0.945 1.00 0.00
#> TCGA.UF.A7JJ.01 2 0.000 0.995 0.00 1.00
#> TCGA.P3.A6T4.01 2 0.000 0.995 0.00 1.00
#> TCGA.UF.A7JK.01 1 0.000 0.945 1.00 0.00
#> TCGA.HD.7831.01 2 0.000 0.995 0.00 1.00
#> TCGA.D6.A6EQ.01 1 0.000 0.945 1.00 0.00
#> TCGA.CV.A6K2.01 1 0.795 0.716 0.76 0.24
#> TCGA.CV.A6K1.01 1 0.000 0.945 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CV.6937.01 3 0 1 0 0 1
#> TCGA.CN.5358.01 3 0 1 0 0 1
#> TCGA.CR.7372.01 1 0 1 1 0 0
#> TCGA.CV.5444.01 2 0 1 0 1 0
#> TCGA.CV.5436.01 2 0 1 0 1 0
#> TCGA.CV.6961.01 3 0 1 0 0 1
#> TCGA.BB.4227.01 1 0 1 1 0 0
#> TCGA.F7.A623.01 3 0 1 0 0 1
#> TCGA.T3.A92M.01 2 0 1 0 1 0
#> TCGA.CV.A468.01 3 0 1 0 0 1
#> TCGA.QK.AA3K.01 2 0 1 0 1 0
#> TCGA.4P.AA8J.01 2 0 1 0 1 0
#> TCGA.CV.A460.01 2 0 1 0 1 0
#> TCGA.BA.A4II.01 3 0 1 0 0 1
#> TCGA.F7.A50I.01 2 0 1 0 1 0
#> TCGA.IQ.A61O.01 1 0 1 1 0 0
#> TCGA.CV.A45X.01 2 0 1 0 1 0
#> TCGA.IQ.A6SH.01 1 0 1 1 0 0
#> TCGA.UF.A7JJ.01 2 0 1 0 1 0
#> TCGA.P3.A6T4.01 2 0 1 0 1 0
#> TCGA.UF.A7JK.01 1 0 1 1 0 0
#> TCGA.HD.7831.01 3 0 1 0 0 1
#> TCGA.D6.A6EQ.01 1 0 1 1 0 0
#> TCGA.CV.A6K2.01 2 0 1 0 1 0
#> TCGA.CV.A6K1.01 1 0 1 1 0 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.CV.6937.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.CN.5358.01 4 0.6594 0.775 0.00 0.24 0.14 0.62
#> TCGA.CR.7372.01 2 0.4713 0.328 0.36 0.64 0.00 0.00
#> TCGA.CV.5444.01 2 0.0000 0.706 0.00 1.00 0.00 0.00
#> TCGA.CV.5436.01 2 0.3975 0.601 0.00 0.76 0.00 0.24
#> TCGA.CV.6961.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.BB.4227.01 1 0.4134 0.758 0.74 0.00 0.00 0.26
#> TCGA.F7.A623.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.T3.A92M.01 4 0.5355 0.872 0.00 0.36 0.02 0.62
#> TCGA.CV.A468.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.QK.AA3K.01 4 0.4790 0.851 0.00 0.38 0.00 0.62
#> TCGA.4P.AA8J.01 4 0.5355 0.872 0.00 0.36 0.02 0.62
#> TCGA.CV.A460.01 2 0.2647 0.620 0.00 0.88 0.00 0.12
#> TCGA.BA.A4II.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.F7.A50I.01 2 0.2647 0.620 0.00 0.88 0.00 0.12
#> TCGA.IQ.A61O.01 1 0.2647 0.808 0.88 0.12 0.00 0.00
#> TCGA.CV.A45X.01 2 0.4134 0.522 0.26 0.74 0.00 0.00
#> TCGA.IQ.A6SH.01 1 0.0707 0.850 0.98 0.02 0.00 0.00
#> TCGA.UF.A7JJ.01 4 0.5355 0.872 0.00 0.36 0.02 0.62
#> TCGA.P3.A6T4.01 4 0.4713 0.858 0.00 0.36 0.00 0.64
#> TCGA.UF.A7JK.01 1 0.4134 0.758 0.74 0.00 0.00 0.26
#> TCGA.HD.7831.01 4 0.6201 0.575 0.00 0.08 0.30 0.62
#> TCGA.D6.A6EQ.01 1 0.2345 0.822 0.90 0.10 0.00 0.00
#> TCGA.CV.A6K2.01 2 0.0000 0.706 0.00 1.00 0.00 0.00
#> TCGA.CV.A6K1.01 1 0.0707 0.850 0.98 0.02 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CV.6937.01 3 0.0000 0.974 0.00 0.00 1.00 0.00 0.00
#> TCGA.CN.5358.01 4 0.0000 0.968 0.00 0.00 0.00 1.00 0.00
#> TCGA.CR.7372.01 2 0.4540 0.345 0.34 0.64 0.00 0.00 0.02
#> TCGA.CV.5444.01 2 0.2516 0.757 0.00 0.86 0.00 0.14 0.00
#> TCGA.CV.5436.01 5 0.4818 0.000 0.00 0.46 0.00 0.02 0.52
#> TCGA.CV.6961.01 3 0.2280 0.888 0.00 0.00 0.88 0.00 0.12
#> TCGA.BB.4227.01 1 0.3983 0.672 0.66 0.00 0.00 0.00 0.34
#> TCGA.F7.A623.01 3 0.0000 0.974 0.00 0.00 1.00 0.00 0.00
#> TCGA.T3.A92M.01 4 0.0000 0.968 0.00 0.00 0.00 1.00 0.00
#> TCGA.CV.A468.01 3 0.0000 0.974 0.00 0.00 1.00 0.00 0.00
#> TCGA.QK.AA3K.01 4 0.1410 0.911 0.00 0.06 0.00 0.94 0.00
#> TCGA.4P.AA8J.01 4 0.0000 0.968 0.00 0.00 0.00 1.00 0.00
#> TCGA.CV.A460.01 2 0.2732 0.747 0.00 0.84 0.00 0.16 0.00
#> TCGA.BA.A4II.01 3 0.0000 0.974 0.00 0.00 1.00 0.00 0.00
#> TCGA.F7.A50I.01 2 0.2732 0.747 0.00 0.84 0.00 0.16 0.00
#> TCGA.IQ.A61O.01 1 0.1216 0.826 0.96 0.02 0.00 0.00 0.02
#> TCGA.CV.A45X.01 2 0.3106 0.594 0.14 0.84 0.00 0.00 0.02
#> TCGA.IQ.A6SH.01 1 0.0000 0.837 1.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A7JJ.01 4 0.0000 0.968 0.00 0.00 0.00 1.00 0.00
#> TCGA.P3.A6T4.01 4 0.0609 0.957 0.00 0.02 0.00 0.98 0.00
#> TCGA.UF.A7JK.01 1 0.4456 0.672 0.66 0.02 0.00 0.00 0.32
#> TCGA.HD.7831.01 4 0.1410 0.904 0.00 0.00 0.06 0.94 0.00
#> TCGA.D6.A6EQ.01 1 0.1216 0.826 0.96 0.02 0.00 0.00 0.02
#> TCGA.CV.A6K2.01 2 0.3106 0.755 0.00 0.84 0.00 0.14 0.02
#> TCGA.CV.A6K1.01 1 0.0000 0.837 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.CV.6937.01 3 0.0000 0.950 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CN.5358.01 4 0.0000 0.862 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CR.7372.01 1 0.3309 0.514 0.72 0.28 0.00 0.00 0.00 0.00
#> TCGA.CV.5444.01 2 0.0547 0.980 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.CV.5436.01 5 0.1814 0.000 0.00 0.10 0.00 0.00 0.90 0.00
#> TCGA.CV.6961.01 3 0.3475 0.798 0.14 0.00 0.80 0.00 0.06 0.00
#> TCGA.BB.4227.01 6 0.0547 0.985 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.F7.A623.01 3 0.0547 0.943 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.T3.A92M.01 4 0.2048 0.825 0.12 0.00 0.00 0.88 0.00 0.00
#> TCGA.CV.A468.01 3 0.0000 0.950 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.QK.AA3K.01 4 0.5555 0.278 0.14 0.38 0.00 0.48 0.00 0.00
#> TCGA.4P.AA8J.01 4 0.0000 0.862 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.A460.01 2 0.0000 0.972 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A4II.01 3 0.0000 0.950 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.F7.A50I.01 2 0.0547 0.955 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.IQ.A61O.01 1 0.3309 0.854 0.72 0.00 0.00 0.00 0.00 0.28
#> TCGA.CV.A45X.01 2 0.0547 0.980 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.IQ.A6SH.01 1 0.3409 0.847 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.UF.A7JJ.01 4 0.0000 0.862 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.P3.A6T4.01 4 0.2581 0.815 0.12 0.02 0.00 0.86 0.00 0.00
#> TCGA.UF.A7JK.01 6 0.0000 0.985 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.HD.7831.01 4 0.0000 0.862 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D6.A6EQ.01 1 0.3309 0.854 0.72 0.00 0.00 0.00 0.00 0.28
#> TCGA.CV.A6K2.01 2 0.0547 0.980 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.CV.A6K1.01 1 0.3409 0.847 0.70 0.00 0.00 0.00 0.00 0.30
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.CV.6937.01 3 0.0000 0.920 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.CN.5358.01 4 0.3496 1.000 0.00 0.00 0.00 0.58 0 0.00 0.42
#> TCGA.CR.7372.01 1 0.3841 0.564 0.68 0.28 0.00 0.04 0 0.00 0.00
#> TCGA.CV.5444.01 2 0.0000 0.937 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.CV.5436.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.CV.6961.01 3 0.4348 0.642 0.00 0.00 0.68 0.18 0 0.14 0.00
#> TCGA.BB.4227.01 6 0.2832 0.968 0.24 0.00 0.00 0.00 0 0.76 0.00
#> TCGA.F7.A623.01 3 0.0504 0.913 0.00 0.00 0.98 0.00 0 0.02 0.00
#> TCGA.T3.A92M.01 7 0.2422 0.134 0.00 0.00 0.00 0.18 0 0.00 0.82
#> TCGA.CV.A468.01 3 0.0000 0.920 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.QK.AA3K.01 7 0.5897 0.329 0.00 0.26 0.00 0.20 0 0.04 0.50
#> TCGA.4P.AA8J.01 4 0.3496 1.000 0.00 0.00 0.00 0.58 0 0.00 0.42
#> TCGA.CV.A460.01 2 0.1433 0.916 0.00 0.92 0.00 0.00 0 0.00 0.08
#> TCGA.BA.A4II.01 3 0.0000 0.920 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.F7.A50I.01 2 0.1928 0.903 0.00 0.90 0.00 0.00 0 0.02 0.08
#> TCGA.IQ.A61O.01 1 0.1718 0.819 0.92 0.04 0.00 0.04 0 0.00 0.00
#> TCGA.CV.A45X.01 2 0.0863 0.911 0.00 0.96 0.00 0.04 0 0.00 0.00
#> TCGA.IQ.A6SH.01 1 0.0504 0.829 0.98 0.00 0.00 0.02 0 0.00 0.00
#> TCGA.UF.A7JJ.01 4 0.3496 1.000 0.00 0.00 0.00 0.58 0 0.00 0.42
#> TCGA.P3.A6T4.01 7 0.0863 0.415 0.00 0.00 0.00 0.00 0 0.04 0.96
#> TCGA.UF.A7JK.01 6 0.3637 0.968 0.24 0.00 0.00 0.04 0 0.72 0.00
#> TCGA.HD.7831.01 4 0.3496 1.000 0.00 0.00 0.00 0.58 0 0.00 0.42
#> TCGA.D6.A6EQ.01 1 0.0504 0.838 0.98 0.02 0.00 0.00 0 0.00 0.00
#> TCGA.CV.A6K2.01 2 0.0000 0.937 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.CV.A6K1.01 1 0.0863 0.821 0.96 0.00 0.00 0.04 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.CV.6937.01 3 0.000 0.875 0.00 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CN.5358.01 4 0.000 0.848 0.00 0.00 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CR.7372.01 1 0.514 0.451 0.44 0.24 0.00 0.00 0 0.32 0.00 0.00
#> TCGA.CV.5444.01 2 0.000 0.876 0.00 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.CV.5436.01 5 0.000 0.000 0.00 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.CV.6961.01 3 0.391 0.526 0.00 0.00 0.58 0.00 0 0.38 0.04 0.00
#> TCGA.BB.4227.01 8 0.156 0.899 0.10 0.00 0.00 0.00 0 0.00 0.00 0.90
#> TCGA.F7.A623.01 3 0.216 0.825 0.00 0.00 0.88 0.00 0 0.00 0.06 0.06
#> TCGA.T3.A92M.01 4 0.327 -0.103 0.00 0.00 0.00 0.58 0 0.00 0.42 0.00
#> TCGA.CV.A468.01 3 0.000 0.875 0.00 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.QK.AA3K.01 7 0.623 0.431 0.00 0.10 0.00 0.14 0 0.20 0.52 0.04
#> TCGA.4P.AA8J.01 4 0.000 0.848 0.00 0.00 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CV.A460.01 2 0.241 0.838 0.00 0.86 0.00 0.00 0 0.06 0.08 0.00
#> TCGA.BA.A4II.01 3 0.000 0.875 0.00 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.F7.A50I.01 2 0.241 0.838 0.00 0.86 0.00 0.00 0 0.06 0.08 0.00
#> TCGA.IQ.A61O.01 1 0.276 0.732 0.74 0.00 0.00 0.00 0 0.26 0.00 0.00
#> TCGA.CV.A45X.01 2 0.156 0.842 0.00 0.90 0.00 0.00 0 0.10 0.00 0.00
#> TCGA.IQ.A6SH.01 1 0.000 0.727 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.UF.A7JJ.01 4 0.000 0.848 0.00 0.00 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.P3.A6T4.01 7 0.375 0.341 0.00 0.04 0.00 0.32 0 0.00 0.64 0.00
#> TCGA.UF.A7JK.01 8 0.363 0.899 0.10 0.00 0.00 0.00 0 0.04 0.08 0.78
#> TCGA.HD.7831.01 4 0.000 0.848 0.00 0.00 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.D6.A6EQ.01 1 0.227 0.752 0.82 0.00 0.00 0.00 0 0.18 0.00 0.00
#> TCGA.CV.A6K2.01 2 0.109 0.865 0.00 0.94 0.00 0.00 0 0.06 0.00 0.00
#> TCGA.CV.A6K1.01 1 0.109 0.694 0.94 0.00 0.00 0.00 0 0.06 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-leaf , Node021 , Node022 , Node023 , Node031-leaf , Node032-leaf , Node033 , Node034-leaf , Node041-leaf , Node042-leaf , Node043 , Node051 , Node052 , Node053-leaf .
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 268 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 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 0.999 0.999 0.4487 0.552 0.552
#> 3 3 1.000 0.977 0.981 0.4571 0.790 0.619
#> 4 4 0.792 0.805 0.807 0.1080 0.939 0.822
#> 5 5 0.729 0.707 0.782 0.0663 0.899 0.657
#> 6 6 0.735 0.653 0.785 0.0486 0.947 0.762
#> 7 7 0.735 0.590 0.768 0.0263 0.950 0.762
#> 8 8 0.778 0.647 0.765 0.0260 0.928 0.635
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.CQ.5327.01 1 0.00 1.000 1.00 0.00
#> TCGA.HD.7753.01 2 0.00 0.999 0.00 1.00
#> TCGA.CQ.5325.01 2 0.00 0.999 0.00 1.00
#> TCGA.CR.7391.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.7415.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.6011.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.6436.01 2 0.00 0.999 0.00 1.00
#> TCGA.DQ.7592.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.7416.01 1 0.00 1.000 1.00 0.00
#> TCGA.H7.7774.01 1 0.00 1.000 1.00 0.00
#> TCGA.CQ.5330.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.7427.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.5979.01 2 0.00 0.999 0.00 1.00
#> TCGA.CQ.6221.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.7425.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.6441.01 2 0.00 0.999 0.00 1.00
#> TCGA.IQ.7630.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.5977.01 2 0.00 0.999 0.00 1.00
#> TCGA.CQ.5324.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.7407.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.5971.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.5970.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.6016.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.6003.01 1 0.00 1.000 1.00 0.00
#> TCGA.CN.6021.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.5434.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.6017.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.7235.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.5439.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.6020.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.7423.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.6023.01 2 0.00 0.999 0.00 1.00
#> TCGA.CR.7365.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.6024.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.5978.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.7089.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.6018.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.5966.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.5976.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.7411.01 1 0.00 1.000 1.00 0.00
#> TCGA.CQ.5323.01 2 0.00 0.999 0.00 1.00
#> TCGA.BB.4217.01 2 0.00 0.999 0.00 1.00
#> TCGA.CQ.7068.01 1 0.00 1.000 1.00 0.00
#> TCGA.CN.6995.01 2 0.00 0.999 0.00 1.00
#> TCGA.CQ.5334.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.7410.01 2 0.00 0.999 0.00 1.00
#> TCGA.DQ.7588.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.5973.01 1 0.00 1.000 1.00 0.00
#> TCGA.DQ.7591.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.5430.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.5435.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.5440.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.7104.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.7100.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.7095.01 1 0.00 1.000 1.00 0.00
#> TCGA.CR.7373.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.7178.01 1 0.00 1.000 1.00 0.00
#> TCGA.CN.6998.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.7252.01 1 0.00 1.000 1.00 0.00
#> TCGA.CR.6478.01 1 0.00 1.000 1.00 0.00
#> TCGA.CR.7380.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.7183.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.7102.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.7254.01 2 0.00 0.999 0.00 1.00
#> TCGA.CR.7394.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.6955.01 1 0.00 1.000 1.00 0.00
#> TCGA.BA.5556.01 1 0.00 1.000 1.00 0.00
#> TCGA.CR.7386.01 2 0.00 0.999 0.00 1.00
#> TCGA.CR.6474.01 2 0.00 0.999 0.00 1.00
#> TCGA.BA.5557.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.7247.01 2 0.00 0.999 0.00 1.00
#> TCGA.CR.7377.01 2 0.00 0.999 0.00 1.00
#> TCGA.HD.7229.01 2 0.00 0.999 0.00 1.00
#> TCGA.D6.6515.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.7238.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.7097.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.5370.01 2 0.00 0.999 0.00 1.00
#> TCGA.CR.7367.01 2 0.00 0.999 0.00 1.00
#> TCGA.CR.7401.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.6942.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.7177.01 1 0.00 1.000 1.00 0.00
#> TCGA.CR.7395.01 1 0.00 1.000 1.00 0.00
#> TCGA.BA.5558.01 2 0.00 0.999 0.00 1.00
#> TCGA.CX.7085.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.7099.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.7090.01 2 0.00 0.999 0.00 1.00
#> TCGA.CX.7219.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.7243.01 2 0.00 0.999 0.00 1.00
#> TCGA.BA.6871.01 2 0.00 0.999 0.00 1.00
#> TCGA.CQ.6218.01 1 0.00 1.000 1.00 0.00
#> TCGA.C9.A47Z.01 1 0.00 1.000 1.00 0.00
#> TCGA.DQ.5625.01 1 0.00 1.000 1.00 0.00
#> TCGA.CR.6480.01 2 0.00 0.999 0.00 1.00
#> TCGA.D6.6825.01 2 0.00 0.999 0.00 1.00
#> TCGA.C9.A480.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.6952.01 1 0.00 1.000 1.00 0.00
#> TCGA.CQ.6222.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.A49C.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.6994.01 2 0.00 0.999 0.00 1.00
#> TCGA.CR.6491.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.6950.01 2 0.00 0.999 0.00 1.00
#> TCGA.CR.6473.01 2 0.00 0.999 0.00 1.00
#> TCGA.CQ.5331.01 1 0.00 1.000 1.00 0.00
#> TCGA.D6.6826.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.6935.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.6953.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.6945.01 2 0.00 0.999 0.00 1.00
#> TCGA.DQ.5630.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.6943.01 2 0.00 0.999 0.00 1.00
#> TCGA.BA.6870.01 1 0.00 1.000 1.00 0.00
#> TCGA.CR.6477.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.A45O.01 2 0.00 0.999 0.00 1.00
#> TCGA.CQ.6219.01 1 0.00 1.000 1.00 0.00
#> TCGA.CN.4733.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.A498.01 1 0.00 1.000 1.00 0.00
#> TCGA.CN.6989.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.6953.11 1 0.00 1.000 1.00 0.00
#> TCGA.D6.6517.01 2 0.00 0.999 0.00 1.00
#> TCGA.CQ.6220.01 2 0.00 0.999 0.00 1.00
#> TCGA.HD.A4C1.01 1 0.00 1.000 1.00 0.00
#> TCGA.CR.6493.01 2 0.00 0.999 0.00 1.00
#> TCGA.D6.6516.01 2 0.00 0.999 0.00 1.00
#> TCGA.CQ.6227.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.A45P.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.A45Q.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.A45T.01 1 0.00 1.000 1.00 0.00
#> TCGA.CN.6996.01 1 0.00 1.000 1.00 0.00
#> TCGA.BA.6873.01 2 0.00 0.999 0.00 1.00
#> TCGA.CR.6467.01 2 0.00 0.999 0.00 1.00
#> TCGA.BA.6868.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.6959.01 2 0.00 0.999 0.00 1.00
#> TCGA.CQ.6229.01 2 0.00 0.999 0.00 1.00
#> TCGA.CQ.6224.01 2 0.00 0.999 0.00 1.00
#> TCGA.CQ.6223.01 2 0.00 0.999 0.00 1.00
#> TCGA.DQ.5624.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.A45R.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.A499.01 1 0.00 1.000 1.00 0.00
#> TCGA.CN.A49B.01 2 0.00 0.999 0.00 1.00
#> TCGA.BA.5152.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.6938.01 2 0.00 0.999 0.00 1.00
#> TCGA.CQ.5326.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.6940.01 1 0.00 1.000 1.00 0.00
#> TCGA.CR.6471.01 2 0.00 0.999 0.00 1.00
#> TCGA.BA.6872.01 2 0.00 0.999 0.00 1.00
#> TCGA.CQ.A4C6.01 2 0.00 0.999 0.00 1.00
#> TCGA.CQ.7064.01 1 0.00 1.000 1.00 0.00
#> TCGA.IQ.A61K.01 1 0.00 1.000 1.00 0.00
#> TCGA.HD.A633.01 2 0.00 0.999 0.00 1.00
#> TCGA.F7.A61W.01 2 0.00 0.999 0.00 1.00
#> TCGA.BA.A6DF.01 1 0.00 1.000 1.00 0.00
#> TCGA.D6.A4ZB.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.A45Y.01 2 0.00 0.999 0.00 1.00
#> TCGA.BB.A5HU.01 2 0.00 0.999 0.00 1.00
#> TCGA.CQ.A4C7.01 2 0.00 0.999 0.00 1.00
#> TCGA.P3.A5Q6.01 2 0.00 0.999 0.00 1.00
#> TCGA.CQ.A4CD.01 2 0.00 0.999 0.00 1.00
#> TCGA.BA.A6DB.01 1 0.00 1.000 1.00 0.00
#> TCGA.F7.A620.01 2 0.00 0.999 0.00 1.00
#> TCGA.CX.A4AQ.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.A464.01 2 0.00 0.999 0.00 1.00
#> TCGA.IQ.A61L.01 1 0.00 1.000 1.00 0.00
#> TCGA.QK.A8Z9.01 2 0.00 0.999 0.00 1.00
#> TCGA.BB.A5HY.01 2 0.00 0.999 0.00 1.00
#> TCGA.HD.8635.01 1 0.00 1.000 1.00 0.00
#> TCGA.QK.A652.01 2 0.00 0.999 0.00 1.00
#> TCGA.MT.A67G.01 1 0.00 1.000 1.00 0.00
#> TCGA.QK.A64Z.01 1 0.00 1.000 1.00 0.00
#> TCGA.HD.8634.01 1 0.00 1.000 1.00 0.00
#> TCGA.CQ.7063.01 1 0.00 1.000 1.00 0.00
#> TCGA.F7.A50J.01 1 0.00 1.000 1.00 0.00
#> TCGA.F7.8298.01 2 0.00 0.999 0.00 1.00
#> TCGA.F7.8489.01 2 0.00 0.999 0.00 1.00
#> TCGA.F7.A50G.01 2 0.00 0.999 0.00 1.00
#> TCGA.CQ.A4CA.01 2 0.00 0.999 0.00 1.00
#> TCGA.T3.A92N.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.A63Y.01 2 0.00 0.999 0.00 1.00
#> TCGA.CQ.5333.01 2 0.00 0.999 0.00 1.00
#> TCGA.P3.A5QE.01 2 0.00 0.999 0.00 1.00
#> TCGA.BA.A6DJ.01 2 0.68 0.780 0.18 0.82
#> TCGA.MT.A51W.01 1 0.00 1.000 1.00 0.00
#> TCGA.IQ.A61G.01 2 0.00 0.999 0.00 1.00
#> TCGA.IQ.A61J.01 2 0.00 0.999 0.00 1.00
#> TCGA.BA.A6DG.01 2 0.00 0.999 0.00 1.00
#> TCGA.CQ.A4CH.01 2 0.00 0.999 0.00 1.00
#> TCGA.CQ.A4CB.01 2 0.00 0.999 0.00 1.00
#> TCGA.D6.8569.01 2 0.00 0.999 0.00 1.00
#> TCGA.IQ.A61I.01 2 0.00 0.999 0.00 1.00
#> TCGA.D6.A4Z9.01 2 0.00 0.999 0.00 1.00
#> TCGA.CQ.7071.01 1 0.00 1.000 1.00 0.00
#> TCGA.H7.8501.01 2 0.00 0.999 0.00 1.00
#> TCGA.BB.8601.01 2 0.00 0.999 0.00 1.00
#> TCGA.H7.8502.01 2 0.00 0.999 0.00 1.00
#> TCGA.F7.A61S.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.A463.01 1 0.00 1.000 1.00 0.00
#> TCGA.D6.8568.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.A642.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.5367.01 1 0.00 1.000 1.00 0.00
#> TCGA.P3.A6T2.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.A6V7.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.A640.01 1 0.00 1.000 1.00 0.00
#> TCGA.DQ.7589.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.4725.01 2 0.00 0.999 0.00 1.00
#> TCGA.HL.7533.01 2 0.00 0.999 0.00 1.00
#> TCGA.UF.A7JO.01 1 0.00 1.000 1.00 0.00
#> TCGA.UF.A7JV.01 1 0.00 1.000 1.00 0.00
#> TCGA.CN.4729.01 2 0.00 0.999 0.00 1.00
#> TCGA.IQ.A6SG.01 1 0.00 1.000 1.00 0.00
#> TCGA.MT.A67A.01 1 0.00 1.000 1.00 0.00
#> TCGA.CN.5361.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.5359.01 2 0.00 0.999 0.00 1.00
#> TCGA.BB.7861.01 2 0.00 0.999 0.00 1.00
#> TCGA.BB.A6UO.01 1 0.00 1.000 1.00 0.00
#> TCGA.CN.4734.01 2 0.00 0.999 0.00 1.00
#> TCGA.BA.4075.01 2 0.00 0.999 0.00 1.00
#> TCGA.BB.7871.01 1 0.00 1.000 1.00 0.00
#> TCGA.CN.4726.01 2 0.00 0.999 0.00 1.00
#> TCGA.UF.A7JS.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.4736.01 1 0.00 1.000 1.00 0.00
#> TCGA.CN.5355.01 2 0.00 0.999 0.00 1.00
#> TCGA.DQ.7590.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.5369.01 1 0.00 1.000 1.00 0.00
#> TCGA.BA.5151.01 2 0.00 0.999 0.00 1.00
#> TCGA.IQ.A61E.01 1 0.00 1.000 1.00 0.00
#> TCGA.BA.4076.01 2 0.00 0.999 0.00 1.00
#> TCGA.MZ.A7D7.01 2 0.00 0.999 0.00 1.00
#> TCGA.UF.A7JT.01 1 0.00 1.000 1.00 0.00
#> TCGA.CN.5373.01 1 0.00 1.000 1.00 0.00
#> TCGA.BB.7863.01 1 0.00 1.000 1.00 0.00
#> TCGA.CN.5363.01 2 0.00 0.999 0.00 1.00
#> TCGA.BA.4077.01 1 0.00 1.000 1.00 0.00
#> TCGA.BB.7872.01 2 0.00 0.999 0.00 1.00
#> TCGA.H7.A6C4.01 1 0.00 1.000 1.00 0.00
#> TCGA.T2.A6X2.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.4741.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.A6JO.01 2 0.00 0.999 0.00 1.00
#> TCGA.BB.7866.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.5365.01 2 0.00 0.999 0.00 1.00
#> TCGA.BB.4224.01 2 0.00 0.999 0.00 1.00
#> TCGA.MT.A67F.01 1 0.00 1.000 1.00 0.00
#> TCGA.CN.5366.01 2 0.00 0.999 0.00 1.00
#> TCGA.QK.A6V9.01 2 0.00 0.999 0.00 1.00
#> TCGA.T2.A6WX.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.A6JZ.01 2 0.00 0.999 0.00 1.00
#> TCGA.CN.A6V1.01 2 0.00 0.999 0.00 1.00
#> TCGA.HD.A6I0.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.7430.01 2 0.00 0.999 0.00 1.00
#> TCGA.CR.7383.01 1 0.00 1.000 1.00 0.00
#> TCGA.UF.A7JC.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.7568.01 2 0.00 0.999 0.00 1.00
#> TCGA.QK.A6IF.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.A6JT.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.7438.01 1 0.00 1.000 1.00 0.00
#> TCGA.D6.A6EN.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.7429.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.7437.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.A6JD.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.A6JN.01 2 0.00 0.999 0.00 1.00
#> TCGA.CV.7434.01 2 0.00 0.999 0.00 1.00
#> TCGA.D6.A6EK.01 2 0.00 0.999 0.00 1.00
#> TCGA.HD.7832.01 2 0.00 0.999 0.00 1.00
#> TCGA.P3.A6SX.01 2 0.00 0.999 0.00 1.00
#> TCGA.QK.A6II.01 2 0.00 0.999 0.00 1.00
#> TCGA.P3.A6T7.01 2 0.00 0.999 0.00 1.00
#> TCGA.CR.7382.01 2 0.00 0.999 0.00 1.00
#> TCGA.T2.A6WZ.01 2 0.00 0.999 0.00 1.00
#> TCGA.P3.A6T5.01 1 0.00 1.000 1.00 0.00
#> TCGA.CV.7433.01 2 0.00 0.999 0.00 1.00
#> TCGA.CR.7376.01 2 0.00 0.999 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CQ.5327.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.HD.7753.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CQ.5325.01 2 0.0892 0.9745 0.00 0.98 0.02
#> TCGA.CR.7391.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CV.7415.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CN.6011.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.6436.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.DQ.7592.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.7416.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.H7.7774.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.CQ.5330.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.CV.7427.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.CV.5979.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CQ.6221.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.7425.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.CV.6441.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.IQ.7630.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CV.5977.01 3 0.0000 0.9496 0.00 0.00 1.00
#> TCGA.CQ.5324.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CV.7407.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CV.5971.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.5970.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CN.6016.01 2 0.2959 0.8859 0.00 0.90 0.10
#> TCGA.CV.6003.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CN.6021.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CV.5434.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CN.6017.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.7235.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.5439.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CN.6020.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.7423.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CN.6023.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CR.7365.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CN.6024.01 2 0.0892 0.9745 0.00 0.98 0.02
#> TCGA.CV.5978.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CV.7089.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CN.6018.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CV.5966.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.CV.5976.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CV.7411.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CQ.5323.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.BB.4217.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CQ.7068.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.CN.6995.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CQ.5334.01 3 0.0000 0.9496 0.00 0.00 1.00
#> TCGA.CV.7410.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.DQ.7588.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.5973.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.DQ.7591.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.5430.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.5435.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CV.5440.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.7104.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CV.7100.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.7095.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.CR.7373.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CV.7178.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CN.6998.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CV.7252.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.CR.6478.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CR.7380.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CV.7183.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CV.7102.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CV.7254.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CR.7394.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CV.6955.01 1 0.0892 0.9839 0.98 0.00 0.02
#> TCGA.BA.5556.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.CR.7386.01 2 0.4002 0.8048 0.00 0.84 0.16
#> TCGA.CR.6474.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.BA.5557.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CV.7247.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CR.7377.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.HD.7229.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.D6.6515.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CV.7238.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CV.7097.01 3 0.0892 0.9656 0.00 0.02 0.98
#> TCGA.CN.5370.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CR.7367.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CR.7401.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.6942.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.CV.7177.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CR.7395.01 1 0.0892 0.9839 0.98 0.00 0.02
#> TCGA.BA.5558.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CX.7085.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CV.7099.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.CV.7090.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CX.7219.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.7243.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.BA.6871.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CQ.6218.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.C9.A47Z.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.DQ.5625.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CR.6480.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.D6.6825.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.C9.A480.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CV.6952.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.CQ.6222.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CN.A49C.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CN.6994.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CR.6491.01 3 0.0000 0.9496 0.00 0.00 1.00
#> TCGA.CV.6950.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CR.6473.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CQ.5331.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.D6.6826.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.CV.6935.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.6953.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.CV.6945.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.DQ.5630.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.6943.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.BA.6870.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CR.6477.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CV.A45O.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CQ.6219.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CN.4733.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CN.A498.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CN.6989.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.6953.11 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.D6.6517.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CQ.6220.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.HD.A4C1.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.CR.6493.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.D6.6516.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CQ.6227.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.A45P.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CV.A45Q.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.CV.A45T.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CN.6996.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.BA.6873.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CR.6467.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.BA.6868.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.6959.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CQ.6229.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CQ.6224.01 3 0.3686 0.8721 0.00 0.14 0.86
#> TCGA.CQ.6223.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.DQ.5624.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CV.A45R.01 2 0.2066 0.9328 0.00 0.94 0.06
#> TCGA.CN.A499.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CN.A49B.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.BA.5152.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.6938.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CQ.5326.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.6940.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CR.6471.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.BA.6872.01 3 0.6309 0.0677 0.00 0.50 0.50
#> TCGA.CQ.A4C6.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CQ.7064.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.IQ.A61K.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.HD.A633.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.F7.A61W.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.BA.A6DF.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.D6.A4ZB.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.A45Y.01 2 0.1529 0.9550 0.00 0.96 0.04
#> TCGA.BB.A5HU.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CQ.A4C7.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.P3.A5Q6.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CQ.A4CD.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.BA.A6DB.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.F7.A620.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CX.A4AQ.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.A464.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.IQ.A61L.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.QK.A8Z9.01 3 0.5216 0.6937 0.00 0.26 0.74
#> TCGA.BB.A5HY.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.HD.8635.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.QK.A652.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.MT.A67G.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.QK.A64Z.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.HD.8634.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CQ.7063.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.F7.A50J.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.F7.8298.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.F7.8489.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.F7.A50G.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CQ.A4CA.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.T3.A92N.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CN.A63Y.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CQ.5333.01 3 0.0000 0.9496 0.00 0.00 1.00
#> TCGA.P3.A5QE.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.BA.A6DJ.01 3 0.0000 0.9496 0.00 0.00 1.00
#> TCGA.MT.A51W.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.IQ.A61G.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.IQ.A61J.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.BA.A6DG.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CQ.A4CH.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CQ.A4CB.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.D6.8569.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.IQ.A61I.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.D6.A4Z9.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CQ.7071.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.H7.8501.01 3 0.0892 0.9656 0.00 0.02 0.98
#> TCGA.BB.8601.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.H7.8502.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.F7.A61S.01 2 0.4555 0.7400 0.00 0.80 0.20
#> TCGA.CV.A463.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.D6.8568.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CN.A642.01 3 0.0000 0.9496 0.00 0.00 1.00
#> TCGA.CN.5367.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.P3.A6T2.01 3 0.0000 0.9496 0.00 0.00 1.00
#> TCGA.CN.A6V7.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CN.A640.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.DQ.7589.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CN.4725.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.HL.7533.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.UF.A7JO.01 1 0.0892 0.9839 0.98 0.00 0.02
#> TCGA.UF.A7JV.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CN.4729.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.IQ.A6SG.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.MT.A67A.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.CN.5361.01 2 0.0892 0.9745 0.00 0.98 0.02
#> TCGA.CN.5359.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.BB.7861.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.BB.A6UO.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.CN.4734.01 3 0.0000 0.9496 0.00 0.00 1.00
#> TCGA.BA.4075.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.BB.7871.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CN.4726.01 3 0.0892 0.9656 0.00 0.02 0.98
#> TCGA.UF.A7JS.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CN.4736.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CN.5355.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.DQ.7590.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CN.5369.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.BA.5151.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.IQ.A61E.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.BA.4076.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.MZ.A7D7.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.UF.A7JT.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.CN.5373.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.BB.7863.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.CN.5363.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.BA.4077.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.BB.7872.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.H7.A6C4.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.T2.A6X2.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CN.4741.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CV.A6JO.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.BB.7866.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CN.5365.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.BB.4224.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.MT.A67F.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.CN.5366.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.QK.A6V9.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.T2.A6WX.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.CV.A6JZ.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CN.A6V1.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.HD.A6I0.01 3 0.0000 0.9496 0.00 0.00 1.00
#> TCGA.CV.7430.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CR.7383.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.UF.A7JC.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.7568.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.QK.A6IF.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.A6JT.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CV.7438.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.D6.A6EN.01 3 0.0000 0.9496 0.00 0.00 1.00
#> TCGA.CV.7429.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.7437.01 2 0.2066 0.9337 0.00 0.94 0.06
#> TCGA.CV.A6JD.01 1 0.1529 0.9793 0.96 0.00 0.04
#> TCGA.CV.A6JN.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CV.7434.01 3 0.0892 0.9656 0.00 0.02 0.98
#> TCGA.D6.A6EK.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.HD.7832.01 3 0.0000 0.9496 0.00 0.00 1.00
#> TCGA.P3.A6SX.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.QK.A6II.01 2 0.2066 0.9335 0.00 0.94 0.06
#> TCGA.P3.A6T7.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.CR.7382.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.T2.A6WZ.01 3 0.1529 0.9788 0.00 0.04 0.96
#> TCGA.P3.A6T5.01 1 0.0000 0.9879 1.00 0.00 0.00
#> TCGA.CV.7433.01 2 0.0000 0.9928 0.00 1.00 0.00
#> TCGA.CR.7376.01 2 0.0000 0.9928 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.CQ.5327.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.HD.7753.01 2 0.1211 0.81871 0.00 0.96 0.00 0.04
#> TCGA.CQ.5325.01 2 0.1211 0.79660 0.00 0.96 0.04 0.00
#> TCGA.CR.7391.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CV.7415.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.CN.6011.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.CV.6436.01 3 0.4406 0.66364 0.00 0.30 0.70 0.00
#> TCGA.DQ.7592.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.CV.7416.01 4 0.5000 0.85926 0.50 0.00 0.00 0.50
#> TCGA.H7.7774.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.CQ.5330.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.CV.7427.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.CV.5979.01 2 0.0707 0.81086 0.00 0.98 0.02 0.00
#> TCGA.CQ.6221.01 2 0.4277 0.79390 0.00 0.72 0.00 0.28
#> TCGA.CV.7425.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.CV.6441.01 3 0.1637 0.91576 0.00 0.00 0.94 0.06
#> TCGA.IQ.7630.01 3 0.3975 0.73771 0.00 0.24 0.76 0.00
#> TCGA.CV.5977.01 3 0.0707 0.92944 0.00 0.00 0.98 0.02
#> TCGA.CQ.5324.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.CV.7407.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CV.5971.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.CV.5970.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.CN.6016.01 2 0.1637 0.77956 0.00 0.94 0.06 0.00
#> TCGA.CV.6003.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CN.6021.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CV.5434.01 2 0.4948 0.74945 0.00 0.56 0.00 0.44
#> TCGA.CN.6017.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.CV.7235.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.CV.5439.01 2 0.3172 0.80955 0.00 0.84 0.00 0.16
#> TCGA.CN.6020.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.CV.7423.01 2 0.0707 0.81086 0.00 0.98 0.02 0.00
#> TCGA.CN.6023.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.CR.7365.01 3 0.0707 0.92944 0.00 0.00 0.98 0.02
#> TCGA.CN.6024.01 2 0.4977 0.74014 0.00 0.54 0.00 0.46
#> TCGA.CV.5978.01 4 0.4713 0.72544 0.36 0.00 0.00 0.64
#> TCGA.CV.7089.01 3 0.0707 0.92944 0.00 0.00 0.98 0.02
#> TCGA.CN.6018.01 1 0.1211 0.81024 0.96 0.00 0.00 0.04
#> TCGA.CV.5966.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.CV.5976.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.CV.7411.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CQ.5323.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.BB.4217.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.CQ.7068.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.CN.6995.01 3 0.4134 0.71529 0.00 0.26 0.74 0.00
#> TCGA.CQ.5334.01 3 0.0707 0.92944 0.00 0.00 0.98 0.02
#> TCGA.CV.7410.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.DQ.7588.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.CV.5973.01 1 0.4522 -0.10879 0.68 0.00 0.00 0.32
#> TCGA.DQ.7591.01 2 0.4977 0.74014 0.00 0.54 0.00 0.46
#> TCGA.CV.5430.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.CV.5435.01 3 0.1637 0.91576 0.00 0.00 0.94 0.06
#> TCGA.CV.5440.01 2 0.4624 0.78393 0.00 0.66 0.00 0.34
#> TCGA.CV.7104.01 1 0.4406 0.00689 0.70 0.00 0.00 0.30
#> TCGA.CV.7100.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.CV.7095.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.CR.7373.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.CV.7178.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CN.6998.01 3 0.4855 0.50801 0.00 0.40 0.60 0.00
#> TCGA.CV.7252.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.CR.6478.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CR.7380.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.CV.7183.01 3 0.3610 0.77910 0.00 0.20 0.80 0.00
#> TCGA.CV.7102.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CV.7254.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.CR.7394.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CV.6955.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.BA.5556.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.CR.7386.01 2 0.3610 0.60410 0.00 0.80 0.20 0.00
#> TCGA.CR.6474.01 2 0.2921 0.81192 0.00 0.86 0.00 0.14
#> TCGA.BA.5557.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CV.7247.01 2 0.4406 0.79097 0.00 0.70 0.00 0.30
#> TCGA.CR.7377.01 2 0.0707 0.81086 0.00 0.98 0.02 0.00
#> TCGA.HD.7229.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.D6.6515.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CV.7238.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CV.7097.01 3 0.0707 0.92944 0.00 0.00 0.98 0.02
#> TCGA.CN.5370.01 2 0.0707 0.81086 0.00 0.98 0.02 0.00
#> TCGA.CR.7367.01 3 0.0707 0.92944 0.00 0.00 0.98 0.02
#> TCGA.CR.7401.01 2 0.0707 0.81086 0.00 0.98 0.02 0.00
#> TCGA.CV.6942.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.CV.7177.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CR.7395.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.BA.5558.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.CX.7085.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CV.7099.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.CV.7090.01 2 0.1211 0.81866 0.00 0.96 0.00 0.04
#> TCGA.CX.7219.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.CV.7243.01 3 0.4134 0.71529 0.00 0.26 0.74 0.00
#> TCGA.BA.6871.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.CQ.6218.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.C9.A47Z.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.DQ.5625.01 1 0.4277 0.11758 0.72 0.00 0.00 0.28
#> TCGA.CR.6480.01 3 0.1637 0.91576 0.00 0.00 0.94 0.06
#> TCGA.D6.6825.01 2 0.0707 0.81086 0.00 0.98 0.02 0.00
#> TCGA.C9.A480.01 1 0.4790 -0.44111 0.62 0.00 0.00 0.38
#> TCGA.CV.6952.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.CQ.6222.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.CN.A49C.01 3 0.1637 0.91576 0.00 0.00 0.94 0.06
#> TCGA.CN.6994.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.CR.6491.01 3 0.0707 0.92944 0.00 0.00 0.98 0.02
#> TCGA.CV.6950.01 2 0.0707 0.81086 0.00 0.98 0.02 0.00
#> TCGA.CR.6473.01 3 0.1637 0.91576 0.00 0.00 0.94 0.06
#> TCGA.CQ.5331.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.D6.6826.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.CV.6935.01 2 0.4977 0.74014 0.00 0.54 0.00 0.46
#> TCGA.CV.6953.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.CV.6945.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.DQ.5630.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.CV.6943.01 2 0.0707 0.81086 0.00 0.98 0.02 0.00
#> TCGA.BA.6870.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CR.6477.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CV.A45O.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.CQ.6219.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CN.4733.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.CN.A498.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CN.6989.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.CV.6953.11 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.D6.6517.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.CQ.6220.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.HD.A4C1.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.CR.6493.01 3 0.1637 0.89527 0.00 0.06 0.94 0.00
#> TCGA.D6.6516.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.CQ.6227.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.CV.A45P.01 1 0.4522 -0.10879 0.68 0.00 0.00 0.32
#> TCGA.CV.A45Q.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.CV.A45T.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CN.6996.01 1 0.4522 -0.10879 0.68 0.00 0.00 0.32
#> TCGA.BA.6873.01 3 0.4713 0.57491 0.00 0.36 0.64 0.00
#> TCGA.CR.6467.01 3 0.1637 0.91576 0.00 0.00 0.94 0.06
#> TCGA.BA.6868.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.CV.6959.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.CQ.6229.01 2 0.0707 0.81086 0.00 0.98 0.02 0.00
#> TCGA.CQ.6224.01 3 0.4948 0.41883 0.00 0.44 0.56 0.00
#> TCGA.CQ.6223.01 2 0.0707 0.81086 0.00 0.98 0.02 0.00
#> TCGA.DQ.5624.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CV.A45R.01 2 0.1637 0.78183 0.00 0.94 0.06 0.00
#> TCGA.CN.A499.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CN.A49B.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.BA.5152.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.CV.6938.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.CQ.5326.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.CV.6940.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CR.6471.01 2 0.0707 0.81086 0.00 0.98 0.02 0.00
#> TCGA.BA.6872.01 2 0.4994 -0.16569 0.00 0.52 0.48 0.00
#> TCGA.CQ.A4C6.01 3 0.4134 0.71529 0.00 0.26 0.74 0.00
#> TCGA.CQ.7064.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.IQ.A61K.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.HD.A633.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.F7.A61W.01 2 0.4406 0.79097 0.00 0.70 0.00 0.30
#> TCGA.BA.A6DF.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.D6.A4ZB.01 2 0.5487 0.76677 0.00 0.58 0.02 0.40
#> TCGA.CV.A45Y.01 2 0.0707 0.81086 0.00 0.98 0.02 0.00
#> TCGA.BB.A5HU.01 2 0.1211 0.81866 0.00 0.96 0.00 0.04
#> TCGA.CQ.A4C7.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.P3.A5Q6.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.CQ.A4CD.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.BA.A6DB.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.F7.A620.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.CX.A4AQ.01 2 0.4948 0.74945 0.00 0.56 0.00 0.44
#> TCGA.CV.A464.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.IQ.A61L.01 1 0.4624 -0.23072 0.66 0.00 0.00 0.34
#> TCGA.QK.A8Z9.01 3 0.3198 0.83602 0.00 0.08 0.88 0.04
#> TCGA.BB.A5HY.01 3 0.1637 0.91576 0.00 0.00 0.94 0.06
#> TCGA.HD.8635.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.QK.A652.01 2 0.0707 0.81086 0.00 0.98 0.02 0.00
#> TCGA.MT.A67G.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.QK.A64Z.01 1 0.4522 -0.10879 0.68 0.00 0.00 0.32
#> TCGA.HD.8634.01 1 0.2011 0.74452 0.92 0.00 0.00 0.08
#> TCGA.CQ.7063.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.F7.A50J.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.F7.8298.01 2 0.4406 0.79158 0.00 0.70 0.00 0.30
#> TCGA.F7.8489.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.F7.A50G.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.CQ.A4CA.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.T3.A92N.01 2 0.4948 0.74945 0.00 0.56 0.00 0.44
#> TCGA.CN.A63Y.01 2 0.4406 0.79097 0.00 0.70 0.00 0.30
#> TCGA.CQ.5333.01 3 0.0707 0.92944 0.00 0.00 0.98 0.02
#> TCGA.P3.A5QE.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.BA.A6DJ.01 3 0.0707 0.92944 0.00 0.00 0.98 0.02
#> TCGA.MT.A51W.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.IQ.A61G.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.IQ.A61J.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.BA.A6DG.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.CQ.A4CH.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.CQ.A4CB.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.D6.8569.01 2 0.0707 0.81086 0.00 0.98 0.02 0.00
#> TCGA.IQ.A61I.01 3 0.1637 0.91576 0.00 0.00 0.94 0.06
#> TCGA.D6.A4Z9.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.CQ.7071.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.H7.8501.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.BB.8601.01 2 0.4948 0.74945 0.00 0.56 0.00 0.44
#> TCGA.H7.8502.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.F7.A61S.01 2 0.3172 0.66651 0.00 0.84 0.16 0.00
#> TCGA.CV.A463.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.D6.8568.01 2 0.0707 0.81086 0.00 0.98 0.02 0.00
#> TCGA.CN.A642.01 3 0.0707 0.92944 0.00 0.00 0.98 0.02
#> TCGA.CN.5367.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.P3.A6T2.01 3 0.0707 0.92944 0.00 0.00 0.98 0.02
#> TCGA.CN.A6V7.01 3 0.1637 0.91576 0.00 0.00 0.94 0.06
#> TCGA.CN.A640.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.DQ.7589.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.CN.4725.01 2 0.0707 0.81086 0.00 0.98 0.02 0.00
#> TCGA.HL.7533.01 2 0.3610 0.80460 0.00 0.80 0.00 0.20
#> TCGA.UF.A7JO.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.UF.A7JV.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CN.4729.01 2 0.0707 0.81086 0.00 0.98 0.02 0.00
#> TCGA.IQ.A6SG.01 4 0.4406 0.60394 0.30 0.00 0.00 0.70
#> TCGA.MT.A67A.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.CN.5361.01 2 0.0707 0.81086 0.00 0.98 0.02 0.00
#> TCGA.CN.5359.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.BB.7861.01 2 0.2921 0.81167 0.00 0.86 0.00 0.14
#> TCGA.BB.A6UO.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.CN.4734.01 3 0.0707 0.92944 0.00 0.00 0.98 0.02
#> TCGA.BA.4075.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.BB.7871.01 4 0.1637 0.27450 0.06 0.00 0.00 0.94
#> TCGA.CN.4726.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.UF.A7JS.01 2 0.0707 0.81086 0.00 0.98 0.02 0.00
#> TCGA.CN.4736.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CN.5355.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.DQ.7590.01 2 0.4948 0.74945 0.00 0.56 0.00 0.44
#> TCGA.CN.5369.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.BA.5151.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.IQ.A61E.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.BA.4076.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.MZ.A7D7.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.UF.A7JT.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.CN.5373.01 1 0.4522 -0.10879 0.68 0.00 0.00 0.32
#> TCGA.BB.7863.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.CN.5363.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.BA.4077.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.BB.7872.01 2 0.0707 0.81086 0.00 0.98 0.02 0.00
#> TCGA.H7.A6C4.01 1 0.0707 0.83787 0.98 0.00 0.00 0.02
#> TCGA.T2.A6X2.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.CN.4741.01 3 0.1637 0.91576 0.00 0.00 0.94 0.06
#> TCGA.CV.A6JO.01 3 0.4134 0.71529 0.00 0.26 0.74 0.00
#> TCGA.BB.7866.01 3 0.1637 0.91576 0.00 0.00 0.94 0.06
#> TCGA.CN.5365.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.BB.4224.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.MT.A67F.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.CN.5366.01 3 0.0707 0.92944 0.00 0.00 0.98 0.02
#> TCGA.QK.A6V9.01 3 0.1637 0.91576 0.00 0.00 0.94 0.06
#> TCGA.T2.A6WX.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.CV.A6JZ.01 3 0.0707 0.92944 0.00 0.00 0.98 0.02
#> TCGA.CN.A6V1.01 2 0.1211 0.81888 0.00 0.96 0.00 0.04
#> TCGA.HD.A6I0.01 3 0.0707 0.92944 0.00 0.00 0.98 0.02
#> TCGA.CV.7430.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.CR.7383.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.UF.A7JC.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.CV.7568.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.QK.A6IF.01 2 0.4713 0.77995 0.00 0.64 0.00 0.36
#> TCGA.CV.A6JT.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.CV.7438.01 1 0.4522 -0.10879 0.68 0.00 0.00 0.32
#> TCGA.D6.A6EN.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.CV.7429.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.CV.7437.01 2 0.4977 0.74014 0.00 0.54 0.00 0.46
#> TCGA.CV.A6JD.01 1 0.0000 0.86228 1.00 0.00 0.00 0.00
#> TCGA.CV.A6JN.01 2 0.0707 0.81086 0.00 0.98 0.02 0.00
#> TCGA.CV.7434.01 3 0.0707 0.92944 0.00 0.00 0.98 0.02
#> TCGA.D6.A6EK.01 2 0.0000 0.81740 0.00 1.00 0.00 0.00
#> TCGA.HD.7832.01 3 0.0707 0.92944 0.00 0.00 0.98 0.02
#> TCGA.P3.A6SX.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.QK.A6II.01 2 0.2345 0.74375 0.00 0.90 0.10 0.00
#> TCGA.P3.A6T7.01 3 0.0000 0.93079 0.00 0.00 1.00 0.00
#> TCGA.CR.7382.01 3 0.4855 0.50801 0.00 0.40 0.60 0.00
#> TCGA.T2.A6WZ.01 3 0.0707 0.92944 0.00 0.00 0.98 0.02
#> TCGA.P3.A6T5.01 4 0.4977 0.95362 0.46 0.00 0.00 0.54
#> TCGA.CV.7433.01 2 0.4855 0.77088 0.00 0.60 0.00 0.40
#> TCGA.CR.7376.01 2 0.0000 0.81740 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.CQ.5327.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.HD.7753.01 2 0.5351 0.7272 0.00 0.56 0.00 0.06 0.38
#> TCGA.CQ.5325.01 2 0.5788 0.7156 0.00 0.58 0.12 0.00 0.30
#> TCGA.CR.7391.01 4 0.3796 0.9563 0.30 0.00 0.00 0.70 0.00
#> TCGA.CV.7415.01 5 0.0609 0.7553 0.00 0.00 0.00 0.02 0.98
#> TCGA.CN.6011.01 5 0.0000 0.7624 0.00 0.00 0.00 0.00 1.00
#> TCGA.CV.6436.01 3 0.3983 0.5075 0.00 0.34 0.66 0.00 0.00
#> TCGA.DQ.7592.01 2 0.5351 0.7272 0.00 0.56 0.00 0.06 0.38
#> TCGA.CV.7416.01 4 0.4540 0.8878 0.34 0.02 0.00 0.64 0.00
#> TCGA.H7.7774.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.5330.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7427.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5979.01 2 0.3895 0.8022 0.00 0.68 0.00 0.00 0.32
#> TCGA.CQ.6221.01 5 0.5156 0.0806 0.00 0.32 0.00 0.06 0.62
#> TCGA.CV.7425.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6441.01 3 0.6532 0.5552 0.00 0.28 0.48 0.24 0.00
#> TCGA.IQ.7630.01 3 0.3561 0.6420 0.00 0.26 0.74 0.00 0.00
#> TCGA.CV.5977.01 3 0.1732 0.8237 0.00 0.00 0.92 0.08 0.00
#> TCGA.CQ.5324.01 3 0.0609 0.8392 0.00 0.02 0.98 0.00 0.00
#> TCGA.CV.7407.01 4 0.4360 0.9507 0.30 0.02 0.00 0.68 0.00
#> TCGA.CV.5971.01 2 0.5232 0.7757 0.00 0.60 0.00 0.06 0.34
#> TCGA.CV.5970.01 2 0.5232 0.7757 0.00 0.60 0.00 0.06 0.34
#> TCGA.CN.6016.01 2 0.6033 0.6021 0.00 0.58 0.22 0.00 0.20
#> TCGA.CV.6003.01 4 0.4360 0.9498 0.30 0.02 0.00 0.68 0.00
#> TCGA.CN.6021.01 4 0.4360 0.9507 0.30 0.02 0.00 0.68 0.00
#> TCGA.CV.5434.01 5 0.4096 0.6075 0.00 0.20 0.00 0.04 0.76
#> TCGA.CN.6017.01 2 0.5297 0.7574 0.00 0.58 0.00 0.06 0.36
#> TCGA.CV.7235.01 5 0.0000 0.7624 0.00 0.00 0.00 0.00 1.00
#> TCGA.CV.5439.01 5 0.5351 -0.1875 0.00 0.38 0.00 0.06 0.56
#> TCGA.CN.6020.01 2 0.3983 0.7981 0.00 0.66 0.00 0.00 0.34
#> TCGA.CV.7423.01 2 0.3895 0.8022 0.00 0.68 0.00 0.00 0.32
#> TCGA.CN.6023.01 5 0.0000 0.7624 0.00 0.00 0.00 0.00 1.00
#> TCGA.CR.7365.01 3 0.0000 0.8379 0.00 0.00 1.00 0.00 0.00
#> TCGA.CN.6024.01 5 0.4966 0.5597 0.00 0.24 0.02 0.04 0.70
#> TCGA.CV.5978.01 4 0.5441 0.8245 0.22 0.02 0.00 0.68 0.08
#> TCGA.CV.7089.01 3 0.1732 0.8237 0.00 0.00 0.92 0.08 0.00
#> TCGA.CN.6018.01 1 0.2331 0.7666 0.90 0.02 0.00 0.08 0.00
#> TCGA.CV.5966.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5976.01 3 0.1043 0.8338 0.00 0.04 0.96 0.00 0.00
#> TCGA.CV.7411.01 4 0.4360 0.9498 0.30 0.02 0.00 0.68 0.00
#> TCGA.CQ.5323.01 5 0.0609 0.7524 0.00 0.02 0.00 0.00 0.98
#> TCGA.BB.4217.01 2 0.5297 0.7574 0.00 0.58 0.00 0.06 0.36
#> TCGA.CQ.7068.01 1 0.3110 0.6762 0.86 0.00 0.06 0.08 0.00
#> TCGA.CN.6995.01 3 0.3895 0.5460 0.00 0.32 0.68 0.00 0.00
#> TCGA.CQ.5334.01 3 0.1732 0.8237 0.00 0.00 0.92 0.08 0.00
#> TCGA.CV.7410.01 2 0.5351 0.7272 0.00 0.56 0.00 0.06 0.38
#> TCGA.DQ.7588.01 5 0.0000 0.7624 0.00 0.00 0.00 0.00 1.00
#> TCGA.CV.5973.01 1 0.4726 -0.1102 0.58 0.02 0.00 0.40 0.00
#> TCGA.DQ.7591.01 5 0.6054 0.4663 0.00 0.28 0.00 0.16 0.56
#> TCGA.CV.5430.01 5 0.0000 0.7624 0.00 0.00 0.00 0.00 1.00
#> TCGA.CV.5435.01 3 0.5680 0.6546 0.00 0.24 0.62 0.14 0.00
#> TCGA.CV.5440.01 5 0.4728 0.3423 0.00 0.24 0.00 0.06 0.70
#> TCGA.CV.7104.01 1 0.4456 0.2412 0.66 0.02 0.00 0.32 0.00
#> TCGA.CV.7100.01 2 0.5297 0.7574 0.00 0.58 0.00 0.06 0.36
#> TCGA.CV.7095.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7373.01 3 0.0609 0.8392 0.00 0.02 0.98 0.00 0.00
#> TCGA.CV.7178.01 4 0.3796 0.9563 0.30 0.00 0.00 0.70 0.00
#> TCGA.CN.6998.01 2 0.4287 0.0591 0.00 0.54 0.46 0.00 0.00
#> TCGA.CV.7252.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.CR.6478.01 4 0.3796 0.9563 0.30 0.00 0.00 0.70 0.00
#> TCGA.CR.7380.01 3 0.0609 0.8392 0.00 0.02 0.98 0.00 0.00
#> TCGA.CV.7183.01 3 0.3424 0.6692 0.00 0.24 0.76 0.00 0.00
#> TCGA.CV.7102.01 4 0.3796 0.9563 0.30 0.00 0.00 0.70 0.00
#> TCGA.CV.7254.01 5 0.0000 0.7624 0.00 0.00 0.00 0.00 1.00
#> TCGA.CR.7394.01 4 0.4360 0.9498 0.30 0.02 0.00 0.68 0.00
#> TCGA.CV.6955.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.BA.5556.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7386.01 2 0.5048 0.3173 0.00 0.58 0.38 0.00 0.04
#> TCGA.CR.6474.01 5 0.5351 -0.1889 0.00 0.38 0.00 0.06 0.56
#> TCGA.BA.5557.01 4 0.4360 0.9498 0.30 0.02 0.00 0.68 0.00
#> TCGA.CV.7247.01 5 0.5068 0.1588 0.00 0.30 0.00 0.06 0.64
#> TCGA.CR.7377.01 2 0.5788 0.7156 0.00 0.58 0.12 0.00 0.30
#> TCGA.HD.7229.01 3 0.0609 0.8392 0.00 0.02 0.98 0.00 0.00
#> TCGA.D6.6515.01 4 0.3796 0.9563 0.30 0.00 0.00 0.70 0.00
#> TCGA.CV.7238.01 4 0.4360 0.9498 0.30 0.02 0.00 0.68 0.00
#> TCGA.CV.7097.01 3 0.1732 0.8237 0.00 0.00 0.92 0.08 0.00
#> TCGA.CN.5370.01 2 0.4360 0.7943 0.00 0.68 0.02 0.00 0.30
#> TCGA.CR.7367.01 3 0.0609 0.8355 0.00 0.00 0.98 0.02 0.00
#> TCGA.CR.7401.01 2 0.3895 0.8022 0.00 0.68 0.00 0.00 0.32
#> TCGA.CV.6942.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7177.01 4 0.4360 0.9507 0.30 0.02 0.00 0.68 0.00
#> TCGA.CR.7395.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.BA.5558.01 3 0.1732 0.8192 0.00 0.08 0.92 0.00 0.00
#> TCGA.CX.7085.01 4 0.4360 0.9498 0.30 0.02 0.00 0.68 0.00
#> TCGA.CV.7099.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7090.01 5 0.5457 -0.4855 0.00 0.46 0.00 0.06 0.48
#> TCGA.CX.7219.01 5 0.0000 0.7624 0.00 0.00 0.00 0.00 1.00
#> TCGA.CV.7243.01 3 0.3895 0.5467 0.00 0.32 0.68 0.00 0.00
#> TCGA.BA.6871.01 5 0.0000 0.7624 0.00 0.00 0.00 0.00 1.00
#> TCGA.CQ.6218.01 4 0.3796 0.9563 0.30 0.00 0.00 0.70 0.00
#> TCGA.C9.A47Z.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.5625.01 1 0.4540 0.1663 0.64 0.02 0.00 0.34 0.00
#> TCGA.CR.6480.01 3 0.6532 0.5552 0.00 0.28 0.48 0.24 0.00
#> TCGA.D6.6825.01 2 0.3895 0.8022 0.00 0.68 0.00 0.00 0.32
#> TCGA.C9.A480.01 1 0.4818 -0.3845 0.52 0.02 0.00 0.46 0.00
#> TCGA.CV.6952.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.6222.01 2 0.4921 0.7877 0.00 0.62 0.00 0.04 0.34
#> TCGA.CN.A49C.01 3 0.6532 0.5552 0.00 0.28 0.48 0.24 0.00
#> TCGA.CN.6994.01 5 0.0609 0.7481 0.00 0.02 0.00 0.00 0.98
#> TCGA.CR.6491.01 3 0.1732 0.8237 0.00 0.00 0.92 0.08 0.00
#> TCGA.CV.6950.01 2 0.4456 0.7948 0.00 0.66 0.02 0.00 0.32
#> TCGA.CR.6473.01 3 0.6532 0.5552 0.00 0.28 0.48 0.24 0.00
#> TCGA.CQ.5331.01 4 0.4360 0.9498 0.30 0.02 0.00 0.68 0.00
#> TCGA.D6.6826.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6935.01 5 0.4966 0.5597 0.00 0.24 0.02 0.04 0.70
#> TCGA.CV.6953.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6945.01 5 0.0609 0.7553 0.00 0.00 0.00 0.02 0.98
#> TCGA.DQ.5630.01 2 0.4921 0.7877 0.00 0.62 0.00 0.04 0.34
#> TCGA.CV.6943.01 2 0.3895 0.8022 0.00 0.68 0.00 0.00 0.32
#> TCGA.BA.6870.01 4 0.4360 0.9507 0.30 0.02 0.00 0.68 0.00
#> TCGA.CR.6477.01 4 0.4360 0.9507 0.30 0.02 0.00 0.68 0.00
#> TCGA.CV.A45O.01 3 0.1043 0.8339 0.00 0.04 0.96 0.00 0.00
#> TCGA.CQ.6219.01 4 0.4360 0.9498 0.30 0.02 0.00 0.68 0.00
#> TCGA.CN.4733.01 2 0.5297 0.7574 0.00 0.58 0.00 0.06 0.36
#> TCGA.CN.A498.01 4 0.4360 0.9507 0.30 0.02 0.00 0.68 0.00
#> TCGA.CN.6989.01 5 0.0000 0.7624 0.00 0.00 0.00 0.00 1.00
#> TCGA.CV.6953.11 4 0.3796 0.9563 0.30 0.00 0.00 0.70 0.00
#> TCGA.D6.6517.01 2 0.3983 0.7981 0.00 0.66 0.00 0.00 0.34
#> TCGA.CQ.6220.01 2 0.4540 0.7950 0.00 0.64 0.00 0.02 0.34
#> TCGA.HD.A4C1.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.CR.6493.01 3 0.2929 0.7398 0.00 0.18 0.82 0.00 0.00
#> TCGA.D6.6516.01 5 0.0000 0.7624 0.00 0.00 0.00 0.00 1.00
#> TCGA.CQ.6227.01 2 0.4921 0.7877 0.00 0.62 0.00 0.04 0.34
#> TCGA.CV.A45P.01 1 0.4726 -0.1102 0.58 0.02 0.00 0.40 0.00
#> TCGA.CV.A45Q.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A45T.01 4 0.4360 0.9498 0.30 0.02 0.00 0.68 0.00
#> TCGA.CN.6996.01 1 0.4675 -0.0143 0.60 0.02 0.00 0.38 0.00
#> TCGA.BA.6873.01 2 0.4307 -0.0876 0.00 0.50 0.50 0.00 0.00
#> TCGA.CR.6467.01 3 0.6532 0.5552 0.00 0.28 0.48 0.24 0.00
#> TCGA.BA.6868.01 5 0.0000 0.7624 0.00 0.00 0.00 0.00 1.00
#> TCGA.CV.6959.01 3 0.1732 0.8171 0.00 0.08 0.92 0.00 0.00
#> TCGA.CQ.6229.01 2 0.5579 0.7354 0.00 0.60 0.10 0.00 0.30
#> TCGA.CQ.6224.01 2 0.4726 0.2545 0.00 0.58 0.40 0.00 0.02
#> TCGA.CQ.6223.01 2 0.5425 0.7500 0.00 0.60 0.08 0.00 0.32
#> TCGA.DQ.5624.01 4 0.3796 0.9563 0.30 0.00 0.00 0.70 0.00
#> TCGA.CV.A45R.01 2 0.5892 0.6014 0.00 0.60 0.22 0.00 0.18
#> TCGA.CN.A499.01 4 0.4360 0.9507 0.30 0.02 0.00 0.68 0.00
#> TCGA.CN.A49B.01 5 0.0000 0.7624 0.00 0.00 0.00 0.00 1.00
#> TCGA.BA.5152.01 2 0.3983 0.7981 0.00 0.66 0.00 0.00 0.34
#> TCGA.CV.6938.01 3 0.0609 0.8392 0.00 0.02 0.98 0.00 0.00
#> TCGA.CQ.5326.01 5 0.1410 0.7326 0.00 0.00 0.00 0.06 0.94
#> TCGA.CV.6940.01 4 0.4360 0.9507 0.30 0.02 0.00 0.68 0.00
#> TCGA.CR.6471.01 2 0.4456 0.7948 0.00 0.66 0.02 0.00 0.32
#> TCGA.BA.6872.01 3 0.5178 -0.0206 0.00 0.48 0.48 0.00 0.04
#> TCGA.CQ.A4C6.01 3 0.3895 0.5467 0.00 0.32 0.68 0.00 0.00
#> TCGA.CQ.7064.01 4 0.4360 0.9498 0.30 0.02 0.00 0.68 0.00
#> TCGA.IQ.A61K.01 1 0.1216 0.8290 0.96 0.02 0.00 0.02 0.00
#> TCGA.HD.A633.01 3 0.0609 0.8392 0.00 0.02 0.98 0.00 0.00
#> TCGA.F7.A61W.01 5 0.5156 0.0806 0.00 0.32 0.00 0.06 0.62
#> TCGA.BA.A6DF.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.D6.A4ZB.01 5 0.1410 0.7138 0.00 0.06 0.00 0.00 0.94
#> TCGA.CV.A45Y.01 2 0.5888 0.6952 0.00 0.58 0.14 0.00 0.28
#> TCGA.BB.A5HU.01 5 0.5457 -0.4855 0.00 0.46 0.00 0.06 0.48
#> TCGA.CQ.A4C7.01 3 0.0609 0.8392 0.00 0.02 0.98 0.00 0.00
#> TCGA.P3.A5Q6.01 2 0.5297 0.7574 0.00 0.58 0.00 0.06 0.36
#> TCGA.CQ.A4CD.01 3 0.1732 0.8192 0.00 0.08 0.92 0.00 0.00
#> TCGA.BA.A6DB.01 4 0.3796 0.9563 0.30 0.00 0.00 0.70 0.00
#> TCGA.F7.A620.01 3 0.0609 0.8392 0.00 0.02 0.98 0.00 0.00
#> TCGA.CX.A4AQ.01 5 0.4096 0.6075 0.00 0.20 0.00 0.04 0.76
#> TCGA.CV.A464.01 2 0.5297 0.7574 0.00 0.58 0.00 0.06 0.36
#> TCGA.IQ.A61L.01 1 0.4726 -0.1102 0.58 0.02 0.00 0.40 0.00
#> TCGA.QK.A8Z9.01 3 0.3037 0.7914 0.00 0.10 0.86 0.00 0.04
#> TCGA.BB.A5HY.01 3 0.5484 0.6670 0.00 0.24 0.64 0.12 0.00
#> TCGA.HD.8635.01 4 0.4360 0.9507 0.30 0.02 0.00 0.68 0.00
#> TCGA.QK.A652.01 2 0.3895 0.8022 0.00 0.68 0.00 0.00 0.32
#> TCGA.MT.A67G.01 4 0.4360 0.9507 0.30 0.02 0.00 0.68 0.00
#> TCGA.QK.A64Z.01 1 0.4540 0.1663 0.64 0.02 0.00 0.34 0.00
#> TCGA.HD.8634.01 1 0.2616 0.7402 0.88 0.02 0.00 0.10 0.00
#> TCGA.CQ.7063.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.F7.A50J.01 4 0.4360 0.9498 0.30 0.02 0.00 0.68 0.00
#> TCGA.F7.8298.01 5 0.3274 0.4656 0.00 0.22 0.00 0.00 0.78
#> TCGA.F7.8489.01 2 0.5232 0.7757 0.00 0.60 0.00 0.06 0.34
#> TCGA.F7.A50G.01 2 0.3983 0.7981 0.00 0.66 0.00 0.00 0.34
#> TCGA.CQ.A4CA.01 2 0.5297 0.7574 0.00 0.58 0.00 0.06 0.36
#> TCGA.T3.A92N.01 5 0.4096 0.6075 0.00 0.20 0.00 0.04 0.76
#> TCGA.CN.A63Y.01 5 0.5068 0.1574 0.00 0.30 0.00 0.06 0.64
#> TCGA.CQ.5333.01 3 0.1732 0.8237 0.00 0.00 0.92 0.08 0.00
#> TCGA.P3.A5QE.01 5 0.0000 0.7624 0.00 0.00 0.00 0.00 1.00
#> TCGA.BA.A6DJ.01 3 0.1732 0.8237 0.00 0.00 0.92 0.08 0.00
#> TCGA.MT.A51W.01 4 0.4360 0.9507 0.30 0.02 0.00 0.68 0.00
#> TCGA.IQ.A61G.01 5 0.1648 0.7259 0.00 0.04 0.00 0.02 0.94
#> TCGA.IQ.A61J.01 2 0.4921 0.7877 0.00 0.62 0.00 0.04 0.34
#> TCGA.BA.A6DG.01 2 0.4921 0.7877 0.00 0.62 0.00 0.04 0.34
#> TCGA.CQ.A4CH.01 2 0.5297 0.7574 0.00 0.58 0.00 0.06 0.36
#> TCGA.CQ.A4CB.01 3 0.0609 0.8392 0.00 0.02 0.98 0.00 0.00
#> TCGA.D6.8569.01 2 0.4456 0.7948 0.00 0.66 0.02 0.00 0.32
#> TCGA.IQ.A61I.01 3 0.6532 0.5552 0.00 0.28 0.48 0.24 0.00
#> TCGA.D6.A4Z9.01 3 0.1732 0.8199 0.00 0.08 0.92 0.00 0.00
#> TCGA.CQ.7071.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.H7.8501.01 3 0.0609 0.8392 0.00 0.02 0.98 0.00 0.00
#> TCGA.BB.8601.01 5 0.4096 0.6075 0.00 0.20 0.00 0.04 0.76
#> TCGA.H7.8502.01 5 0.0609 0.7525 0.00 0.02 0.00 0.00 0.98
#> TCGA.F7.A61S.01 2 0.5579 0.5080 0.00 0.60 0.30 0.00 0.10
#> TCGA.CV.A463.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.D6.8568.01 2 0.3895 0.8022 0.00 0.68 0.00 0.00 0.32
#> TCGA.CN.A642.01 3 0.0609 0.8355 0.00 0.00 0.98 0.02 0.00
#> TCGA.CN.5367.01 4 0.3796 0.9563 0.30 0.00 0.00 0.70 0.00
#> TCGA.P3.A6T2.01 3 0.1732 0.8237 0.00 0.00 0.92 0.08 0.00
#> TCGA.CN.A6V7.01 3 0.6532 0.5552 0.00 0.28 0.48 0.24 0.00
#> TCGA.CN.A640.01 1 0.0609 0.8444 0.98 0.02 0.00 0.00 0.00
#> TCGA.DQ.7589.01 5 0.0000 0.7624 0.00 0.00 0.00 0.00 1.00
#> TCGA.CN.4725.01 2 0.3895 0.8022 0.00 0.68 0.00 0.00 0.32
#> TCGA.HL.7533.01 5 0.5297 -0.1034 0.00 0.36 0.00 0.06 0.58
#> TCGA.UF.A7JO.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A7JV.01 4 0.4360 0.9498 0.30 0.02 0.00 0.68 0.00
#> TCGA.CN.4729.01 2 0.4840 0.7827 0.00 0.64 0.04 0.00 0.32
#> TCGA.IQ.A6SG.01 4 0.5441 0.8245 0.22 0.02 0.00 0.68 0.08
#> TCGA.MT.A67A.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.5361.01 2 0.4840 0.7828 0.00 0.64 0.04 0.00 0.32
#> TCGA.CN.5359.01 5 0.0000 0.7624 0.00 0.00 0.00 0.00 1.00
#> TCGA.BB.7861.01 5 0.5351 -0.1920 0.00 0.38 0.00 0.06 0.56
#> TCGA.BB.A6UO.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4734.01 3 0.1732 0.8237 0.00 0.00 0.92 0.08 0.00
#> TCGA.BA.4075.01 3 0.1410 0.8266 0.00 0.06 0.94 0.00 0.00
#> TCGA.BB.7871.01 4 0.4360 0.4778 0.00 0.02 0.00 0.68 0.30
#> TCGA.CN.4726.01 3 0.0609 0.8392 0.00 0.02 0.98 0.00 0.00
#> TCGA.UF.A7JS.01 2 0.5727 0.7143 0.00 0.56 0.10 0.00 0.34
#> TCGA.CN.4736.01 4 0.3796 0.9563 0.30 0.00 0.00 0.70 0.00
#> TCGA.CN.5355.01 3 0.2516 0.7780 0.00 0.14 0.86 0.00 0.00
#> TCGA.DQ.7590.01 5 0.4096 0.6075 0.00 0.20 0.00 0.04 0.76
#> TCGA.CN.5369.01 4 0.3796 0.9563 0.30 0.00 0.00 0.70 0.00
#> TCGA.BA.5151.01 3 0.0609 0.8392 0.00 0.02 0.98 0.00 0.00
#> TCGA.IQ.A61E.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.BA.4076.01 5 0.0000 0.7624 0.00 0.00 0.00 0.00 1.00
#> TCGA.MZ.A7D7.01 5 0.0000 0.7624 0.00 0.00 0.00 0.00 1.00
#> TCGA.UF.A7JT.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.5373.01 1 0.4726 -0.1102 0.58 0.02 0.00 0.40 0.00
#> TCGA.BB.7863.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.5363.01 3 0.1410 0.8266 0.00 0.06 0.94 0.00 0.00
#> TCGA.BA.4077.01 4 0.4360 0.9507 0.30 0.02 0.00 0.68 0.00
#> TCGA.BB.7872.01 2 0.3895 0.8022 0.00 0.68 0.00 0.00 0.32
#> TCGA.H7.A6C4.01 1 0.2012 0.7900 0.92 0.02 0.00 0.06 0.00
#> TCGA.T2.A6X2.01 3 0.0609 0.8392 0.00 0.02 0.98 0.00 0.00
#> TCGA.CN.4741.01 3 0.6532 0.5552 0.00 0.28 0.48 0.24 0.00
#> TCGA.CV.A6JO.01 3 0.3895 0.5467 0.00 0.32 0.68 0.00 0.00
#> TCGA.BB.7866.01 3 0.6532 0.5552 0.00 0.28 0.48 0.24 0.00
#> TCGA.CN.5365.01 5 0.0609 0.7553 0.00 0.00 0.00 0.02 0.98
#> TCGA.BB.4224.01 2 0.4540 0.7950 0.00 0.64 0.00 0.02 0.34
#> TCGA.MT.A67F.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.5366.01 3 0.1732 0.8237 0.00 0.00 0.92 0.08 0.00
#> TCGA.QK.A6V9.01 3 0.7048 0.5311 0.00 0.28 0.46 0.24 0.02
#> TCGA.T2.A6WX.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A6JZ.01 3 0.0609 0.8392 0.00 0.02 0.98 0.00 0.00
#> TCGA.CN.A6V1.01 2 0.5394 0.6889 0.00 0.54 0.00 0.06 0.40
#> TCGA.HD.A6I0.01 3 0.0000 0.8379 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.7430.01 5 0.0000 0.7624 0.00 0.00 0.00 0.00 1.00
#> TCGA.CR.7383.01 4 0.4360 0.9507 0.30 0.02 0.00 0.68 0.00
#> TCGA.UF.A7JC.01 2 0.5297 0.7574 0.00 0.58 0.00 0.06 0.36
#> TCGA.CV.7568.01 5 0.1410 0.7326 0.00 0.00 0.00 0.06 0.94
#> TCGA.QK.A6IF.01 5 0.4854 0.2863 0.00 0.26 0.00 0.06 0.68
#> TCGA.CV.A6JT.01 3 0.1732 0.8171 0.00 0.08 0.92 0.00 0.00
#> TCGA.CV.7438.01 1 0.4726 -0.1102 0.58 0.02 0.00 0.40 0.00
#> TCGA.D6.A6EN.01 3 0.0000 0.8379 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.7429.01 5 0.2797 0.6739 0.00 0.06 0.00 0.06 0.88
#> TCGA.CV.7437.01 5 0.5358 0.5403 0.00 0.24 0.04 0.04 0.68
#> TCGA.CV.A6JD.01 1 0.0000 0.8579 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A6JN.01 2 0.5579 0.7354 0.00 0.60 0.10 0.00 0.30
#> TCGA.CV.7434.01 3 0.1732 0.8237 0.00 0.00 0.92 0.08 0.00
#> TCGA.D6.A6EK.01 2 0.4540 0.7952 0.00 0.64 0.00 0.02 0.34
#> TCGA.HD.7832.01 3 0.4725 0.7277 0.00 0.08 0.72 0.20 0.00
#> TCGA.P3.A6SX.01 5 0.0000 0.7624 0.00 0.00 0.00 0.00 1.00
#> TCGA.QK.A6II.01 2 0.6033 0.6256 0.00 0.58 0.20 0.00 0.22
#> TCGA.P3.A6T7.01 3 0.1410 0.8266 0.00 0.06 0.94 0.00 0.00
#> TCGA.CR.7382.01 2 0.4302 -0.0125 0.00 0.52 0.48 0.00 0.00
#> TCGA.T2.A6WZ.01 3 0.0609 0.8392 0.00 0.02 0.98 0.00 0.00
#> TCGA.P3.A6T5.01 4 0.4360 0.9498 0.30 0.02 0.00 0.68 0.00
#> TCGA.CV.7433.01 5 0.1410 0.7326 0.00 0.00 0.00 0.06 0.94
#> TCGA.CR.7376.01 2 0.5351 0.7272 0.00 0.56 0.00 0.06 0.38
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.CQ.5327.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HD.7753.01 2 0.3854 0.6408 0.00 0.80 0.00 0.04 0.12 0.04
#> TCGA.CQ.5325.01 2 0.5618 0.5326 0.00 0.64 0.20 0.10 0.00 0.06
#> TCGA.CR.7391.01 4 0.3711 0.8699 0.26 0.00 0.00 0.72 0.00 0.02
#> TCGA.CV.7415.01 5 0.1480 0.8962 0.00 0.04 0.00 0.00 0.94 0.02
#> TCGA.CN.6011.01 5 0.1865 0.8931 0.00 0.04 0.00 0.04 0.92 0.00
#> TCGA.CV.6436.01 3 0.6273 0.1113 0.00 0.38 0.46 0.10 0.00 0.06
#> TCGA.DQ.7592.01 2 0.4055 0.6184 0.00 0.78 0.00 0.04 0.14 0.04
#> TCGA.CV.7416.01 4 0.5747 0.7249 0.30 0.00 0.00 0.50 0.00 0.20
#> TCGA.H7.7774.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.5330.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7427.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5979.01 2 0.2512 0.7160 0.00 0.88 0.00 0.06 0.00 0.06
#> TCGA.CQ.6221.01 2 0.5405 0.0954 0.00 0.50 0.00 0.04 0.42 0.04
#> TCGA.CV.7425.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6441.01 6 0.5210 0.8902 0.00 0.00 0.26 0.06 0.04 0.64
#> TCGA.IQ.7630.01 3 0.6100 0.3255 0.00 0.30 0.54 0.10 0.00 0.06
#> TCGA.CV.5977.01 3 0.3475 0.5223 0.00 0.00 0.80 0.06 0.00 0.14
#> TCGA.CQ.5324.01 3 0.0547 0.6819 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.CV.7407.01 4 0.3198 0.8689 0.26 0.00 0.00 0.74 0.00 0.00
#> TCGA.CV.5971.01 2 0.2403 0.7011 0.00 0.90 0.00 0.04 0.02 0.04
#> TCGA.CV.5970.01 2 0.1480 0.7115 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.CN.6016.01 2 0.6029 0.3928 0.00 0.56 0.28 0.10 0.00 0.06
#> TCGA.CV.6003.01 4 0.5608 0.7894 0.26 0.00 0.00 0.54 0.00 0.20
#> TCGA.CN.6021.01 4 0.3198 0.8689 0.26 0.00 0.00 0.74 0.00 0.00
#> TCGA.CV.5434.01 5 0.3045 0.7714 0.00 0.00 0.00 0.06 0.84 0.10
#> TCGA.CN.6017.01 2 0.2784 0.6949 0.00 0.88 0.00 0.04 0.04 0.04
#> TCGA.CV.7235.01 5 0.0937 0.9041 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.CV.5439.01 2 0.5302 0.2668 0.00 0.56 0.00 0.04 0.36 0.04
#> TCGA.CN.6020.01 2 0.2794 0.7119 0.00 0.86 0.00 0.08 0.00 0.06
#> TCGA.CV.7423.01 2 0.2794 0.7119 0.00 0.86 0.00 0.08 0.00 0.06
#> TCGA.CN.6023.01 5 0.0937 0.9041 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.CR.7365.01 3 0.1267 0.6663 0.00 0.00 0.94 0.06 0.00 0.00
#> TCGA.CN.6024.01 5 0.3572 0.7528 0.00 0.02 0.00 0.06 0.82 0.10
#> TCGA.CV.5978.01 4 0.4165 0.7428 0.16 0.00 0.00 0.74 0.10 0.00
#> TCGA.CV.7089.01 3 0.3475 0.5223 0.00 0.00 0.80 0.06 0.00 0.14
#> TCGA.CN.6018.01 1 0.4244 0.5524 0.72 0.00 0.00 0.08 0.00 0.20
#> TCGA.CV.5966.01 1 0.0937 0.8014 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.CV.5976.01 3 0.2020 0.6802 0.00 0.02 0.92 0.04 0.00 0.02
#> TCGA.CV.7411.01 4 0.5608 0.7894 0.26 0.00 0.00 0.54 0.00 0.20
#> TCGA.CQ.5323.01 5 0.1092 0.8875 0.00 0.02 0.00 0.02 0.96 0.00
#> TCGA.BB.4217.01 2 0.2784 0.6949 0.00 0.88 0.00 0.04 0.04 0.04
#> TCGA.CQ.7068.01 1 0.3795 0.5325 0.80 0.00 0.12 0.06 0.00 0.02
#> TCGA.CN.6995.01 3 0.6294 -0.0245 0.00 0.42 0.42 0.10 0.00 0.06
#> TCGA.CQ.5334.01 3 0.2794 0.5963 0.00 0.00 0.86 0.06 0.00 0.08
#> TCGA.CV.7410.01 2 0.3631 0.6566 0.00 0.82 0.00 0.04 0.10 0.04
#> TCGA.DQ.7588.01 5 0.0937 0.9041 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.CV.5973.01 1 0.5865 -0.3616 0.44 0.00 0.00 0.36 0.00 0.20
#> TCGA.DQ.7591.01 6 0.4282 0.1179 0.00 0.00 0.00 0.02 0.42 0.56
#> TCGA.CV.5430.01 5 0.0937 0.9041 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.CV.5435.01 3 0.5669 -0.0430 0.00 0.00 0.60 0.10 0.04 0.26
#> TCGA.CV.5440.01 2 0.5405 0.0954 0.00 0.50 0.00 0.04 0.42 0.04
#> TCGA.CV.7104.01 1 0.5747 -0.1310 0.50 0.00 0.00 0.30 0.00 0.20
#> TCGA.CV.7100.01 2 0.3382 0.6735 0.00 0.84 0.00 0.04 0.08 0.04
#> TCGA.CV.7095.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7373.01 3 0.1092 0.6895 0.00 0.02 0.96 0.02 0.00 0.00
#> TCGA.CV.7178.01 4 0.3198 0.8689 0.26 0.00 0.00 0.74 0.00 0.00
#> TCGA.CN.6998.01 2 0.6246 0.1875 0.00 0.48 0.36 0.10 0.00 0.06
#> TCGA.CV.7252.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.6478.01 4 0.3198 0.8689 0.26 0.00 0.00 0.74 0.00 0.00
#> TCGA.CR.7380.01 3 0.1092 0.6895 0.00 0.02 0.96 0.02 0.00 0.00
#> TCGA.CV.7183.01 3 0.5849 0.4423 0.00 0.24 0.60 0.10 0.00 0.06
#> TCGA.CV.7102.01 4 0.4613 0.8456 0.26 0.00 0.00 0.66 0.00 0.08
#> TCGA.CV.7254.01 5 0.0937 0.9041 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.CR.7394.01 4 0.5608 0.7894 0.26 0.00 0.00 0.54 0.00 0.20
#> TCGA.CV.6955.01 1 0.0937 0.8014 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.BA.5556.01 1 0.1267 0.7901 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.CR.7386.01 2 0.6029 0.3909 0.00 0.56 0.28 0.10 0.00 0.06
#> TCGA.CR.6474.01 2 0.5248 0.3134 0.00 0.58 0.00 0.04 0.34 0.04
#> TCGA.BA.5557.01 4 0.5608 0.7894 0.26 0.00 0.00 0.54 0.00 0.20
#> TCGA.CV.7247.01 2 0.5405 0.0954 0.00 0.50 0.00 0.04 0.42 0.04
#> TCGA.CR.7377.01 2 0.5740 0.5036 0.00 0.62 0.22 0.10 0.00 0.06
#> TCGA.HD.7229.01 3 0.1480 0.6854 0.00 0.02 0.94 0.04 0.00 0.00
#> TCGA.D6.6515.01 4 0.3711 0.8699 0.26 0.00 0.00 0.72 0.00 0.02
#> TCGA.CV.7238.01 4 0.5608 0.7894 0.26 0.00 0.00 0.54 0.00 0.20
#> TCGA.CV.7097.01 3 0.3475 0.5223 0.00 0.00 0.80 0.06 0.00 0.14
#> TCGA.CN.5370.01 2 0.3572 0.6942 0.00 0.82 0.02 0.10 0.00 0.06
#> TCGA.CR.7367.01 3 0.1480 0.6635 0.00 0.00 0.94 0.04 0.00 0.02
#> TCGA.CR.7401.01 2 0.2794 0.7119 0.00 0.86 0.00 0.08 0.00 0.06
#> TCGA.CV.6942.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7177.01 4 0.3198 0.8689 0.26 0.00 0.00 0.74 0.00 0.00
#> TCGA.CR.7395.01 1 0.1267 0.7901 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.BA.5558.01 3 0.3572 0.6280 0.00 0.02 0.82 0.10 0.00 0.06
#> TCGA.CX.7085.01 4 0.5608 0.7894 0.26 0.00 0.00 0.54 0.00 0.20
#> TCGA.CV.7099.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7090.01 2 0.4574 0.4816 0.00 0.68 0.00 0.02 0.26 0.04
#> TCGA.CX.7219.01 5 0.0937 0.9041 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.CV.7243.01 3 0.6100 0.3255 0.00 0.30 0.54 0.10 0.00 0.06
#> TCGA.BA.6871.01 5 0.2020 0.8880 0.00 0.04 0.00 0.02 0.92 0.02
#> TCGA.CQ.6218.01 4 0.3198 0.8689 0.26 0.00 0.00 0.74 0.00 0.00
#> TCGA.C9.A47Z.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.5625.01 1 0.5747 -0.1319 0.50 0.00 0.00 0.30 0.00 0.20
#> TCGA.CR.6480.01 6 0.4574 0.9178 0.00 0.00 0.26 0.02 0.04 0.68
#> TCGA.D6.6825.01 2 0.3572 0.6942 0.00 0.82 0.02 0.10 0.00 0.06
#> TCGA.C9.A480.01 4 0.5888 0.4743 0.40 0.00 0.00 0.40 0.00 0.20
#> TCGA.CV.6952.01 1 0.0937 0.8014 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.CQ.6222.01 2 0.1092 0.7158 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.CN.A49C.01 6 0.4067 0.9173 0.00 0.00 0.26 0.00 0.04 0.70
#> TCGA.CN.6994.01 5 0.1865 0.8931 0.00 0.04 0.00 0.04 0.92 0.00
#> TCGA.CR.6491.01 3 0.3475 0.5223 0.00 0.00 0.80 0.06 0.00 0.14
#> TCGA.CV.6950.01 2 0.4251 0.6689 0.00 0.78 0.06 0.10 0.00 0.06
#> TCGA.CR.6473.01 6 0.4067 0.9173 0.00 0.00 0.26 0.00 0.04 0.70
#> TCGA.CQ.5331.01 4 0.5608 0.7894 0.26 0.00 0.00 0.54 0.00 0.20
#> TCGA.D6.6826.01 1 0.0547 0.8085 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CV.6935.01 5 0.3475 0.7232 0.00 0.00 0.00 0.06 0.80 0.14
#> TCGA.CV.6953.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6945.01 5 0.1807 0.8854 0.00 0.06 0.00 0.00 0.92 0.02
#> TCGA.DQ.5630.01 2 0.0000 0.7197 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6943.01 2 0.2512 0.7160 0.00 0.88 0.00 0.06 0.00 0.06
#> TCGA.BA.6870.01 4 0.3198 0.8689 0.26 0.00 0.00 0.74 0.00 0.00
#> TCGA.CR.6477.01 4 0.3198 0.8689 0.26 0.00 0.00 0.74 0.00 0.00
#> TCGA.CV.A45O.01 3 0.1480 0.6854 0.00 0.02 0.94 0.04 0.00 0.00
#> TCGA.CQ.6219.01 4 0.5608 0.7894 0.26 0.00 0.00 0.54 0.00 0.20
#> TCGA.CN.4733.01 2 0.2784 0.6949 0.00 0.88 0.00 0.04 0.04 0.04
#> TCGA.CN.A498.01 4 0.3198 0.8689 0.26 0.00 0.00 0.74 0.00 0.00
#> TCGA.CN.6989.01 5 0.0937 0.9041 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.CV.6953.11 4 0.3711 0.8699 0.26 0.00 0.00 0.72 0.00 0.02
#> TCGA.D6.6517.01 2 0.0547 0.7184 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CQ.6220.01 2 0.0937 0.7203 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.HD.A4C1.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.6493.01 3 0.5618 0.4947 0.00 0.20 0.64 0.10 0.00 0.06
#> TCGA.D6.6516.01 5 0.1480 0.8998 0.00 0.04 0.00 0.02 0.94 0.00
#> TCGA.CQ.6227.01 2 0.1092 0.7158 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.CV.A45P.01 1 0.5798 -0.2078 0.48 0.00 0.00 0.32 0.00 0.20
#> TCGA.CV.A45Q.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A45T.01 4 0.5608 0.7894 0.26 0.00 0.00 0.54 0.00 0.20
#> TCGA.CN.6996.01 1 0.5798 -0.2078 0.48 0.00 0.00 0.32 0.00 0.20
#> TCGA.BA.6873.01 2 0.6273 0.1300 0.00 0.46 0.38 0.10 0.00 0.06
#> TCGA.CR.6467.01 6 0.4067 0.9173 0.00 0.00 0.26 0.00 0.04 0.70
#> TCGA.BA.6868.01 5 0.0937 0.9041 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.CV.6959.01 3 0.4756 0.5731 0.00 0.10 0.74 0.10 0.00 0.06
#> TCGA.CQ.6229.01 2 0.5157 0.5982 0.00 0.70 0.14 0.10 0.00 0.06
#> TCGA.CQ.6224.01 2 0.6246 0.1875 0.00 0.48 0.36 0.10 0.00 0.06
#> TCGA.CQ.6223.01 2 0.5813 0.5228 0.00 0.62 0.20 0.12 0.00 0.06
#> TCGA.DQ.5624.01 4 0.3711 0.8699 0.26 0.00 0.00 0.72 0.00 0.02
#> TCGA.CV.A45R.01 2 0.5740 0.5020 0.00 0.62 0.22 0.10 0.00 0.06
#> TCGA.CN.A499.01 4 0.3198 0.8689 0.26 0.00 0.00 0.74 0.00 0.00
#> TCGA.CN.A49B.01 5 0.2020 0.8880 0.00 0.04 0.00 0.02 0.92 0.02
#> TCGA.BA.5152.01 2 0.2190 0.7191 0.00 0.90 0.00 0.06 0.00 0.04
#> TCGA.CV.6938.01 3 0.0547 0.6905 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.CQ.5326.01 5 0.2882 0.8346 0.00 0.10 0.00 0.02 0.86 0.02
#> TCGA.CV.6940.01 4 0.3198 0.8689 0.26 0.00 0.00 0.74 0.00 0.00
#> TCGA.CR.6471.01 2 0.3572 0.6942 0.00 0.82 0.02 0.10 0.00 0.06
#> TCGA.BA.6872.01 3 0.6294 -0.0319 0.00 0.42 0.42 0.10 0.00 0.06
#> TCGA.CQ.A4C6.01 3 0.6100 0.3255 0.00 0.30 0.54 0.10 0.00 0.06
#> TCGA.CQ.7064.01 4 0.5608 0.7894 0.26 0.00 0.00 0.54 0.00 0.20
#> TCGA.IQ.A61K.01 1 0.2631 0.6902 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.HD.A633.01 3 0.1092 0.6895 0.00 0.02 0.96 0.02 0.00 0.00
#> TCGA.F7.A61W.01 2 0.5405 0.0954 0.00 0.50 0.00 0.04 0.42 0.04
#> TCGA.BA.A6DF.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D6.A4ZB.01 5 0.3942 0.8104 0.00 0.10 0.00 0.06 0.80 0.04
#> TCGA.CV.A45Y.01 2 0.5480 0.5542 0.00 0.66 0.18 0.10 0.00 0.06
#> TCGA.BB.A5HU.01 2 0.4574 0.4816 0.00 0.68 0.00 0.02 0.26 0.04
#> TCGA.CQ.A4C7.01 3 0.0937 0.6850 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.P3.A5Q6.01 2 0.2403 0.7011 0.00 0.90 0.00 0.04 0.02 0.04
#> TCGA.CQ.A4CD.01 3 0.3258 0.6402 0.00 0.04 0.84 0.10 0.00 0.02
#> TCGA.BA.A6DB.01 4 0.3711 0.8699 0.26 0.00 0.00 0.72 0.00 0.02
#> TCGA.F7.A620.01 3 0.1092 0.6891 0.00 0.02 0.96 0.02 0.00 0.00
#> TCGA.CX.A4AQ.01 5 0.3045 0.7714 0.00 0.00 0.00 0.06 0.84 0.10
#> TCGA.CV.A464.01 2 0.2784 0.6949 0.00 0.88 0.00 0.04 0.04 0.04
#> TCGA.IQ.A61L.01 1 0.5798 -0.2078 0.48 0.00 0.00 0.32 0.00 0.20
#> TCGA.QK.A8Z9.01 3 0.5653 0.5402 0.00 0.08 0.70 0.10 0.08 0.04
#> TCGA.BB.A5HY.01 3 0.5857 -0.0642 0.00 0.00 0.58 0.12 0.04 0.26
#> TCGA.HD.8635.01 4 0.3198 0.8689 0.26 0.00 0.00 0.74 0.00 0.00
#> TCGA.QK.A652.01 2 0.2512 0.7160 0.00 0.88 0.00 0.06 0.00 0.06
#> TCGA.MT.A67G.01 4 0.3198 0.8689 0.26 0.00 0.00 0.74 0.00 0.00
#> TCGA.QK.A64Z.01 1 0.5747 -0.1310 0.50 0.00 0.00 0.30 0.00 0.20
#> TCGA.HD.8634.01 1 0.4244 0.5524 0.72 0.00 0.00 0.08 0.00 0.20
#> TCGA.CQ.7063.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F7.A50J.01 4 0.5608 0.7894 0.26 0.00 0.00 0.54 0.00 0.20
#> TCGA.F7.8298.01 5 0.4695 0.7116 0.00 0.16 0.02 0.06 0.74 0.02
#> TCGA.F7.8489.01 2 0.1865 0.7064 0.00 0.92 0.00 0.04 0.00 0.04
#> TCGA.F7.A50G.01 2 0.2794 0.7119 0.00 0.86 0.00 0.08 0.00 0.06
#> TCGA.CQ.A4CA.01 2 0.2784 0.6949 0.00 0.88 0.00 0.04 0.04 0.04
#> TCGA.T3.A92N.01 5 0.3045 0.7714 0.00 0.00 0.00 0.06 0.84 0.10
#> TCGA.CN.A63Y.01 2 0.5405 0.0954 0.00 0.50 0.00 0.04 0.42 0.04
#> TCGA.CQ.5333.01 3 0.3475 0.5223 0.00 0.00 0.80 0.06 0.00 0.14
#> TCGA.P3.A5QE.01 5 0.1480 0.8975 0.00 0.04 0.00 0.02 0.94 0.00
#> TCGA.BA.A6DJ.01 3 0.3475 0.5223 0.00 0.00 0.80 0.06 0.00 0.14
#> TCGA.MT.A51W.01 4 0.3198 0.8689 0.26 0.00 0.00 0.74 0.00 0.00
#> TCGA.IQ.A61G.01 5 0.1807 0.8852 0.00 0.06 0.00 0.00 0.92 0.02
#> TCGA.IQ.A61J.01 2 0.1092 0.7158 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.BA.A6DG.01 2 0.1092 0.7158 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.CQ.A4CH.01 2 0.2784 0.6949 0.00 0.88 0.00 0.04 0.04 0.04
#> TCGA.CQ.A4CB.01 3 0.1480 0.6854 0.00 0.02 0.94 0.04 0.00 0.00
#> TCGA.D6.8569.01 2 0.3572 0.6942 0.00 0.82 0.02 0.10 0.00 0.06
#> TCGA.IQ.A61I.01 6 0.4067 0.9173 0.00 0.00 0.26 0.00 0.04 0.70
#> TCGA.D6.A4Z9.01 3 0.2882 0.6508 0.00 0.02 0.86 0.10 0.00 0.02
#> TCGA.CQ.7071.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.H7.8501.01 3 0.1267 0.6663 0.00 0.00 0.94 0.06 0.00 0.00
#> TCGA.BB.8601.01 5 0.3045 0.7714 0.00 0.00 0.00 0.06 0.84 0.10
#> TCGA.H7.8502.01 5 0.2345 0.8585 0.00 0.02 0.00 0.06 0.90 0.02
#> TCGA.F7.A61S.01 2 0.5740 0.5020 0.00 0.62 0.22 0.10 0.00 0.06
#> TCGA.CV.A463.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D6.8568.01 2 0.2512 0.7160 0.00 0.88 0.00 0.06 0.00 0.06
#> TCGA.CN.A642.01 3 0.2190 0.6362 0.00 0.00 0.90 0.06 0.00 0.04
#> TCGA.CN.5367.01 4 0.3711 0.8699 0.26 0.00 0.00 0.72 0.00 0.02
#> TCGA.P3.A6T2.01 3 0.3475 0.5223 0.00 0.00 0.80 0.06 0.00 0.14
#> TCGA.CN.A6V7.01 6 0.4574 0.9178 0.00 0.00 0.26 0.02 0.04 0.68
#> TCGA.CN.A640.01 1 0.2260 0.7280 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.DQ.7589.01 5 0.0937 0.9041 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.CN.4725.01 2 0.2794 0.7119 0.00 0.86 0.00 0.08 0.00 0.06
#> TCGA.HL.7533.01 2 0.5248 0.2988 0.00 0.58 0.00 0.04 0.34 0.04
#> TCGA.UF.A7JO.01 1 0.0937 0.8014 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.UF.A7JV.01 4 0.5608 0.7894 0.26 0.00 0.00 0.54 0.00 0.20
#> TCGA.CN.4729.01 2 0.3942 0.6821 0.00 0.80 0.04 0.10 0.00 0.06
#> TCGA.IQ.A6SG.01 4 0.4200 0.7134 0.14 0.00 0.00 0.74 0.12 0.00
#> TCGA.MT.A67A.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.5361.01 2 0.4519 0.6536 0.00 0.76 0.08 0.10 0.00 0.06
#> TCGA.CN.5359.01 5 0.0937 0.9041 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.BB.7861.01 2 0.4403 0.5723 0.00 0.74 0.00 0.04 0.18 0.04
#> TCGA.BB.A6UO.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4734.01 3 0.3475 0.5223 0.00 0.00 0.80 0.06 0.00 0.14
#> TCGA.BA.4075.01 3 0.3324 0.6413 0.00 0.02 0.84 0.08 0.00 0.06
#> TCGA.BB.7871.01 4 0.3198 0.5050 0.00 0.00 0.00 0.74 0.26 0.00
#> TCGA.CN.4726.01 3 0.0937 0.6747 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.UF.A7JS.01 2 0.6453 0.5031 0.00 0.60 0.20 0.10 0.04 0.06
#> TCGA.CN.4736.01 4 0.3711 0.8699 0.26 0.00 0.00 0.72 0.00 0.02
#> TCGA.CN.5355.01 3 0.5327 0.5255 0.00 0.16 0.68 0.10 0.00 0.06
#> TCGA.DQ.7590.01 5 0.3592 0.6274 0.00 0.00 0.00 0.02 0.74 0.24
#> TCGA.CN.5369.01 4 0.3711 0.8699 0.26 0.00 0.00 0.72 0.00 0.02
#> TCGA.BA.5151.01 3 0.0547 0.6905 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.IQ.A61E.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.4076.01 5 0.1480 0.8998 0.00 0.04 0.00 0.02 0.94 0.00
#> TCGA.MZ.A7D7.01 5 0.0937 0.9041 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.UF.A7JT.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.5373.01 1 0.5798 -0.2078 0.48 0.00 0.00 0.32 0.00 0.20
#> TCGA.BB.7863.01 1 0.0937 0.8014 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.CN.5363.01 3 0.2020 0.6802 0.00 0.02 0.92 0.04 0.00 0.02
#> TCGA.BA.4077.01 4 0.3198 0.8689 0.26 0.00 0.00 0.74 0.00 0.00
#> TCGA.BB.7872.01 2 0.2512 0.7160 0.00 0.88 0.00 0.06 0.00 0.06
#> TCGA.H7.A6C4.01 1 0.4244 0.5524 0.72 0.00 0.00 0.08 0.00 0.20
#> TCGA.T2.A6X2.01 3 0.1267 0.6663 0.00 0.00 0.94 0.06 0.00 0.00
#> TCGA.CN.4741.01 6 0.4574 0.9178 0.00 0.00 0.26 0.02 0.04 0.68
#> TCGA.CV.A6JO.01 3 0.6160 0.2780 0.00 0.32 0.52 0.10 0.00 0.06
#> TCGA.BB.7866.01 6 0.4067 0.9173 0.00 0.00 0.26 0.00 0.04 0.70
#> TCGA.CN.5365.01 5 0.0937 0.9041 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.BB.4224.01 2 0.0547 0.7184 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.MT.A67F.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.5366.01 3 0.3475 0.5223 0.00 0.00 0.80 0.06 0.00 0.14
#> TCGA.QK.A6V9.01 6 0.4574 0.9178 0.00 0.00 0.26 0.02 0.04 0.68
#> TCGA.T2.A6WX.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A6JZ.01 3 0.0547 0.6807 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.CN.A6V1.01 2 0.4055 0.6212 0.00 0.78 0.00 0.04 0.14 0.04
#> TCGA.HD.A6I0.01 3 0.1267 0.6663 0.00 0.00 0.94 0.06 0.00 0.00
#> TCGA.CV.7430.01 5 0.0937 0.9041 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.CR.7383.01 4 0.3198 0.8689 0.26 0.00 0.00 0.74 0.00 0.00
#> TCGA.UF.A7JC.01 2 0.2725 0.6954 0.00 0.88 0.00 0.02 0.06 0.04
#> TCGA.CV.7568.01 5 0.3111 0.8143 0.00 0.12 0.00 0.02 0.84 0.02
#> TCGA.QK.A6IF.01 2 0.5302 0.2394 0.00 0.56 0.00 0.04 0.36 0.04
#> TCGA.CV.A6JT.01 3 0.4756 0.5731 0.00 0.10 0.74 0.10 0.00 0.06
#> TCGA.CV.7438.01 1 0.5865 -0.3616 0.44 0.00 0.00 0.36 0.00 0.20
#> TCGA.D6.A6EN.01 3 0.1267 0.6663 0.00 0.00 0.94 0.06 0.00 0.00
#> TCGA.CV.7429.01 5 0.4574 0.5867 0.00 0.26 0.00 0.02 0.68 0.04
#> TCGA.CV.7437.01 5 0.3997 0.7013 0.00 0.02 0.00 0.06 0.78 0.14
#> TCGA.CV.A6JD.01 1 0.0000 0.8145 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A6JN.01 2 0.5618 0.5326 0.00 0.64 0.20 0.10 0.00 0.06
#> TCGA.CV.7434.01 3 0.3475 0.5223 0.00 0.00 0.80 0.06 0.00 0.14
#> TCGA.D6.A6EK.01 2 0.0547 0.7196 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.HD.7832.01 3 0.4806 -0.1748 0.00 0.00 0.56 0.06 0.00 0.38
#> TCGA.P3.A6SX.01 5 0.0937 0.9041 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.QK.A6II.01 2 0.6100 0.3483 0.00 0.54 0.30 0.10 0.00 0.06
#> TCGA.P3.A6T7.01 3 0.1092 0.6891 0.00 0.02 0.96 0.02 0.00 0.00
#> TCGA.CR.7382.01 2 0.6246 0.1875 0.00 0.48 0.36 0.10 0.00 0.06
#> TCGA.T2.A6WZ.01 3 0.0937 0.6858 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.P3.A6T5.01 4 0.5490 0.8005 0.26 0.00 0.00 0.56 0.00 0.18
#> TCGA.CV.7433.01 5 0.3111 0.8143 0.00 0.12 0.00 0.02 0.84 0.02
#> TCGA.CR.7376.01 2 0.3631 0.6566 0.00 0.82 0.00 0.04 0.10 0.04
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.CQ.5327.01 1 0.2081 0.94302 0.86 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.HD.7753.01 2 0.5180 -0.29974 0.02 0.54 0.00 0.00 0.10 0.00 0.34
#> TCGA.CQ.5325.01 2 0.2906 0.50643 0.00 0.80 0.18 0.00 0.00 0.00 0.02
#> TCGA.CR.7391.01 4 0.3815 0.73076 0.00 0.00 0.00 0.62 0.00 0.02 0.36
#> TCGA.CV.7415.01 5 0.2803 0.72284 0.00 0.06 0.00 0.00 0.84 0.00 0.10
#> TCGA.CN.6011.01 5 0.1166 0.78830 0.00 0.06 0.00 0.00 0.94 0.00 0.00
#> TCGA.CV.6436.01 2 0.4408 -0.01540 0.02 0.52 0.44 0.00 0.00 0.00 0.02
#> TCGA.DQ.7592.01 2 0.5040 -0.28458 0.02 0.54 0.00 0.00 0.08 0.00 0.36
#> TCGA.CV.7416.01 4 0.1363 0.68669 0.02 0.00 0.00 0.94 0.04 0.00 0.00
#> TCGA.H7.7774.01 1 0.2081 0.94302 0.86 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.CQ.5330.01 1 0.2081 0.94302 0.86 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.CV.7427.01 1 0.2081 0.94302 0.86 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.CV.5979.01 2 0.0863 0.55074 0.04 0.96 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.6221.01 7 0.5416 0.79361 0.00 0.38 0.00 0.00 0.20 0.00 0.42
#> TCGA.CV.7425.01 1 0.3055 0.93354 0.82 0.00 0.00 0.14 0.02 0.00 0.02
#> TCGA.CV.6441.01 6 0.2864 0.88538 0.02 0.00 0.12 0.00 0.00 0.84 0.02
#> TCGA.IQ.7630.01 3 0.4386 0.30816 0.02 0.42 0.54 0.00 0.00 0.00 0.02
#> TCGA.CV.5977.01 3 0.3722 0.57941 0.04 0.00 0.76 0.00 0.00 0.18 0.02
#> TCGA.CQ.5324.01 3 0.1006 0.75156 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.CV.7407.01 4 0.4381 0.71772 0.00 0.00 0.00 0.58 0.00 0.06 0.36
#> TCGA.CV.5971.01 2 0.3413 0.02556 0.00 0.62 0.00 0.00 0.00 0.00 0.38
#> TCGA.CV.5970.01 2 0.3517 0.23806 0.02 0.70 0.00 0.00 0.00 0.00 0.28
#> TCGA.CN.6016.01 2 0.3517 0.43057 0.00 0.70 0.28 0.00 0.00 0.00 0.02
#> TCGA.CV.6003.01 4 0.0863 0.69644 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.CN.6021.01 4 0.4381 0.71772 0.00 0.00 0.00 0.58 0.00 0.06 0.36
#> TCGA.CV.5434.01 5 0.4590 0.74577 0.06 0.02 0.00 0.00 0.74 0.06 0.12
#> TCGA.CN.6017.01 2 0.3867 -0.05182 0.00 0.60 0.00 0.00 0.02 0.00 0.38
#> TCGA.CV.7235.01 5 0.1664 0.78596 0.00 0.06 0.00 0.00 0.92 0.00 0.02
#> TCGA.CV.5439.01 7 0.5976 0.80777 0.02 0.34 0.00 0.00 0.26 0.00 0.38
#> TCGA.CN.6020.01 2 0.1006 0.54752 0.02 0.96 0.00 0.00 0.02 0.00 0.00
#> TCGA.CV.7423.01 2 0.1363 0.55239 0.04 0.94 0.00 0.00 0.00 0.00 0.02
#> TCGA.CN.6023.01 5 0.3833 0.78846 0.04 0.06 0.00 0.00 0.78 0.00 0.12
#> TCGA.CR.7365.01 3 0.1363 0.74771 0.04 0.00 0.94 0.00 0.00 0.00 0.02
#> TCGA.CN.6024.01 5 0.4927 0.72460 0.06 0.02 0.00 0.00 0.70 0.06 0.16
#> TCGA.CV.5978.01 4 0.5602 0.63864 0.04 0.00 0.00 0.50 0.02 0.06 0.38
#> TCGA.CV.7089.01 3 0.3566 0.60569 0.04 0.00 0.78 0.00 0.00 0.16 0.02
#> TCGA.CN.6018.01 4 0.3496 -0.25320 0.42 0.00 0.00 0.58 0.00 0.00 0.00
#> TCGA.CV.5966.01 1 0.2422 0.92306 0.82 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.CV.5976.01 3 0.1166 0.74785 0.00 0.06 0.94 0.00 0.00 0.00 0.00
#> TCGA.CV.7411.01 4 0.0504 0.69641 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.CQ.5323.01 5 0.4654 0.77266 0.04 0.06 0.00 0.00 0.72 0.02 0.16
#> TCGA.BB.4217.01 2 0.3867 -0.05182 0.00 0.60 0.00 0.00 0.02 0.00 0.38
#> TCGA.CQ.7068.01 1 0.2654 0.71497 0.86 0.00 0.10 0.00 0.02 0.00 0.02
#> TCGA.CN.6995.01 2 0.3968 -0.01797 0.00 0.54 0.44 0.00 0.00 0.00 0.02
#> TCGA.CQ.5334.01 3 0.3566 0.60570 0.04 0.00 0.78 0.00 0.00 0.16 0.02
#> TCGA.CV.7410.01 2 0.3943 -0.18947 0.00 0.56 0.00 0.00 0.02 0.00 0.42
#> TCGA.DQ.7588.01 5 0.1664 0.78596 0.00 0.06 0.00 0.00 0.92 0.00 0.02
#> TCGA.CV.5973.01 4 0.2912 0.56810 0.14 0.00 0.00 0.82 0.04 0.00 0.00
#> TCGA.DQ.7591.01 6 0.3908 0.48244 0.00 0.00 0.00 0.00 0.20 0.72 0.08
#> TCGA.CV.5430.01 5 0.3630 0.78655 0.04 0.06 0.00 0.00 0.80 0.00 0.10
#> TCGA.CV.5435.01 3 0.4765 0.33409 0.02 0.00 0.64 0.00 0.02 0.28 0.04
#> TCGA.CV.5440.01 7 0.6382 0.84497 0.02 0.30 0.00 0.00 0.28 0.02 0.38
#> TCGA.CV.7104.01 4 0.3052 0.46053 0.20 0.00 0.00 0.78 0.02 0.00 0.00
#> TCGA.CV.7100.01 2 0.3943 -0.18947 0.00 0.56 0.00 0.00 0.02 0.00 0.42
#> TCGA.CV.7095.01 1 0.2081 0.94302 0.86 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.CR.7373.01 3 0.0000 0.75394 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7178.01 4 0.4328 0.72761 0.00 0.00 0.00 0.60 0.00 0.06 0.34
#> TCGA.CN.6998.01 2 0.4146 0.33473 0.02 0.64 0.32 0.00 0.00 0.00 0.02
#> TCGA.CV.7252.01 1 0.2081 0.94302 0.86 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.CR.6478.01 4 0.4328 0.72761 0.00 0.00 0.00 0.60 0.00 0.06 0.34
#> TCGA.CR.7380.01 3 0.1006 0.75161 0.02 0.00 0.96 0.00 0.00 0.00 0.02
#> TCGA.CV.7183.01 3 0.4356 0.35163 0.02 0.40 0.56 0.00 0.00 0.00 0.02
#> TCGA.CV.7102.01 4 0.3770 0.72840 0.00 0.00 0.00 0.74 0.00 0.08 0.18
#> TCGA.CV.7254.01 5 0.3833 0.78846 0.04 0.06 0.00 0.00 0.78 0.00 0.12
#> TCGA.CR.7394.01 4 0.0504 0.69943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CV.6955.01 1 0.2572 0.90839 0.80 0.00 0.00 0.20 0.00 0.00 0.00
#> TCGA.BA.5556.01 1 0.2572 0.90839 0.80 0.00 0.00 0.20 0.00 0.00 0.00
#> TCGA.CR.7386.01 2 0.3047 0.44086 0.00 0.72 0.28 0.00 0.00 0.00 0.00
#> TCGA.CR.6474.01 2 0.5871 -0.61902 0.02 0.42 0.00 0.00 0.22 0.00 0.34
#> TCGA.BA.5557.01 4 0.0504 0.69943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CV.7247.01 7 0.5976 0.82272 0.02 0.26 0.00 0.00 0.34 0.00 0.38
#> TCGA.CR.7377.01 2 0.2708 0.49724 0.00 0.78 0.22 0.00 0.00 0.00 0.00
#> TCGA.HD.7229.01 3 0.0504 0.75446 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.D6.6515.01 4 0.3815 0.73076 0.00 0.00 0.00 0.62 0.00 0.02 0.36
#> TCGA.CV.7238.01 4 0.0504 0.69943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CV.7097.01 3 0.3722 0.59680 0.04 0.00 0.76 0.00 0.00 0.18 0.02
#> TCGA.CN.5370.01 2 0.1006 0.55437 0.02 0.96 0.00 0.00 0.00 0.00 0.02
#> TCGA.CR.7367.01 3 0.1006 0.74922 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.CR.7401.01 2 0.0504 0.55495 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6942.01 1 0.3055 0.93354 0.82 0.00 0.00 0.14 0.02 0.00 0.02
#> TCGA.CV.7177.01 4 0.4681 0.71817 0.00 0.00 0.00 0.58 0.00 0.10 0.32
#> TCGA.CR.7395.01 1 0.2832 0.86597 0.76 0.00 0.00 0.24 0.00 0.00 0.00
#> TCGA.BA.5558.01 3 0.1886 0.71579 0.00 0.12 0.88 0.00 0.00 0.00 0.00
#> TCGA.CX.7085.01 4 0.0504 0.69943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CV.7099.01 1 0.2569 0.93963 0.84 0.00 0.00 0.14 0.02 0.00 0.00
#> TCGA.CV.7090.01 2 0.5908 -0.62384 0.02 0.42 0.00 0.00 0.24 0.00 0.32
#> TCGA.CX.7219.01 5 0.1166 0.78830 0.00 0.06 0.00 0.00 0.94 0.00 0.00
#> TCGA.CV.7243.01 3 0.4386 0.30816 0.02 0.42 0.54 0.00 0.00 0.00 0.02
#> TCGA.BA.6871.01 5 0.5254 0.67791 0.04 0.06 0.00 0.00 0.62 0.02 0.26
#> TCGA.CQ.6218.01 4 0.4418 0.72863 0.00 0.00 0.00 0.62 0.00 0.08 0.30
#> TCGA.C9.A47Z.01 1 0.3055 0.93354 0.82 0.00 0.00 0.14 0.02 0.00 0.02
#> TCGA.DQ.5625.01 4 0.2259 0.53334 0.16 0.00 0.00 0.84 0.00 0.00 0.00
#> TCGA.CR.6480.01 6 0.1886 0.89895 0.00 0.00 0.12 0.00 0.00 0.88 0.00
#> TCGA.D6.6825.01 2 0.0000 0.55506 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.C9.A480.01 4 0.1671 0.61279 0.10 0.00 0.00 0.90 0.00 0.00 0.00
#> TCGA.CV.6952.01 1 0.2422 0.92306 0.82 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.CQ.6222.01 2 0.2832 0.35045 0.00 0.76 0.00 0.00 0.00 0.00 0.24
#> TCGA.CN.A49C.01 6 0.2081 0.90169 0.00 0.00 0.14 0.00 0.00 0.86 0.00
#> TCGA.CN.6994.01 5 0.1664 0.78370 0.00 0.06 0.00 0.00 0.92 0.00 0.02
#> TCGA.CR.6491.01 3 0.3722 0.57941 0.04 0.00 0.76 0.00 0.00 0.18 0.02
#> TCGA.CV.6950.01 2 0.2003 0.54631 0.02 0.92 0.02 0.00 0.02 0.00 0.02
#> TCGA.CR.6473.01 6 0.2081 0.90169 0.00 0.00 0.14 0.00 0.00 0.86 0.00
#> TCGA.CQ.5331.01 4 0.0504 0.69943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.D6.6826.01 1 0.2906 0.91335 0.80 0.00 0.00 0.18 0.00 0.02 0.00
#> TCGA.CV.6935.01 5 0.4536 0.71609 0.06 0.00 0.00 0.00 0.72 0.08 0.14
#> TCGA.CV.6953.01 1 0.3055 0.93354 0.82 0.00 0.00 0.14 0.02 0.00 0.02
#> TCGA.CV.6945.01 5 0.3370 0.65586 0.00 0.06 0.00 0.00 0.78 0.00 0.16
#> TCGA.DQ.5630.01 2 0.2259 0.45194 0.00 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.CV.6943.01 2 0.1166 0.53754 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.BA.6870.01 4 0.4381 0.71772 0.00 0.00 0.00 0.58 0.00 0.06 0.36
#> TCGA.CR.6477.01 4 0.4175 0.72039 0.00 0.00 0.00 0.58 0.00 0.04 0.38
#> TCGA.CV.A45O.01 3 0.1166 0.74785 0.00 0.06 0.94 0.00 0.00 0.00 0.00
#> TCGA.CQ.6219.01 4 0.0504 0.69943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CN.4733.01 2 0.3867 -0.05182 0.00 0.60 0.00 0.00 0.02 0.00 0.38
#> TCGA.CN.A498.01 4 0.4681 0.71817 0.00 0.00 0.00 0.58 0.00 0.10 0.32
#> TCGA.CN.6989.01 5 0.3833 0.78846 0.04 0.06 0.00 0.00 0.78 0.00 0.12
#> TCGA.CV.6953.11 4 0.3815 0.73076 0.00 0.00 0.00 0.62 0.00 0.02 0.36
#> TCGA.D6.6517.01 2 0.2159 0.51975 0.02 0.90 0.00 0.00 0.02 0.00 0.06
#> TCGA.CQ.6220.01 2 0.1860 0.53180 0.02 0.92 0.00 0.00 0.02 0.00 0.04
#> TCGA.HD.A4C1.01 1 0.3055 0.93354 0.82 0.00 0.00 0.14 0.02 0.00 0.02
#> TCGA.CR.6493.01 3 0.4356 0.35813 0.02 0.40 0.56 0.00 0.00 0.00 0.02
#> TCGA.D6.6516.01 5 0.1664 0.77968 0.02 0.06 0.00 0.00 0.92 0.00 0.00
#> TCGA.CQ.6227.01 2 0.2945 0.31790 0.00 0.74 0.00 0.00 0.00 0.00 0.26
#> TCGA.CV.A45P.01 4 0.2081 0.56390 0.14 0.00 0.00 0.86 0.00 0.00 0.00
#> TCGA.CV.A45Q.01 1 0.3055 0.93354 0.82 0.00 0.00 0.14 0.02 0.00 0.02
#> TCGA.CV.A45T.01 4 0.0504 0.69943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CN.6996.01 4 0.2081 0.56390 0.14 0.00 0.00 0.86 0.00 0.00 0.00
#> TCGA.BA.6873.01 2 0.4269 0.24482 0.02 0.60 0.36 0.00 0.00 0.00 0.02
#> TCGA.CR.6467.01 6 0.2081 0.90169 0.00 0.00 0.14 0.00 0.00 0.86 0.00
#> TCGA.BA.6868.01 5 0.1166 0.78830 0.00 0.06 0.00 0.00 0.94 0.00 0.00
#> TCGA.CV.6959.01 3 0.3887 0.56165 0.02 0.26 0.70 0.00 0.00 0.00 0.02
#> TCGA.CQ.6229.01 2 0.1928 0.54702 0.02 0.90 0.08 0.00 0.00 0.00 0.00
#> TCGA.CQ.6224.01 2 0.4146 0.33473 0.02 0.64 0.32 0.00 0.00 0.00 0.02
#> TCGA.CQ.6223.01 2 0.3661 0.49268 0.02 0.74 0.22 0.00 0.00 0.00 0.02
#> TCGA.DQ.5624.01 4 0.3815 0.73076 0.00 0.00 0.00 0.62 0.00 0.02 0.36
#> TCGA.CV.A45R.01 2 0.3661 0.49211 0.02 0.74 0.22 0.00 0.00 0.00 0.02
#> TCGA.CN.A499.01 4 0.4681 0.71817 0.00 0.00 0.00 0.58 0.00 0.10 0.32
#> TCGA.CN.A49B.01 5 0.5026 0.65764 0.02 0.06 0.00 0.00 0.62 0.02 0.28
#> TCGA.BA.5152.01 2 0.1505 0.54306 0.02 0.94 0.00 0.00 0.02 0.00 0.02
#> TCGA.CV.6938.01 3 0.0000 0.75394 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.5326.01 5 0.4264 0.47118 0.02 0.06 0.00 0.00 0.70 0.00 0.22
#> TCGA.CV.6940.01 4 0.5023 0.72883 0.00 0.00 0.00 0.62 0.04 0.08 0.26
#> TCGA.CR.6471.01 2 0.1006 0.54974 0.00 0.96 0.02 0.00 0.00 0.02 0.00
#> TCGA.BA.6872.01 2 0.4070 0.25855 0.00 0.62 0.34 0.00 0.00 0.00 0.04
#> TCGA.CQ.A4C6.01 3 0.3994 0.19525 0.00 0.48 0.50 0.00 0.00 0.00 0.02
#> TCGA.CQ.7064.01 4 0.0000 0.69486 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.IQ.A61K.01 1 0.4283 0.39450 0.48 0.00 0.00 0.48 0.04 0.00 0.00
#> TCGA.HD.A633.01 3 0.0504 0.75336 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.F7.A61W.01 7 0.5976 0.82272 0.02 0.26 0.00 0.00 0.34 0.00 0.38
#> TCGA.BA.A6DF.01 1 0.2081 0.94302 0.86 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.D6.A4ZB.01 5 0.4905 0.73152 0.06 0.10 0.00 0.00 0.68 0.00 0.16
#> TCGA.CV.A45Y.01 2 0.2906 0.50643 0.00 0.80 0.18 0.00 0.00 0.00 0.02
#> TCGA.BB.A5HU.01 2 0.5908 -0.62384 0.02 0.42 0.00 0.00 0.24 0.00 0.32
#> TCGA.CQ.A4C7.01 3 0.0504 0.75280 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.P3.A5Q6.01 2 0.4764 -0.20587 0.02 0.56 0.00 0.00 0.02 0.02 0.38
#> TCGA.CQ.A4CD.01 3 0.2912 0.69550 0.00 0.14 0.82 0.00 0.00 0.00 0.04
#> TCGA.BA.A6DB.01 4 0.3815 0.73076 0.00 0.00 0.00 0.62 0.00 0.02 0.36
#> TCGA.F7.A620.01 3 0.1664 0.74490 0.00 0.06 0.92 0.00 0.00 0.00 0.02
#> TCGA.CX.A4AQ.01 5 0.4831 0.73931 0.06 0.02 0.00 0.00 0.72 0.08 0.12
#> TCGA.CV.A464.01 2 0.3413 0.02556 0.00 0.62 0.00 0.00 0.00 0.00 0.38
#> TCGA.IQ.A61L.01 4 0.2081 0.56390 0.14 0.00 0.00 0.86 0.00 0.00 0.00
#> TCGA.QK.A8Z9.01 3 0.5409 0.47467 0.00 0.18 0.60 0.00 0.18 0.00 0.04
#> TCGA.BB.A5HY.01 3 0.5159 0.40244 0.06 0.00 0.64 0.00 0.02 0.24 0.04
#> TCGA.HD.8635.01 4 0.4681 0.71817 0.00 0.00 0.00 0.58 0.00 0.10 0.32
#> TCGA.QK.A652.01 2 0.1363 0.54346 0.02 0.94 0.00 0.00 0.00 0.00 0.04
#> TCGA.MT.A67G.01 4 0.4538 0.72287 0.00 0.00 0.00 0.62 0.00 0.10 0.28
#> TCGA.QK.A64Z.01 4 0.2259 0.53334 0.16 0.00 0.00 0.84 0.00 0.00 0.00
#> TCGA.HD.8634.01 4 0.3459 -0.18711 0.40 0.00 0.00 0.60 0.00 0.00 0.00
#> TCGA.CQ.7063.01 1 0.2081 0.94302 0.86 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.F7.A50J.01 4 0.0863 0.69644 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.F7.8298.01 5 0.3863 0.58259 0.02 0.20 0.00 0.00 0.74 0.00 0.04
#> TCGA.F7.8489.01 2 0.3294 0.13856 0.00 0.66 0.00 0.00 0.00 0.00 0.34
#> TCGA.F7.A50G.01 2 0.0504 0.55174 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.A4CA.01 2 0.3867 -0.05182 0.00 0.60 0.00 0.00 0.02 0.00 0.38
#> TCGA.T3.A92N.01 5 0.4590 0.74577 0.06 0.02 0.00 0.00 0.74 0.06 0.12
#> TCGA.CN.A63Y.01 7 0.5819 0.81137 0.00 0.36 0.00 0.00 0.20 0.02 0.42
#> TCGA.CQ.5333.01 3 0.3722 0.57941 0.04 0.00 0.76 0.00 0.00 0.18 0.02
#> TCGA.P3.A5QE.01 5 0.5159 0.70246 0.04 0.06 0.00 0.00 0.64 0.02 0.24
#> TCGA.BA.A6DJ.01 3 0.4197 0.55229 0.04 0.00 0.74 0.00 0.02 0.18 0.02
#> TCGA.MT.A51W.01 4 0.4175 0.72039 0.00 0.00 0.00 0.58 0.00 0.04 0.38
#> TCGA.IQ.A61G.01 5 0.4565 0.57409 0.02 0.08 0.00 0.00 0.72 0.02 0.16
#> TCGA.IQ.A61J.01 2 0.2832 0.35045 0.00 0.76 0.00 0.00 0.00 0.00 0.24
#> TCGA.BA.A6DG.01 2 0.2832 0.35045 0.00 0.76 0.00 0.00 0.00 0.00 0.24
#> TCGA.CQ.A4CH.01 2 0.3867 -0.05182 0.00 0.60 0.00 0.00 0.02 0.00 0.38
#> TCGA.CQ.A4CB.01 3 0.1664 0.74490 0.00 0.06 0.92 0.00 0.00 0.00 0.02
#> TCGA.D6.8569.01 2 0.0504 0.55495 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.IQ.A61I.01 6 0.2081 0.90169 0.00 0.00 0.14 0.00 0.00 0.86 0.00
#> TCGA.D6.A4Z9.01 3 0.2163 0.72420 0.00 0.10 0.88 0.00 0.00 0.00 0.02
#> TCGA.CQ.7071.01 1 0.2569 0.93963 0.84 0.00 0.00 0.14 0.02 0.00 0.00
#> TCGA.H7.8501.01 3 0.1363 0.74237 0.04 0.00 0.94 0.00 0.00 0.02 0.00
#> TCGA.BB.8601.01 5 0.4590 0.74577 0.06 0.02 0.00 0.00 0.74 0.06 0.12
#> TCGA.H7.8502.01 5 0.3289 0.79368 0.02 0.06 0.00 0.00 0.82 0.00 0.10
#> TCGA.F7.A61S.01 2 0.3887 0.45057 0.02 0.70 0.26 0.00 0.00 0.00 0.02
#> TCGA.CV.A463.01 1 0.3055 0.93354 0.82 0.00 0.00 0.14 0.02 0.00 0.02
#> TCGA.D6.8568.01 2 0.0863 0.54638 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.CN.A642.01 3 0.1718 0.73143 0.04 0.00 0.92 0.00 0.00 0.04 0.00
#> TCGA.CN.5367.01 4 0.4264 0.73140 0.00 0.00 0.00 0.62 0.00 0.06 0.32
#> TCGA.P3.A6T2.01 3 0.3722 0.57941 0.04 0.00 0.76 0.00 0.00 0.18 0.02
#> TCGA.CN.A6V7.01 6 0.1886 0.89895 0.00 0.00 0.12 0.00 0.00 0.88 0.00
#> TCGA.CN.A640.01 1 0.3525 0.54736 0.56 0.00 0.00 0.44 0.00 0.00 0.00
#> TCGA.DQ.7589.01 5 0.3630 0.78655 0.04 0.06 0.00 0.00 0.80 0.00 0.10
#> TCGA.CN.4725.01 2 0.1363 0.55239 0.04 0.94 0.00 0.00 0.00 0.00 0.02
#> TCGA.HL.7533.01 2 0.6073 -0.68032 0.02 0.42 0.00 0.00 0.16 0.02 0.38
#> TCGA.UF.A7JO.01 1 0.2572 0.90839 0.80 0.00 0.00 0.20 0.00 0.00 0.00
#> TCGA.UF.A7JV.01 4 0.0504 0.69943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CN.4729.01 2 0.1166 0.55133 0.00 0.94 0.06 0.00 0.00 0.00 0.00
#> TCGA.IQ.A6SG.01 4 0.5602 0.63864 0.04 0.00 0.00 0.50 0.02 0.06 0.38
#> TCGA.MT.A67A.01 1 0.3055 0.93354 0.82 0.00 0.00 0.14 0.02 0.00 0.02
#> TCGA.CN.5361.01 2 0.2213 0.53514 0.00 0.90 0.04 0.00 0.00 0.02 0.04
#> TCGA.CN.5359.01 5 0.2313 0.76113 0.00 0.06 0.00 0.00 0.88 0.00 0.06
#> TCGA.BB.7861.01 2 0.4923 -0.40903 0.00 0.50 0.00 0.00 0.06 0.02 0.42
#> TCGA.BB.A6UO.01 1 0.3055 0.93354 0.82 0.00 0.00 0.14 0.02 0.00 0.02
#> TCGA.CN.4734.01 3 0.3722 0.57941 0.04 0.00 0.76 0.00 0.00 0.18 0.02
#> TCGA.BA.4075.01 3 0.1928 0.73887 0.00 0.08 0.90 0.00 0.00 0.00 0.02
#> TCGA.BB.7871.01 4 0.6313 0.54913 0.04 0.00 0.00 0.44 0.08 0.06 0.38
#> TCGA.CN.4726.01 3 0.0504 0.75280 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.UF.A7JS.01 2 0.4992 0.40882 0.00 0.66 0.16 0.00 0.14 0.00 0.04
#> TCGA.CN.4736.01 4 0.3815 0.73076 0.00 0.00 0.00 0.62 0.00 0.02 0.36
#> TCGA.CN.5355.01 3 0.3909 0.40630 0.00 0.40 0.58 0.00 0.00 0.00 0.02
#> TCGA.DQ.7590.01 5 0.5453 0.70730 0.04 0.02 0.00 0.00 0.64 0.14 0.16
#> TCGA.CN.5369.01 4 0.3685 0.73394 0.00 0.00 0.00 0.66 0.00 0.02 0.32
#> TCGA.BA.5151.01 3 0.0504 0.75604 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.IQ.A61E.01 1 0.2081 0.94302 0.86 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.BA.4076.01 5 0.1166 0.78830 0.00 0.06 0.00 0.00 0.94 0.00 0.00
#> TCGA.MZ.A7D7.01 5 0.1664 0.78596 0.00 0.06 0.00 0.00 0.92 0.00 0.02
#> TCGA.UF.A7JT.01 1 0.2081 0.94302 0.86 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.CN.5373.01 4 0.2912 0.56810 0.14 0.00 0.00 0.82 0.04 0.00 0.00
#> TCGA.BB.7863.01 1 0.2081 0.94302 0.86 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.CN.5363.01 3 0.2016 0.74361 0.00 0.06 0.90 0.00 0.00 0.00 0.04
#> TCGA.BA.4077.01 4 0.4681 0.71817 0.00 0.00 0.00 0.58 0.00 0.10 0.32
#> TCGA.BB.7872.01 2 0.0863 0.55074 0.04 0.96 0.00 0.00 0.00 0.00 0.00
#> TCGA.H7.A6C4.01 4 0.3496 -0.25320 0.42 0.00 0.00 0.58 0.00 0.00 0.00
#> TCGA.T2.A6X2.01 3 0.1363 0.74237 0.04 0.00 0.94 0.00 0.00 0.02 0.00
#> TCGA.CN.4741.01 6 0.1886 0.89895 0.00 0.00 0.12 0.00 0.00 0.88 0.00
#> TCGA.CV.A6JO.01 3 0.3546 0.26901 0.00 0.46 0.54 0.00 0.00 0.00 0.00
#> TCGA.BB.7866.01 6 0.2081 0.90169 0.00 0.00 0.14 0.00 0.00 0.86 0.00
#> TCGA.CN.5365.01 5 0.1664 0.78596 0.00 0.06 0.00 0.00 0.92 0.00 0.02
#> TCGA.BB.4224.01 2 0.2769 0.48599 0.02 0.86 0.00 0.00 0.04 0.00 0.08
#> TCGA.MT.A67F.01 1 0.2081 0.94302 0.86 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.CN.5366.01 3 0.3566 0.60569 0.04 0.00 0.78 0.00 0.00 0.16 0.02
#> TCGA.QK.A6V9.01 6 0.2722 0.87603 0.00 0.00 0.12 0.00 0.00 0.84 0.04
#> TCGA.T2.A6WX.01 1 0.2081 0.94302 0.86 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.CV.A6JZ.01 3 0.1006 0.75143 0.00 0.02 0.96 0.00 0.00 0.00 0.02
#> TCGA.CN.A6V1.01 2 0.4684 -0.32450 0.00 0.52 0.00 0.00 0.04 0.02 0.42
#> TCGA.HD.A6I0.01 3 0.1363 0.74237 0.04 0.00 0.94 0.00 0.00 0.02 0.00
#> TCGA.CV.7430.01 5 0.4466 0.75750 0.04 0.06 0.00 0.00 0.70 0.00 0.20
#> TCGA.CR.7383.01 4 0.4681 0.71817 0.00 0.00 0.00 0.58 0.00 0.10 0.32
#> TCGA.UF.A7JC.01 2 0.4212 0.00126 0.02 0.62 0.00 0.00 0.02 0.00 0.34
#> TCGA.CV.7568.01 5 0.3911 0.45467 0.00 0.06 0.00 0.00 0.70 0.00 0.24
#> TCGA.QK.A6IF.01 7 0.5756 0.81938 0.00 0.28 0.00 0.00 0.22 0.02 0.48
#> TCGA.CV.A6JT.01 3 0.3228 0.65921 0.02 0.16 0.80 0.00 0.00 0.00 0.02
#> TCGA.CV.7438.01 4 0.2912 0.56810 0.14 0.00 0.00 0.82 0.04 0.00 0.00
#> TCGA.D6.A6EN.01 3 0.1363 0.74237 0.04 0.00 0.94 0.00 0.00 0.02 0.00
#> TCGA.CV.7429.01 5 0.4992 0.03606 0.02 0.10 0.00 0.00 0.60 0.00 0.28
#> TCGA.CV.7437.01 5 0.4696 0.70470 0.06 0.00 0.00 0.00 0.70 0.08 0.16
#> TCGA.CV.A6JD.01 1 0.2081 0.94302 0.86 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.CV.A6JN.01 2 0.3228 0.51596 0.02 0.80 0.16 0.00 0.00 0.00 0.02
#> TCGA.CV.7434.01 3 0.3244 0.60071 0.04 0.00 0.78 0.00 0.00 0.18 0.00
#> TCGA.D6.A6EK.01 2 0.2804 0.48580 0.02 0.86 0.00 0.00 0.06 0.00 0.06
#> TCGA.HD.7832.01 6 0.4278 0.19484 0.04 0.00 0.46 0.00 0.00 0.50 0.00
#> TCGA.P3.A6SX.01 5 0.1664 0.78596 0.00 0.06 0.00 0.00 0.92 0.00 0.02
#> TCGA.QK.A6II.01 2 0.3606 0.38930 0.00 0.68 0.30 0.00 0.00 0.00 0.02
#> TCGA.P3.A6T7.01 3 0.1664 0.74490 0.00 0.06 0.92 0.00 0.00 0.00 0.02
#> TCGA.CR.7382.01 2 0.3294 0.32451 0.00 0.66 0.34 0.00 0.00 0.00 0.00
#> TCGA.T2.A6WZ.01 3 0.1363 0.74876 0.00 0.04 0.94 0.00 0.00 0.00 0.02
#> TCGA.P3.A6T5.01 4 0.0863 0.69644 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.CV.7433.01 5 0.3911 0.45467 0.00 0.06 0.00 0.00 0.70 0.00 0.24
#> TCGA.CR.7376.01 2 0.3909 -0.12866 0.00 0.58 0.00 0.00 0.02 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.CQ.5327.01 1 0.1804 0.8965 0.90 0.00 0.00 0.08 0.00 0.00 0.00 0.02
#> TCGA.HD.7753.01 7 0.4960 0.6904 0.00 0.28 0.00 0.00 0.04 0.00 0.58 0.10
#> TCGA.CQ.5325.01 2 0.2719 0.6919 0.00 0.80 0.18 0.00 0.00 0.00 0.00 0.02
#> TCGA.CR.7391.01 4 0.0471 0.7328 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CV.7415.01 5 0.4982 0.7087 0.00 0.02 0.00 0.00 0.58 0.00 0.18 0.22
#> TCGA.CN.6011.01 5 0.3991 0.7352 0.00 0.02 0.00 0.00 0.70 0.00 0.06 0.22
#> TCGA.CV.6436.01 2 0.2938 0.6091 0.00 0.70 0.30 0.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.7592.01 7 0.4826 0.7146 0.02 0.30 0.00 0.00 0.04 0.00 0.60 0.04
#> TCGA.CV.7416.01 4 0.5430 -0.2519 0.04 0.00 0.00 0.48 0.00 0.02 0.08 0.38
#> TCGA.H7.7774.01 1 0.2132 0.8928 0.88 0.00 0.00 0.08 0.00 0.00 0.00 0.04
#> TCGA.CQ.5330.01 1 0.2407 0.8849 0.86 0.00 0.00 0.08 0.00 0.00 0.00 0.06
#> TCGA.CV.7427.01 1 0.1341 0.8968 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.CV.5979.01 2 0.2680 0.5321 0.02 0.84 0.00 0.00 0.00 0.00 0.12 0.02
#> TCGA.CQ.6221.01 7 0.3421 0.6200 0.00 0.08 0.00 0.00 0.08 0.00 0.80 0.04
#> TCGA.CV.7425.01 1 0.1341 0.8968 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.CV.6441.01 6 0.2864 0.8546 0.00 0.00 0.02 0.00 0.08 0.84 0.00 0.06
#> TCGA.IQ.7630.01 2 0.3193 0.4721 0.00 0.62 0.38 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5977.01 3 0.4046 0.7453 0.06 0.00 0.74 0.00 0.00 0.02 0.02 0.16
#> TCGA.CQ.5324.01 3 0.1741 0.7984 0.04 0.02 0.92 0.00 0.00 0.00 0.00 0.02
#> TCGA.CV.7407.01 4 0.1275 0.7156 0.00 0.00 0.00 0.94 0.04 0.00 0.02 0.00
#> TCGA.CV.5971.01 7 0.3570 0.6820 0.02 0.36 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.CV.5970.01 7 0.4125 0.5589 0.02 0.44 0.00 0.00 0.00 0.00 0.52 0.02
#> TCGA.CN.6016.01 2 0.2981 0.6848 0.00 0.76 0.22 0.00 0.00 0.00 0.00 0.02
#> TCGA.CV.6003.01 4 0.4717 0.0946 0.00 0.00 0.00 0.54 0.00 0.02 0.08 0.36
#> TCGA.CN.6021.01 4 0.1275 0.7156 0.00 0.00 0.00 0.94 0.04 0.00 0.02 0.00
#> TCGA.CV.5434.01 5 0.2862 0.5967 0.00 0.00 0.00 0.00 0.82 0.10 0.00 0.08
#> TCGA.CN.6017.01 7 0.3570 0.6820 0.02 0.36 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.CV.7235.01 5 0.4467 0.7417 0.00 0.02 0.00 0.00 0.66 0.00 0.12 0.20
#> TCGA.CV.5439.01 7 0.4873 0.5558 0.00 0.12 0.00 0.00 0.12 0.00 0.66 0.10
#> TCGA.CN.6020.01 2 0.2862 0.5789 0.00 0.82 0.00 0.00 0.00 0.00 0.08 0.10
#> TCGA.CV.7423.01 2 0.1091 0.6208 0.00 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.CN.6023.01 5 0.2484 0.7466 0.00 0.02 0.00 0.00 0.86 0.00 0.10 0.02
#> TCGA.CR.7365.01 3 0.2025 0.7933 0.02 0.00 0.88 0.00 0.00 0.00 0.00 0.10
#> TCGA.CN.6024.01 5 0.3314 0.5972 0.00 0.00 0.00 0.00 0.80 0.10 0.02 0.08
#> TCGA.CV.5978.01 4 0.1804 0.6752 0.00 0.00 0.00 0.90 0.08 0.00 0.02 0.00
#> TCGA.CV.7089.01 3 0.3311 0.7642 0.02 0.00 0.80 0.00 0.00 0.02 0.02 0.14
#> TCGA.CN.6018.01 8 0.4680 0.3944 0.40 0.00 0.00 0.12 0.00 0.00 0.00 0.48
#> TCGA.CV.5966.01 1 0.3227 0.8197 0.78 0.00 0.00 0.08 0.00 0.00 0.00 0.14
#> TCGA.CV.5976.01 3 0.1563 0.7515 0.00 0.10 0.90 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7411.01 4 0.3714 0.0094 0.00 0.00 0.00 0.54 0.00 0.00 0.02 0.44
#> TCGA.CQ.5323.01 5 0.4057 0.6955 0.00 0.02 0.00 0.00 0.72 0.02 0.20 0.04
#> TCGA.BB.4217.01 7 0.3570 0.6820 0.02 0.36 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.CQ.7068.01 1 0.0471 0.7811 0.98 0.00 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.6995.01 2 0.3449 0.6090 0.00 0.66 0.32 0.00 0.00 0.00 0.00 0.02
#> TCGA.CQ.5334.01 3 0.4046 0.7453 0.06 0.00 0.74 0.00 0.00 0.02 0.02 0.16
#> TCGA.CV.7410.01 7 0.4106 0.7181 0.02 0.30 0.00 0.00 0.04 0.00 0.64 0.00
#> TCGA.DQ.7588.01 5 0.4621 0.7348 0.00 0.02 0.00 0.00 0.64 0.00 0.14 0.20
#> TCGA.CV.5973.01 8 0.6295 0.7236 0.16 0.00 0.00 0.36 0.00 0.02 0.08 0.38
#> TCGA.DQ.7591.01 6 0.1341 0.8819 0.00 0.00 0.00 0.00 0.08 0.92 0.00 0.00
#> TCGA.CV.5430.01 5 0.0941 0.7296 0.00 0.02 0.00 0.00 0.96 0.00 0.02 0.00
#> TCGA.CV.5435.01 3 0.5288 0.5219 0.02 0.00 0.64 0.00 0.10 0.14 0.00 0.10
#> TCGA.CV.5440.01 7 0.3586 0.5632 0.00 0.06 0.00 0.00 0.12 0.00 0.78 0.04
#> TCGA.CV.7104.01 8 0.5342 0.8004 0.18 0.00 0.00 0.34 0.00 0.00 0.02 0.46
#> TCGA.CV.7100.01 7 0.3615 0.7192 0.00 0.20 0.00 0.00 0.04 0.00 0.74 0.02
#> TCGA.CV.7095.01 1 0.1804 0.8965 0.90 0.00 0.00 0.08 0.00 0.00 0.00 0.02
#> TCGA.CR.7373.01 3 0.1408 0.7993 0.02 0.02 0.94 0.00 0.00 0.00 0.00 0.02
#> TCGA.CV.7178.01 4 0.1408 0.7283 0.00 0.00 0.00 0.94 0.00 0.02 0.02 0.02
#> TCGA.CN.6998.01 2 0.2534 0.6826 0.00 0.78 0.22 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7252.01 1 0.2132 0.8930 0.88 0.00 0.00 0.08 0.00 0.00 0.00 0.04
#> TCGA.CR.6478.01 4 0.0471 0.7328 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CR.7380.01 3 0.1275 0.8015 0.02 0.00 0.94 0.00 0.00 0.00 0.00 0.04
#> TCGA.CV.7183.01 2 0.3272 0.3794 0.00 0.58 0.42 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7102.01 4 0.3169 0.5903 0.00 0.00 0.00 0.78 0.00 0.02 0.02 0.18
#> TCGA.CV.7254.01 5 0.2484 0.7466 0.00 0.02 0.00 0.00 0.86 0.00 0.10 0.02
#> TCGA.CR.7394.01 4 0.3237 0.1955 0.00 0.00 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.CV.6955.01 1 0.3528 0.7640 0.74 0.00 0.00 0.08 0.00 0.00 0.00 0.18
#> TCGA.BA.5556.01 1 0.3385 0.7937 0.76 0.00 0.00 0.08 0.00 0.00 0.00 0.16
#> TCGA.CR.7386.01 2 0.2569 0.6969 0.00 0.82 0.16 0.00 0.00 0.00 0.00 0.02
#> TCGA.CR.6474.01 7 0.5028 0.5289 0.00 0.10 0.00 0.00 0.14 0.00 0.64 0.12
#> TCGA.BA.5557.01 4 0.3237 0.1955 0.00 0.00 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.CV.7247.01 7 0.3630 0.6060 0.00 0.08 0.00 0.00 0.10 0.00 0.78 0.04
#> TCGA.CR.7377.01 2 0.2856 0.6894 0.00 0.78 0.20 0.00 0.00 0.00 0.00 0.02
#> TCGA.HD.7229.01 3 0.0808 0.7907 0.00 0.04 0.96 0.00 0.00 0.00 0.00 0.00
#> TCGA.D6.6515.01 4 0.0808 0.7274 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CV.7238.01 4 0.3237 0.1955 0.00 0.00 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.CV.7097.01 3 0.3627 0.7597 0.04 0.00 0.78 0.00 0.00 0.02 0.02 0.14
#> TCGA.CN.5370.01 2 0.0471 0.6531 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.CR.7367.01 3 0.1275 0.8002 0.02 0.00 0.94 0.00 0.00 0.00 0.00 0.04
#> TCGA.CR.7401.01 2 0.1091 0.6208 0.00 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.CV.6942.01 1 0.1341 0.8968 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.CV.7177.01 4 0.0941 0.7269 0.00 0.00 0.00 0.96 0.02 0.00 0.02 0.00
#> TCGA.CR.7395.01 1 0.3774 0.6930 0.70 0.00 0.00 0.08 0.00 0.00 0.00 0.22
#> TCGA.BA.5558.01 3 0.2856 0.5912 0.00 0.20 0.78 0.00 0.00 0.00 0.00 0.02
#> TCGA.CX.7085.01 4 0.3299 0.0306 0.00 0.00 0.00 0.56 0.00 0.00 0.00 0.44
#> TCGA.CV.7099.01 1 0.1341 0.8968 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.CV.7090.01 7 0.6211 0.1381 0.00 0.14 0.00 0.00 0.22 0.00 0.44 0.20
#> TCGA.CX.7219.01 5 0.4621 0.7348 0.00 0.02 0.00 0.00 0.64 0.00 0.14 0.20
#> TCGA.CV.7243.01 2 0.3193 0.4721 0.00 0.62 0.38 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.6871.01 5 0.4106 0.6539 0.00 0.02 0.00 0.00 0.64 0.00 0.30 0.04
#> TCGA.CQ.6218.01 4 0.1408 0.7283 0.00 0.00 0.00 0.94 0.00 0.02 0.02 0.02
#> TCGA.C9.A47Z.01 1 0.1341 0.8968 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.DQ.5625.01 8 0.4943 0.8000 0.18 0.00 0.00 0.34 0.00 0.00 0.00 0.48
#> TCGA.CR.6480.01 6 0.0471 0.9561 0.00 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.D6.6825.01 2 0.1275 0.6487 0.00 0.94 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.C9.A480.01 8 0.4873 0.7996 0.16 0.00 0.00 0.36 0.00 0.00 0.00 0.48
#> TCGA.CV.6952.01 1 0.3227 0.8197 0.78 0.00 0.00 0.08 0.00 0.00 0.00 0.14
#> TCGA.CQ.6222.01 2 0.4137 -0.4344 0.02 0.50 0.00 0.00 0.00 0.00 0.46 0.02
#> TCGA.CN.A49C.01 6 0.1408 0.9560 0.00 0.00 0.02 0.00 0.00 0.94 0.02 0.02
#> TCGA.CN.6994.01 5 0.4147 0.7200 0.00 0.04 0.00 0.00 0.68 0.00 0.04 0.24
#> TCGA.CR.6491.01 3 0.4046 0.7453 0.06 0.00 0.74 0.00 0.00 0.02 0.02 0.16
#> TCGA.CV.6950.01 2 0.1887 0.6762 0.00 0.90 0.04 0.00 0.00 0.00 0.00 0.06
#> TCGA.CR.6473.01 6 0.1408 0.9560 0.00 0.00 0.02 0.00 0.00 0.94 0.02 0.02
#> TCGA.CQ.5331.01 4 0.3237 0.1955 0.00 0.00 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.D6.6826.01 1 0.3227 0.8197 0.78 0.00 0.00 0.08 0.00 0.00 0.00 0.14
#> TCGA.CV.6935.01 5 0.2862 0.5967 0.00 0.00 0.00 0.00 0.82 0.10 0.00 0.08
#> TCGA.CV.6953.01 1 0.1341 0.8968 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.CV.6945.01 5 0.4882 0.6956 0.00 0.02 0.00 0.00 0.60 0.00 0.20 0.18
#> TCGA.DQ.5630.01 2 0.3570 -0.1375 0.02 0.62 0.00 0.00 0.00 0.00 0.36 0.00
#> TCGA.CV.6943.01 2 0.2859 0.5328 0.02 0.82 0.00 0.00 0.00 0.00 0.14 0.02
#> TCGA.BA.6870.01 4 0.0941 0.7269 0.00 0.00 0.00 0.96 0.02 0.00 0.02 0.00
#> TCGA.CR.6477.01 4 0.0000 0.7311 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A45O.01 3 0.1091 0.7819 0.00 0.06 0.94 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.6219.01 4 0.3237 0.1955 0.00 0.00 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.CN.4733.01 7 0.3570 0.6820 0.02 0.36 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.CN.A498.01 4 0.0941 0.7269 0.00 0.00 0.00 0.96 0.02 0.00 0.02 0.00
#> TCGA.CN.6989.01 5 0.2484 0.7466 0.00 0.02 0.00 0.00 0.86 0.00 0.10 0.02
#> TCGA.CV.6953.11 4 0.0471 0.7328 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.D6.6517.01 2 0.3021 0.4487 0.02 0.80 0.00 0.00 0.00 0.00 0.16 0.02
#> TCGA.CQ.6220.01 2 0.2680 0.5275 0.02 0.84 0.00 0.00 0.00 0.00 0.12 0.02
#> TCGA.HD.A4C1.01 1 0.1341 0.8968 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.CR.6493.01 2 0.3272 0.3794 0.00 0.58 0.42 0.00 0.00 0.00 0.00 0.00
#> TCGA.D6.6516.01 5 0.4180 0.7305 0.00 0.04 0.00 0.00 0.70 0.00 0.06 0.20
#> TCGA.CQ.6227.01 7 0.4141 0.4723 0.02 0.48 0.00 0.00 0.00 0.00 0.48 0.02
#> TCGA.CV.A45P.01 8 0.4873 0.7996 0.16 0.00 0.00 0.36 0.00 0.00 0.00 0.48
#> TCGA.CV.A45Q.01 1 0.1341 0.8968 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.CV.A45T.01 4 0.3237 0.1955 0.00 0.00 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.CN.6996.01 8 0.4873 0.7996 0.16 0.00 0.00 0.36 0.00 0.00 0.00 0.48
#> TCGA.BA.6873.01 2 0.2852 0.6350 0.00 0.72 0.28 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.6467.01 6 0.1408 0.9560 0.00 0.00 0.02 0.00 0.00 0.94 0.02 0.02
#> TCGA.BA.6868.01 5 0.4467 0.7387 0.00 0.02 0.00 0.00 0.66 0.00 0.12 0.20
#> TCGA.CV.6959.01 2 0.3329 0.2420 0.00 0.52 0.48 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.6229.01 2 0.0808 0.6796 0.00 0.96 0.04 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.6224.01 2 0.2534 0.6842 0.00 0.78 0.22 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.6223.01 2 0.3891 0.6782 0.00 0.76 0.14 0.00 0.02 0.00 0.02 0.06
#> TCGA.DQ.5624.01 4 0.0471 0.7328 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CV.A45R.01 2 0.1563 0.6960 0.00 0.90 0.10 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.A499.01 4 0.0941 0.7269 0.00 0.00 0.00 0.96 0.02 0.00 0.02 0.00
#> TCGA.CN.A49B.01 5 0.4174 0.6125 0.00 0.02 0.00 0.00 0.62 0.00 0.32 0.04
#> TCGA.BA.5152.01 2 0.2547 0.5560 0.00 0.84 0.00 0.00 0.00 0.00 0.12 0.04
#> TCGA.CV.6938.01 3 0.0808 0.7907 0.00 0.04 0.96 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.5326.01 5 0.5329 0.6216 0.00 0.02 0.00 0.00 0.50 0.00 0.26 0.22
#> TCGA.CV.6940.01 4 0.2224 0.6832 0.00 0.00 0.00 0.86 0.00 0.02 0.12 0.00
#> TCGA.CR.6471.01 2 0.2674 0.6630 0.00 0.86 0.04 0.00 0.00 0.00 0.04 0.06
#> TCGA.BA.6872.01 2 0.4504 0.6445 0.00 0.64 0.24 0.00 0.00 0.00 0.02 0.10
#> TCGA.CQ.A4C6.01 2 0.3658 0.4878 0.00 0.58 0.40 0.00 0.00 0.00 0.00 0.02
#> TCGA.CQ.7064.01 4 0.3714 0.0094 0.00 0.00 0.00 0.54 0.00 0.00 0.02 0.44
#> TCGA.IQ.A61K.01 1 0.5264 -0.1722 0.46 0.00 0.00 0.08 0.00 0.00 0.06 0.40
#> TCGA.HD.A633.01 3 0.0941 0.7988 0.02 0.02 0.96 0.00 0.00 0.00 0.00 0.00
#> TCGA.F7.A61W.01 7 0.4079 0.5809 0.00 0.08 0.00 0.00 0.12 0.00 0.74 0.06
#> TCGA.BA.A6DF.01 1 0.1341 0.8968 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.D6.A4ZB.01 5 0.4160 0.6101 0.00 0.06 0.04 0.00 0.76 0.04 0.00 0.10
#> TCGA.CV.A45Y.01 2 0.2719 0.6919 0.00 0.80 0.18 0.00 0.00 0.00 0.00 0.02
#> TCGA.BB.A5HU.01 7 0.6211 0.1381 0.00 0.14 0.00 0.00 0.22 0.00 0.44 0.20
#> TCGA.CQ.A4C7.01 3 0.1275 0.7943 0.00 0.04 0.94 0.00 0.00 0.00 0.00 0.02
#> TCGA.P3.A5Q6.01 7 0.3975 0.6793 0.00 0.26 0.00 0.00 0.00 0.00 0.66 0.08
#> TCGA.CQ.A4CD.01 3 0.2981 0.5518 0.00 0.22 0.76 0.00 0.00 0.00 0.00 0.02
#> TCGA.BA.A6DB.01 4 0.0471 0.7328 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.F7.A620.01 3 0.0808 0.7907 0.00 0.04 0.96 0.00 0.00 0.00 0.00 0.00
#> TCGA.CX.A4AQ.01 5 0.3073 0.5998 0.00 0.00 0.00 0.00 0.80 0.10 0.00 0.10
#> TCGA.CV.A464.01 7 0.3570 0.6820 0.02 0.36 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.IQ.A61L.01 8 0.5273 0.7887 0.16 0.00 0.00 0.36 0.00 0.00 0.02 0.46
#> TCGA.QK.A8Z9.01 3 0.6556 0.1733 0.00 0.20 0.44 0.00 0.18 0.00 0.02 0.16
#> TCGA.BB.A5HY.01 3 0.5591 0.5169 0.02 0.00 0.60 0.00 0.10 0.12 0.00 0.16
#> TCGA.HD.8635.01 4 0.1408 0.7256 0.00 0.00 0.00 0.94 0.02 0.00 0.02 0.02
#> TCGA.QK.A652.01 2 0.1804 0.5961 0.02 0.90 0.00 0.00 0.00 0.00 0.08 0.00
#> TCGA.MT.A67G.01 4 0.2020 0.7062 0.00 0.00 0.00 0.90 0.02 0.00 0.02 0.06
#> TCGA.QK.A64Z.01 8 0.4873 0.7996 0.16 0.00 0.00 0.36 0.00 0.00 0.00 0.48
#> TCGA.HD.8634.01 8 0.4873 0.5351 0.36 0.00 0.00 0.16 0.00 0.00 0.00 0.48
#> TCGA.CQ.7063.01 1 0.1804 0.8965 0.90 0.00 0.00 0.08 0.00 0.00 0.00 0.02
#> TCGA.F7.A50J.01 4 0.4717 0.0946 0.00 0.00 0.00 0.54 0.00 0.02 0.08 0.36
#> TCGA.F7.8298.01 5 0.5528 0.6140 0.00 0.14 0.02 0.00 0.56 0.00 0.04 0.24
#> TCGA.F7.8489.01 7 0.4383 0.5700 0.02 0.42 0.00 0.00 0.00 0.00 0.52 0.04
#> TCGA.F7.A50G.01 2 0.1341 0.6096 0.00 0.92 0.00 0.00 0.00 0.00 0.08 0.00
#> TCGA.CQ.A4CA.01 7 0.3570 0.6820 0.02 0.36 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.T3.A92N.01 5 0.3523 0.6008 0.00 0.00 0.00 0.00 0.78 0.10 0.02 0.10
#> TCGA.CN.A63Y.01 7 0.3397 0.6428 0.00 0.10 0.00 0.00 0.06 0.00 0.80 0.04
#> TCGA.CQ.5333.01 3 0.4046 0.7453 0.06 0.00 0.74 0.00 0.00 0.02 0.02 0.16
#> TCGA.P3.A5QE.01 5 0.4028 0.6521 0.00 0.02 0.00 0.00 0.66 0.00 0.28 0.04
#> TCGA.BA.A6DJ.01 3 0.4046 0.7453 0.06 0.00 0.74 0.00 0.00 0.02 0.02 0.16
#> TCGA.MT.A51W.01 4 0.0000 0.7311 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.IQ.A61G.01 5 0.5342 0.6208 0.00 0.02 0.00 0.00 0.46 0.00 0.34 0.18
#> TCGA.IQ.A61J.01 7 0.4141 0.4723 0.02 0.48 0.00 0.00 0.00 0.00 0.48 0.02
#> TCGA.BA.A6DG.01 2 0.3737 -0.4719 0.02 0.50 0.00 0.00 0.00 0.00 0.48 0.00
#> TCGA.CQ.A4CH.01 7 0.3570 0.6820 0.02 0.36 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.CQ.A4CB.01 3 0.1091 0.7819 0.00 0.06 0.94 0.00 0.00 0.00 0.00 0.00
#> TCGA.D6.8569.01 2 0.0471 0.6531 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.IQ.A61I.01 6 0.1408 0.9560 0.00 0.00 0.02 0.00 0.00 0.94 0.02 0.02
#> TCGA.D6.A4Z9.01 3 0.2856 0.5972 0.00 0.20 0.78 0.00 0.00 0.00 0.00 0.02
#> TCGA.CQ.7071.01 1 0.1341 0.8968 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.H7.8501.01 3 0.2818 0.7826 0.06 0.00 0.82 0.00 0.00 0.00 0.00 0.12
#> TCGA.BB.8601.01 5 0.2862 0.5967 0.00 0.00 0.00 0.00 0.82 0.10 0.00 0.08
#> TCGA.H7.8502.01 5 0.3021 0.7231 0.00 0.02 0.00 0.00 0.80 0.00 0.02 0.16
#> TCGA.F7.A61S.01 2 0.1947 0.6968 0.00 0.86 0.14 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A463.01 1 0.1341 0.8968 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.D6.8568.01 2 0.2807 0.5741 0.02 0.84 0.00 0.00 0.00 0.00 0.10 0.04
#> TCGA.CN.A642.01 3 0.3444 0.7692 0.06 0.00 0.78 0.00 0.00 0.00 0.02 0.14
#> TCGA.CN.5367.01 4 0.1408 0.7283 0.00 0.00 0.00 0.94 0.00 0.02 0.02 0.02
#> TCGA.P3.A6T2.01 3 0.4046 0.7453 0.06 0.00 0.74 0.00 0.00 0.02 0.02 0.16
#> TCGA.CN.A6V7.01 6 0.0471 0.9561 0.00 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.CN.A640.01 1 0.4391 0.0123 0.50 0.00 0.00 0.08 0.00 0.00 0.00 0.42
#> TCGA.DQ.7589.01 5 0.1275 0.7367 0.00 0.02 0.00 0.00 0.94 0.00 0.04 0.00
#> TCGA.CN.4725.01 2 0.1091 0.6208 0.00 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.HL.7533.01 7 0.3397 0.6428 0.00 0.10 0.00 0.00 0.06 0.00 0.80 0.04
#> TCGA.UF.A7JO.01 1 0.3528 0.7640 0.74 0.00 0.00 0.08 0.00 0.00 0.00 0.18
#> TCGA.UF.A7JV.01 4 0.3237 0.1955 0.00 0.00 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.CN.4729.01 2 0.2591 0.6778 0.00 0.86 0.08 0.00 0.00 0.00 0.02 0.04
#> TCGA.IQ.A6SG.01 4 0.1804 0.6752 0.00 0.00 0.00 0.90 0.08 0.00 0.02 0.00
#> TCGA.MT.A67A.01 1 0.1341 0.8968 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.CN.5361.01 2 0.3178 0.6789 0.00 0.80 0.14 0.00 0.00 0.00 0.02 0.04
#> TCGA.CN.5359.01 5 0.4621 0.7334 0.00 0.02 0.00 0.00 0.64 0.00 0.14 0.20
#> TCGA.BB.7861.01 7 0.3794 0.7043 0.00 0.18 0.00 0.00 0.04 0.00 0.74 0.04
#> TCGA.BB.A6UO.01 1 0.1341 0.8968 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.CN.4734.01 3 0.4046 0.7453 0.06 0.00 0.74 0.00 0.00 0.02 0.02 0.16
#> TCGA.BA.4075.01 3 0.1765 0.7295 0.00 0.12 0.88 0.00 0.00 0.00 0.00 0.00
#> TCGA.BB.7871.01 4 0.2025 0.6482 0.00 0.00 0.00 0.88 0.10 0.00 0.02 0.00
#> TCGA.CN.4726.01 3 0.2591 0.7972 0.04 0.02 0.86 0.00 0.00 0.00 0.00 0.08
#> TCGA.UF.A7JS.01 2 0.5589 0.5240 0.00 0.56 0.18 0.00 0.04 0.00 0.02 0.20
#> TCGA.CN.4736.01 4 0.0471 0.7328 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CN.5355.01 2 0.3714 0.3686 0.00 0.54 0.44 0.00 0.00 0.00 0.00 0.02
#> TCGA.DQ.7590.01 5 0.5518 0.3747 0.00 0.00 0.00 0.00 0.50 0.26 0.20 0.04
#> TCGA.CN.5369.01 4 0.1091 0.7172 0.00 0.00 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.BA.5151.01 3 0.0471 0.7956 0.00 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.IQ.A61E.01 1 0.2648 0.8727 0.84 0.00 0.00 0.08 0.00 0.00 0.00 0.08
#> TCGA.BA.4076.01 5 0.3970 0.7467 0.00 0.02 0.00 0.00 0.72 0.00 0.08 0.18
#> TCGA.MZ.A7D7.01 5 0.4345 0.7443 0.00 0.02 0.00 0.00 0.68 0.00 0.12 0.18
#> TCGA.UF.A7JT.01 1 0.1341 0.8968 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.CN.5373.01 8 0.6129 0.7509 0.16 0.00 0.00 0.36 0.00 0.02 0.06 0.40
#> TCGA.BB.7863.01 1 0.2862 0.8566 0.82 0.00 0.00 0.08 0.00 0.00 0.00 0.10
#> TCGA.CN.5363.01 3 0.2132 0.7507 0.00 0.08 0.88 0.00 0.00 0.00 0.00 0.04
#> TCGA.BA.4077.01 4 0.0471 0.7290 0.00 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.BB.7872.01 2 0.2025 0.5616 0.02 0.88 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.H7.A6C4.01 8 0.4786 0.4724 0.38 0.00 0.00 0.14 0.00 0.00 0.00 0.48
#> TCGA.T2.A6X2.01 3 0.2818 0.7826 0.06 0.00 0.82 0.00 0.00 0.00 0.00 0.12
#> TCGA.CN.4741.01 6 0.0471 0.9561 0.00 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.CV.A6JO.01 2 0.3658 0.4870 0.00 0.58 0.40 0.00 0.00 0.00 0.00 0.02
#> TCGA.BB.7866.01 6 0.1408 0.9560 0.00 0.00 0.02 0.00 0.00 0.94 0.02 0.02
#> TCGA.CN.5365.01 5 0.4760 0.7246 0.00 0.02 0.00 0.00 0.62 0.00 0.16 0.20
#> TCGA.BB.4224.01 2 0.3735 0.2561 0.02 0.72 0.00 0.00 0.00 0.00 0.22 0.04
#> TCGA.MT.A67F.01 1 0.2407 0.8849 0.86 0.00 0.00 0.08 0.00 0.00 0.00 0.06
#> TCGA.CN.5366.01 3 0.3311 0.7642 0.02 0.00 0.80 0.00 0.00 0.02 0.02 0.14
#> TCGA.QK.A6V9.01 6 0.0471 0.9561 0.00 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.T2.A6WX.01 1 0.2132 0.8928 0.88 0.00 0.00 0.08 0.00 0.00 0.00 0.04
#> TCGA.CV.A6JZ.01 3 0.0808 0.7907 0.00 0.04 0.96 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.A6V1.01 7 0.3483 0.7137 0.00 0.18 0.00 0.00 0.04 0.00 0.76 0.02
#> TCGA.HD.A6I0.01 3 0.3444 0.7692 0.06 0.00 0.78 0.00 0.00 0.00 0.02 0.14
#> TCGA.CV.7430.01 5 0.3537 0.7006 0.00 0.02 0.00 0.00 0.72 0.00 0.24 0.02
#> TCGA.CR.7383.01 4 0.0941 0.7269 0.00 0.00 0.00 0.96 0.02 0.00 0.02 0.00
#> TCGA.UF.A7JC.01 7 0.4367 0.6925 0.02 0.34 0.00 0.00 0.02 0.00 0.60 0.02
#> TCGA.CV.7568.01 5 0.5264 0.5671 0.00 0.02 0.00 0.00 0.50 0.00 0.30 0.18
#> TCGA.QK.A6IF.01 7 0.4188 0.5949 0.00 0.10 0.00 0.00 0.14 0.00 0.72 0.04
#> TCGA.CV.A6JT.01 3 0.3015 0.3465 0.00 0.32 0.68 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7438.01 8 0.5743 0.7720 0.16 0.00 0.00 0.36 0.00 0.00 0.06 0.42
#> TCGA.D6.A6EN.01 3 0.3444 0.7692 0.06 0.00 0.78 0.00 0.00 0.00 0.02 0.14
#> TCGA.CV.7429.01 7 0.5827 -0.2934 0.00 0.06 0.00 0.00 0.36 0.00 0.40 0.18
#> TCGA.CV.7437.01 5 0.2862 0.5967 0.00 0.00 0.00 0.00 0.82 0.10 0.00 0.08
#> TCGA.CV.A6JD.01 1 0.2132 0.8928 0.88 0.00 0.00 0.08 0.00 0.00 0.00 0.04
#> TCGA.CV.A6JN.01 2 0.1563 0.6960 0.00 0.90 0.10 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7434.01 3 0.4046 0.7453 0.06 0.00 0.74 0.00 0.00 0.02 0.02 0.16
#> TCGA.D6.A6EK.01 2 0.3528 0.3868 0.00 0.74 0.00 0.00 0.00 0.00 0.18 0.08
#> TCGA.HD.7832.01 3 0.5473 0.5357 0.04 0.00 0.58 0.00 0.00 0.20 0.02 0.16
#> TCGA.P3.A6SX.01 5 0.4621 0.7348 0.00 0.02 0.00 0.00 0.64 0.00 0.14 0.20
#> TCGA.QK.A6II.01 2 0.3426 0.6803 0.00 0.74 0.22 0.00 0.00 0.00 0.02 0.02
#> TCGA.P3.A6T7.01 3 0.1091 0.7819 0.00 0.06 0.94 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7382.01 2 0.3449 0.6161 0.00 0.66 0.32 0.00 0.00 0.00 0.00 0.02
#> TCGA.T2.A6WZ.01 3 0.1804 0.7552 0.00 0.08 0.90 0.00 0.00 0.00 0.00 0.02
#> TCGA.P3.A6T5.01 4 0.4593 0.3317 0.00 0.00 0.00 0.62 0.00 0.02 0.10 0.26
#> TCGA.CV.7433.01 5 0.5264 0.5671 0.00 0.02 0.00 0.00 0.50 0.00 0.30 0.18
#> TCGA.CR.7376.01 7 0.4106 0.7181 0.02 0.30 0.00 0.00 0.04 0.00 0.64 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: Node02. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0121 , Node0122 , Node0211 , Node0212 , Node0213 , Node0221 , Node0222 , Node0223 , Node0224 , Node0225-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0511 , Node0512 , Node0521-leaf , Node0522 , Node0523-leaf , Node0524-leaf .
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 90 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 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 0.979 0.992 0.4663 0.530 0.530
#> 3 3 1.000 0.963 0.985 0.4385 0.726 0.517
#> 4 4 0.670 0.741 0.836 0.0993 0.904 0.718
#> 5 5 0.655 0.640 0.805 0.0643 0.961 0.854
#> 6 6 0.673 0.572 0.742 0.0375 0.951 0.797
#> 7 7 0.700 0.505 0.701 0.0246 0.952 0.775
#> 8 8 0.732 0.494 0.684 0.0246 0.896 0.511
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.CQ.5327.01 1 0.000 0.979 1.00 0.00
#> TCGA.CR.7391.01 2 0.000 0.999 0.00 1.00
#> TCGA.CV.7416.01 2 0.000 0.999 0.00 1.00
#> TCGA.H7.7774.01 1 0.000 0.979 1.00 0.00
#> TCGA.CQ.5330.01 1 0.000 0.979 1.00 0.00
#> TCGA.CV.7427.01 1 0.000 0.979 1.00 0.00
#> TCGA.CV.7425.01 1 0.000 0.979 1.00 0.00
#> TCGA.CV.7407.01 2 0.000 0.999 0.00 1.00
#> TCGA.CV.6003.01 2 0.000 0.999 0.00 1.00
#> TCGA.CN.6021.01 2 0.000 0.999 0.00 1.00
#> TCGA.CV.5978.01 2 0.000 0.999 0.00 1.00
#> TCGA.CN.6018.01 2 0.000 0.999 0.00 1.00
#> TCGA.CV.5966.01 1 0.000 0.979 1.00 0.00
#> TCGA.CV.7411.01 2 0.000 0.999 0.00 1.00
#> TCGA.CQ.7068.01 1 0.000 0.979 1.00 0.00
#> TCGA.CV.5973.01 2 0.000 0.999 0.00 1.00
#> TCGA.CV.7104.01 2 0.000 0.999 0.00 1.00
#> TCGA.CV.7095.01 1 0.000 0.979 1.00 0.00
#> TCGA.CV.7178.01 2 0.000 0.999 0.00 1.00
#> TCGA.CV.7252.01 1 0.000 0.979 1.00 0.00
#> TCGA.CR.6478.01 2 0.000 0.999 0.00 1.00
#> TCGA.CV.7102.01 2 0.000 0.999 0.00 1.00
#> TCGA.CR.7394.01 2 0.000 0.999 0.00 1.00
#> TCGA.CV.6955.01 2 0.000 0.999 0.00 1.00
#> TCGA.BA.5556.01 1 0.000 0.979 1.00 0.00
#> TCGA.BA.5557.01 2 0.000 0.999 0.00 1.00
#> TCGA.D6.6515.01 2 0.000 0.999 0.00 1.00
#> TCGA.CV.7238.01 2 0.000 0.999 0.00 1.00
#> TCGA.CV.6942.01 1 0.000 0.979 1.00 0.00
#> TCGA.CV.7177.01 2 0.000 0.999 0.00 1.00
#> TCGA.CR.7395.01 1 0.000 0.979 1.00 0.00
#> TCGA.CX.7085.01 2 0.000 0.999 0.00 1.00
#> TCGA.CV.7099.01 1 0.000 0.979 1.00 0.00
#> TCGA.CQ.6218.01 2 0.000 0.999 0.00 1.00
#> TCGA.C9.A47Z.01 1 0.000 0.979 1.00 0.00
#> TCGA.DQ.5625.01 2 0.000 0.999 0.00 1.00
#> TCGA.C9.A480.01 2 0.000 0.999 0.00 1.00
#> TCGA.CV.6952.01 1 0.000 0.979 1.00 0.00
#> TCGA.CQ.5331.01 2 0.000 0.999 0.00 1.00
#> TCGA.D6.6826.01 1 0.722 0.746 0.80 0.20
#> TCGA.CV.6953.01 1 0.000 0.979 1.00 0.00
#> TCGA.BA.6870.01 2 0.000 0.999 0.00 1.00
#> TCGA.CR.6477.01 2 0.000 0.999 0.00 1.00
#> TCGA.CQ.6219.01 2 0.000 0.999 0.00 1.00
#> TCGA.CN.A498.01 2 0.000 0.999 0.00 1.00
#> TCGA.CV.6953.11 2 0.000 0.999 0.00 1.00
#> TCGA.HD.A4C1.01 1 0.000 0.979 1.00 0.00
#> TCGA.CV.A45P.01 2 0.000 0.999 0.00 1.00
#> TCGA.CV.A45Q.01 1 0.000 0.979 1.00 0.00
#> TCGA.CV.A45T.01 2 0.000 0.999 0.00 1.00
#> TCGA.CN.6996.01 2 0.000 0.999 0.00 1.00
#> TCGA.DQ.5624.01 2 0.000 0.999 0.00 1.00
#> TCGA.CN.A499.01 2 0.000 0.999 0.00 1.00
#> TCGA.CV.6940.01 2 0.000 0.999 0.00 1.00
#> TCGA.CQ.7064.01 2 0.000 0.999 0.00 1.00
#> TCGA.IQ.A61K.01 2 0.327 0.935 0.06 0.94
#> TCGA.BA.A6DF.01 1 0.000 0.979 1.00 0.00
#> TCGA.BA.A6DB.01 2 0.000 0.999 0.00 1.00
#> TCGA.IQ.A61L.01 2 0.000 0.999 0.00 1.00
#> TCGA.HD.8635.01 2 0.000 0.999 0.00 1.00
#> TCGA.MT.A67G.01 2 0.000 0.999 0.00 1.00
#> TCGA.QK.A64Z.01 2 0.000 0.999 0.00 1.00
#> TCGA.HD.8634.01 2 0.000 0.999 0.00 1.00
#> TCGA.CQ.7063.01 1 0.000 0.979 1.00 0.00
#> TCGA.F7.A50J.01 2 0.000 0.999 0.00 1.00
#> TCGA.MT.A51W.01 2 0.000 0.999 0.00 1.00
#> TCGA.CQ.7071.01 1 0.000 0.979 1.00 0.00
#> TCGA.CV.A463.01 1 0.000 0.979 1.00 0.00
#> TCGA.CN.5367.01 2 0.000 0.999 0.00 1.00
#> TCGA.CN.A640.01 1 0.000 0.979 1.00 0.00
#> TCGA.UF.A7JO.01 1 0.995 0.164 0.54 0.46
#> TCGA.UF.A7JV.01 2 0.000 0.999 0.00 1.00
#> TCGA.IQ.A6SG.01 2 0.000 0.999 0.00 1.00
#> TCGA.MT.A67A.01 1 0.000 0.979 1.00 0.00
#> TCGA.BB.A6UO.01 1 0.000 0.979 1.00 0.00
#> TCGA.BB.7871.01 2 0.000 0.999 0.00 1.00
#> TCGA.CN.4736.01 2 0.000 0.999 0.00 1.00
#> TCGA.CN.5369.01 2 0.000 0.999 0.00 1.00
#> TCGA.IQ.A61E.01 1 0.000 0.979 1.00 0.00
#> TCGA.UF.A7JT.01 1 0.000 0.979 1.00 0.00
#> TCGA.CN.5373.01 2 0.000 0.999 0.00 1.00
#> TCGA.BB.7863.01 1 0.000 0.979 1.00 0.00
#> TCGA.BA.4077.01 2 0.000 0.999 0.00 1.00
#> TCGA.H7.A6C4.01 2 0.000 0.999 0.00 1.00
#> TCGA.MT.A67F.01 1 0.000 0.979 1.00 0.00
#> TCGA.T2.A6WX.01 1 0.000 0.979 1.00 0.00
#> TCGA.CR.7383.01 2 0.000 0.999 0.00 1.00
#> TCGA.CV.7438.01 2 0.000 0.999 0.00 1.00
#> TCGA.CV.A6JD.01 1 0.000 0.979 1.00 0.00
#> TCGA.P3.A6T5.01 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.CQ.5327.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.CR.7391.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.CV.7416.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.H7.7774.01 1 0.3340 0.866 0.88 0.12 0.00
#> TCGA.CQ.5330.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.CV.7427.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.CV.7425.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.CV.7407.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.CV.6003.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.CN.6021.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.CV.5978.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.CN.6018.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.CV.5966.01 2 0.5835 0.477 0.34 0.66 0.00
#> TCGA.CV.7411.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.CQ.7068.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.CV.5973.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.CV.7104.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.CV.7095.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.CV.7178.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.CV.7252.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.CR.6478.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.CV.7102.01 3 0.4002 0.801 0.00 0.16 0.84
#> TCGA.CR.7394.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.CV.6955.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.BA.5556.01 1 0.0892 0.975 0.98 0.02 0.00
#> TCGA.BA.5557.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.D6.6515.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.CV.7238.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.CV.6942.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.CV.7177.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.CR.7395.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.CX.7085.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.CV.7099.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.CQ.6218.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.C9.A47Z.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.DQ.5625.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.C9.A480.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.CV.6952.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.CQ.5331.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.D6.6826.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.CV.6953.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.BA.6870.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.CR.6477.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.CQ.6219.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.CN.A498.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.CV.6953.11 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.HD.A4C1.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.CV.A45P.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.CV.A45Q.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.CV.A45T.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.CN.6996.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.DQ.5624.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.CN.A499.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.CV.6940.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.CQ.7064.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.IQ.A61K.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.BA.A6DF.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.BA.A6DB.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.IQ.A61L.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.HD.8635.01 2 0.5016 0.669 0.00 0.76 0.24
#> TCGA.MT.A67G.01 3 0.6192 0.271 0.00 0.42 0.58
#> TCGA.QK.A64Z.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.HD.8634.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.CQ.7063.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.F7.A50J.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.MT.A51W.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.CQ.7071.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.CV.A463.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.CN.5367.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.CN.A640.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.UF.A7JO.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.UF.A7JV.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.IQ.A6SG.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.MT.A67A.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.BB.A6UO.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.BB.7871.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.CN.4736.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.CN.5369.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.IQ.A61E.01 1 0.2066 0.936 0.94 0.06 0.00
#> TCGA.UF.A7JT.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.CN.5373.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.BB.7863.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.BA.4077.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.H7.A6C4.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.MT.A67F.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.T2.A6WX.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.CR.7383.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.CV.7438.01 2 0.0000 0.982 0.00 1.00 0.00
#> TCGA.CV.A6JD.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.P3.A6T5.01 3 0.0000 0.977 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.CQ.5327.01 1 0.0000 0.910 1.00 0.00 0.00 0.00
#> TCGA.CR.7391.01 3 0.2011 0.859 0.00 0.08 0.92 0.00
#> TCGA.CV.7416.01 2 0.1637 0.841 0.00 0.94 0.00 0.06
#> TCGA.H7.7774.01 4 0.5661 0.588 0.22 0.08 0.00 0.70
#> TCGA.CQ.5330.01 4 0.5594 0.257 0.46 0.02 0.00 0.52
#> TCGA.CV.7427.01 1 0.4994 -0.116 0.52 0.00 0.00 0.48
#> TCGA.CV.7425.01 1 0.0000 0.910 1.00 0.00 0.00 0.00
#> TCGA.CV.7407.01 3 0.2921 0.830 0.00 0.00 0.86 0.14
#> TCGA.CV.6003.01 2 0.2011 0.780 0.00 0.92 0.08 0.00
#> TCGA.CN.6021.01 3 0.2921 0.830 0.00 0.00 0.86 0.14
#> TCGA.CV.5978.01 3 0.2921 0.830 0.00 0.00 0.86 0.14
#> TCGA.CN.6018.01 2 0.3801 0.815 0.00 0.78 0.00 0.22
#> TCGA.CV.5966.01 4 0.5291 0.583 0.08 0.18 0.00 0.74
#> TCGA.CV.7411.01 2 0.1211 0.817 0.00 0.96 0.04 0.00
#> TCGA.CQ.7068.01 1 0.0000 0.910 1.00 0.00 0.00 0.00
#> TCGA.CV.5973.01 2 0.1637 0.841 0.00 0.94 0.00 0.06
#> TCGA.CV.7104.01 2 0.4790 0.604 0.00 0.62 0.00 0.38
#> TCGA.CV.7095.01 1 0.0707 0.896 0.98 0.00 0.00 0.02
#> TCGA.CV.7178.01 3 0.3198 0.853 0.00 0.08 0.88 0.04
#> TCGA.CV.7252.01 1 0.3801 0.670 0.78 0.00 0.00 0.22
#> TCGA.CR.6478.01 3 0.3972 0.845 0.00 0.08 0.84 0.08
#> TCGA.CV.7102.01 3 0.5767 0.695 0.00 0.06 0.66 0.28
#> TCGA.CR.7394.01 2 0.3821 0.848 0.00 0.84 0.04 0.12
#> TCGA.CV.6955.01 4 0.3801 0.520 0.00 0.22 0.00 0.78
#> TCGA.BA.5556.01 4 0.5962 0.571 0.26 0.08 0.00 0.66
#> TCGA.BA.5557.01 2 0.3821 0.848 0.00 0.84 0.04 0.12
#> TCGA.D6.6515.01 3 0.2011 0.859 0.00 0.08 0.92 0.00
#> TCGA.CV.7238.01 2 0.4088 0.843 0.00 0.82 0.04 0.14
#> TCGA.CV.6942.01 1 0.0000 0.910 1.00 0.00 0.00 0.00
#> TCGA.CV.7177.01 3 0.3610 0.818 0.00 0.00 0.80 0.20
#> TCGA.CR.7395.01 4 0.4994 0.108 0.48 0.00 0.00 0.52
#> TCGA.CX.7085.01 2 0.2647 0.858 0.00 0.88 0.00 0.12
#> TCGA.CV.7099.01 1 0.0000 0.910 1.00 0.00 0.00 0.00
#> TCGA.CQ.6218.01 3 0.3972 0.845 0.00 0.08 0.84 0.08
#> TCGA.C9.A47Z.01 1 0.0707 0.896 0.98 0.00 0.00 0.02
#> TCGA.DQ.5625.01 2 0.4406 0.743 0.00 0.70 0.00 0.30
#> TCGA.C9.A480.01 2 0.2011 0.865 0.00 0.92 0.00 0.08
#> TCGA.CV.6952.01 4 0.4134 0.471 0.00 0.26 0.00 0.74
#> TCGA.CQ.5331.01 2 0.3606 0.850 0.00 0.84 0.02 0.14
#> TCGA.D6.6826.01 4 0.3610 0.533 0.00 0.20 0.00 0.80
#> TCGA.CV.6953.01 1 0.0000 0.910 1.00 0.00 0.00 0.00
#> TCGA.BA.6870.01 3 0.2921 0.830 0.00 0.00 0.86 0.14
#> TCGA.CR.6477.01 3 0.0707 0.860 0.00 0.02 0.98 0.00
#> TCGA.CQ.6219.01 2 0.4088 0.843 0.00 0.82 0.04 0.14
#> TCGA.CN.A498.01 3 0.3975 0.795 0.00 0.00 0.76 0.24
#> TCGA.CV.6953.11 3 0.2011 0.859 0.00 0.08 0.92 0.00
#> TCGA.HD.A4C1.01 1 0.0000 0.910 1.00 0.00 0.00 0.00
#> TCGA.CV.A45P.01 2 0.2011 0.849 0.00 0.92 0.00 0.08
#> TCGA.CV.A45Q.01 1 0.0000 0.910 1.00 0.00 0.00 0.00
#> TCGA.CV.A45T.01 2 0.3821 0.848 0.00 0.84 0.04 0.12
#> TCGA.CN.6996.01 2 0.3610 0.831 0.00 0.80 0.00 0.20
#> TCGA.DQ.5624.01 3 0.2011 0.859 0.00 0.08 0.92 0.00
#> TCGA.CN.A499.01 3 0.3400 0.826 0.00 0.00 0.82 0.18
#> TCGA.CV.6940.01 3 0.5383 0.791 0.00 0.16 0.74 0.10
#> TCGA.CQ.7064.01 2 0.1211 0.817 0.00 0.96 0.04 0.00
#> TCGA.IQ.A61K.01 2 0.2011 0.831 0.00 0.92 0.00 0.08
#> TCGA.BA.A6DF.01 1 0.0000 0.910 1.00 0.00 0.00 0.00
#> TCGA.BA.A6DB.01 3 0.2011 0.859 0.00 0.08 0.92 0.00
#> TCGA.IQ.A61L.01 2 0.1211 0.844 0.00 0.96 0.00 0.04
#> TCGA.HD.8635.01 4 0.5606 -0.476 0.00 0.02 0.48 0.50
#> TCGA.MT.A67G.01 3 0.6074 0.609 0.00 0.06 0.60 0.34
#> TCGA.QK.A64Z.01 2 0.2921 0.853 0.00 0.86 0.00 0.14
#> TCGA.HD.8634.01 2 0.3801 0.815 0.00 0.78 0.00 0.22
#> TCGA.CQ.7063.01 1 0.0000 0.910 1.00 0.00 0.00 0.00
#> TCGA.F7.A50J.01 2 0.2706 0.762 0.00 0.90 0.08 0.02
#> TCGA.MT.A51W.01 3 0.1637 0.860 0.00 0.06 0.94 0.00
#> TCGA.CQ.7071.01 1 0.0000 0.910 1.00 0.00 0.00 0.00
#> TCGA.CV.A463.01 1 0.0000 0.910 1.00 0.00 0.00 0.00
#> TCGA.CN.5367.01 3 0.3972 0.845 0.00 0.08 0.84 0.08
#> TCGA.CN.A640.01 4 0.4713 0.285 0.00 0.36 0.00 0.64
#> TCGA.UF.A7JO.01 4 0.3801 0.520 0.00 0.22 0.00 0.78
#> TCGA.UF.A7JV.01 2 0.2921 0.851 0.00 0.86 0.00 0.14
#> TCGA.IQ.A6SG.01 3 0.2921 0.830 0.00 0.00 0.86 0.14
#> TCGA.MT.A67A.01 1 0.0707 0.896 0.98 0.00 0.00 0.02
#> TCGA.BB.A6UO.01 1 0.0000 0.910 1.00 0.00 0.00 0.00
#> TCGA.BB.7871.01 3 0.2921 0.830 0.00 0.00 0.86 0.14
#> TCGA.CN.4736.01 3 0.2011 0.859 0.00 0.08 0.92 0.00
#> TCGA.CN.5369.01 3 0.2706 0.854 0.00 0.08 0.90 0.02
#> TCGA.IQ.A61E.01 4 0.6510 0.425 0.38 0.08 0.00 0.54
#> TCGA.UF.A7JT.01 1 0.0707 0.896 0.98 0.00 0.00 0.02
#> TCGA.CN.5373.01 2 0.2345 0.824 0.00 0.90 0.00 0.10
#> TCGA.BB.7863.01 1 0.3801 0.670 0.78 0.00 0.00 0.22
#> TCGA.BA.4077.01 3 0.2345 0.840 0.00 0.00 0.90 0.10
#> TCGA.H7.A6C4.01 2 0.3801 0.815 0.00 0.78 0.00 0.22
#> TCGA.MT.A67F.01 1 0.4855 0.181 0.60 0.00 0.00 0.40
#> TCGA.T2.A6WX.01 4 0.5606 0.196 0.48 0.02 0.00 0.50
#> TCGA.CR.7383.01 3 0.3821 0.852 0.00 0.04 0.84 0.12
#> TCGA.CV.7438.01 2 0.1637 0.841 0.00 0.94 0.00 0.06
#> TCGA.CV.A6JD.01 4 0.6299 0.360 0.42 0.06 0.00 0.52
#> TCGA.P3.A6T5.01 3 0.5957 0.412 0.00 0.42 0.54 0.04
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CQ.5327.01 1 0.2020 0.87677 0.90 0.00 0.00 0.10 0.00
#> TCGA.CR.7391.01 3 0.1732 0.57467 0.00 0.08 0.92 0.00 0.00
#> TCGA.CV.7416.01 2 0.4728 0.70239 0.00 0.70 0.00 0.06 0.24
#> TCGA.H7.7774.01 4 0.3110 0.81917 0.08 0.00 0.00 0.86 0.06
#> TCGA.CQ.5330.01 4 0.3106 0.81949 0.14 0.00 0.00 0.84 0.02
#> TCGA.CV.7427.01 4 0.2732 0.81013 0.16 0.00 0.00 0.84 0.00
#> TCGA.CV.7425.01 1 0.0000 0.91909 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7407.01 3 0.4287 -0.17222 0.00 0.00 0.54 0.00 0.46
#> TCGA.CV.6003.01 2 0.3109 0.73006 0.00 0.80 0.00 0.00 0.20
#> TCGA.CN.6021.01 3 0.4287 -0.17222 0.00 0.00 0.54 0.00 0.46
#> TCGA.CV.5978.01 3 0.4287 -0.17222 0.00 0.00 0.54 0.00 0.46
#> TCGA.CN.6018.01 2 0.3561 0.75788 0.00 0.74 0.00 0.26 0.00
#> TCGA.CV.5966.01 4 0.1043 0.79516 0.00 0.00 0.00 0.96 0.04
#> TCGA.CV.7411.01 2 0.2610 0.80427 0.00 0.90 0.02 0.02 0.06
#> TCGA.CQ.7068.01 1 0.0000 0.91909 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5973.01 2 0.4263 0.74159 0.00 0.76 0.00 0.06 0.18
#> TCGA.CV.7104.01 2 0.5156 0.63660 0.00 0.62 0.00 0.32 0.06
#> TCGA.CV.7095.01 1 0.3291 0.83721 0.84 0.00 0.00 0.12 0.04
#> TCGA.CV.7178.01 3 0.2331 0.53861 0.00 0.02 0.90 0.00 0.08
#> TCGA.CV.7252.01 1 0.5068 0.54207 0.64 0.00 0.00 0.30 0.06
#> TCGA.CR.6478.01 3 0.3390 0.51627 0.00 0.06 0.84 0.00 0.10
#> TCGA.CV.7102.01 3 0.6880 0.13042 0.00 0.08 0.56 0.10 0.26
#> TCGA.CR.7394.01 2 0.4389 0.78796 0.00 0.80 0.10 0.06 0.04
#> TCGA.CV.6955.01 4 0.3106 0.74095 0.00 0.02 0.00 0.84 0.14
#> TCGA.BA.5556.01 4 0.2012 0.82405 0.06 0.00 0.00 0.92 0.02
#> TCGA.BA.5557.01 2 0.3977 0.79129 0.00 0.82 0.10 0.06 0.02
#> TCGA.D6.6515.01 3 0.2873 0.54978 0.00 0.12 0.86 0.00 0.02
#> TCGA.CV.7238.01 2 0.4690 0.78730 0.00 0.78 0.10 0.08 0.04
#> TCGA.CV.6942.01 1 0.0000 0.91909 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7177.01 5 0.4227 0.28316 0.00 0.00 0.42 0.00 0.58
#> TCGA.CR.7395.01 4 0.3513 0.78633 0.18 0.00 0.00 0.80 0.02
#> TCGA.CX.7085.01 2 0.4281 0.78900 0.00 0.80 0.10 0.08 0.02
#> TCGA.CV.7099.01 1 0.1043 0.90808 0.96 0.00 0.00 0.04 0.00
#> TCGA.CQ.6218.01 3 0.3731 0.47989 0.00 0.04 0.80 0.00 0.16
#> TCGA.C9.A47Z.01 1 0.2438 0.87526 0.90 0.00 0.00 0.04 0.06
#> TCGA.DQ.5625.01 2 0.4748 0.70868 0.00 0.66 0.00 0.30 0.04
#> TCGA.C9.A480.01 2 0.2927 0.81492 0.00 0.88 0.02 0.08 0.02
#> TCGA.CV.6952.01 4 0.1216 0.78996 0.00 0.02 0.00 0.96 0.02
#> TCGA.CQ.5331.01 2 0.4690 0.78730 0.00 0.78 0.10 0.08 0.04
#> TCGA.D6.6826.01 4 0.2873 0.75750 0.00 0.02 0.00 0.86 0.12
#> TCGA.CV.6953.01 1 0.0000 0.91909 1.00 0.00 0.00 0.00 0.00
#> TCGA.BA.6870.01 3 0.4287 -0.17222 0.00 0.00 0.54 0.00 0.46
#> TCGA.CR.6477.01 3 0.2020 0.50445 0.00 0.00 0.90 0.00 0.10
#> TCGA.CQ.6219.01 2 0.4690 0.78730 0.00 0.78 0.10 0.08 0.04
#> TCGA.CN.A498.01 5 0.5304 0.40029 0.00 0.02 0.42 0.02 0.54
#> TCGA.CV.6953.11 3 0.1732 0.57467 0.00 0.08 0.92 0.00 0.00
#> TCGA.HD.A4C1.01 1 0.0000 0.91909 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A45P.01 2 0.1410 0.82060 0.00 0.94 0.00 0.06 0.00
#> TCGA.CV.A45Q.01 1 0.0000 0.91909 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A45T.01 2 0.4690 0.78730 0.00 0.78 0.10 0.08 0.04
#> TCGA.CN.6996.01 2 0.2732 0.81215 0.00 0.84 0.00 0.16 0.00
#> TCGA.DQ.5624.01 3 0.1732 0.57467 0.00 0.08 0.92 0.00 0.00
#> TCGA.CN.A499.01 3 0.4126 0.00915 0.00 0.00 0.62 0.00 0.38
#> TCGA.CV.6940.01 3 0.5972 0.20620 0.00 0.14 0.56 0.00 0.30
#> TCGA.CQ.7064.01 2 0.1820 0.81194 0.00 0.94 0.02 0.02 0.02
#> TCGA.IQ.A61K.01 2 0.4982 0.70838 0.00 0.70 0.00 0.10 0.20
#> TCGA.BA.A6DF.01 1 0.0609 0.91474 0.98 0.00 0.00 0.02 0.00
#> TCGA.BA.A6DB.01 3 0.1732 0.57467 0.00 0.08 0.92 0.00 0.00
#> TCGA.IQ.A61L.01 2 0.2438 0.80021 0.00 0.90 0.00 0.06 0.04
#> TCGA.HD.8635.01 5 0.6311 0.41424 0.00 0.04 0.10 0.26 0.60
#> TCGA.MT.A67G.01 5 0.6520 0.49804 0.00 0.12 0.26 0.04 0.58
#> TCGA.QK.A64Z.01 2 0.2516 0.81053 0.00 0.86 0.00 0.14 0.00
#> TCGA.HD.8634.01 2 0.3895 0.70504 0.00 0.68 0.00 0.32 0.00
#> TCGA.CQ.7063.01 1 0.3291 0.83721 0.84 0.00 0.00 0.12 0.04
#> TCGA.F7.A50J.01 2 0.3106 0.76101 0.00 0.84 0.02 0.00 0.14
#> TCGA.MT.A51W.01 3 0.1648 0.55002 0.00 0.02 0.94 0.00 0.04
#> TCGA.CQ.7071.01 1 0.0000 0.91909 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A463.01 1 0.0000 0.91909 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.5367.01 3 0.3390 0.51627 0.00 0.06 0.84 0.00 0.10
#> TCGA.CN.A640.01 4 0.2616 0.74456 0.00 0.10 0.00 0.88 0.02
#> TCGA.UF.A7JO.01 4 0.2873 0.75750 0.00 0.02 0.00 0.86 0.12
#> TCGA.UF.A7JV.01 2 0.4008 0.79710 0.00 0.82 0.08 0.08 0.02
#> TCGA.IQ.A6SG.01 3 0.4287 -0.17222 0.00 0.00 0.54 0.00 0.46
#> TCGA.MT.A67A.01 1 0.0609 0.91105 0.98 0.00 0.00 0.00 0.02
#> TCGA.BB.A6UO.01 1 0.0000 0.91909 1.00 0.00 0.00 0.00 0.00
#> TCGA.BB.7871.01 3 0.4287 -0.17222 0.00 0.00 0.54 0.00 0.46
#> TCGA.CN.4736.01 3 0.1732 0.57467 0.00 0.08 0.92 0.00 0.00
#> TCGA.CN.5369.01 3 0.3106 0.53913 0.00 0.14 0.84 0.00 0.02
#> TCGA.IQ.A61E.01 4 0.2873 0.82629 0.12 0.00 0.00 0.86 0.02
#> TCGA.UF.A7JT.01 1 0.2020 0.87640 0.90 0.00 0.00 0.10 0.00
#> TCGA.CN.5373.01 2 0.4170 0.75089 0.00 0.78 0.00 0.08 0.14
#> TCGA.BB.7863.01 1 0.5068 0.54207 0.64 0.00 0.00 0.30 0.06
#> TCGA.BA.4077.01 3 0.2929 0.35041 0.00 0.00 0.82 0.00 0.18
#> TCGA.H7.A6C4.01 2 0.3561 0.75788 0.00 0.74 0.00 0.26 0.00
#> TCGA.MT.A67F.01 4 0.3983 0.52053 0.34 0.00 0.00 0.66 0.00
#> TCGA.T2.A6WX.01 4 0.4096 0.75994 0.20 0.00 0.00 0.76 0.04
#> TCGA.CR.7383.01 3 0.3999 0.38688 0.00 0.02 0.74 0.00 0.24
#> TCGA.CV.7438.01 2 0.2438 0.80021 0.00 0.90 0.00 0.06 0.04
#> TCGA.CV.A6JD.01 4 0.3731 0.80360 0.16 0.00 0.00 0.80 0.04
#> TCGA.P3.A6T5.01 3 0.6398 0.20314 0.00 0.30 0.50 0.00 0.20
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.CQ.5327.01 1 0.4983 0.6759 0.68 0.00 0.00 0.04 0.06 0.22
#> TCGA.CR.7391.01 3 0.1556 0.6629 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.CV.7416.01 2 0.4873 0.3807 0.00 0.52 0.00 0.06 0.00 0.42
#> TCGA.H7.7774.01 4 0.2725 0.5664 0.00 0.06 0.00 0.88 0.04 0.02
#> TCGA.CQ.5330.01 4 0.7394 0.5697 0.18 0.08 0.00 0.48 0.04 0.22
#> TCGA.CV.7427.01 4 0.5955 0.5859 0.16 0.00 0.00 0.62 0.08 0.14
#> TCGA.CV.7425.01 1 0.0000 0.8351 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7407.01 5 0.3499 0.7315 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.CV.6003.01 2 0.6564 0.3223 0.00 0.42 0.14 0.06 0.00 0.38
#> TCGA.CN.6021.01 5 0.3499 0.7315 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.CV.5978.01 5 0.3499 0.7315 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.CN.6018.01 2 0.2190 0.7001 0.00 0.90 0.00 0.06 0.00 0.04
#> TCGA.CV.5966.01 4 0.1267 0.5924 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.CV.7411.01 2 0.4200 0.6888 0.00 0.74 0.14 0.00 0.00 0.12
#> TCGA.CQ.7068.01 1 0.0000 0.8351 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5973.01 2 0.4078 0.5193 0.00 0.64 0.00 0.00 0.02 0.34
#> TCGA.CV.7104.01 2 0.4675 0.4660 0.00 0.66 0.00 0.28 0.02 0.04
#> TCGA.CV.7095.01 1 0.5740 0.5991 0.62 0.00 0.00 0.10 0.06 0.22
#> TCGA.CV.7178.01 3 0.4475 0.3248 0.00 0.00 0.70 0.00 0.10 0.20
#> TCGA.CV.7252.01 1 0.6516 0.3674 0.52 0.00 0.00 0.26 0.08 0.14
#> TCGA.CR.6478.01 3 0.4536 0.3102 0.00 0.00 0.70 0.00 0.12 0.18
#> TCGA.CV.7102.01 6 0.8463 0.5099 0.00 0.06 0.24 0.20 0.20 0.30
#> TCGA.CR.7394.01 2 0.3409 0.6635 0.00 0.70 0.30 0.00 0.00 0.00
#> TCGA.CV.6955.01 4 0.3942 0.5061 0.00 0.10 0.00 0.80 0.04 0.06
#> TCGA.BA.5556.01 4 0.7166 0.6293 0.10 0.10 0.00 0.54 0.06 0.20
#> TCGA.BA.5557.01 2 0.3409 0.6635 0.00 0.70 0.30 0.00 0.00 0.00
#> TCGA.D6.6515.01 3 0.0000 0.6211 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.7238.01 2 0.3409 0.6635 0.00 0.70 0.30 0.00 0.00 0.00
#> TCGA.CV.6942.01 1 0.0000 0.8351 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7177.01 5 0.2631 0.6091 0.00 0.00 0.18 0.00 0.82 0.00
#> TCGA.CR.7395.01 4 0.6321 0.5628 0.16 0.00 0.00 0.58 0.10 0.16
#> TCGA.CX.7085.01 2 0.3309 0.6740 0.00 0.72 0.28 0.00 0.00 0.00
#> TCGA.CV.7099.01 1 0.3997 0.7584 0.78 0.00 0.00 0.02 0.06 0.14
#> TCGA.CQ.6218.01 3 0.4989 0.2036 0.00 0.00 0.64 0.00 0.14 0.22
#> TCGA.C9.A47Z.01 1 0.2794 0.7863 0.86 0.00 0.00 0.00 0.06 0.08
#> TCGA.DQ.5625.01 2 0.3821 0.5437 0.00 0.74 0.00 0.22 0.00 0.04
#> TCGA.C9.A480.01 2 0.1814 0.7254 0.00 0.90 0.10 0.00 0.00 0.00
#> TCGA.CV.6952.01 4 0.3787 0.5892 0.00 0.12 0.00 0.78 0.00 0.10
#> TCGA.CQ.5331.01 2 0.3409 0.6635 0.00 0.70 0.30 0.00 0.00 0.00
#> TCGA.D6.6826.01 4 0.3382 0.5487 0.00 0.08 0.00 0.84 0.04 0.04
#> TCGA.CV.6953.01 1 0.0000 0.8351 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.6870.01 5 0.3499 0.7315 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.CR.6477.01 3 0.2454 0.5689 0.00 0.00 0.84 0.00 0.16 0.00
#> TCGA.CQ.6219.01 2 0.3409 0.6635 0.00 0.70 0.30 0.00 0.00 0.00
#> TCGA.CN.A498.01 5 0.6097 0.0482 0.00 0.00 0.14 0.08 0.60 0.18
#> TCGA.CV.6953.11 3 0.1556 0.6629 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.HD.A4C1.01 1 0.0000 0.8351 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A45P.01 2 0.0937 0.7178 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CV.A45Q.01 1 0.0000 0.8351 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A45T.01 2 0.3409 0.6635 0.00 0.70 0.30 0.00 0.00 0.00
#> TCGA.CN.6996.01 2 0.1480 0.7103 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.DQ.5624.01 3 0.1556 0.6629 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.CN.A499.01 5 0.5692 0.0879 0.00 0.00 0.32 0.00 0.50 0.18
#> TCGA.CV.6940.01 6 0.7197 0.4608 0.00 0.10 0.26 0.00 0.24 0.40
#> TCGA.CQ.7064.01 2 0.3163 0.7141 0.00 0.82 0.14 0.00 0.00 0.04
#> TCGA.IQ.A61K.01 2 0.4420 0.5369 0.00 0.66 0.00 0.02 0.02 0.30
#> TCGA.BA.A6DF.01 1 0.1807 0.8214 0.92 0.00 0.00 0.00 0.02 0.06
#> TCGA.BA.A6DB.01 3 0.1556 0.6629 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.IQ.A61L.01 2 0.1267 0.7185 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.HD.8635.01 4 0.6677 -0.2248 0.00 0.02 0.06 0.48 0.34 0.10
#> TCGA.MT.A67G.01 5 0.6869 -0.1205 0.00 0.08 0.08 0.08 0.58 0.18
#> TCGA.QK.A64Z.01 2 0.0547 0.7204 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.HD.8634.01 2 0.3163 0.6653 0.00 0.82 0.00 0.14 0.00 0.04
#> TCGA.CQ.7063.01 1 0.5523 0.6252 0.64 0.00 0.00 0.08 0.06 0.22
#> TCGA.F7.A50J.01 2 0.4863 0.6382 0.00 0.66 0.14 0.00 0.00 0.20
#> TCGA.MT.A51W.01 3 0.1556 0.6629 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.CQ.7071.01 1 0.0937 0.8327 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.CV.A463.01 1 0.0000 0.8351 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.5367.01 3 0.4810 0.2417 0.00 0.00 0.66 0.00 0.12 0.22
#> TCGA.CN.A640.01 4 0.5523 0.4004 0.00 0.36 0.00 0.50 0.00 0.14
#> TCGA.UF.A7JO.01 4 0.3007 0.5571 0.00 0.08 0.00 0.86 0.04 0.02
#> TCGA.UF.A7JV.01 2 0.4326 0.6646 0.00 0.68 0.28 0.02 0.00 0.02
#> TCGA.IQ.A6SG.01 5 0.3499 0.7315 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.MT.A67A.01 1 0.1092 0.8142 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.BB.A6UO.01 1 0.1480 0.8238 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.BB.7871.01 5 0.3499 0.7315 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.CN.4736.01 3 0.1267 0.6551 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.CN.5369.01 3 0.0547 0.6008 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.IQ.A61E.01 4 0.7564 0.6182 0.10 0.12 0.00 0.50 0.08 0.20
#> TCGA.UF.A7JT.01 1 0.4430 0.7457 0.76 0.00 0.00 0.04 0.08 0.12
#> TCGA.CN.5373.01 2 0.3711 0.5793 0.00 0.72 0.00 0.00 0.02 0.26
#> TCGA.BB.7863.01 1 0.6516 0.3674 0.52 0.00 0.00 0.26 0.08 0.14
#> TCGA.BA.4077.01 3 0.5569 -0.1690 0.00 0.00 0.52 0.00 0.32 0.16
#> TCGA.H7.A6C4.01 2 0.2474 0.6921 0.00 0.88 0.00 0.08 0.00 0.04
#> TCGA.MT.A67F.01 4 0.6771 0.4407 0.26 0.00 0.00 0.48 0.08 0.18
#> TCGA.T2.A6WX.01 4 0.7432 0.5415 0.18 0.06 0.00 0.48 0.06 0.22
#> TCGA.CR.7383.01 3 0.5841 -0.1651 0.00 0.00 0.48 0.00 0.30 0.22
#> TCGA.CV.7438.01 2 0.0937 0.7178 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CV.A6JD.01 4 0.7314 0.5663 0.16 0.06 0.00 0.50 0.06 0.22
#> TCGA.P3.A6T5.01 3 0.6071 -0.1618 0.00 0.12 0.52 0.00 0.04 0.32
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.CQ.5327.01 1 0.391 0.5158 0.58 0.00 0.00 0.02 0.00 0.00 0.40
#> TCGA.CR.7391.01 3 0.421 0.8840 0.00 0.04 0.56 0.00 0.40 0.00 0.00
#> TCGA.CV.7416.01 7 0.731 -0.3311 0.00 0.28 0.14 0.02 0.00 0.28 0.28
#> TCGA.H7.7774.01 4 0.186 0.4372 0.02 0.00 0.00 0.92 0.00 0.02 0.04
#> TCGA.CQ.5330.01 4 0.660 0.2072 0.06 0.02 0.10 0.44 0.00 0.02 0.36
#> TCGA.CV.7427.01 4 0.499 0.1633 0.08 0.00 0.02 0.56 0.00 0.00 0.34
#> TCGA.CV.7425.01 1 0.000 0.7765 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7407.01 5 0.000 0.7179 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.6003.01 2 0.716 0.0921 0.00 0.34 0.12 0.02 0.00 0.30 0.22
#> TCGA.CN.6021.01 5 0.000 0.7179 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.5978.01 5 0.000 0.7179 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CN.6018.01 2 0.388 0.6832 0.00 0.78 0.04 0.02 0.00 0.02 0.14
#> TCGA.CV.5966.01 4 0.420 0.4297 0.00 0.02 0.04 0.74 0.00 0.02 0.18
#> TCGA.CV.7411.01 2 0.339 0.6695 0.00 0.78 0.02 0.02 0.00 0.18 0.00
#> TCGA.CQ.7068.01 1 0.000 0.7765 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5973.01 2 0.684 0.1301 0.00 0.32 0.12 0.00 0.00 0.28 0.28
#> TCGA.CV.7104.01 2 0.510 0.4061 0.00 0.52 0.02 0.40 0.00 0.04 0.02
#> TCGA.CV.7095.01 1 0.428 0.3981 0.50 0.00 0.00 0.04 0.00 0.00 0.46
#> TCGA.CV.7178.01 6 0.534 0.2833 0.00 0.00 0.32 0.00 0.20 0.48 0.00
#> TCGA.CV.7252.01 1 0.682 0.2440 0.40 0.00 0.18 0.18 0.00 0.00 0.24
#> TCGA.CR.6478.01 6 0.642 0.2682 0.00 0.08 0.30 0.00 0.20 0.42 0.00
#> TCGA.CV.7102.01 6 0.470 0.4439 0.00 0.04 0.04 0.30 0.00 0.62 0.00
#> TCGA.CR.7394.01 2 0.189 0.7265 0.00 0.88 0.12 0.00 0.00 0.00 0.00
#> TCGA.CV.6955.01 4 0.202 0.4135 0.00 0.06 0.00 0.90 0.00 0.04 0.00
#> TCGA.BA.5556.01 4 0.494 0.0621 0.06 0.00 0.02 0.46 0.00 0.00 0.46
#> TCGA.BA.5557.01 2 0.189 0.7265 0.00 0.88 0.12 0.00 0.00 0.00 0.00
#> TCGA.D6.6515.01 3 0.474 0.8139 0.00 0.10 0.56 0.00 0.34 0.00 0.00
#> TCGA.CV.7238.01 2 0.238 0.7248 0.00 0.86 0.12 0.00 0.00 0.00 0.02
#> TCGA.CV.6942.01 1 0.000 0.7765 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7177.01 5 0.323 0.4709 0.00 0.00 0.02 0.02 0.80 0.16 0.00
#> TCGA.CR.7395.01 4 0.640 0.1727 0.08 0.00 0.18 0.38 0.00 0.00 0.36
#> TCGA.CX.7085.01 2 0.238 0.7248 0.00 0.86 0.12 0.00 0.00 0.00 0.02
#> TCGA.CV.7099.01 1 0.361 0.6379 0.68 0.00 0.00 0.02 0.00 0.00 0.30
#> TCGA.CQ.6218.01 6 0.509 0.5150 0.00 0.02 0.20 0.00 0.16 0.62 0.00
#> TCGA.C9.A47Z.01 1 0.418 0.6099 0.70 0.00 0.18 0.00 0.00 0.00 0.12
#> TCGA.DQ.5625.01 2 0.407 0.5549 0.00 0.66 0.00 0.30 0.00 0.02 0.02
#> TCGA.C9.A480.01 2 0.101 0.7409 0.00 0.96 0.02 0.00 0.00 0.00 0.02
#> TCGA.CV.6952.01 4 0.554 0.4061 0.00 0.06 0.08 0.62 0.00 0.02 0.22
#> TCGA.CQ.5331.01 2 0.238 0.7248 0.00 0.86 0.12 0.00 0.00 0.00 0.02
#> TCGA.D6.6826.01 4 0.200 0.4175 0.00 0.02 0.02 0.92 0.00 0.02 0.02
#> TCGA.CV.6953.01 1 0.000 0.7765 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.6870.01 5 0.000 0.7179 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CR.6477.01 5 0.352 -0.5672 0.00 0.00 0.44 0.00 0.56 0.00 0.00
#> TCGA.CQ.6219.01 2 0.238 0.7248 0.00 0.86 0.12 0.00 0.00 0.00 0.02
#> TCGA.CN.A498.01 6 0.713 0.1810 0.00 0.04 0.06 0.14 0.36 0.38 0.02
#> TCGA.CV.6953.11 3 0.421 0.8840 0.00 0.04 0.56 0.00 0.40 0.00 0.00
#> TCGA.HD.A4C1.01 1 0.000 0.7765 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A45P.01 2 0.143 0.7333 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.CV.A45Q.01 1 0.000 0.7765 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A45T.01 2 0.238 0.7248 0.00 0.86 0.12 0.00 0.00 0.00 0.02
#> TCGA.CN.6996.01 2 0.265 0.7224 0.00 0.86 0.02 0.00 0.00 0.02 0.10
#> TCGA.DQ.5624.01 3 0.439 0.8606 0.00 0.02 0.54 0.00 0.42 0.02 0.00
#> TCGA.CN.A499.01 5 0.606 -0.1622 0.00 0.02 0.16 0.00 0.44 0.36 0.02
#> TCGA.CV.6940.01 6 0.300 0.4746 0.00 0.04 0.02 0.00 0.10 0.84 0.00
#> TCGA.CQ.7064.01 2 0.216 0.7344 0.00 0.90 0.02 0.00 0.00 0.06 0.02
#> TCGA.IQ.A61K.01 2 0.684 0.1205 0.00 0.32 0.12 0.00 0.00 0.26 0.30
#> TCGA.BA.A6DF.01 1 0.166 0.7621 0.92 0.00 0.00 0.02 0.00 0.00 0.06
#> TCGA.BA.A6DB.01 3 0.394 0.8725 0.00 0.02 0.56 0.00 0.42 0.00 0.00
#> TCGA.IQ.A61L.01 2 0.354 0.7001 0.00 0.80 0.02 0.00 0.00 0.08 0.10
#> TCGA.HD.8635.01 4 0.658 0.0461 0.00 0.02 0.02 0.56 0.16 0.14 0.10
#> TCGA.MT.A67G.01 6 0.771 0.2616 0.00 0.12 0.06 0.14 0.28 0.38 0.02
#> TCGA.QK.A64Z.01 2 0.251 0.7268 0.00 0.88 0.02 0.00 0.00 0.04 0.06
#> TCGA.HD.8634.01 2 0.477 0.6234 0.00 0.72 0.04 0.10 0.00 0.02 0.12
#> TCGA.CQ.7063.01 1 0.427 0.4295 0.52 0.00 0.00 0.04 0.00 0.00 0.44
#> TCGA.F7.A50J.01 2 0.457 0.6309 0.00 0.70 0.04 0.00 0.00 0.18 0.08
#> TCGA.MT.A51W.01 3 0.397 0.8420 0.00 0.02 0.54 0.00 0.44 0.00 0.00
#> TCGA.CQ.7071.01 1 0.208 0.7460 0.86 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.CV.A463.01 1 0.000 0.7765 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.5367.01 6 0.550 0.4547 0.00 0.02 0.26 0.00 0.18 0.54 0.00
#> TCGA.CN.A640.01 4 0.701 0.2277 0.00 0.22 0.12 0.42 0.00 0.02 0.22
#> TCGA.UF.A7JO.01 4 0.136 0.4333 0.00 0.04 0.00 0.94 0.00 0.02 0.00
#> TCGA.UF.A7JV.01 2 0.265 0.7261 0.00 0.86 0.10 0.00 0.00 0.02 0.02
#> TCGA.IQ.A6SG.01 5 0.000 0.7179 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.MT.A67A.01 1 0.101 0.7590 0.96 0.00 0.02 0.00 0.00 0.00 0.02
#> TCGA.BB.A6UO.01 1 0.117 0.7681 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.BB.7871.01 5 0.000 0.7179 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CN.4736.01 3 0.466 0.8772 0.00 0.04 0.54 0.00 0.40 0.02 0.00
#> TCGA.CN.5369.01 3 0.542 0.6341 0.00 0.18 0.56 0.00 0.24 0.02 0.00
#> TCGA.IQ.A61E.01 4 0.652 0.2359 0.04 0.02 0.12 0.44 0.00 0.02 0.36
#> TCGA.UF.A7JT.01 1 0.352 0.6514 0.70 0.00 0.00 0.02 0.00 0.00 0.28
#> TCGA.CN.5373.01 2 0.591 0.3859 0.00 0.48 0.04 0.00 0.00 0.30 0.18
#> TCGA.BB.7863.01 1 0.682 0.2440 0.40 0.00 0.18 0.18 0.00 0.00 0.24
#> TCGA.BA.4077.01 5 0.532 0.1442 0.00 0.00 0.22 0.00 0.58 0.18 0.02
#> TCGA.H7.A6C4.01 2 0.388 0.6832 0.00 0.78 0.04 0.02 0.00 0.02 0.14
#> TCGA.MT.A67F.01 4 0.651 -0.0532 0.22 0.00 0.08 0.38 0.00 0.00 0.32
#> TCGA.T2.A6WX.01 7 0.495 -0.1596 0.12 0.00 0.00 0.36 0.00 0.00 0.52
#> TCGA.CR.7383.01 6 0.568 0.4765 0.00 0.04 0.16 0.00 0.26 0.54 0.00
#> TCGA.CV.7438.01 2 0.238 0.7199 0.00 0.86 0.02 0.00 0.00 0.00 0.12
#> TCGA.CV.A6JD.01 7 0.487 -0.2125 0.10 0.00 0.00 0.42 0.00 0.00 0.48
#> TCGA.P3.A6T5.01 6 0.615 0.3147 0.00 0.16 0.20 0.00 0.04 0.56 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.CQ.5327.01 7 0.3272 0.1535 0.42 0.00 0.00 0.00 0.00 0.00 0.58 0.00
#> TCGA.CR.7391.01 5 0.6199 0.2982 0.00 0.08 0.30 0.00 0.32 0.30 0.00 0.00
#> TCGA.CV.7416.01 8 0.3078 0.7126 0.00 0.10 0.06 0.02 0.00 0.00 0.00 0.82
#> TCGA.H7.7774.01 4 0.1765 0.6702 0.00 0.00 0.00 0.88 0.00 0.00 0.12 0.00
#> TCGA.CQ.5330.01 7 0.5289 0.1879 0.00 0.00 0.16 0.20 0.00 0.00 0.58 0.06
#> TCGA.CV.7427.01 7 0.4804 -0.0687 0.00 0.00 0.14 0.40 0.00 0.00 0.46 0.00
#> TCGA.CV.7425.01 1 0.0000 0.8684 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7407.01 5 0.0471 0.4459 0.00 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.CV.6003.01 8 0.3444 0.7435 0.00 0.14 0.06 0.02 0.00 0.00 0.00 0.78
#> TCGA.CN.6021.01 5 0.0000 0.4642 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.5978.01 5 0.0000 0.4642 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CN.6018.01 2 0.3847 0.6548 0.00 0.78 0.02 0.10 0.00 0.00 0.06 0.04
#> TCGA.CV.5966.01 4 0.4885 0.4014 0.00 0.00 0.10 0.60 0.00 0.00 0.26 0.04
#> TCGA.CV.7411.01 2 0.4262 0.6281 0.00 0.74 0.02 0.08 0.00 0.04 0.00 0.12
#> TCGA.CQ.7068.01 1 0.0000 0.8684 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5973.01 8 0.4280 0.7903 0.00 0.24 0.02 0.02 0.00 0.04 0.00 0.68
#> TCGA.CV.7104.01 4 0.4308 0.3168 0.00 0.32 0.02 0.62 0.00 0.00 0.02 0.02
#> TCGA.CV.7095.01 7 0.2406 0.3524 0.20 0.00 0.00 0.00 0.00 0.00 0.80 0.00
#> TCGA.CV.7178.01 6 0.2862 0.4261 0.00 0.00 0.10 0.00 0.08 0.82 0.00 0.00
#> TCGA.CV.7252.01 3 0.6375 0.6586 0.24 0.00 0.46 0.12 0.00 0.00 0.16 0.02
#> TCGA.CR.6478.01 6 0.3421 0.4286 0.00 0.04 0.08 0.00 0.08 0.80 0.00 0.00
#> TCGA.CV.7102.01 6 0.4174 0.4052 0.00 0.02 0.00 0.22 0.02 0.70 0.00 0.04
#> TCGA.CR.7394.01 2 0.2165 0.7706 0.00 0.88 0.06 0.00 0.00 0.06 0.00 0.00
#> TCGA.CV.6955.01 4 0.1804 0.6860 0.00 0.02 0.00 0.90 0.00 0.00 0.08 0.00
#> TCGA.BA.5556.01 7 0.3002 0.3899 0.00 0.00 0.02 0.12 0.00 0.00 0.82 0.04
#> TCGA.BA.5557.01 2 0.2165 0.7706 0.00 0.88 0.06 0.00 0.00 0.06 0.00 0.00
#> TCGA.D6.6515.01 6 0.6398 -0.2902 0.00 0.12 0.30 0.00 0.26 0.32 0.00 0.00
#> TCGA.CV.7238.01 2 0.2407 0.7715 0.00 0.86 0.08 0.00 0.00 0.06 0.00 0.00
#> TCGA.CV.6942.01 1 0.0000 0.8684 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7177.01 5 0.3528 0.1374 0.00 0.00 0.08 0.00 0.74 0.18 0.00 0.00
#> TCGA.CR.7395.01 3 0.5683 0.2020 0.00 0.00 0.42 0.20 0.00 0.00 0.34 0.04
#> TCGA.CX.7085.01 2 0.1887 0.7748 0.00 0.90 0.04 0.00 0.00 0.06 0.00 0.00
#> TCGA.CV.7099.01 7 0.3299 0.0167 0.44 0.00 0.00 0.00 0.00 0.00 0.56 0.00
#> TCGA.CQ.6218.01 6 0.1804 0.5020 0.00 0.00 0.00 0.00 0.08 0.90 0.00 0.02
#> TCGA.C9.A47Z.01 1 0.4137 -0.1896 0.50 0.00 0.46 0.00 0.00 0.00 0.02 0.02
#> TCGA.DQ.5625.01 2 0.4325 0.3010 0.00 0.56 0.00 0.38 0.00 0.00 0.02 0.04
#> TCGA.C9.A480.01 2 0.1741 0.7702 0.00 0.92 0.02 0.00 0.00 0.02 0.00 0.04
#> TCGA.CV.6952.01 4 0.5653 0.2397 0.00 0.00 0.16 0.48 0.00 0.00 0.30 0.06
#> TCGA.CQ.5331.01 2 0.2407 0.7715 0.00 0.86 0.08 0.00 0.00 0.06 0.00 0.00
#> TCGA.D6.6826.01 4 0.2624 0.6475 0.00 0.00 0.06 0.86 0.00 0.02 0.06 0.00
#> TCGA.CV.6953.01 1 0.0000 0.8684 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.6870.01 5 0.0000 0.4642 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CR.6477.01 5 0.5190 0.3148 0.00 0.00 0.26 0.00 0.42 0.32 0.00 0.00
#> TCGA.CQ.6219.01 2 0.2407 0.7715 0.00 0.86 0.08 0.00 0.00 0.06 0.00 0.00
#> TCGA.CN.A498.01 6 0.6547 0.2733 0.00 0.02 0.12 0.06 0.34 0.42 0.00 0.04
#> TCGA.CV.6953.11 5 0.6199 0.2982 0.00 0.08 0.30 0.00 0.32 0.30 0.00 0.00
#> TCGA.HD.A4C1.01 1 0.0000 0.8684 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A45P.01 2 0.0808 0.7558 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.CV.A45Q.01 1 0.0000 0.8684 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A45T.01 2 0.2165 0.7706 0.00 0.88 0.06 0.00 0.00 0.06 0.00 0.00
#> TCGA.CN.6996.01 2 0.2482 0.7305 0.00 0.88 0.02 0.06 0.00 0.00 0.02 0.02
#> TCGA.DQ.5624.01 5 0.6173 0.3056 0.00 0.08 0.26 0.00 0.34 0.32 0.00 0.00
#> TCGA.CN.A499.01 6 0.5639 0.3161 0.00 0.00 0.12 0.02 0.32 0.50 0.00 0.04
#> TCGA.CV.6940.01 6 0.4521 0.4405 0.00 0.02 0.00 0.08 0.06 0.72 0.00 0.12
#> TCGA.CQ.7064.01 2 0.2071 0.7594 0.00 0.90 0.02 0.00 0.00 0.04 0.00 0.04
#> TCGA.IQ.A61K.01 8 0.4806 0.7773 0.00 0.26 0.02 0.02 0.00 0.04 0.02 0.64
#> TCGA.BA.A6DF.01 1 0.2623 0.7655 0.84 0.00 0.06 0.00 0.00 0.00 0.10 0.00
#> TCGA.BA.A6DB.01 5 0.6187 0.3151 0.00 0.08 0.28 0.00 0.34 0.30 0.00 0.00
#> TCGA.IQ.A61L.01 2 0.1947 0.6864 0.00 0.86 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.HD.8635.01 4 0.4087 0.5347 0.00 0.02 0.06 0.78 0.08 0.04 0.00 0.02
#> TCGA.MT.A67G.01 6 0.7321 0.3158 0.00 0.10 0.12 0.08 0.24 0.42 0.00 0.04
#> TCGA.QK.A64Z.01 2 0.1607 0.7433 0.00 0.92 0.00 0.04 0.00 0.00 0.00 0.04
#> TCGA.HD.8634.01 2 0.4988 0.5675 0.00 0.68 0.04 0.14 0.00 0.00 0.08 0.06
#> TCGA.CQ.7063.01 7 0.2406 0.3524 0.20 0.00 0.00 0.00 0.00 0.00 0.80 0.00
#> TCGA.F7.A50J.01 2 0.3449 0.2880 0.00 0.66 0.02 0.00 0.00 0.00 0.00 0.32
#> TCGA.MT.A51W.01 5 0.6032 0.3238 0.00 0.06 0.28 0.00 0.36 0.30 0.00 0.00
#> TCGA.CQ.7071.01 1 0.2407 0.7897 0.86 0.00 0.06 0.00 0.00 0.00 0.08 0.00
#> TCGA.CV.A463.01 1 0.0000 0.8684 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.5367.01 6 0.2864 0.4487 0.00 0.02 0.06 0.00 0.08 0.84 0.00 0.00
#> TCGA.CN.A640.01 7 0.7148 -0.0684 0.00 0.22 0.14 0.24 0.00 0.00 0.34 0.06
#> TCGA.UF.A7JO.01 4 0.1804 0.6860 0.00 0.02 0.00 0.90 0.00 0.00 0.08 0.00
#> TCGA.UF.A7JV.01 2 0.2407 0.7715 0.00 0.86 0.08 0.00 0.00 0.06 0.00 0.00
#> TCGA.IQ.A6SG.01 5 0.0000 0.4642 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MT.A67A.01 1 0.0808 0.8482 0.96 0.00 0.04 0.00 0.00 0.00 0.00 0.00
#> TCGA.BB.A6UO.01 1 0.1947 0.7573 0.86 0.00 0.00 0.00 0.00 0.00 0.14 0.00
#> TCGA.BB.7871.01 5 0.0000 0.4642 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CN.4736.01 5 0.6199 0.2982 0.00 0.08 0.30 0.00 0.32 0.30 0.00 0.00
#> TCGA.CN.5369.01 6 0.6523 -0.1677 0.00 0.20 0.30 0.00 0.18 0.32 0.00 0.00
#> TCGA.IQ.A61E.01 7 0.5385 0.1700 0.00 0.00 0.16 0.22 0.00 0.00 0.56 0.06
#> TCGA.UF.A7JT.01 1 0.3657 0.5976 0.72 0.00 0.08 0.00 0.00 0.00 0.20 0.00
#> TCGA.CN.5373.01 8 0.4834 0.5952 0.00 0.38 0.00 0.04 0.00 0.06 0.00 0.52
#> TCGA.BB.7863.01 3 0.6186 0.6573 0.26 0.00 0.48 0.10 0.00 0.00 0.14 0.02
#> TCGA.BA.4077.01 5 0.5171 -0.0126 0.00 0.00 0.06 0.02 0.54 0.34 0.00 0.04
#> TCGA.H7.A6C4.01 2 0.4077 0.6324 0.00 0.76 0.02 0.10 0.00 0.00 0.08 0.04
#> TCGA.MT.A67F.01 7 0.5560 0.1267 0.06 0.00 0.20 0.10 0.00 0.00 0.60 0.04
#> TCGA.T2.A6WX.01 7 0.0471 0.4220 0.00 0.00 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.CR.7383.01 6 0.3135 0.5041 0.00 0.02 0.00 0.02 0.12 0.82 0.00 0.02
#> TCGA.CV.7438.01 2 0.1947 0.6911 0.00 0.86 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.CV.A6JD.01 7 0.0471 0.4220 0.00 0.00 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.P3.A6T5.01 6 0.5662 -0.0358 0.00 0.10 0.10 0.00 0.00 0.48 0.00 0.32
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: Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node02111-leaf , Node02112-leaf , Node02113-leaf , Node02114-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02124-leaf , Node02131-leaf , Node02132 , Node02133-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02231-leaf , Node02232-leaf , Node02233-leaf , Node02241-leaf , Node02242-leaf , Node02243-leaf , Node02321-leaf , Node02322-leaf , Node02323-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf , Node05114-leaf , Node05121 , Node05122-leaf , Node05123-leaf , Node05221-leaf , Node05222-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0211"]
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 28 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 0.979 0.990 0.3602 0.651 0.651
#> 3 3 0.829 0.842 0.942 0.7197 0.622 0.458
#> 4 4 1.000 0.997 0.999 0.1914 0.831 0.576
#> 5 5 0.809 0.757 0.852 0.0601 1.000 1.000
#> 6 6 0.732 0.715 0.845 0.0475 0.876 0.569
#> 7 7 0.778 0.590 0.804 0.0293 0.950 0.750
#> 8 8 0.792 0.537 0.817 0.0272 0.934 0.627
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.CQ.5327.01 1 0.000 0.986 1.00 0.00
#> TCGA.H7.7774.01 1 0.000 0.986 1.00 0.00
#> TCGA.CQ.5330.01 1 0.000 0.986 1.00 0.00
#> TCGA.CV.7427.01 1 0.000 0.986 1.00 0.00
#> TCGA.CV.7425.01 1 0.000 0.986 1.00 0.00
#> TCGA.CQ.7068.01 1 0.000 0.986 1.00 0.00
#> TCGA.CV.7095.01 1 0.000 0.986 1.00 0.00
#> TCGA.CV.7252.01 2 0.000 1.000 0.00 1.00
#> TCGA.BA.5556.01 1 0.000 0.986 1.00 0.00
#> TCGA.CV.6942.01 1 0.000 0.986 1.00 0.00
#> TCGA.CR.7395.01 1 0.584 0.845 0.86 0.14
#> TCGA.CV.7099.01 1 0.000 0.986 1.00 0.00
#> TCGA.C9.A47Z.01 2 0.000 1.000 0.00 1.00
#> TCGA.CV.6953.01 1 0.000 0.986 1.00 0.00
#> TCGA.HD.A4C1.01 1 0.000 0.986 1.00 0.00
#> TCGA.CV.A45Q.01 1 0.000 0.986 1.00 0.00
#> TCGA.BA.A6DF.01 2 0.000 1.000 0.00 1.00
#> TCGA.CQ.7063.01 1 0.000 0.986 1.00 0.00
#> TCGA.CQ.7071.01 2 0.000 1.000 0.00 1.00
#> TCGA.CV.A463.01 1 0.000 0.986 1.00 0.00
#> TCGA.MT.A67A.01 2 0.000 1.000 0.00 1.00
#> TCGA.BB.A6UO.01 1 0.000 0.986 1.00 0.00
#> TCGA.IQ.A61E.01 1 0.584 0.845 0.86 0.14
#> TCGA.UF.A7JT.01 1 0.000 0.986 1.00 0.00
#> TCGA.BB.7863.01 2 0.000 1.000 0.00 1.00
#> TCGA.MT.A67F.01 1 0.000 0.986 1.00 0.00
#> TCGA.T2.A6WX.01 1 0.000 0.986 1.00 0.00
#> TCGA.CV.A6JD.01 1 0.000 0.986 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CQ.5327.01 1 0.254 0.8624 0.92 0 0.08
#> TCGA.H7.7774.01 3 0.000 0.8557 0.00 0 1.00
#> TCGA.CQ.5330.01 1 0.000 0.9463 1.00 0 0.00
#> TCGA.CV.7427.01 3 0.000 0.8557 0.00 0 1.00
#> TCGA.CV.7425.01 1 0.000 0.9463 1.00 0 0.00
#> TCGA.CQ.7068.01 1 0.000 0.9463 1.00 0 0.00
#> TCGA.CV.7095.01 3 0.000 0.8557 0.00 0 1.00
#> TCGA.CV.7252.01 2 0.000 1.0000 0.00 1 0.00
#> TCGA.BA.5556.01 1 0.628 -0.0645 0.54 0 0.46
#> TCGA.CV.6942.01 1 0.000 0.9463 1.00 0 0.00
#> TCGA.CR.7395.01 3 0.000 0.8557 0.00 0 1.00
#> TCGA.CV.7099.01 3 0.595 0.5064 0.36 0 0.64
#> TCGA.C9.A47Z.01 2 0.000 1.0000 0.00 1 0.00
#> TCGA.CV.6953.01 3 0.595 0.5064 0.36 0 0.64
#> TCGA.HD.A4C1.01 1 0.000 0.9463 1.00 0 0.00
#> TCGA.CV.A45Q.01 1 0.000 0.9463 1.00 0 0.00
#> TCGA.BA.A6DF.01 3 0.000 0.8557 0.00 0 1.00
#> TCGA.CQ.7063.01 1 0.000 0.9463 1.00 0 0.00
#> TCGA.CQ.7071.01 3 0.000 0.8557 0.00 0 1.00
#> TCGA.CV.A463.01 1 0.000 0.9463 1.00 0 0.00
#> TCGA.MT.A67A.01 2 0.000 1.0000 0.00 1 0.00
#> TCGA.BB.A6UO.01 1 0.000 0.9463 1.00 0 0.00
#> TCGA.IQ.A61E.01 3 0.000 0.8557 0.00 0 1.00
#> TCGA.UF.A7JT.01 3 0.000 0.8557 0.00 0 1.00
#> TCGA.BB.7863.01 2 0.000 1.0000 0.00 1 0.00
#> TCGA.MT.A67F.01 1 0.000 0.9463 1.00 0 0.00
#> TCGA.T2.A6WX.01 3 0.595 0.5064 0.36 0 0.64
#> TCGA.CV.A6JD.01 1 0.000 0.9463 1.00 0 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.CQ.5327.01 3 0.000 1.000 0 0 1.00 0.00
#> TCGA.H7.7774.01 4 0.121 0.951 0 0 0.04 0.96
#> TCGA.CQ.5330.01 1 0.000 1.000 1 0 0.00 0.00
#> TCGA.CV.7427.01 3 0.000 1.000 0 0 1.00 0.00
#> TCGA.CV.7425.01 1 0.000 1.000 1 0 0.00 0.00
#> TCGA.CQ.7068.01 1 0.000 1.000 1 0 0.00 0.00
#> TCGA.CV.7095.01 3 0.000 1.000 0 0 1.00 0.00
#> TCGA.CV.7252.01 2 0.000 1.000 0 1 0.00 0.00
#> TCGA.BA.5556.01 3 0.000 1.000 0 0 1.00 0.00
#> TCGA.CV.6942.01 1 0.000 1.000 1 0 0.00 0.00
#> TCGA.CR.7395.01 4 0.000 0.988 0 0 0.00 1.00
#> TCGA.CV.7099.01 3 0.000 1.000 0 0 1.00 0.00
#> TCGA.C9.A47Z.01 2 0.000 1.000 0 1 0.00 0.00
#> TCGA.CV.6953.01 3 0.000 1.000 0 0 1.00 0.00
#> TCGA.HD.A4C1.01 1 0.000 1.000 1 0 0.00 0.00
#> TCGA.CV.A45Q.01 1 0.000 1.000 1 0 0.00 0.00
#> TCGA.BA.A6DF.01 4 0.000 0.988 0 0 0.00 1.00
#> TCGA.CQ.7063.01 1 0.000 1.000 1 0 0.00 0.00
#> TCGA.CQ.7071.01 4 0.000 0.988 0 0 0.00 1.00
#> TCGA.CV.A463.01 1 0.000 1.000 1 0 0.00 0.00
#> TCGA.MT.A67A.01 2 0.000 1.000 0 1 0.00 0.00
#> TCGA.BB.A6UO.01 1 0.000 1.000 1 0 0.00 0.00
#> TCGA.IQ.A61E.01 4 0.000 0.988 0 0 0.00 1.00
#> TCGA.UF.A7JT.01 3 0.000 1.000 0 0 1.00 0.00
#> TCGA.BB.7863.01 2 0.000 1.000 0 1 0.00 0.00
#> TCGA.MT.A67F.01 1 0.000 1.000 1 0 0.00 0.00
#> TCGA.T2.A6WX.01 3 0.000 1.000 0 0 1.00 0.00
#> TCGA.CV.A6JD.01 1 0.000 1.000 1 0 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CQ.5327.01 3 0.418 0.648 0.00 0.40 0.60 0.00 0.0
#> TCGA.H7.7774.01 4 0.546 0.111 0.00 0.06 0.46 0.48 0.0
#> TCGA.CQ.5330.01 1 0.104 0.874 0.96 0.04 0.00 0.00 0.0
#> TCGA.CV.7427.01 3 0.141 0.717 0.00 0.06 0.94 0.00 0.0
#> TCGA.CV.7425.01 1 0.430 0.530 0.52 0.48 0.00 0.00 0.0
#> TCGA.CQ.7068.01 1 0.000 0.879 1.00 0.00 0.00 0.00 0.0
#> TCGA.CV.7095.01 3 0.141 0.709 0.00 0.06 0.94 0.00 0.0
#> TCGA.CV.7252.01 5 0.202 0.949 0.00 0.10 0.00 0.00 0.9
#> TCGA.BA.5556.01 3 0.429 0.637 0.00 0.46 0.54 0.00 0.0
#> TCGA.CV.6942.01 1 0.293 0.801 0.82 0.18 0.00 0.00 0.0
#> TCGA.CR.7395.01 4 0.141 0.767 0.00 0.06 0.00 0.94 0.0
#> TCGA.CV.7099.01 3 0.141 0.723 0.00 0.06 0.94 0.00 0.0
#> TCGA.C9.A47Z.01 5 0.000 0.949 0.00 0.00 0.00 0.00 1.0
#> TCGA.CV.6953.01 3 0.398 0.684 0.00 0.34 0.66 0.00 0.0
#> TCGA.HD.A4C1.01 1 0.141 0.862 0.94 0.06 0.00 0.00 0.0
#> TCGA.CV.A45Q.01 1 0.000 0.879 1.00 0.00 0.00 0.00 0.0
#> TCGA.BA.A6DF.01 4 0.000 0.783 0.00 0.00 0.00 1.00 0.0
#> TCGA.CQ.7063.01 1 0.104 0.874 0.96 0.04 0.00 0.00 0.0
#> TCGA.CQ.7071.01 4 0.368 0.648 0.00 0.28 0.00 0.72 0.0
#> TCGA.CV.A463.01 1 0.141 0.862 0.94 0.06 0.00 0.00 0.0
#> TCGA.MT.A67A.01 5 0.202 0.949 0.00 0.10 0.00 0.00 0.9
#> TCGA.BB.A6UO.01 1 0.000 0.879 1.00 0.00 0.00 0.00 0.0
#> TCGA.IQ.A61E.01 4 0.000 0.783 0.00 0.00 0.00 1.00 0.0
#> TCGA.UF.A7JT.01 3 0.417 0.552 0.00 0.08 0.78 0.14 0.0
#> TCGA.BB.7863.01 5 0.000 0.949 0.00 0.00 0.00 0.00 1.0
#> TCGA.MT.A67F.01 1 0.423 0.565 0.58 0.42 0.00 0.00 0.0
#> TCGA.T2.A6WX.01 3 0.228 0.740 0.00 0.12 0.88 0.00 0.0
#> TCGA.CV.A6JD.01 1 0.000 0.879 1.00 0.00 0.00 0.00 0.0
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.CQ.5327.01 6 0.3756 0.444 0.00 0.00 0.40 0.00 0.00 0.60
#> TCGA.H7.7774.01 3 0.4337 0.476 0.00 0.02 0.50 0.48 0.00 0.00
#> TCGA.CQ.5330.01 1 0.1556 0.863 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.CV.7427.01 3 0.3315 0.691 0.00 0.00 0.78 0.20 0.00 0.02
#> TCGA.CV.7425.01 6 0.3660 0.635 0.16 0.06 0.00 0.00 0.00 0.78
#> TCGA.CQ.7068.01 1 0.0000 0.887 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7095.01 3 0.3198 0.689 0.00 0.00 0.74 0.26 0.00 0.00
#> TCGA.CV.7252.01 5 0.2048 0.930 0.00 0.00 0.00 0.00 0.88 0.12
#> TCGA.BA.5556.01 6 0.3592 0.576 0.00 0.00 0.24 0.02 0.00 0.74
#> TCGA.CV.6942.01 1 0.4144 0.449 0.62 0.02 0.00 0.00 0.00 0.36
#> TCGA.CR.7395.01 4 0.4199 0.938 0.00 0.38 0.00 0.60 0.00 0.02
#> TCGA.CV.7099.01 3 0.0937 0.637 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.C9.A47Z.01 5 0.0000 0.930 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CV.6953.01 3 0.3916 0.129 0.00 0.00 0.68 0.02 0.00 0.30
#> TCGA.HD.A4C1.01 1 0.3258 0.827 0.84 0.02 0.00 0.10 0.00 0.04
#> TCGA.CV.A45Q.01 1 0.0547 0.887 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.BA.A6DF.01 4 0.4246 0.953 0.00 0.40 0.00 0.58 0.00 0.02
#> TCGA.CQ.7063.01 1 0.1556 0.863 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.CQ.7071.01 2 0.1267 0.000 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.CV.A463.01 1 0.3007 0.832 0.86 0.02 0.00 0.08 0.00 0.04
#> TCGA.MT.A67A.01 5 0.2048 0.930 0.00 0.00 0.00 0.00 0.88 0.12
#> TCGA.BB.A6UO.01 1 0.0547 0.887 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.IQ.A61E.01 4 0.3756 0.943 0.00 0.40 0.00 0.60 0.00 0.00
#> TCGA.UF.A7JT.01 3 0.4199 0.636 0.00 0.00 0.60 0.38 0.00 0.02
#> TCGA.BB.7863.01 5 0.0000 0.930 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.MT.A67F.01 6 0.2793 0.630 0.20 0.00 0.00 0.00 0.00 0.80
#> TCGA.T2.A6WX.01 3 0.2260 0.549 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.CV.A6JD.01 1 0.0000 0.887 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.CQ.5327.01 3 0.356 -0.3808 0.00 0.00 0.52 0.00 0.00 0.48 0.00
#> TCGA.H7.7774.01 7 0.328 0.6768 0.00 0.00 0.10 0.10 0.00 0.00 0.80
#> TCGA.CQ.5330.01 1 0.117 0.8181 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.CV.7427.01 3 0.399 -0.4451 0.00 0.00 0.50 0.00 0.00 0.02 0.48
#> TCGA.CV.7425.01 6 0.360 0.6122 0.08 0.02 0.04 0.00 0.00 0.82 0.04
#> TCGA.CQ.7068.01 1 0.000 0.8329 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7095.01 7 0.361 0.5831 0.00 0.00 0.30 0.00 0.00 0.02 0.68
#> TCGA.CV.7252.01 5 0.000 0.8986 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BA.5556.01 6 0.329 0.4065 0.00 0.00 0.34 0.00 0.00 0.66 0.00
#> TCGA.CV.6942.01 1 0.399 0.2347 0.52 0.02 0.00 0.00 0.00 0.46 0.00
#> TCGA.CR.7395.01 4 0.000 0.9520 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.7099.01 3 0.322 -0.0224 0.00 0.00 0.68 0.00 0.00 0.00 0.32
#> TCGA.C9.A47Z.01 5 0.306 0.8986 0.00 0.02 0.00 0.00 0.84 0.08 0.06
#> TCGA.CV.6953.01 3 0.189 0.4669 0.00 0.00 0.88 0.00 0.00 0.12 0.00
#> TCGA.HD.A4C1.01 1 0.530 0.6540 0.66 0.06 0.02 0.00 0.00 0.18 0.08
#> TCGA.CV.A45Q.01 1 0.101 0.8291 0.96 0.02 0.00 0.00 0.00 0.00 0.02
#> TCGA.BA.A6DF.01 4 0.000 0.9520 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CQ.7063.01 1 0.117 0.8181 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.CQ.7071.01 2 0.143 0.0000 0.00 0.92 0.00 0.08 0.00 0.00 0.00
#> TCGA.CV.A463.01 1 0.465 0.6851 0.72 0.04 0.02 0.00 0.00 0.16 0.06
#> TCGA.MT.A67A.01 5 0.000 0.8986 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BB.A6UO.01 1 0.101 0.8291 0.96 0.02 0.00 0.00 0.00 0.00 0.02
#> TCGA.IQ.A61E.01 4 0.143 0.9024 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.UF.A7JT.01 7 0.465 0.5560 0.00 0.00 0.30 0.06 0.00 0.02 0.62
#> TCGA.BB.7863.01 5 0.306 0.8986 0.00 0.02 0.00 0.00 0.84 0.08 0.06
#> TCGA.MT.A67F.01 6 0.420 0.6450 0.16 0.00 0.14 0.00 0.00 0.70 0.00
#> TCGA.T2.A6WX.01 3 0.238 0.4755 0.00 0.00 0.86 0.00 0.00 0.12 0.02
#> TCGA.CV.A6JD.01 1 0.000 0.8329 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.CQ.5327.01 3 0.3272 0.1957 0.00 0.00 0.58 0.00 0.00 0.42 0.00 0.00
#> TCGA.H7.7774.01 7 0.3856 0.6332 0.00 0.00 0.10 0.20 0.00 0.00 0.70 0.00
#> TCGA.CQ.5330.01 1 0.1947 0.6248 0.86 0.00 0.00 0.00 0.00 0.14 0.00 0.00
#> TCGA.CV.7427.01 7 0.3329 0.3588 0.00 0.00 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.CV.7425.01 6 0.4880 0.4715 0.00 0.06 0.00 0.00 0.00 0.58 0.06 0.30
#> TCGA.CQ.7068.01 1 0.0000 0.7058 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7095.01 7 0.3757 0.5021 0.00 0.00 0.26 0.00 0.00 0.00 0.68 0.06
#> TCGA.CV.7252.01 5 0.0471 0.8266 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.BA.5556.01 6 0.2725 0.4833 0.00 0.00 0.14 0.00 0.00 0.82 0.04 0.00
#> TCGA.CV.6942.01 6 0.4588 0.0363 0.34 0.00 0.00 0.00 0.00 0.54 0.00 0.12
#> TCGA.CR.7395.01 4 0.0808 0.8737 0.00 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.CV.7099.01 3 0.1341 0.6446 0.00 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.C9.A47Z.01 5 0.3483 0.8321 0.00 0.00 0.00 0.00 0.76 0.02 0.04 0.18
#> TCGA.CV.6953.01 3 0.0471 0.6922 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.HD.A4C1.01 8 0.3729 0.0000 0.46 0.00 0.00 0.00 0.00 0.02 0.00 0.52
#> TCGA.CV.A45Q.01 1 0.1091 0.6755 0.94 0.00 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.BA.A6DF.01 4 0.0000 0.8832 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.7063.01 1 0.1947 0.6248 0.86 0.00 0.00 0.00 0.00 0.14 0.00 0.00
#> TCGA.CQ.7071.01 2 0.1091 0.0000 0.00 0.94 0.00 0.06 0.00 0.00 0.00 0.00
#> TCGA.CV.A463.01 1 0.3618 -0.7336 0.60 0.00 0.00 0.00 0.00 0.02 0.00 0.38
#> TCGA.MT.A67A.01 5 0.0471 0.8266 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.BB.A6UO.01 1 0.1091 0.6755 0.94 0.00 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.IQ.A61E.01 4 0.2623 0.8132 0.00 0.00 0.00 0.84 0.00 0.00 0.10 0.06
#> TCGA.UF.A7JT.01 7 0.4081 0.6528 0.00 0.00 0.16 0.16 0.00 0.00 0.68 0.00
#> TCGA.BB.7863.01 5 0.3483 0.8321 0.00 0.00 0.00 0.00 0.76 0.02 0.04 0.18
#> TCGA.MT.A67F.01 6 0.0941 0.5693 0.02 0.00 0.02 0.00 0.00 0.96 0.00 0.00
#> TCGA.T2.A6WX.01 3 0.1804 0.6261 0.00 0.00 0.90 0.00 0.00 0.02 0.08 0.00
#> TCGA.CV.A6JD.01 1 0.0000 0.7058 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: Node021. Child nodes: Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node02111-leaf , Node02112-leaf , Node02113-leaf , Node02114-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02124-leaf , Node02131-leaf , Node02132 , Node02133-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02231-leaf , Node02232-leaf , Node02233-leaf , Node02241-leaf , Node02242-leaf , Node02243-leaf , Node02321-leaf , Node02322-leaf , Node02323-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf , Node05114-leaf , Node05121 , Node05122-leaf , Node05123-leaf , Node05221-leaf , Node05222-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 34 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 0.984 0.993 0.3286 0.663 0.663
#> 3 3 1.000 0.997 0.998 0.4383 0.834 0.756
#> 4 4 1.000 0.998 0.999 0.5234 0.750 0.529
#> 5 5 0.764 0.729 0.816 0.0764 0.959 0.865
#> 6 6 0.764 0.619 0.805 0.0496 0.829 0.458
#> 7 7 0.776 0.800 0.855 0.0392 0.934 0.644
#> 8 8 0.857 0.808 0.891 0.0256 0.955 0.702
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.CV.7416.01 2 0.000 0.960 0.00 1.00
#> TCGA.CV.6003.01 2 0.000 0.960 0.00 1.00
#> TCGA.CN.6018.01 1 0.000 1.000 1.00 0.00
#> TCGA.CV.5966.01 1 0.000 1.000 1.00 0.00
#> TCGA.CV.7411.01 1 0.000 1.000 1.00 0.00
#> TCGA.CV.5973.01 2 0.000 0.960 0.00 1.00
#> TCGA.CV.7104.01 2 0.795 0.684 0.24 0.76
#> TCGA.CR.7394.01 1 0.000 1.000 1.00 0.00
#> TCGA.CV.6955.01 1 0.000 1.000 1.00 0.00
#> TCGA.BA.5557.01 1 0.000 1.000 1.00 0.00
#> TCGA.CV.7238.01 1 0.000 1.000 1.00 0.00
#> TCGA.CX.7085.01 1 0.000 1.000 1.00 0.00
#> TCGA.DQ.5625.01 1 0.000 1.000 1.00 0.00
#> TCGA.C9.A480.01 1 0.000 1.000 1.00 0.00
#> TCGA.CV.6952.01 1 0.000 1.000 1.00 0.00
#> TCGA.CQ.5331.01 1 0.000 1.000 1.00 0.00
#> TCGA.D6.6826.01 1 0.000 1.000 1.00 0.00
#> TCGA.CQ.6219.01 1 0.000 1.000 1.00 0.00
#> TCGA.CV.A45P.01 1 0.000 1.000 1.00 0.00
#> TCGA.CV.A45T.01 1 0.000 1.000 1.00 0.00
#> TCGA.CN.6996.01 1 0.000 1.000 1.00 0.00
#> TCGA.CQ.7064.01 1 0.000 1.000 1.00 0.00
#> TCGA.IQ.A61K.01 2 0.000 0.960 0.00 1.00
#> TCGA.IQ.A61L.01 2 0.000 0.960 0.00 1.00
#> TCGA.HD.8635.01 1 0.000 1.000 1.00 0.00
#> TCGA.QK.A64Z.01 1 0.000 1.000 1.00 0.00
#> TCGA.HD.8634.01 1 0.000 1.000 1.00 0.00
#> TCGA.F7.A50J.01 2 0.000 0.960 0.00 1.00
#> TCGA.CN.A640.01 1 0.000 1.000 1.00 0.00
#> TCGA.UF.A7JO.01 1 0.000 1.000 1.00 0.00
#> TCGA.UF.A7JV.01 1 0.000 1.000 1.00 0.00
#> TCGA.CN.5373.01 1 0.000 1.000 1.00 0.00
#> TCGA.H7.A6C4.01 1 0.000 1.000 1.00 0.00
#> TCGA.CV.7438.01 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.CV.7416.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.CV.6003.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.CN.6018.01 1 0.0000 0.997 1.00 0 0.00
#> TCGA.CV.5966.01 1 0.0000 0.997 1.00 0 0.00
#> TCGA.CV.7411.01 3 0.0000 1.000 0.00 0 1.00
#> TCGA.CV.5973.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.CV.7104.01 3 0.0000 1.000 0.00 0 1.00
#> TCGA.CR.7394.01 1 0.0000 0.997 1.00 0 0.00
#> TCGA.CV.6955.01 1 0.0000 0.997 1.00 0 0.00
#> TCGA.BA.5557.01 1 0.0000 0.997 1.00 0 0.00
#> TCGA.CV.7238.01 1 0.0000 0.997 1.00 0 0.00
#> TCGA.CX.7085.01 1 0.0000 0.997 1.00 0 0.00
#> TCGA.DQ.5625.01 1 0.0000 0.997 1.00 0 0.00
#> TCGA.C9.A480.01 1 0.0000 0.997 1.00 0 0.00
#> TCGA.CV.6952.01 1 0.0892 0.981 0.98 0 0.02
#> TCGA.CQ.5331.01 1 0.0000 0.997 1.00 0 0.00
#> TCGA.D6.6826.01 1 0.0000 0.997 1.00 0 0.00
#> TCGA.CQ.6219.01 1 0.0000 0.997 1.00 0 0.00
#> TCGA.CV.A45P.01 1 0.0000 0.997 1.00 0 0.00
#> TCGA.CV.A45T.01 1 0.0000 0.997 1.00 0 0.00
#> TCGA.CN.6996.01 1 0.0000 0.997 1.00 0 0.00
#> TCGA.CQ.7064.01 1 0.0000 0.997 1.00 0 0.00
#> TCGA.IQ.A61K.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.IQ.A61L.01 3 0.0000 1.000 0.00 0 1.00
#> TCGA.HD.8635.01 1 0.0892 0.981 0.98 0 0.02
#> TCGA.QK.A64Z.01 1 0.0892 0.981 0.98 0 0.02
#> TCGA.HD.8634.01 1 0.0000 0.997 1.00 0 0.00
#> TCGA.F7.A50J.01 3 0.0000 1.000 0.00 0 1.00
#> TCGA.CN.A640.01 1 0.0000 0.997 1.00 0 0.00
#> TCGA.UF.A7JO.01 1 0.0000 0.997 1.00 0 0.00
#> TCGA.UF.A7JV.01 1 0.0000 0.997 1.00 0 0.00
#> TCGA.CN.5373.01 3 0.0000 1.000 0.00 0 1.00
#> TCGA.H7.A6C4.01 1 0.0000 0.997 1.00 0 0.00
#> TCGA.CV.7438.01 3 0.0000 1.000 0.00 0 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.CV.7416.01 2 0.0000 1.00 0 1 0.00 0.00
#> TCGA.CV.6003.01 2 0.0000 1.00 0 1 0.00 0.00
#> TCGA.CN.6018.01 1 0.0000 1.00 1 0 0.00 0.00
#> TCGA.CV.5966.01 1 0.0000 1.00 1 0 0.00 0.00
#> TCGA.CV.7411.01 3 0.0707 0.98 0 0 0.98 0.02
#> TCGA.CV.5973.01 2 0.0000 1.00 0 1 0.00 0.00
#> TCGA.CV.7104.01 3 0.0000 0.99 0 0 1.00 0.00
#> TCGA.CR.7394.01 1 0.0000 1.00 1 0 0.00 0.00
#> TCGA.CV.6955.01 4 0.0000 1.00 0 0 0.00 1.00
#> TCGA.BA.5557.01 1 0.0000 1.00 1 0 0.00 0.00
#> TCGA.CV.7238.01 1 0.0000 1.00 1 0 0.00 0.00
#> TCGA.CX.7085.01 1 0.0000 1.00 1 0 0.00 0.00
#> TCGA.DQ.5625.01 4 0.0000 1.00 0 0 0.00 1.00
#> TCGA.C9.A480.01 1 0.0000 1.00 1 0 0.00 0.00
#> TCGA.CV.6952.01 4 0.0000 1.00 0 0 0.00 1.00
#> TCGA.CQ.5331.01 1 0.0000 1.00 1 0 0.00 0.00
#> TCGA.D6.6826.01 1 0.0000 1.00 1 0 0.00 0.00
#> TCGA.CQ.6219.01 1 0.0000 1.00 1 0 0.00 0.00
#> TCGA.CV.A45P.01 1 0.0000 1.00 1 0 0.00 0.00
#> TCGA.CV.A45T.01 1 0.0000 1.00 1 0 0.00 0.00
#> TCGA.CN.6996.01 1 0.0000 1.00 1 0 0.00 0.00
#> TCGA.CQ.7064.01 4 0.0000 1.00 0 0 0.00 1.00
#> TCGA.IQ.A61K.01 2 0.0000 1.00 0 1 0.00 0.00
#> TCGA.IQ.A61L.01 3 0.0000 0.99 0 0 1.00 0.00
#> TCGA.HD.8635.01 4 0.0000 1.00 0 0 0.00 1.00
#> TCGA.QK.A64Z.01 4 0.0000 1.00 0 0 0.00 1.00
#> TCGA.HD.8634.01 4 0.0000 1.00 0 0 0.00 1.00
#> TCGA.F7.A50J.01 3 0.0000 0.99 0 0 1.00 0.00
#> TCGA.CN.A640.01 1 0.0000 1.00 1 0 0.00 0.00
#> TCGA.UF.A7JO.01 4 0.0000 1.00 0 0 0.00 1.00
#> TCGA.UF.A7JV.01 4 0.0000 1.00 0 0 0.00 1.00
#> TCGA.CN.5373.01 3 0.0000 0.99 0 0 1.00 0.00
#> TCGA.H7.A6C4.01 4 0.0000 1.00 0 0 0.00 1.00
#> TCGA.CV.7438.01 3 0.0707 0.98 0 0 0.98 0.02
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CV.7416.01 5 0.000 0.991 0.00 0.00 0.00 0.00 1.00
#> TCGA.CV.6003.01 5 0.000 0.991 0.00 0.00 0.00 0.00 1.00
#> TCGA.CN.6018.01 1 0.173 0.548 0.92 0.00 0.00 0.08 0.00
#> TCGA.CV.5966.01 1 0.327 0.693 0.78 0.22 0.00 0.00 0.00
#> TCGA.CV.7411.01 3 0.489 0.810 0.00 0.14 0.72 0.14 0.00
#> TCGA.CV.5973.01 5 0.000 0.991 0.00 0.00 0.00 0.00 1.00
#> TCGA.CV.7104.01 3 0.000 0.871 0.00 0.00 1.00 0.00 0.00
#> TCGA.CR.7394.01 1 0.524 0.583 0.64 0.28 0.00 0.08 0.00
#> TCGA.CV.6955.01 4 0.000 0.774 0.00 0.00 0.00 1.00 0.00
#> TCGA.BA.5557.01 1 0.426 0.749 0.56 0.44 0.00 0.00 0.00
#> TCGA.CV.7238.01 1 0.426 0.749 0.56 0.44 0.00 0.00 0.00
#> TCGA.CX.7085.01 1 0.426 0.749 0.56 0.44 0.00 0.00 0.00
#> TCGA.DQ.5625.01 4 0.385 0.736 0.22 0.02 0.00 0.76 0.00
#> TCGA.C9.A480.01 1 0.000 0.615 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6952.01 4 0.173 0.735 0.00 0.08 0.00 0.92 0.00
#> TCGA.CQ.5331.01 1 0.426 0.749 0.56 0.44 0.00 0.00 0.00
#> TCGA.D6.6826.01 1 0.356 0.702 0.74 0.26 0.00 0.00 0.00
#> TCGA.CQ.6219.01 1 0.426 0.749 0.56 0.44 0.00 0.00 0.00
#> TCGA.CV.A45P.01 1 0.514 0.543 0.66 0.26 0.00 0.08 0.00
#> TCGA.CV.A45T.01 1 0.426 0.749 0.56 0.44 0.00 0.00 0.00
#> TCGA.CN.6996.01 1 0.173 0.548 0.92 0.00 0.00 0.08 0.00
#> TCGA.CQ.7064.01 4 0.535 0.724 0.22 0.12 0.00 0.66 0.00
#> TCGA.IQ.A61K.01 5 0.104 0.972 0.00 0.04 0.00 0.00 0.96
#> TCGA.IQ.A61L.01 3 0.000 0.871 0.00 0.00 1.00 0.00 0.00
#> TCGA.HD.8635.01 4 0.273 0.728 0.00 0.16 0.00 0.84 0.00
#> TCGA.QK.A64Z.01 4 0.273 0.728 0.00 0.16 0.00 0.84 0.00
#> TCGA.HD.8634.01 4 0.579 0.684 0.26 0.14 0.00 0.60 0.00
#> TCGA.F7.A50J.01 3 0.000 0.871 0.00 0.00 1.00 0.00 0.00
#> TCGA.CN.A640.01 1 0.426 0.749 0.56 0.44 0.00 0.00 0.00
#> TCGA.UF.A7JO.01 4 0.000 0.774 0.00 0.00 0.00 1.00 0.00
#> TCGA.UF.A7JV.01 1 0.659 -0.327 0.44 0.34 0.00 0.22 0.00
#> TCGA.CN.5373.01 3 0.252 0.861 0.00 0.14 0.86 0.00 0.00
#> TCGA.H7.A6C4.01 4 0.535 0.724 0.22 0.12 0.00 0.66 0.00
#> TCGA.CV.7438.01 3 0.489 0.810 0.00 0.14 0.72 0.14 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.CV.7416.01 5 0.0000 0.9795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CV.6003.01 5 0.0000 0.9795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CN.6018.01 6 0.5867 0.2558 0.28 0.00 0.24 0.00 0.00 0.48
#> TCGA.CV.5966.01 1 0.5721 0.2620 0.52 0.00 0.24 0.00 0.00 0.24
#> TCGA.CV.7411.01 3 0.5801 0.4374 0.00 0.24 0.50 0.26 0.00 0.00
#> TCGA.CV.5973.01 5 0.0000 0.9795 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CV.7104.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7394.01 6 0.3578 0.4677 0.34 0.00 0.00 0.00 0.00 0.66
#> TCGA.CV.6955.01 4 0.1267 0.8183 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.BA.5557.01 1 0.0000 0.8298 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7238.01 1 0.0000 0.8298 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CX.7085.01 1 0.0000 0.8298 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.5625.01 4 0.5618 -0.0137 0.00 0.00 0.16 0.50 0.00 0.34
#> TCGA.C9.A480.01 1 0.6010 -0.0968 0.40 0.00 0.24 0.00 0.00 0.36
#> TCGA.CV.6952.01 4 0.0000 0.8276 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CQ.5331.01 1 0.0000 0.8298 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D6.6826.01 1 0.3544 0.6717 0.80 0.00 0.08 0.00 0.00 0.12
#> TCGA.CQ.6219.01 1 0.0000 0.8298 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A45P.01 6 0.3198 0.5476 0.26 0.00 0.00 0.00 0.00 0.74
#> TCGA.CV.A45T.01 1 0.0000 0.8298 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.6996.01 6 0.5712 0.3195 0.26 0.00 0.22 0.00 0.00 0.52
#> TCGA.CQ.7064.01 6 0.3916 0.3961 0.00 0.00 0.02 0.30 0.00 0.68
#> TCGA.IQ.A61K.01 5 0.1807 0.9369 0.00 0.00 0.02 0.00 0.92 0.06
#> TCGA.IQ.A61L.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HD.8635.01 4 0.0547 0.8310 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.QK.A64Z.01 4 0.0547 0.8310 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.HD.8634.01 6 0.3198 0.4448 0.00 0.00 0.00 0.26 0.00 0.74
#> TCGA.F7.A50J.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.A640.01 1 0.0000 0.8298 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A7JO.01 4 0.0937 0.8285 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.UF.A7JV.01 3 0.4902 -0.3480 0.00 0.00 0.48 0.06 0.00 0.46
#> TCGA.CN.5373.01 3 0.4646 0.0504 0.00 0.46 0.50 0.04 0.00 0.00
#> TCGA.H7.A6C4.01 6 0.3916 0.3961 0.00 0.00 0.02 0.30 0.00 0.68
#> TCGA.CV.7438.01 3 0.5801 0.4374 0.00 0.24 0.50 0.26 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.CV.7416.01 5 0.0000 0.961 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.6003.01 5 0.0504 0.957 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.CN.6018.01 7 0.4787 0.633 0.12 0.00 0.00 0.00 0.00 0.30 0.58
#> TCGA.CV.5966.01 7 0.4328 0.500 0.34 0.00 0.00 0.00 0.00 0.06 0.60
#> TCGA.CV.7411.01 3 0.1671 0.900 0.00 0.00 0.90 0.10 0.00 0.00 0.00
#> TCGA.CV.5973.01 5 0.0000 0.961 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.7104.01 2 0.2708 1.000 0.00 0.78 0.22 0.00 0.00 0.00 0.00
#> TCGA.CR.7394.01 6 0.2259 0.748 0.16 0.00 0.00 0.00 0.00 0.84 0.00
#> TCGA.CV.6955.01 4 0.1006 0.839 0.00 0.00 0.02 0.96 0.00 0.02 0.00
#> TCGA.BA.5557.01 1 0.0000 0.934 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7238.01 1 0.0000 0.934 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CX.7085.01 1 0.0000 0.934 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.5625.01 4 0.5233 0.155 0.00 0.00 0.00 0.52 0.00 0.20 0.28
#> TCGA.C9.A480.01 7 0.4873 0.667 0.22 0.00 0.00 0.00 0.00 0.18 0.60
#> TCGA.CV.6952.01 4 0.0504 0.836 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.CQ.5331.01 1 0.0000 0.934 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D6.6826.01 1 0.3755 0.266 0.64 0.00 0.00 0.00 0.00 0.02 0.34
#> TCGA.CQ.6219.01 1 0.0000 0.934 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A45P.01 6 0.1671 0.791 0.10 0.00 0.00 0.00 0.00 0.90 0.00
#> TCGA.CV.A45T.01 1 0.0000 0.934 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.6996.01 7 0.4597 0.556 0.08 0.00 0.00 0.00 0.00 0.36 0.56
#> TCGA.CQ.7064.01 6 0.2569 0.844 0.00 0.00 0.02 0.14 0.00 0.84 0.00
#> TCGA.IQ.A61K.01 5 0.2857 0.892 0.00 0.04 0.00 0.00 0.86 0.06 0.04
#> TCGA.IQ.A61L.01 2 0.2708 1.000 0.00 0.78 0.22 0.00 0.00 0.00 0.00
#> TCGA.HD.8635.01 4 0.1860 0.819 0.00 0.02 0.02 0.92 0.00 0.00 0.04
#> TCGA.QK.A64Z.01 4 0.1860 0.819 0.00 0.02 0.02 0.92 0.00 0.00 0.04
#> TCGA.HD.8634.01 6 0.1671 0.840 0.00 0.00 0.00 0.10 0.00 0.90 0.00
#> TCGA.F7.A50J.01 2 0.2708 1.000 0.00 0.78 0.22 0.00 0.00 0.00 0.00
#> TCGA.CN.A640.01 1 0.0000 0.934 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A7JO.01 4 0.1006 0.839 0.00 0.00 0.02 0.96 0.00 0.02 0.00
#> TCGA.UF.A7JV.01 7 0.5373 0.310 0.00 0.14 0.10 0.00 0.00 0.12 0.64
#> TCGA.CN.5373.01 3 0.2376 0.771 0.00 0.12 0.86 0.02 0.00 0.00 0.00
#> TCGA.H7.A6C4.01 6 0.2569 0.844 0.00 0.00 0.02 0.14 0.00 0.84 0.00
#> TCGA.CV.7438.01 3 0.1671 0.900 0.00 0.00 0.90 0.10 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.CV.7416.01 5 0.0000 0.9472 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.6003.01 5 0.0471 0.9432 0.00 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.CN.6018.01 7 0.2407 0.6450 0.06 0.00 0.00 0.00 0.00 0.08 0.86 0.00
#> TCGA.CV.5966.01 7 0.1563 0.6330 0.10 0.00 0.00 0.00 0.00 0.00 0.90 0.00
#> TCGA.CV.7411.01 3 0.3263 0.9059 0.00 0.12 0.78 0.10 0.00 0.00 0.00 0.00
#> TCGA.CV.5973.01 5 0.0000 0.9472 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.7104.01 2 0.1557 0.9289 0.00 0.92 0.00 0.00 0.00 0.00 0.06 0.02
#> TCGA.CR.7394.01 6 0.3054 0.8051 0.08 0.00 0.00 0.00 0.00 0.80 0.12 0.00
#> TCGA.CV.6955.01 4 0.0000 0.9398 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BA.5557.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7238.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CX.7085.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.5625.01 7 0.6344 -0.0247 0.00 0.00 0.14 0.36 0.00 0.10 0.38 0.02
#> TCGA.C9.A480.01 7 0.1557 0.6424 0.06 0.00 0.00 0.00 0.00 0.02 0.92 0.00
#> TCGA.CV.6952.01 4 0.0000 0.9398 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.5331.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D6.6826.01 7 0.3329 0.0910 0.48 0.00 0.00 0.00 0.00 0.00 0.52 0.00
#> TCGA.CQ.6219.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A45P.01 6 0.2547 0.8336 0.04 0.00 0.00 0.00 0.00 0.84 0.12 0.00
#> TCGA.CV.A45T.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.6996.01 7 0.2623 0.6358 0.06 0.00 0.00 0.00 0.00 0.10 0.84 0.00
#> TCGA.CQ.7064.01 6 0.2132 0.7908 0.00 0.00 0.00 0.08 0.00 0.88 0.00 0.04
#> TCGA.IQ.A61K.01 5 0.3048 0.8502 0.00 0.00 0.04 0.00 0.84 0.02 0.02 0.08
#> TCGA.IQ.A61L.01 2 0.0000 0.9650 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HD.8635.01 4 0.2348 0.9075 0.00 0.00 0.04 0.88 0.00 0.02 0.00 0.06
#> TCGA.QK.A64Z.01 4 0.2348 0.9075 0.00 0.00 0.04 0.88 0.00 0.02 0.00 0.06
#> TCGA.HD.8634.01 6 0.2224 0.8325 0.00 0.00 0.00 0.02 0.00 0.86 0.12 0.00
#> TCGA.F7.A50J.01 2 0.0000 0.9650 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.A640.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A7JO.01 4 0.0000 0.9398 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A7JV.01 8 0.3054 0.0000 0.00 0.00 0.00 0.00 0.00 0.08 0.12 0.80
#> TCGA.CN.5373.01 3 0.3426 0.7971 0.00 0.22 0.74 0.00 0.00 0.02 0.00 0.02
#> TCGA.H7.A6C4.01 6 0.2132 0.7908 0.00 0.00 0.00 0.08 0.00 0.88 0.00 0.04
#> TCGA.CV.7438.01 3 0.3263 0.9059 0.00 0.12 0.78 0.10 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: Node021. Child nodes: Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node02111-leaf , Node02112-leaf , Node02113-leaf , Node02114-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02124-leaf , Node02131-leaf , Node02132 , Node02133-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02231-leaf , Node02232-leaf , Node02233-leaf , Node02241-leaf , Node02242-leaf , Node02243-leaf , Node02321-leaf , Node02322-leaf , Node02323-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf , Node05114-leaf , Node05121 , Node05122-leaf , Node05123-leaf , Node05221-leaf , Node05222-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 28 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 1.000 0.995 0.997 0.4775 0.524 0.524
#> 3 3 1.000 0.974 0.987 0.3630 0.828 0.672
#> 4 4 0.880 0.895 0.940 0.1233 0.934 0.812
#> 5 5 0.969 0.892 0.951 0.1233 0.889 0.611
#> 6 6 0.905 0.836 0.939 0.0323 0.984 0.909
#> 7 7 0.852 0.758 0.900 0.0123 0.989 0.933
#> 8 8 0.860 0.681 0.886 0.0171 0.987 0.911
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
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.CR.7391.01 1 0.000 1.000 1.00 0.00
#> TCGA.CV.7407.01 2 0.141 0.983 0.02 0.98
#> TCGA.CN.6021.01 2 0.000 0.995 0.00 1.00
#> TCGA.CV.5978.01 2 0.141 0.983 0.02 0.98
#> TCGA.CV.7178.01 2 0.000 0.995 0.00 1.00
#> TCGA.CR.6478.01 1 0.000 1.000 1.00 0.00
#> TCGA.CV.7102.01 2 0.000 0.995 0.00 1.00
#> TCGA.D6.6515.01 1 0.000 1.000 1.00 0.00
#> TCGA.CV.7177.01 2 0.000 0.995 0.00 1.00
#> TCGA.CQ.6218.01 2 0.000 0.995 0.00 1.00
#> TCGA.BA.6870.01 2 0.000 0.995 0.00 1.00
#> TCGA.CR.6477.01 1 0.000 1.000 1.00 0.00
#> TCGA.CN.A498.01 2 0.000 0.995 0.00 1.00
#> TCGA.CV.6953.11 1 0.000 1.000 1.00 0.00
#> TCGA.DQ.5624.01 1 0.000 1.000 1.00 0.00
#> TCGA.CN.A499.01 2 0.000 0.995 0.00 1.00
#> TCGA.CV.6940.01 2 0.000 0.995 0.00 1.00
#> TCGA.BA.A6DB.01 1 0.000 1.000 1.00 0.00
#> TCGA.MT.A67G.01 2 0.141 0.983 0.02 0.98
#> TCGA.MT.A51W.01 1 0.000 1.000 1.00 0.00
#> TCGA.CN.5367.01 2 0.000 0.995 0.00 1.00
#> TCGA.IQ.A6SG.01 2 0.000 0.995 0.00 1.00
#> TCGA.BB.7871.01 2 0.000 0.995 0.00 1.00
#> TCGA.CN.4736.01 1 0.000 1.000 1.00 0.00
#> TCGA.CN.5369.01 1 0.000 1.000 1.00 0.00
#> TCGA.BA.4077.01 2 0.000 0.995 0.00 1.00
#> TCGA.CR.7383.01 2 0.141 0.983 0.02 0.98
#> TCGA.P3.A6T5.01 2 0.000 0.995 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CR.7391.01 1 0.0000 0.982 1.00 0.00 0.00
#> TCGA.CV.7407.01 2 0.0000 0.981 0.00 1.00 0.00
#> TCGA.CN.6021.01 2 0.0000 0.981 0.00 1.00 0.00
#> TCGA.CV.5978.01 2 0.0000 0.981 0.00 1.00 0.00
#> TCGA.CV.7178.01 2 0.0892 0.968 0.00 0.98 0.02
#> TCGA.CR.6478.01 1 0.0000 0.982 1.00 0.00 0.00
#> TCGA.CV.7102.01 2 0.2959 0.899 0.00 0.90 0.10
#> TCGA.D6.6515.01 1 0.0000 0.982 1.00 0.00 0.00
#> TCGA.CV.7177.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.CQ.6218.01 2 0.0000 0.981 0.00 1.00 0.00
#> TCGA.BA.6870.01 2 0.0000 0.981 0.00 1.00 0.00
#> TCGA.CR.6477.01 1 0.2066 0.933 0.94 0.06 0.00
#> TCGA.CN.A498.01 2 0.2959 0.899 0.00 0.90 0.10
#> TCGA.CV.6953.11 1 0.0000 0.982 1.00 0.00 0.00
#> TCGA.DQ.5624.01 1 0.2537 0.912 0.92 0.08 0.00
#> TCGA.CN.A499.01 2 0.0000 0.981 0.00 1.00 0.00
#> TCGA.CV.6940.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.BA.A6DB.01 1 0.0000 0.982 1.00 0.00 0.00
#> TCGA.MT.A67G.01 2 0.0000 0.981 0.00 1.00 0.00
#> TCGA.MT.A51W.01 1 0.0000 0.982 1.00 0.00 0.00
#> TCGA.CN.5367.01 2 0.0000 0.981 0.00 1.00 0.00
#> TCGA.IQ.A6SG.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.BB.7871.01 2 0.0000 0.981 0.00 1.00 0.00
#> TCGA.CN.4736.01 1 0.0000 0.982 1.00 0.00 0.00
#> TCGA.CN.5369.01 1 0.0000 0.982 1.00 0.00 0.00
#> TCGA.BA.4077.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.CR.7383.01 2 0.0000 0.981 0.00 1.00 0.00
#> TCGA.P3.A6T5.01 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.CR.7391.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CV.7407.01 2 0.4406 0.711 0.00 0.70 0.00 0.30
#> TCGA.CN.6021.01 2 0.0000 0.876 0.00 1.00 0.00 0.00
#> TCGA.CV.5978.01 2 0.4406 0.711 0.00 0.70 0.00 0.30
#> TCGA.CV.7178.01 2 0.0707 0.870 0.00 0.98 0.02 0.00
#> TCGA.CR.6478.01 4 0.2011 0.880 0.08 0.00 0.00 0.92
#> TCGA.CV.7102.01 2 0.1637 0.849 0.00 0.94 0.06 0.00
#> TCGA.D6.6515.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CV.7177.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.CQ.6218.01 2 0.0000 0.876 0.00 1.00 0.00 0.00
#> TCGA.BA.6870.01 2 0.0707 0.874 0.00 0.98 0.00 0.02
#> TCGA.CR.6477.01 4 0.0000 0.916 0.00 0.00 0.00 1.00
#> TCGA.CN.A498.01 2 0.1637 0.849 0.00 0.94 0.06 0.00
#> TCGA.CV.6953.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DQ.5624.01 4 0.0000 0.916 0.00 0.00 0.00 1.00
#> TCGA.CN.A499.01 2 0.0000 0.876 0.00 1.00 0.00 0.00
#> TCGA.CV.6940.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.BA.A6DB.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.MT.A67G.01 2 0.4277 0.733 0.00 0.72 0.00 0.28
#> TCGA.MT.A51W.01 4 0.0000 0.916 0.00 0.00 0.00 1.00
#> TCGA.CN.5367.01 2 0.0000 0.876 0.00 1.00 0.00 0.00
#> TCGA.IQ.A6SG.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.BB.7871.01 2 0.2011 0.855 0.00 0.92 0.00 0.08
#> TCGA.CN.4736.01 4 0.3610 0.741 0.20 0.00 0.00 0.80
#> TCGA.CN.5369.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BA.4077.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.CR.7383.01 2 0.4277 0.733 0.00 0.72 0.00 0.28
#> TCGA.P3.A6T5.01 3 0.0000 1.000 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.CR.7391.01 1 0.000 1.000 1 0.00 0 0.00 0.00
#> TCGA.CV.7407.01 2 0.141 0.825 0 0.94 0 0.06 0.00
#> TCGA.CN.6021.01 5 0.368 0.566 0 0.28 0 0.00 0.72
#> TCGA.CV.5978.01 2 0.104 0.822 0 0.96 0 0.04 0.00
#> TCGA.CV.7178.01 5 0.000 0.936 0 0.00 0 0.00 1.00
#> TCGA.CR.6478.01 4 0.000 1.000 0 0.00 0 1.00 0.00
#> TCGA.CV.7102.01 5 0.000 0.936 0 0.00 0 0.00 1.00
#> TCGA.D6.6515.01 1 0.000 1.000 1 0.00 0 0.00 0.00
#> TCGA.CV.7177.01 3 0.000 1.000 0 0.00 1 0.00 0.00
#> TCGA.CQ.6218.01 5 0.000 0.936 0 0.00 0 0.00 1.00
#> TCGA.BA.6870.01 2 0.426 0.283 0 0.56 0 0.00 0.44
#> TCGA.CR.6477.01 4 0.000 1.000 0 0.00 0 1.00 0.00
#> TCGA.CN.A498.01 5 0.000 0.936 0 0.00 0 0.00 1.00
#> TCGA.CV.6953.11 1 0.000 1.000 1 0.00 0 0.00 0.00
#> TCGA.DQ.5624.01 4 0.000 1.000 0 0.00 0 1.00 0.00
#> TCGA.CN.A499.01 5 0.000 0.936 0 0.00 0 0.00 1.00
#> TCGA.CV.6940.01 3 0.000 1.000 0 0.00 1 0.00 0.00
#> TCGA.BA.A6DB.01 1 0.000 1.000 1 0.00 0 0.00 0.00
#> TCGA.MT.A67G.01 2 0.141 0.825 0 0.94 0 0.06 0.00
#> TCGA.MT.A51W.01 4 0.000 1.000 0 0.00 0 1.00 0.00
#> TCGA.CN.5367.01 2 0.423 0.346 0 0.58 0 0.00 0.42
#> TCGA.IQ.A6SG.01 3 0.000 1.000 0 0.00 1 0.00 0.00
#> TCGA.BB.7871.01 2 0.000 0.803 0 1.00 0 0.00 0.00
#> TCGA.CN.4736.01 4 0.000 1.000 0 0.00 0 1.00 0.00
#> TCGA.CN.5369.01 1 0.000 1.000 1 0.00 0 0.00 0.00
#> TCGA.BA.4077.01 3 0.000 1.000 0 0.00 1 0.00 0.00
#> TCGA.CR.7383.01 2 0.141 0.825 0 0.94 0 0.06 0.00
#> TCGA.P3.A6T5.01 3 0.000 1.000 0 0.00 1 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.CR.7391.01 1 0.0000 1.000 1 0.00 0.00 0 0.00 0.00
#> TCGA.CV.7407.01 2 0.1814 0.795 0 0.90 0.00 0 0.00 0.10
#> TCGA.CN.6021.01 5 0.5265 0.285 0 0.10 0.00 0 0.50 0.40
#> TCGA.CV.5978.01 2 0.3647 0.431 0 0.64 0.00 0 0.00 0.36
#> TCGA.CV.7178.01 5 0.0547 0.832 0 0.02 0.00 0 0.98 0.00
#> TCGA.CR.6478.01 4 0.0000 1.000 0 0.00 0.00 1 0.00 0.00
#> TCGA.CV.7102.01 5 0.0000 0.827 0 0.00 0.00 0 1.00 0.00
#> TCGA.D6.6515.01 1 0.0000 1.000 1 0.00 0.00 0 0.00 0.00
#> TCGA.CV.7177.01 3 0.0000 0.939 0 0.00 1.00 0 0.00 0.00
#> TCGA.CQ.6218.01 5 0.3315 0.702 0 0.20 0.00 0 0.78 0.02
#> TCGA.BA.6870.01 2 0.2474 0.796 0 0.88 0.00 0 0.08 0.04
#> TCGA.CR.6477.01 4 0.0000 1.000 0 0.00 0.00 1 0.00 0.00
#> TCGA.CN.A498.01 5 0.0000 0.827 0 0.00 0.00 0 1.00 0.00
#> TCGA.CV.6953.11 1 0.0000 1.000 1 0.00 0.00 0 0.00 0.00
#> TCGA.DQ.5624.01 4 0.0000 1.000 0 0.00 0.00 1 0.00 0.00
#> TCGA.CN.A499.01 5 0.1480 0.824 0 0.04 0.00 0 0.94 0.02
#> TCGA.CV.6940.01 3 0.0000 0.939 0 0.00 1.00 0 0.00 0.00
#> TCGA.BA.A6DB.01 1 0.0000 1.000 1 0.00 0.00 0 0.00 0.00
#> TCGA.MT.A67G.01 2 0.0000 0.848 0 1.00 0.00 0 0.00 0.00
#> TCGA.MT.A51W.01 4 0.0000 1.000 0 0.00 0.00 1 0.00 0.00
#> TCGA.CN.5367.01 2 0.1480 0.830 0 0.94 0.00 0 0.04 0.02
#> TCGA.IQ.A6SG.01 3 0.1267 0.918 0 0.00 0.94 0 0.06 0.00
#> TCGA.BB.7871.01 6 0.1267 0.000 0 0.06 0.00 0 0.00 0.94
#> TCGA.CN.4736.01 4 0.0000 1.000 0 0.00 0.00 1 0.00 0.00
#> TCGA.CN.5369.01 1 0.0000 1.000 1 0.00 0.00 0 0.00 0.00
#> TCGA.BA.4077.01 3 0.0000 0.939 0 0.00 1.00 0 0.00 0.00
#> TCGA.CR.7383.01 2 0.0000 0.848 0 1.00 0.00 0 0.00 0.00
#> TCGA.P3.A6T5.01 3 0.2454 0.828 0 0.00 0.84 0 0.16 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.CR.7391.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7407.01 2 0.2016 0.838 0 0.90 0.00 0.00 0.00 0.04 0.06
#> TCGA.CN.6021.01 5 0.6433 0.280 0 0.10 0.00 0.00 0.46 0.20 0.24
#> TCGA.CV.5978.01 2 0.3526 0.715 0 0.76 0.00 0.00 0.00 0.18 0.06
#> TCGA.CV.7178.01 5 0.0504 0.800 0 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.CR.6478.01 4 0.0000 0.995 0 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.7102.01 5 0.0504 0.800 0 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.D6.6515.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7177.01 3 0.2572 0.507 0 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.CQ.6218.01 5 0.3795 0.636 0 0.22 0.00 0.00 0.72 0.00 0.06
#> TCGA.BA.6870.01 2 0.2572 0.819 0 0.86 0.00 0.00 0.06 0.00 0.08
#> TCGA.CR.6477.01 4 0.0000 0.995 0 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CN.A498.01 5 0.0000 0.800 0 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.6953.11 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.5624.01 4 0.0000 0.995 0 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CN.A499.01 5 0.2016 0.779 0 0.04 0.00 0.00 0.90 0.00 0.06
#> TCGA.CV.6940.01 7 0.3459 0.000 0 0.00 0.40 0.00 0.00 0.00 0.60
#> TCGA.BA.A6DB.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MT.A67G.01 2 0.0504 0.859 0 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.MT.A51W.01 4 0.0504 0.982 0 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CN.5367.01 2 0.2722 0.786 0 0.84 0.00 0.00 0.12 0.00 0.04
#> TCGA.IQ.A6SG.01 3 0.1505 0.645 0 0.00 0.94 0.00 0.02 0.02 0.02
#> TCGA.BB.7871.01 6 0.0863 0.000 0 0.04 0.00 0.00 0.00 0.96 0.00
#> TCGA.CN.4736.01 4 0.0000 0.995 0 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CN.5369.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.4077.01 3 0.2422 0.546 0 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.CR.7383.01 2 0.0504 0.858 0 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.P3.A6T5.01 3 0.2313 0.596 0 0.00 0.88 0.00 0.06 0.00 0.06
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.CR.7391.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7407.01 2 0.2624 0.781 0 0.86 0.00 0.00 0.00 0.06 0.02 0.06
#> TCGA.CN.6021.01 8 0.4276 0.000 0 0.04 0.00 0.00 0.18 0.08 0.00 0.70
#> TCGA.CV.5978.01 2 0.3843 0.601 0 0.70 0.00 0.00 0.00 0.24 0.02 0.04
#> TCGA.CV.7178.01 5 0.0808 0.640 0 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.CR.6478.01 4 0.0000 0.972 0 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7102.01 5 0.0000 0.655 0 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D6.6515.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7177.01 3 0.2852 0.502 0 0.00 0.72 0.00 0.00 0.00 0.28 0.00
#> TCGA.CQ.6218.01 5 0.5028 0.174 0 0.36 0.00 0.00 0.52 0.00 0.06 0.06
#> TCGA.BA.6870.01 2 0.2399 0.779 0 0.88 0.00 0.00 0.04 0.00 0.04 0.04
#> TCGA.CR.6477.01 4 0.0000 0.972 0 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.A498.01 5 0.2680 0.610 0 0.00 0.02 0.00 0.84 0.00 0.02 0.12
#> TCGA.CV.6953.11 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.5624.01 4 0.0000 0.972 0 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.A499.01 5 0.4053 0.524 0 0.04 0.00 0.00 0.72 0.00 0.06 0.18
#> TCGA.CV.6940.01 7 0.2267 0.000 0 0.00 0.18 0.00 0.00 0.00 0.82 0.00
#> TCGA.BA.A6DB.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MT.A67G.01 2 0.0941 0.817 0 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.MT.A51W.01 4 0.2132 0.882 0 0.00 0.00 0.88 0.00 0.00 0.04 0.08
#> TCGA.CN.5367.01 2 0.4122 0.663 0 0.74 0.00 0.00 0.08 0.00 0.08 0.10
#> TCGA.IQ.A6SG.01 3 0.0000 0.646 0 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BB.7871.01 6 0.0000 0.000 0 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CN.4736.01 4 0.0000 0.972 0 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.5369.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.4077.01 3 0.3293 0.557 0 0.00 0.74 0.00 0.00 0.00 0.22 0.04
#> TCGA.CR.7383.01 2 0.0471 0.816 0 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.P3.A6T5.01 3 0.3169 0.530 0 0.00 0.78 0.00 0.18 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: Node0213. Child nodes: Node021321-leaf , Node021322-leaf , Node051211-leaf , Node051212-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["02132"]
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 13 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 0.5133 0.487 0.487
#> 3 3 0.705 0.904 0.871 0.2739 0.808 0.605
#> 4 4 0.615 0.823 0.915 0.1388 0.949 0.826
#> 5 5 0.821 0.781 0.897 0.0857 0.859 0.500
#> 6 6 0.769 0.460 0.806 0.0601 0.936 0.667
#> 7 7 0.821 0.637 0.848 0.0388 0.897 0.385
#> 8 8 0.833 0.507 0.746 0.0251 0.987 0.857
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.CV.7407.01 2 0 1 0 1
#> TCGA.CN.6021.01 2 0 1 0 1
#> TCGA.CV.5978.01 2 0 1 0 1
#> TCGA.CV.7178.01 1 0 1 1 0
#> TCGA.CV.7102.01 1 0 1 1 0
#> TCGA.CQ.6218.01 1 0 1 1 0
#> TCGA.BA.6870.01 1 0 1 1 0
#> TCGA.CN.A498.01 1 0 1 1 0
#> TCGA.CN.A499.01 1 0 1 1 0
#> TCGA.MT.A67G.01 2 0 1 0 1
#> TCGA.CN.5367.01 1 0 1 1 0
#> TCGA.BB.7871.01 2 0 1 0 1
#> TCGA.CR.7383.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CV.7407.01 2 0.000 0.926 0.00 1.00 0.00
#> TCGA.CN.6021.01 2 0.000 0.926 0.00 1.00 0.00
#> TCGA.CV.5978.01 2 0.000 0.926 0.00 1.00 0.00
#> TCGA.CV.7178.01 3 0.604 1.000 0.38 0.00 0.62
#> TCGA.CV.7102.01 3 0.604 1.000 0.38 0.00 0.62
#> TCGA.CQ.6218.01 3 0.604 1.000 0.38 0.00 0.62
#> TCGA.BA.6870.01 1 0.000 0.932 1.00 0.00 0.00
#> TCGA.CN.A498.01 1 0.000 0.932 1.00 0.00 0.00
#> TCGA.CN.A499.01 1 0.000 0.932 1.00 0.00 0.00
#> TCGA.MT.A67G.01 2 0.604 0.664 0.00 0.62 0.38
#> TCGA.CN.5367.01 1 0.400 0.652 0.84 0.00 0.16
#> TCGA.BB.7871.01 2 0.000 0.926 0.00 1.00 0.00
#> TCGA.CR.7383.01 1 0.000 0.932 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.CV.7407.01 2 0.265 0.868 0.00 0.88 0.12 0.00
#> TCGA.CN.6021.01 2 0.000 0.958 0.00 1.00 0.00 0.00
#> TCGA.CV.5978.01 2 0.000 0.958 0.00 1.00 0.00 0.00
#> TCGA.CV.7178.01 3 0.265 1.000 0.12 0.00 0.88 0.00
#> TCGA.CV.7102.01 3 0.265 1.000 0.12 0.00 0.88 0.00
#> TCGA.CQ.6218.01 3 0.265 1.000 0.12 0.00 0.88 0.00
#> TCGA.BA.6870.01 1 0.000 0.860 1.00 0.00 0.00 0.00
#> TCGA.CN.A498.01 1 0.265 0.849 0.88 0.00 0.00 0.12
#> TCGA.CN.A499.01 1 0.265 0.849 0.88 0.00 0.00 0.12
#> TCGA.MT.A67G.01 4 0.265 0.000 0.00 0.12 0.00 0.88
#> TCGA.CN.5367.01 1 0.413 0.535 0.74 0.00 0.26 0.00
#> TCGA.BB.7871.01 2 0.000 0.958 0.00 1.00 0.00 0.00
#> TCGA.CR.7383.01 1 0.000 0.860 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.CV.7407.01 2 0.3274 0.794 0.00 0.78 0.00 0 0.22
#> TCGA.CN.6021.01 2 0.1410 0.906 0.06 0.94 0.00 0 0.00
#> TCGA.CV.5978.01 2 0.0000 0.919 0.00 1.00 0.00 0 0.00
#> TCGA.CV.7178.01 3 0.0000 0.821 0.00 0.00 1.00 0 0.00
#> TCGA.CV.7102.01 3 0.0000 0.821 0.00 0.00 1.00 0 0.00
#> TCGA.CQ.6218.01 3 0.0609 0.817 0.00 0.00 0.98 0 0.02
#> TCGA.BA.6870.01 1 0.1410 1.000 0.94 0.00 0.06 0 0.00
#> TCGA.CN.A498.01 5 0.4263 1.000 0.18 0.00 0.06 0 0.76
#> TCGA.CN.A499.01 5 0.4263 1.000 0.18 0.00 0.06 0 0.76
#> TCGA.MT.A67G.01 4 0.0000 0.000 0.00 0.00 0.00 1 0.00
#> TCGA.CN.5367.01 3 0.4767 0.154 0.42 0.00 0.56 0 0.02
#> TCGA.BB.7871.01 2 0.0000 0.919 0.00 1.00 0.00 0 0.00
#> TCGA.CR.7383.01 1 0.1410 1.000 0.94 0.00 0.06 0 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.CV.7407.01 2 0.350 0.685 0.32 0.68 0.00 0 0.00 0.00
#> TCGA.CN.6021.01 2 0.209 0.852 0.00 0.90 0.00 0 0.08 0.02
#> TCGA.CV.5978.01 2 0.000 0.876 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.CV.7178.01 3 0.000 0.764 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.CV.7102.01 3 0.000 0.764 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.CQ.6218.01 3 0.376 0.409 0.00 0.00 0.60 0 0.00 0.40
#> TCGA.BA.6870.01 1 0.463 0.000 0.52 0.00 0.00 0 0.04 0.44
#> TCGA.CN.A498.01 5 0.393 0.861 0.16 0.00 0.00 0 0.76 0.08
#> TCGA.CN.A499.01 5 0.156 0.861 0.00 0.00 0.00 0 0.92 0.08
#> TCGA.MT.A67G.01 4 0.000 0.000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.CN.5367.01 6 0.320 -0.125 0.00 0.00 0.26 0 0.00 0.74
#> TCGA.BB.7871.01 2 0.000 0.876 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.CR.7383.01 6 0.453 -0.841 0.38 0.00 0.00 0 0.04 0.58
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.CV.7407.01 7 0.3413 0.000 0.00 0.38 0.00 0 0.0 0.00 0.62
#> TCGA.CN.6021.01 2 0.2259 0.746 0.00 0.84 0.00 0 0.0 0.16 0.00
#> TCGA.CV.5978.01 2 0.0000 0.881 0.00 1.00 0.00 0 0.0 0.00 0.00
#> TCGA.CV.7178.01 3 0.0504 0.977 0.00 0.00 0.98 0 0.0 0.00 0.02
#> TCGA.CV.7102.01 3 0.0000 0.977 0.00 0.00 1.00 0 0.0 0.00 0.00
#> TCGA.CQ.6218.01 6 0.3546 0.449 0.00 0.00 0.46 0 0.0 0.54 0.00
#> TCGA.BA.6870.01 1 0.4535 0.657 0.64 0.00 0.00 0 0.0 0.24 0.12
#> TCGA.CN.A498.01 5 0.3911 0.731 0.00 0.00 0.00 0 0.7 0.06 0.24
#> TCGA.CN.A499.01 5 0.0000 0.731 0.00 0.00 0.00 0 1.0 0.00 0.00
#> TCGA.MT.A67G.01 4 0.0000 0.000 0.00 0.00 0.00 1 0.0 0.00 0.00
#> TCGA.CN.5367.01 6 0.5164 0.587 0.26 0.00 0.20 0 0.0 0.54 0.00
#> TCGA.BB.7871.01 2 0.0000 0.881 0.00 1.00 0.00 0 0.0 0.00 0.00
#> TCGA.CR.7383.01 1 0.0000 0.661 1.00 0.00 0.00 0 0.0 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.CV.7407.01 7 0.2650 0.000 0.00 0.24 0.00 0 0.00 0.00 0.76 0.00
#> TCGA.CN.6021.01 2 0.4059 0.505 0.00 0.64 0.00 0 0.00 0.08 0.00 0.28
#> TCGA.CV.5978.01 2 0.0808 0.757 0.00 0.96 0.00 0 0.00 0.04 0.00 0.00
#> TCGA.CV.7178.01 3 0.1275 0.941 0.00 0.00 0.94 0 0.00 0.00 0.04 0.02
#> TCGA.CV.7102.01 3 0.0000 0.941 0.00 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CQ.6218.01 6 0.3374 0.787 0.00 0.00 0.30 0 0.00 0.68 0.02 0.00
#> TCGA.BA.6870.01 1 0.3909 0.547 0.70 0.00 0.00 0 0.00 0.00 0.18 0.12
#> TCGA.CN.A498.01 5 0.0000 0.000 0.00 0.00 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.CN.A499.01 8 0.3272 0.000 0.00 0.00 0.00 0 0.42 0.00 0.00 0.58
#> TCGA.MT.A67G.01 4 0.0000 0.000 0.00 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.CN.5367.01 6 0.3036 0.807 0.04 0.00 0.18 0 0.00 0.78 0.00 0.00
#> TCGA.BB.7871.01 2 0.0000 0.757 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CR.7383.01 1 0.2267 0.548 0.82 0.00 0.00 0 0.00 0.18 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: Node02. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0121 , Node0122 , Node0211 , Node0212 , Node0213 , Node0221 , Node0222 , Node0223 , Node0224 , Node0225-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0511 , Node0512 , Node0521-leaf , Node0522 , Node0523-leaf , Node0524-leaf .
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 109 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 0.961 0.947 0.979 0.4930 0.508 0.508
#> 3 3 1.000 0.987 0.996 0.3389 0.673 0.443
#> 4 4 1.000 0.987 0.994 0.1450 0.829 0.547
#> 5 5 1.000 0.959 0.984 0.0273 0.971 0.883
#> 6 6 0.831 0.749 0.886 0.0471 0.940 0.745
#> 7 7 0.817 0.687 0.794 0.0316 0.906 0.569
#> 8 8 0.826 0.715 0.857 0.0188 0.968 0.805
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.HD.7753.01 1 0.000 0.979 1.00 0.00
#> TCGA.CQ.5325.01 2 0.000 0.976 0.00 1.00
#> TCGA.CV.7415.01 1 0.000 0.979 1.00 0.00
#> TCGA.CN.6011.01 1 0.000 0.979 1.00 0.00
#> TCGA.DQ.7592.01 1 0.000 0.979 1.00 0.00
#> TCGA.CV.5979.01 1 0.000 0.979 1.00 0.00
#> TCGA.CQ.6221.01 1 0.680 0.777 0.82 0.18
#> TCGA.CV.5971.01 2 0.000 0.976 0.00 1.00
#> TCGA.CV.5970.01 2 0.981 0.273 0.42 0.58
#> TCGA.CN.6016.01 2 0.000 0.976 0.00 1.00
#> TCGA.CV.5434.01 1 0.000 0.979 1.00 0.00
#> TCGA.CN.6017.01 2 0.000 0.976 0.00 1.00
#> TCGA.CV.7235.01 1 0.000 0.979 1.00 0.00
#> TCGA.CV.5439.01 1 0.000 0.979 1.00 0.00
#> TCGA.CN.6020.01 2 0.000 0.976 0.00 1.00
#> TCGA.CV.7423.01 1 0.000 0.979 1.00 0.00
#> TCGA.CN.6023.01 2 0.000 0.976 0.00 1.00
#> TCGA.CN.6024.01 1 0.000 0.979 1.00 0.00
#> TCGA.CQ.5323.01 1 0.000 0.979 1.00 0.00
#> TCGA.BB.4217.01 2 0.000 0.976 0.00 1.00
#> TCGA.CV.7410.01 2 0.000 0.976 0.00 1.00
#> TCGA.DQ.7588.01 1 0.000 0.979 1.00 0.00
#> TCGA.DQ.7591.01 1 0.000 0.979 1.00 0.00
#> TCGA.CV.5430.01 1 0.000 0.979 1.00 0.00
#> TCGA.CV.5440.01 1 0.000 0.979 1.00 0.00
#> TCGA.CV.7100.01 2 0.000 0.976 0.00 1.00
#> TCGA.CV.7254.01 2 0.000 0.976 0.00 1.00
#> TCGA.CR.7386.01 2 0.000 0.976 0.00 1.00
#> TCGA.CR.6474.01 2 0.000 0.976 0.00 1.00
#> TCGA.CV.7247.01 1 0.000 0.979 1.00 0.00
#> TCGA.CR.7377.01 2 0.000 0.976 0.00 1.00
#> TCGA.CN.5370.01 2 0.000 0.976 0.00 1.00
#> TCGA.CR.7401.01 2 0.000 0.976 0.00 1.00
#> TCGA.CV.7090.01 2 0.000 0.976 0.00 1.00
#> TCGA.CX.7219.01 2 0.000 0.976 0.00 1.00
#> TCGA.BA.6871.01 1 0.000 0.979 1.00 0.00
#> TCGA.D6.6825.01 2 0.000 0.976 0.00 1.00
#> TCGA.CQ.6222.01 2 0.000 0.976 0.00 1.00
#> TCGA.CN.6994.01 1 0.000 0.979 1.00 0.00
#> TCGA.CV.6950.01 1 0.000 0.979 1.00 0.00
#> TCGA.CV.6935.01 1 0.000 0.979 1.00 0.00
#> TCGA.CV.6945.01 2 0.000 0.976 0.00 1.00
#> TCGA.DQ.5630.01 2 0.000 0.976 0.00 1.00
#> TCGA.CV.6943.01 2 0.000 0.976 0.00 1.00
#> TCGA.CN.4733.01 2 0.000 0.976 0.00 1.00
#> TCGA.CN.6989.01 2 0.000 0.976 0.00 1.00
#> TCGA.D6.6517.01 2 0.000 0.976 0.00 1.00
#> TCGA.CQ.6220.01 2 0.000 0.976 0.00 1.00
#> TCGA.D6.6516.01 1 0.000 0.979 1.00 0.00
#> TCGA.CQ.6227.01 2 0.000 0.976 0.00 1.00
#> TCGA.BA.6868.01 1 0.000 0.979 1.00 0.00
#> TCGA.CQ.6229.01 2 0.000 0.976 0.00 1.00
#> TCGA.CQ.6223.01 1 0.000 0.979 1.00 0.00
#> TCGA.CV.A45R.01 1 0.529 0.855 0.88 0.12
#> TCGA.CN.A49B.01 1 0.000 0.979 1.00 0.00
#> TCGA.BA.5152.01 2 0.000 0.976 0.00 1.00
#> TCGA.CQ.5326.01 2 0.000 0.976 0.00 1.00
#> TCGA.CR.6471.01 2 0.000 0.976 0.00 1.00
#> TCGA.F7.A61W.01 1 0.000 0.979 1.00 0.00
#> TCGA.D6.A4ZB.01 2 0.000 0.976 0.00 1.00
#> TCGA.CV.A45Y.01 2 0.000 0.976 0.00 1.00
#> TCGA.BB.A5HU.01 2 0.000 0.976 0.00 1.00
#> TCGA.P3.A5Q6.01 1 0.000 0.979 1.00 0.00
#> TCGA.CX.A4AQ.01 2 0.904 0.524 0.32 0.68
#> TCGA.CV.A464.01 2 0.000 0.976 0.00 1.00
#> TCGA.QK.A652.01 2 0.000 0.976 0.00 1.00
#> TCGA.F7.8298.01 1 0.925 0.484 0.66 0.34
#> TCGA.F7.8489.01 2 0.000 0.976 0.00 1.00
#> TCGA.F7.A50G.01 2 0.000 0.976 0.00 1.00
#> TCGA.CQ.A4CA.01 2 0.000 0.976 0.00 1.00
#> TCGA.T3.A92N.01 1 0.000 0.979 1.00 0.00
#> TCGA.CN.A63Y.01 2 0.000 0.976 0.00 1.00
#> TCGA.P3.A5QE.01 2 0.000 0.976 0.00 1.00
#> TCGA.IQ.A61G.01 1 0.000 0.979 1.00 0.00
#> TCGA.IQ.A61J.01 2 0.000 0.976 0.00 1.00
#> TCGA.BA.A6DG.01 2 0.000 0.976 0.00 1.00
#> TCGA.CQ.A4CH.01 2 0.000 0.976 0.00 1.00
#> TCGA.D6.8569.01 1 0.000 0.979 1.00 0.00
#> TCGA.BB.8601.01 1 0.000 0.979 1.00 0.00
#> TCGA.H7.8502.01 1 0.000 0.979 1.00 0.00
#> TCGA.F7.A61S.01 2 0.000 0.976 0.00 1.00
#> TCGA.D6.8568.01 2 0.000 0.976 0.00 1.00
#> TCGA.DQ.7589.01 1 0.000 0.979 1.00 0.00
#> TCGA.CN.4725.01 1 0.000 0.979 1.00 0.00
#> TCGA.HL.7533.01 1 0.000 0.979 1.00 0.00
#> TCGA.CN.4729.01 2 0.000 0.976 0.00 1.00
#> TCGA.CN.5361.01 2 0.981 0.273 0.42 0.58
#> TCGA.CN.5359.01 2 0.000 0.976 0.00 1.00
#> TCGA.BB.7861.01 2 0.000 0.976 0.00 1.00
#> TCGA.UF.A7JS.01 1 0.000 0.979 1.00 0.00
#> TCGA.DQ.7590.01 2 0.000 0.976 0.00 1.00
#> TCGA.BA.4076.01 1 0.000 0.979 1.00 0.00
#> TCGA.MZ.A7D7.01 1 0.000 0.979 1.00 0.00
#> TCGA.BB.7872.01 2 0.000 0.976 0.00 1.00
#> TCGA.CN.5365.01 2 0.000 0.976 0.00 1.00
#> TCGA.BB.4224.01 1 0.000 0.979 1.00 0.00
#> TCGA.CN.A6V1.01 2 0.000 0.976 0.00 1.00
#> TCGA.CV.7430.01 1 0.000 0.979 1.00 0.00
#> TCGA.UF.A7JC.01 1 0.000 0.979 1.00 0.00
#> TCGA.CV.7568.01 2 0.000 0.976 0.00 1.00
#> TCGA.QK.A6IF.01 2 0.000 0.976 0.00 1.00
#> TCGA.CV.7429.01 2 0.000 0.976 0.00 1.00
#> TCGA.CV.7437.01 1 0.000 0.979 1.00 0.00
#> TCGA.CV.A6JN.01 2 0.795 0.675 0.24 0.76
#> TCGA.D6.A6EK.01 2 0.000 0.976 0.00 1.00
#> TCGA.P3.A6SX.01 1 0.000 0.979 1.00 0.00
#> TCGA.QK.A6II.01 1 0.827 0.649 0.74 0.26
#> TCGA.CV.7433.01 2 0.000 0.976 0.00 1.00
#> TCGA.CR.7376.01 2 0.000 0.976 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.HD.7753.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CQ.5325.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.CV.7415.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CN.6011.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.DQ.7592.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CV.5979.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CQ.6221.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CV.5971.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.CV.5970.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CN.6016.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.CV.5434.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CN.6017.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.CV.7235.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CV.5439.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CN.6020.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CV.7423.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CN.6023.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CN.6024.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CQ.5323.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.BB.4217.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.CV.7410.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.DQ.7588.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.DQ.7591.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CV.5430.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CV.5440.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CV.7100.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CV.7254.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CR.7386.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.CR.6474.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.CV.7247.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CR.7377.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.CN.5370.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CR.7401.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CV.7090.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CX.7219.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.BA.6871.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.D6.6825.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.CQ.6222.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.CN.6994.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CV.6950.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CV.6935.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CV.6945.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.DQ.5630.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.CV.6943.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.CN.4733.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.CN.6989.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.D6.6517.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CQ.6220.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.D6.6516.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CQ.6227.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.BA.6868.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CQ.6229.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.CQ.6223.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CV.A45R.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CN.A49B.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.BA.5152.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CQ.5326.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.CR.6471.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.F7.A61W.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.D6.A4ZB.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CV.A45Y.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.BB.A5HU.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.P3.A5Q6.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CX.A4AQ.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CV.A464.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.QK.A652.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.F7.8298.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.F7.8489.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.F7.A50G.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CQ.A4CA.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.T3.A92N.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CN.A63Y.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.P3.A5QE.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.IQ.A61G.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.IQ.A61J.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.BA.A6DG.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.CQ.A4CH.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.D6.8569.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.BB.8601.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.H7.8502.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.F7.A61S.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.D6.8568.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.DQ.7589.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CN.4725.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.HL.7533.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CN.4729.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CN.5361.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CN.5359.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.BB.7861.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.UF.A7JS.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.DQ.7590.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.BA.4076.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.MZ.A7D7.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.BB.7872.01 2 0.628 0.148 0 0.54 0.46
#> TCGA.CN.5365.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.BB.4224.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CN.A6V1.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.CV.7430.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.UF.A7JC.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CV.7568.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.QK.A6IF.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CV.7429.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CV.7437.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CV.A6JN.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.D6.A6EK.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.P3.A6SX.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.QK.A6II.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.CV.7433.01 2 0.000 0.983 0 1.00 0.00
#> TCGA.CR.7376.01 2 0.000 0.983 0 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.HD.7753.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.CQ.5325.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CV.7415.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.CN.6011.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.DQ.7592.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.CV.5979.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CQ.6221.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.CV.5971.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CV.5970.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.CN.6016.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.CV.5434.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CN.6017.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CV.7235.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.CV.5439.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.CN.6020.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.CV.7423.01 1 0.1211 0.951 0.96 0 0.00 0.04
#> TCGA.CN.6023.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.CN.6024.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CQ.5323.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.BB.4217.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CV.7410.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.DQ.7588.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.DQ.7591.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.CV.5430.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.CV.5440.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CV.7100.01 4 0.3400 0.779 0.00 0 0.18 0.82
#> TCGA.CV.7254.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.CR.7386.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CR.6474.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CV.7247.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CR.7377.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CN.5370.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.CR.7401.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.CV.7090.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.CX.7219.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.BA.6871.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.D6.6825.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.CQ.6222.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CN.6994.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CV.6950.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.CV.6935.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CV.6945.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.DQ.5630.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CV.6943.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CN.4733.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CN.6989.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.D6.6517.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.CQ.6220.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.D6.6516.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.CQ.6227.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.BA.6868.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CQ.6229.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CQ.6223.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.CV.A45R.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.CN.A49B.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.BA.5152.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.CQ.5326.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.CR.6471.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.F7.A61W.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.D6.A4ZB.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.CV.A45Y.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.BB.A5HU.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.P3.A5Q6.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.CX.A4AQ.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.CV.A464.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.QK.A652.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.F7.8298.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.F7.8489.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.F7.A50G.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.CQ.A4CA.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.T3.A92N.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CN.A63Y.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.P3.A5QE.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.IQ.A61G.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.IQ.A61J.01 3 0.2647 0.862 0.00 0 0.88 0.12
#> TCGA.BA.A6DG.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CQ.A4CH.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.D6.8569.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.BB.8601.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.H7.8502.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.F7.A61S.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.D6.8568.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.DQ.7589.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CN.4725.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.HL.7533.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.CN.4729.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.CN.5361.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.CN.5359.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.BB.7861.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.UF.A7JS.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.DQ.7590.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.BA.4076.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.MZ.A7D7.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.BB.7872.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.CN.5365.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.BB.4224.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CN.A6V1.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CV.7430.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.UF.A7JC.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CV.7568.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.QK.A6IF.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.CV.7429.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.CV.7437.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CV.A6JN.01 4 0.0707 0.972 0.00 0 0.02 0.98
#> TCGA.D6.A6EK.01 3 0.0000 0.996 0.00 0 1.00 0.00
#> TCGA.P3.A6SX.01 1 0.4134 0.654 0.74 0 0.00 0.26
#> TCGA.QK.A6II.01 4 0.0000 0.991 0.00 0 0.00 1.00
#> TCGA.CV.7433.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CR.7376.01 2 0.0000 1.000 0.00 1 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.HD.7753.01 4 0.0609 0.949 0.00 0 0.00 0.98 0.02
#> TCGA.CQ.5325.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CV.7415.01 4 0.0609 0.949 0.00 0 0.00 0.98 0.02
#> TCGA.CN.6011.01 1 0.0000 0.973 1.00 0 0.00 0.00 0.00
#> TCGA.DQ.7592.01 4 0.0000 0.948 0.00 0 0.00 1.00 0.00
#> TCGA.CV.5979.01 1 0.0000 0.973 1.00 0 0.00 0.00 0.00
#> TCGA.CQ.6221.01 4 0.0000 0.948 0.00 0 0.00 1.00 0.00
#> TCGA.CV.5971.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CV.5970.01 4 0.0000 0.948 0.00 0 0.00 1.00 0.00
#> TCGA.CN.6016.01 3 0.0000 0.985 0.00 0 1.00 0.00 0.00
#> TCGA.CV.5434.01 1 0.0609 0.954 0.98 0 0.00 0.00 0.02
#> TCGA.CN.6017.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CV.7235.01 4 0.0609 0.949 0.00 0 0.00 0.98 0.02
#> TCGA.CV.5439.01 4 0.0609 0.949 0.00 0 0.00 0.98 0.02
#> TCGA.CN.6020.01 3 0.0000 0.985 0.00 0 1.00 0.00 0.00
#> TCGA.CV.7423.01 1 0.2616 0.834 0.88 0 0.00 0.10 0.02
#> TCGA.CN.6023.01 3 0.0000 0.985 0.00 0 1.00 0.00 0.00
#> TCGA.CN.6024.01 1 0.0000 0.973 1.00 0 0.00 0.00 0.00
#> TCGA.CQ.5323.01 1 0.0000 0.973 1.00 0 0.00 0.00 0.00
#> TCGA.BB.4217.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CV.7410.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.DQ.7588.01 1 0.0000 0.973 1.00 0 0.00 0.00 0.00
#> TCGA.DQ.7591.01 5 0.0000 0.988 0.00 0 0.00 0.00 1.00
#> TCGA.CV.5430.01 5 0.0000 0.988 0.00 0 0.00 0.00 1.00
#> TCGA.CV.5440.01 1 0.0000 0.973 1.00 0 0.00 0.00 0.00
#> TCGA.CV.7100.01 4 0.2732 0.739 0.00 0 0.16 0.84 0.00
#> TCGA.CV.7254.01 3 0.0000 0.985 0.00 0 1.00 0.00 0.00
#> TCGA.CR.7386.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CR.6474.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CV.7247.01 1 0.0000 0.973 1.00 0 0.00 0.00 0.00
#> TCGA.CR.7377.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CN.5370.01 3 0.0000 0.985 0.00 0 1.00 0.00 0.00
#> TCGA.CR.7401.01 3 0.0000 0.985 0.00 0 1.00 0.00 0.00
#> TCGA.CV.7090.01 3 0.0609 0.972 0.00 0 0.98 0.02 0.00
#> TCGA.CX.7219.01 3 0.0609 0.972 0.00 0 0.98 0.02 0.00
#> TCGA.BA.6871.01 5 0.0000 0.988 0.00 0 0.00 0.00 1.00
#> TCGA.D6.6825.01 3 0.0000 0.985 0.00 0 1.00 0.00 0.00
#> TCGA.CQ.6222.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CN.6994.01 1 0.0000 0.973 1.00 0 0.00 0.00 0.00
#> TCGA.CV.6950.01 4 0.0609 0.949 0.00 0 0.00 0.98 0.02
#> TCGA.CV.6935.01 1 0.0000 0.973 1.00 0 0.00 0.00 0.00
#> TCGA.CV.6945.01 3 0.3109 0.726 0.00 0 0.80 0.20 0.00
#> TCGA.DQ.5630.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CV.6943.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CN.4733.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CN.6989.01 3 0.0000 0.985 0.00 0 1.00 0.00 0.00
#> TCGA.D6.6517.01 3 0.0000 0.985 0.00 0 1.00 0.00 0.00
#> TCGA.CQ.6220.01 3 0.0000 0.985 0.00 0 1.00 0.00 0.00
#> TCGA.D6.6516.01 4 0.0000 0.948 0.00 0 0.00 1.00 0.00
#> TCGA.CQ.6227.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.BA.6868.01 1 0.0000 0.973 1.00 0 0.00 0.00 0.00
#> TCGA.CQ.6229.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CQ.6223.01 4 0.0609 0.949 0.00 0 0.00 0.98 0.02
#> TCGA.CV.A45R.01 4 0.0000 0.948 0.00 0 0.00 1.00 0.00
#> TCGA.CN.A49B.01 4 0.0609 0.949 0.00 0 0.00 0.98 0.02
#> TCGA.BA.5152.01 3 0.0000 0.985 0.00 0 1.00 0.00 0.00
#> TCGA.CQ.5326.01 3 0.0000 0.985 0.00 0 1.00 0.00 0.00
#> TCGA.CR.6471.01 3 0.0609 0.972 0.00 0 0.98 0.02 0.00
#> TCGA.F7.A61W.01 1 0.0000 0.973 1.00 0 0.00 0.00 0.00
#> TCGA.D6.A4ZB.01 3 0.0000 0.985 0.00 0 1.00 0.00 0.00
#> TCGA.CV.A45Y.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.BB.A5HU.01 3 0.0000 0.985 0.00 0 1.00 0.00 0.00
#> TCGA.P3.A5Q6.01 4 0.0609 0.949 0.00 0 0.00 0.98 0.02
#> TCGA.CX.A4AQ.01 5 0.0609 0.982 0.00 0 0.00 0.02 0.98
#> TCGA.CV.A464.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.QK.A652.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.F7.8298.01 4 0.0000 0.948 0.00 0 0.00 1.00 0.00
#> TCGA.F7.8489.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.F7.A50G.01 3 0.0000 0.985 0.00 0 1.00 0.00 0.00
#> TCGA.CQ.A4CA.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.T3.A92N.01 1 0.0000 0.973 1.00 0 0.00 0.00 0.00
#> TCGA.CN.A63Y.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.P3.A5QE.01 5 0.0609 0.982 0.00 0 0.00 0.02 0.98
#> TCGA.IQ.A61G.01 1 0.0000 0.973 1.00 0 0.00 0.00 0.00
#> TCGA.IQ.A61J.01 4 0.4287 0.130 0.00 0 0.46 0.54 0.00
#> TCGA.BA.A6DG.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CQ.A4CH.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.D6.8569.01 4 0.0000 0.948 0.00 0 0.00 1.00 0.00
#> TCGA.BB.8601.01 1 0.0000 0.973 1.00 0 0.00 0.00 0.00
#> TCGA.H7.8502.01 1 0.0000 0.973 1.00 0 0.00 0.00 0.00
#> TCGA.F7.A61S.01 3 0.0609 0.972 0.00 0 0.98 0.02 0.00
#> TCGA.D6.8568.01 3 0.0000 0.985 0.00 0 1.00 0.00 0.00
#> TCGA.DQ.7589.01 1 0.0000 0.973 1.00 0 0.00 0.00 0.00
#> TCGA.CN.4725.01 1 0.0000 0.973 1.00 0 0.00 0.00 0.00
#> TCGA.HL.7533.01 4 0.0609 0.949 0.00 0 0.00 0.98 0.02
#> TCGA.CN.4729.01 3 0.0000 0.985 0.00 0 1.00 0.00 0.00
#> TCGA.CN.5361.01 4 0.0000 0.948 0.00 0 0.00 1.00 0.00
#> TCGA.CN.5359.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.BB.7861.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.UF.A7JS.01 4 0.0609 0.949 0.00 0 0.00 0.98 0.02
#> TCGA.DQ.7590.01 3 0.0000 0.985 0.00 0 1.00 0.00 0.00
#> TCGA.BA.4076.01 1 0.0000 0.973 1.00 0 0.00 0.00 0.00
#> TCGA.MZ.A7D7.01 4 0.0609 0.949 0.00 0 0.00 0.98 0.02
#> TCGA.BB.7872.01 3 0.0000 0.985 0.00 0 1.00 0.00 0.00
#> TCGA.CN.5365.01 3 0.0609 0.972 0.00 0 0.98 0.02 0.00
#> TCGA.BB.4224.01 1 0.0000 0.973 1.00 0 0.00 0.00 0.00
#> TCGA.CN.A6V1.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CV.7430.01 1 0.0000 0.973 1.00 0 0.00 0.00 0.00
#> TCGA.UF.A7JC.01 1 0.0000 0.973 1.00 0 0.00 0.00 0.00
#> TCGA.CV.7568.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.QK.A6IF.01 3 0.1043 0.951 0.00 0 0.96 0.00 0.04
#> TCGA.CV.7429.01 3 0.0000 0.985 0.00 0 1.00 0.00 0.00
#> TCGA.CV.7437.01 1 0.0000 0.973 1.00 0 0.00 0.00 0.00
#> TCGA.CV.A6JN.01 4 0.0609 0.930 0.00 0 0.02 0.98 0.00
#> TCGA.D6.A6EK.01 3 0.0000 0.985 0.00 0 1.00 0.00 0.00
#> TCGA.P3.A6SX.01 1 0.4613 0.412 0.62 0 0.00 0.36 0.02
#> TCGA.QK.A6II.01 4 0.0000 0.948 0.00 0 0.00 1.00 0.00
#> TCGA.CV.7433.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CR.7376.01 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.HD.7753.01 4 0.3851 -0.0949 0.00 0.00 0.00 0.54 0.00 0.46
#> TCGA.CQ.5325.01 2 0.0937 0.9243 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CV.7415.01 6 0.3851 0.2196 0.00 0.00 0.00 0.46 0.00 0.54
#> TCGA.CN.6011.01 1 0.2454 0.8286 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.DQ.7592.01 4 0.0937 0.7564 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.CV.5979.01 1 0.0000 0.8734 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.6221.01 4 0.0547 0.7667 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.CV.5971.01 2 0.0937 0.9243 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CV.5970.01 4 0.0000 0.7697 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CN.6016.01 3 0.1480 0.8493 0.00 0.04 0.94 0.00 0.00 0.02
#> TCGA.CV.5434.01 6 0.3647 0.1102 0.36 0.00 0.00 0.00 0.00 0.64
#> TCGA.CN.6017.01 2 0.0937 0.9243 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CV.7235.01 6 0.1556 0.7229 0.00 0.00 0.00 0.08 0.00 0.92
#> TCGA.CV.5439.01 6 0.3864 0.1707 0.00 0.00 0.00 0.48 0.00 0.52
#> TCGA.CN.6020.01 3 0.0000 0.8828 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.7423.01 6 0.1807 0.6860 0.06 0.00 0.00 0.02 0.00 0.92
#> TCGA.CN.6023.01 3 0.0547 0.8790 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CN.6024.01 1 0.1556 0.8635 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.CQ.5323.01 1 0.3756 0.5512 0.60 0.00 0.00 0.00 0.00 0.40
#> TCGA.BB.4217.01 2 0.0937 0.9243 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CV.7410.01 2 0.0937 0.9243 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.DQ.7588.01 1 0.2260 0.8400 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.DQ.7591.01 5 0.0547 0.8599 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.CV.5430.01 5 0.2941 0.7716 0.00 0.00 0.00 0.00 0.78 0.22
#> TCGA.CV.5440.01 1 0.0000 0.8734 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7100.01 4 0.0547 0.7628 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.CV.7254.01 3 0.0000 0.8828 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CR.7386.01 2 0.2790 0.8270 0.00 0.84 0.14 0.00 0.00 0.02
#> TCGA.CR.6474.01 2 0.3819 0.6359 0.00 0.70 0.28 0.00 0.00 0.02
#> TCGA.CV.7247.01 6 0.2260 0.5962 0.14 0.00 0.00 0.00 0.00 0.86
#> TCGA.CR.7377.01 2 0.0000 0.9209 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.5370.01 3 0.0547 0.8790 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CR.7401.01 3 0.0547 0.8790 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CV.7090.01 3 0.3076 0.6926 0.00 0.00 0.76 0.24 0.00 0.00
#> TCGA.CX.7219.01 4 0.3869 -0.1842 0.00 0.00 0.50 0.50 0.00 0.00
#> TCGA.BA.6871.01 5 0.3409 0.6739 0.00 0.00 0.00 0.00 0.70 0.30
#> TCGA.D6.6825.01 3 0.1092 0.8664 0.00 0.02 0.96 0.00 0.00 0.02
#> TCGA.CQ.6222.01 2 0.0937 0.9243 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CN.6994.01 1 0.1556 0.8635 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.CV.6950.01 4 0.3864 -0.1572 0.00 0.00 0.00 0.52 0.00 0.48
#> TCGA.CV.6935.01 1 0.0547 0.8724 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CV.6945.01 4 0.2048 0.6865 0.00 0.00 0.12 0.88 0.00 0.00
#> TCGA.DQ.5630.01 2 0.1480 0.9015 0.00 0.94 0.04 0.00 0.00 0.02
#> TCGA.CV.6943.01 2 0.0937 0.9243 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CN.4733.01 2 0.0937 0.9243 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CN.6989.01 3 0.0547 0.8840 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.D6.6517.01 3 0.0547 0.8790 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CQ.6220.01 3 0.2454 0.7874 0.00 0.00 0.84 0.16 0.00 0.00
#> TCGA.D6.6516.01 4 0.0937 0.7564 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.CQ.6227.01 2 0.2350 0.8657 0.00 0.88 0.10 0.00 0.00 0.02
#> TCGA.BA.6868.01 1 0.2260 0.8400 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.CQ.6229.01 2 0.1807 0.8925 0.00 0.92 0.06 0.00 0.00 0.02
#> TCGA.CQ.6223.01 6 0.1556 0.7229 0.00 0.00 0.00 0.08 0.00 0.92
#> TCGA.CV.A45R.01 4 0.0547 0.7667 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.CN.A49B.01 6 0.1814 0.7122 0.00 0.00 0.00 0.10 0.00 0.90
#> TCGA.BA.5152.01 3 0.0547 0.8840 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.CQ.5326.01 3 0.0547 0.8790 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CR.6471.01 3 0.3578 0.5280 0.00 0.00 0.66 0.34 0.00 0.00
#> TCGA.F7.A61W.01 1 0.0000 0.8734 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D6.A4ZB.01 3 0.2048 0.8204 0.00 0.00 0.88 0.12 0.00 0.00
#> TCGA.CV.A45Y.01 2 0.1807 0.8925 0.00 0.92 0.06 0.00 0.00 0.02
#> TCGA.BB.A5HU.01 3 0.0547 0.8840 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.P3.A5Q6.01 4 0.3828 -0.0377 0.00 0.00 0.00 0.56 0.00 0.44
#> TCGA.CX.A4AQ.01 5 0.0000 0.8604 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CV.A464.01 2 0.2350 0.8657 0.00 0.88 0.10 0.00 0.00 0.02
#> TCGA.QK.A652.01 2 0.3592 0.6988 0.00 0.74 0.24 0.00 0.00 0.02
#> TCGA.F7.8298.01 4 0.0000 0.7697 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.F7.8489.01 2 0.2094 0.8802 0.00 0.90 0.08 0.00 0.00 0.02
#> TCGA.F7.A50G.01 3 0.0547 0.8840 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.CQ.A4CA.01 2 0.0000 0.9209 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.T3.A92N.01 1 0.2793 0.7978 0.80 0.00 0.00 0.00 0.00 0.20
#> TCGA.CN.A63Y.01 2 0.2350 0.8657 0.00 0.88 0.10 0.00 0.00 0.02
#> TCGA.P3.A5QE.01 5 0.0000 0.8604 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.IQ.A61G.01 1 0.0000 0.8734 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IQ.A61J.01 4 0.1556 0.7217 0.00 0.00 0.08 0.92 0.00 0.00
#> TCGA.BA.A6DG.01 2 0.0937 0.9243 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CQ.A4CH.01 2 0.0937 0.9243 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.D6.8569.01 4 0.0937 0.7564 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.BB.8601.01 1 0.0000 0.8734 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.H7.8502.01 1 0.0000 0.8734 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F7.A61S.01 4 0.3756 0.1616 0.00 0.00 0.40 0.60 0.00 0.00
#> TCGA.D6.8568.01 3 0.0547 0.8840 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.DQ.7589.01 1 0.3797 0.5107 0.58 0.00 0.00 0.00 0.00 0.42
#> TCGA.CN.4725.01 1 0.3409 0.6953 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.HL.7533.01 6 0.1556 0.7229 0.00 0.00 0.00 0.08 0.00 0.92
#> TCGA.CN.4729.01 3 0.0547 0.8840 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.CN.5361.01 4 0.0000 0.7697 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CN.5359.01 2 0.0000 0.9209 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BB.7861.01 2 0.0937 0.9243 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.UF.A7JS.01 6 0.3864 0.1707 0.00 0.00 0.00 0.48 0.00 0.52
#> TCGA.DQ.7590.01 3 0.3409 0.5656 0.00 0.00 0.70 0.00 0.30 0.00
#> TCGA.BA.4076.01 1 0.0000 0.8734 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MZ.A7D7.01 6 0.1556 0.7229 0.00 0.00 0.00 0.08 0.00 0.92
#> TCGA.BB.7872.01 3 0.0547 0.8790 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CN.5365.01 3 0.3828 0.2946 0.00 0.00 0.56 0.44 0.00 0.00
#> TCGA.BB.4224.01 1 0.0000 0.8734 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.A6V1.01 2 0.0937 0.9243 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CV.7430.01 1 0.0000 0.8734 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A7JC.01 1 0.0000 0.8734 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7568.01 2 0.0000 0.9209 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QK.A6IF.01 3 0.4144 0.4471 0.00 0.00 0.62 0.00 0.36 0.02
#> TCGA.CV.7429.01 3 0.1814 0.8361 0.00 0.00 0.90 0.10 0.00 0.00
#> TCGA.CV.7437.01 1 0.3706 0.5841 0.62 0.00 0.00 0.00 0.00 0.38
#> TCGA.CV.A6JN.01 4 0.0547 0.7628 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.D6.A6EK.01 3 0.0547 0.8840 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.P3.A6SX.01 6 0.1807 0.6860 0.06 0.00 0.00 0.02 0.00 0.92
#> TCGA.QK.A6II.01 4 0.0547 0.7667 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.CV.7433.01 2 0.0000 0.9209 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7376.01 2 0.0937 0.9243 0.00 0.96 0.00 0.00 0.00 0.04
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.HD.7753.01 4 0.4883 0.60535 0.00 0.00 0.00 0.60 0.00 0.20 0.20
#> TCGA.CQ.5325.01 2 0.0000 0.94477 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7415.01 4 0.5164 0.55555 0.00 0.00 0.00 0.54 0.00 0.26 0.20
#> TCGA.CN.6011.01 6 0.3525 0.26037 0.44 0.00 0.00 0.00 0.00 0.56 0.00
#> TCGA.DQ.7592.01 4 0.0504 0.80498 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CV.5979.01 1 0.0000 0.86337 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.6221.01 4 0.0000 0.80733 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.5971.01 2 0.0000 0.94477 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5970.01 4 0.0000 0.80733 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CN.6016.01 7 0.3546 -0.04858 0.00 0.00 0.46 0.00 0.00 0.00 0.54
#> TCGA.CV.5434.01 6 0.3519 0.58166 0.22 0.00 0.00 0.00 0.00 0.74 0.04
#> TCGA.CN.6017.01 2 0.0000 0.94477 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7235.01 6 0.3388 0.53542 0.00 0.00 0.00 0.04 0.00 0.76 0.20
#> TCGA.CV.5439.01 4 0.5164 0.55555 0.00 0.00 0.00 0.54 0.00 0.26 0.20
#> TCGA.CN.6020.01 3 0.0000 0.77983 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7423.01 6 0.1006 0.63071 0.02 0.00 0.00 0.02 0.00 0.96 0.00
#> TCGA.CN.6023.01 3 0.0000 0.77983 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.6024.01 1 0.3943 0.15478 0.56 0.00 0.00 0.00 0.00 0.42 0.02
#> TCGA.CQ.5323.01 6 0.3517 0.53924 0.28 0.00 0.00 0.00 0.00 0.70 0.02
#> TCGA.BB.4217.01 2 0.0000 0.94477 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7410.01 2 0.0000 0.94477 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.7588.01 6 0.3558 0.12813 0.48 0.00 0.00 0.00 0.00 0.52 0.00
#> TCGA.DQ.7591.01 5 0.0863 0.74589 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.CV.5430.01 5 0.2803 0.70837 0.00 0.00 0.00 0.00 0.84 0.06 0.10
#> TCGA.CV.5440.01 1 0.0000 0.86337 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7100.01 4 0.0504 0.79442 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.CV.7254.01 3 0.0000 0.77983 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7386.01 7 0.4244 0.81581 0.00 0.42 0.04 0.00 0.00 0.00 0.54
#> TCGA.CR.6474.01 7 0.5164 0.66959 0.00 0.26 0.20 0.00 0.00 0.00 0.54
#> TCGA.CV.7247.01 6 0.0863 0.63679 0.04 0.00 0.00 0.00 0.00 0.96 0.00
#> TCGA.CR.7377.01 2 0.2081 0.78532 0.00 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.CN.5370.01 3 0.3047 0.55496 0.00 0.00 0.72 0.00 0.00 0.00 0.28
#> TCGA.CR.7401.01 3 0.3413 0.39430 0.00 0.00 0.62 0.00 0.00 0.00 0.38
#> TCGA.CV.7090.01 3 0.1433 0.74833 0.00 0.00 0.92 0.08 0.00 0.00 0.00
#> TCGA.CX.7219.01 3 0.3496 0.37953 0.00 0.00 0.58 0.42 0.00 0.00 0.00
#> TCGA.BA.6871.01 5 0.4990 0.47295 0.00 0.00 0.00 0.00 0.58 0.22 0.20
#> TCGA.D6.6825.01 3 0.3546 0.19874 0.00 0.00 0.54 0.00 0.00 0.00 0.46
#> TCGA.CQ.6222.01 2 0.0000 0.94477 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.6994.01 1 0.3358 0.33646 0.64 0.00 0.00 0.00 0.00 0.36 0.00
#> TCGA.CV.6950.01 4 0.5164 0.55555 0.00 0.00 0.00 0.54 0.00 0.26 0.20
#> TCGA.CV.6935.01 1 0.1664 0.81178 0.92 0.00 0.00 0.00 0.00 0.06 0.02
#> TCGA.CV.6945.01 4 0.1671 0.71426 0.00 0.00 0.10 0.90 0.00 0.00 0.00
#> TCGA.DQ.5630.01 7 0.3968 0.80806 0.00 0.44 0.02 0.00 0.00 0.00 0.54
#> TCGA.CV.6943.01 2 0.0000 0.94477 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4733.01 2 0.0000 0.94477 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.6989.01 3 0.0504 0.77975 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.D6.6517.01 3 0.0504 0.77157 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CQ.6220.01 3 0.0863 0.77099 0.00 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.D6.6516.01 4 0.2722 0.75613 0.00 0.00 0.00 0.84 0.00 0.04 0.12
#> TCGA.CQ.6227.01 7 0.4244 0.81581 0.00 0.42 0.04 0.00 0.00 0.00 0.54
#> TCGA.BA.6868.01 1 0.3525 0.06872 0.56 0.00 0.00 0.00 0.00 0.44 0.00
#> TCGA.CQ.6229.01 7 0.3968 0.80806 0.00 0.44 0.02 0.00 0.00 0.00 0.54
#> TCGA.CQ.6223.01 6 0.3388 0.53542 0.00 0.00 0.00 0.04 0.00 0.76 0.20
#> TCGA.CV.A45R.01 4 0.0000 0.80733 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CN.A49B.01 6 0.3667 0.51233 0.00 0.00 0.00 0.06 0.00 0.74 0.20
#> TCGA.BA.5152.01 3 0.0000 0.77983 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.5326.01 3 0.3358 0.43318 0.00 0.00 0.64 0.00 0.00 0.00 0.36
#> TCGA.CR.6471.01 3 0.2708 0.61941 0.00 0.00 0.78 0.22 0.00 0.00 0.00
#> TCGA.F7.A61W.01 1 0.0000 0.86337 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D6.A4ZB.01 3 0.0504 0.77975 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.CV.A45Y.01 7 0.3968 0.80806 0.00 0.44 0.02 0.00 0.00 0.00 0.54
#> TCGA.BB.A5HU.01 3 0.0504 0.77975 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.P3.A5Q6.01 4 0.3985 0.68578 0.00 0.00 0.00 0.72 0.00 0.18 0.10
#> TCGA.CX.A4AQ.01 5 0.1886 0.74873 0.00 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.CV.A464.01 7 0.4244 0.81581 0.00 0.42 0.04 0.00 0.00 0.00 0.54
#> TCGA.QK.A652.01 7 0.4998 0.73190 0.00 0.32 0.14 0.00 0.00 0.00 0.54
#> TCGA.F7.8298.01 4 0.0000 0.80733 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.F7.8489.01 7 0.3968 0.80806 0.00 0.44 0.02 0.00 0.00 0.00 0.54
#> TCGA.F7.A50G.01 3 0.0504 0.77975 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.CQ.A4CA.01 2 0.1671 0.84986 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.T3.A92N.01 6 0.3909 0.34374 0.40 0.00 0.00 0.00 0.00 0.58 0.02
#> TCGA.CN.A63Y.01 7 0.3968 0.80806 0.00 0.44 0.02 0.00 0.00 0.00 0.54
#> TCGA.P3.A5QE.01 5 0.2081 0.74462 0.00 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.IQ.A61G.01 1 0.0000 0.86337 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IQ.A61J.01 4 0.0863 0.77693 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.BA.A6DG.01 2 0.0000 0.94477 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.A4CH.01 2 0.0000 0.94477 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D6.8569.01 4 0.1664 0.78860 0.00 0.00 0.00 0.92 0.00 0.02 0.06
#> TCGA.BB.8601.01 1 0.0504 0.85300 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.H7.8502.01 1 0.0000 0.86337 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F7.A61S.01 3 0.3562 0.18142 0.00 0.00 0.50 0.50 0.00 0.00 0.00
#> TCGA.D6.8568.01 3 0.0000 0.77983 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.7589.01 6 0.3745 0.55354 0.26 0.00 0.00 0.00 0.00 0.70 0.04
#> TCGA.CN.4725.01 6 0.3294 0.47532 0.34 0.00 0.00 0.00 0.00 0.66 0.00
#> TCGA.HL.7533.01 6 0.3388 0.53542 0.00 0.00 0.00 0.04 0.00 0.76 0.20
#> TCGA.CN.4729.01 3 0.0504 0.77975 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.CN.5361.01 4 0.0000 0.80733 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CN.5359.01 2 0.1671 0.84986 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.BB.7861.01 2 0.0000 0.94477 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A7JS.01 4 0.5083 0.57298 0.00 0.00 0.00 0.56 0.00 0.24 0.20
#> TCGA.DQ.7590.01 3 0.5173 -0.00841 0.00 0.00 0.50 0.00 0.34 0.00 0.16
#> TCGA.BA.4076.01 1 0.0000 0.86337 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MZ.A7D7.01 6 0.3530 0.52671 0.00 0.00 0.00 0.02 0.02 0.76 0.20
#> TCGA.BB.7872.01 3 0.3358 0.43318 0.00 0.00 0.64 0.00 0.00 0.00 0.36
#> TCGA.CN.5365.01 3 0.3139 0.52930 0.00 0.00 0.70 0.30 0.00 0.00 0.00
#> TCGA.BB.4224.01 1 0.0000 0.86337 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.A6V1.01 2 0.0000 0.94477 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7430.01 1 0.0504 0.85300 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.UF.A7JC.01 1 0.0000 0.86337 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7568.01 2 0.1886 0.82223 0.00 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.QK.A6IF.01 5 0.5247 0.14259 0.00 0.00 0.40 0.00 0.44 0.00 0.16
#> TCGA.CV.7429.01 3 0.1166 0.76032 0.00 0.00 0.94 0.06 0.00 0.00 0.00
#> TCGA.CV.7437.01 6 0.3745 0.55354 0.26 0.00 0.00 0.00 0.00 0.70 0.04
#> TCGA.CV.A6JN.01 4 0.0504 0.79558 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.D6.A6EK.01 3 0.0000 0.77983 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.P3.A6SX.01 6 0.1860 0.62071 0.02 0.00 0.00 0.02 0.00 0.92 0.04
#> TCGA.QK.A6II.01 4 0.0000 0.80733 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.7433.01 2 0.1886 0.82223 0.00 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.CR.7376.01 2 0.0000 0.94477 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.HD.7753.01 4 0.4570 0.5238 0.00 0.00 0.00 0.60 0.20 0.20 0.00 0.00
#> TCGA.CQ.5325.01 2 0.0000 0.9474 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7415.01 4 0.4849 0.4636 0.00 0.00 0.00 0.54 0.22 0.24 0.00 0.00
#> TCGA.CN.6011.01 6 0.3272 0.3345 0.42 0.00 0.00 0.00 0.00 0.58 0.00 0.00
#> TCGA.DQ.7592.01 4 0.0941 0.7768 0.00 0.00 0.02 0.96 0.02 0.00 0.00 0.00
#> TCGA.CV.5979.01 1 0.0000 0.8754 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.6221.01 4 0.0471 0.7781 0.00 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.CV.5971.01 2 0.0000 0.9474 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5970.01 4 0.0471 0.7781 0.00 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.CN.6016.01 7 0.1947 0.7128 0.00 0.00 0.14 0.00 0.00 0.00 0.86 0.00
#> TCGA.CV.5434.01 6 0.2591 0.6069 0.08 0.00 0.00 0.00 0.02 0.86 0.04 0.00
#> TCGA.CN.6017.01 2 0.0000 0.9474 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7235.01 6 0.3293 0.4610 0.00 0.00 0.00 0.04 0.22 0.74 0.00 0.00
#> TCGA.CV.5439.01 4 0.4921 0.4371 0.00 0.00 0.00 0.52 0.22 0.26 0.00 0.00
#> TCGA.CN.6020.01 3 0.1091 0.8648 0.00 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.CV.7423.01 6 0.0941 0.5874 0.00 0.00 0.00 0.02 0.02 0.96 0.00 0.00
#> TCGA.CN.6023.01 3 0.1563 0.8324 0.00 0.00 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.CN.6024.01 6 0.4399 0.1343 0.44 0.00 0.00 0.00 0.02 0.50 0.04 0.00
#> TCGA.CQ.5323.01 6 0.3426 0.5668 0.22 0.00 0.00 0.00 0.02 0.74 0.02 0.00
#> TCGA.BB.4217.01 2 0.0000 0.9474 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7410.01 2 0.0000 0.9474 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.7588.01 6 0.3237 0.3556 0.40 0.00 0.00 0.00 0.00 0.60 0.00 0.00
#> TCGA.DQ.7591.01 5 0.4050 0.4713 0.00 0.00 0.00 0.00 0.60 0.00 0.06 0.34
#> TCGA.CV.5430.01 5 0.3494 0.6942 0.00 0.00 0.00 0.00 0.78 0.04 0.04 0.14
#> TCGA.CV.5440.01 1 0.0000 0.8754 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7100.01 4 0.2114 0.6713 0.00 0.00 0.16 0.84 0.00 0.00 0.00 0.00
#> TCGA.CV.7254.01 3 0.1091 0.8648 0.00 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.CR.7386.01 7 0.2114 0.8109 0.00 0.16 0.00 0.00 0.00 0.00 0.84 0.00
#> TCGA.CR.6474.01 7 0.2350 0.7898 0.00 0.10 0.04 0.00 0.00 0.00 0.86 0.00
#> TCGA.CV.7247.01 6 0.0000 0.5918 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CR.7377.01 2 0.2114 0.8408 0.00 0.84 0.00 0.00 0.00 0.00 0.16 0.00
#> TCGA.CN.5370.01 3 0.3318 0.0233 0.00 0.00 0.54 0.00 0.00 0.00 0.46 0.00
#> TCGA.CR.7401.01 7 0.3142 0.4636 0.00 0.00 0.36 0.00 0.00 0.00 0.64 0.00
#> TCGA.CV.7090.01 3 0.0000 0.8682 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CX.7219.01 3 0.2756 0.5927 0.00 0.00 0.74 0.26 0.00 0.00 0.00 0.00
#> TCGA.BA.6871.01 5 0.2864 0.6748 0.00 0.00 0.00 0.00 0.84 0.06 0.08 0.02
#> TCGA.D6.6825.01 7 0.2938 0.5714 0.00 0.00 0.30 0.00 0.00 0.00 0.70 0.00
#> TCGA.CQ.6222.01 2 0.0000 0.9474 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.6994.01 1 0.3318 -0.0180 0.54 0.00 0.00 0.00 0.00 0.46 0.00 0.00
#> TCGA.CV.6950.01 4 0.4849 0.4636 0.00 0.00 0.00 0.54 0.22 0.24 0.00 0.00
#> TCGA.CV.6935.01 1 0.2265 0.7962 0.88 0.00 0.00 0.00 0.02 0.08 0.02 0.00
#> TCGA.CV.6945.01 4 0.2534 0.5919 0.00 0.00 0.22 0.78 0.00 0.00 0.00 0.00
#> TCGA.DQ.5630.01 7 0.2114 0.8109 0.00 0.16 0.00 0.00 0.00 0.00 0.84 0.00
#> TCGA.CV.6943.01 2 0.0000 0.9474 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4733.01 2 0.0000 0.9474 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.6989.01 3 0.0808 0.8713 0.00 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.D6.6517.01 3 0.2650 0.6380 0.00 0.00 0.76 0.00 0.00 0.00 0.24 0.00
#> TCGA.CQ.6220.01 3 0.0000 0.8682 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D6.6516.01 4 0.1563 0.7410 0.00 0.00 0.00 0.90 0.10 0.00 0.00 0.00
#> TCGA.CQ.6227.01 7 0.2114 0.8109 0.00 0.16 0.00 0.00 0.00 0.00 0.84 0.00
#> TCGA.BA.6868.01 1 0.3318 -0.0829 0.54 0.00 0.00 0.00 0.00 0.46 0.00 0.00
#> TCGA.CQ.6229.01 7 0.2114 0.8109 0.00 0.16 0.00 0.00 0.00 0.00 0.84 0.00
#> TCGA.CQ.6223.01 6 0.3293 0.4610 0.00 0.00 0.00 0.04 0.22 0.74 0.00 0.00
#> TCGA.CV.A45R.01 4 0.0471 0.7781 0.00 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.CN.A49B.01 6 0.3774 0.4140 0.00 0.00 0.00 0.08 0.22 0.70 0.00 0.00
#> TCGA.BA.5152.01 3 0.1091 0.8618 0.00 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.CQ.5326.01 7 0.3299 0.2567 0.00 0.00 0.44 0.00 0.00 0.00 0.56 0.00
#> TCGA.CR.6471.01 3 0.1563 0.7964 0.00 0.00 0.90 0.10 0.00 0.00 0.00 0.00
#> TCGA.F7.A61W.01 1 0.0000 0.8754 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D6.A4ZB.01 3 0.0000 0.8682 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A45Y.01 7 0.2114 0.8109 0.00 0.16 0.00 0.00 0.00 0.00 0.84 0.00
#> TCGA.BB.A5HU.01 3 0.0471 0.8719 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.P3.A5Q6.01 4 0.2725 0.6863 0.00 0.00 0.00 0.82 0.04 0.14 0.00 0.00
#> TCGA.CX.A4AQ.01 8 0.3002 0.7351 0.00 0.00 0.00 0.02 0.12 0.00 0.04 0.82
#> TCGA.CV.A464.01 7 0.2114 0.8109 0.00 0.16 0.00 0.00 0.00 0.00 0.84 0.00
#> TCGA.QK.A652.01 7 0.2224 0.7996 0.00 0.12 0.02 0.00 0.00 0.00 0.86 0.00
#> TCGA.F7.8298.01 4 0.0808 0.7715 0.00 0.00 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.F7.8489.01 7 0.2114 0.8109 0.00 0.16 0.00 0.00 0.00 0.00 0.84 0.00
#> TCGA.F7.A50G.01 3 0.0471 0.8719 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.CQ.A4CA.01 2 0.1947 0.8582 0.00 0.86 0.00 0.00 0.00 0.00 0.14 0.00
#> TCGA.T3.A92N.01 6 0.3514 0.4382 0.34 0.00 0.00 0.00 0.02 0.64 0.00 0.00
#> TCGA.CN.A63Y.01 7 0.2114 0.8109 0.00 0.16 0.00 0.00 0.00 0.00 0.84 0.00
#> TCGA.P3.A5QE.01 8 0.0000 0.8638 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.IQ.A61G.01 1 0.0000 0.8754 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IQ.A61J.01 4 0.1341 0.7479 0.00 0.00 0.08 0.92 0.00 0.00 0.00 0.00
#> TCGA.BA.A6DG.01 2 0.0000 0.9474 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.A4CH.01 2 0.0000 0.9474 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D6.8569.01 4 0.0808 0.7652 0.00 0.00 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.BB.8601.01 1 0.1408 0.8440 0.94 0.00 0.00 0.00 0.02 0.02 0.02 0.00
#> TCGA.H7.8502.01 1 0.0000 0.8754 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F7.A61S.01 3 0.3083 0.4686 0.00 0.00 0.66 0.34 0.00 0.00 0.00 0.00
#> TCGA.D6.8568.01 3 0.1091 0.8648 0.00 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.DQ.7589.01 6 0.4041 0.5550 0.22 0.00 0.00 0.00 0.04 0.70 0.04 0.00
#> TCGA.CN.4725.01 6 0.3015 0.4951 0.32 0.00 0.00 0.00 0.00 0.68 0.00 0.00
#> TCGA.HL.7533.01 6 0.3551 0.4404 0.00 0.00 0.00 0.06 0.22 0.72 0.00 0.00
#> TCGA.CN.4729.01 3 0.0471 0.8719 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.CN.5361.01 4 0.0471 0.7781 0.00 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.CN.5359.01 2 0.1765 0.8731 0.00 0.88 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.BB.7861.01 2 0.0000 0.9474 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A7JS.01 4 0.4765 0.4845 0.00 0.00 0.00 0.56 0.22 0.22 0.00 0.00
#> TCGA.DQ.7590.01 8 0.1091 0.8280 0.00 0.00 0.06 0.00 0.00 0.00 0.00 0.94
#> TCGA.BA.4076.01 1 0.0000 0.8754 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MZ.A7D7.01 6 0.3941 0.4073 0.00 0.00 0.00 0.04 0.26 0.68 0.02 0.00
#> TCGA.BB.7872.01 7 0.2938 0.5731 0.00 0.00 0.30 0.00 0.00 0.00 0.70 0.00
#> TCGA.CN.5365.01 3 0.1765 0.7689 0.00 0.00 0.88 0.12 0.00 0.00 0.00 0.00
#> TCGA.BB.4224.01 1 0.0000 0.8754 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.A6V1.01 2 0.0000 0.9474 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7430.01 1 0.1408 0.8440 0.94 0.00 0.00 0.00 0.02 0.02 0.02 0.00
#> TCGA.UF.A7JC.01 1 0.0000 0.8754 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7568.01 2 0.2114 0.8408 0.00 0.84 0.00 0.00 0.00 0.00 0.16 0.00
#> TCGA.QK.A6IF.01 8 0.0471 0.8758 0.00 0.00 0.02 0.00 0.00 0.00 0.00 0.98
#> TCGA.CV.7429.01 3 0.0000 0.8682 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7437.01 6 0.3426 0.5668 0.22 0.00 0.00 0.00 0.02 0.74 0.02 0.00
#> TCGA.CV.A6JN.01 4 0.1341 0.7479 0.00 0.00 0.08 0.92 0.00 0.00 0.00 0.00
#> TCGA.D6.A6EK.01 3 0.0808 0.8690 0.00 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.P3.A6SX.01 6 0.0941 0.5874 0.00 0.00 0.00 0.02 0.02 0.96 0.00 0.00
#> TCGA.QK.A6II.01 4 0.0471 0.7781 0.00 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.CV.7433.01 2 0.2114 0.8408 0.00 0.84 0.00 0.00 0.00 0.00 0.16 0.00
#> TCGA.CR.7376.01 2 0.0000 0.9474 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: Node022. Child nodes: Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node02111-leaf , Node02112-leaf , Node02113-leaf , Node02114-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02124-leaf , Node02131-leaf , Node02132 , Node02133-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02231-leaf , Node02232-leaf , Node02233-leaf , Node02241-leaf , Node02242-leaf , Node02243-leaf , Node02321-leaf , Node02322-leaf , Node02323-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf , Node05114-leaf , Node05121 , Node05122-leaf , Node05123-leaf , Node05221-leaf , Node05222-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 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 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 1.000 1.000 0.5005 0.500 0.500
#> 3 3 1.000 0.980 0.991 0.3726 0.813 0.627
#> 4 4 0.925 0.742 0.887 0.0513 0.977 0.926
#> 5 5 0.933 0.788 0.930 0.0429 0.907 0.705
#> 6 6 0.909 0.699 0.859 0.0224 0.987 0.947
#> 7 7 0.846 0.706 0.886 0.0268 0.957 0.829
#> 8 8 0.887 0.633 0.887 0.0163 0.977 0.897
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
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.CN.6011.01 2 0 1 0 1
#> TCGA.CV.5979.01 2 0 1 0 1
#> TCGA.CV.5434.01 1 0 1 1 0
#> TCGA.CV.7423.01 2 0 1 0 1
#> TCGA.CN.6024.01 1 0 1 1 0
#> TCGA.CQ.5323.01 1 0 1 1 0
#> TCGA.DQ.7588.01 2 0 1 0 1
#> TCGA.CV.5440.01 1 0 1 1 0
#> TCGA.CV.7247.01 2 0 1 0 1
#> TCGA.CN.6994.01 2 0 1 0 1
#> TCGA.CV.6935.01 1 0 1 1 0
#> TCGA.BA.6868.01 2 0 1 0 1
#> TCGA.F7.A61W.01 2 0 1 0 1
#> TCGA.T3.A92N.01 1 0 1 1 0
#> TCGA.IQ.A61G.01 2 0 1 0 1
#> TCGA.BB.8601.01 1 0 1 1 0
#> TCGA.H7.8502.01 2 0 1 0 1
#> TCGA.DQ.7589.01 1 0 1 1 0
#> TCGA.CN.4725.01 2 0 1 0 1
#> TCGA.BA.4076.01 2 0 1 0 1
#> TCGA.BB.4224.01 2 0 1 0 1
#> TCGA.CV.7430.01 1 0 1 1 0
#> TCGA.UF.A7JC.01 2 0 1 0 1
#> TCGA.CV.7437.01 1 0 1 1 0
#> TCGA.P3.A6SX.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CN.6011.01 2 0.00 0.968 0 1.00 0.00
#> TCGA.CV.5979.01 3 0.00 1.000 0 0.00 1.00
#> TCGA.CV.5434.01 1 0.00 1.000 1 0.00 0.00
#> TCGA.CV.7423.01 3 0.00 1.000 0 0.00 1.00
#> TCGA.CN.6024.01 1 0.00 1.000 1 0.00 0.00
#> TCGA.CQ.5323.01 1 0.00 1.000 1 0.00 0.00
#> TCGA.DQ.7588.01 3 0.00 1.000 0 0.00 1.00
#> TCGA.CV.5440.01 1 0.00 1.000 1 0.00 0.00
#> TCGA.CV.7247.01 3 0.00 1.000 0 0.00 1.00
#> TCGA.CN.6994.01 2 0.00 0.968 0 1.00 0.00
#> TCGA.CV.6935.01 1 0.00 1.000 1 0.00 0.00
#> TCGA.BA.6868.01 2 0.00 0.968 0 1.00 0.00
#> TCGA.F7.A61W.01 3 0.00 1.000 0 0.00 1.00
#> TCGA.T3.A92N.01 1 0.00 1.000 1 0.00 0.00
#> TCGA.IQ.A61G.01 2 0.00 0.968 0 1.00 0.00
#> TCGA.BB.8601.01 1 0.00 1.000 1 0.00 0.00
#> TCGA.H7.8502.01 2 0.00 0.968 0 1.00 0.00
#> TCGA.DQ.7589.01 1 0.00 1.000 1 0.00 0.00
#> TCGA.CN.4725.01 3 0.00 1.000 0 0.00 1.00
#> TCGA.BA.4076.01 2 0.00 0.968 0 1.00 0.00
#> TCGA.BB.4224.01 3 0.00 1.000 0 0.00 1.00
#> TCGA.CV.7430.01 1 0.00 1.000 1 0.00 0.00
#> TCGA.UF.A7JC.01 2 0.00 0.968 0 1.00 0.00
#> TCGA.CV.7437.01 1 0.00 1.000 1 0.00 0.00
#> TCGA.P3.A6SX.01 2 0.48 0.718 0 0.78 0.22
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.CN.6011.01 2 0.0707 0.6339 0.00 0.98 0.00 0.02
#> TCGA.CV.5979.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.CV.5434.01 1 0.0000 0.9503 1.00 0.00 0.00 0.00
#> TCGA.CV.7423.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.CN.6024.01 1 0.0000 0.9503 1.00 0.00 0.00 0.00
#> TCGA.CQ.5323.01 1 0.0000 0.9503 1.00 0.00 0.00 0.00
#> TCGA.DQ.7588.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.CV.5440.01 1 0.4994 0.3673 0.52 0.00 0.00 0.48
#> TCGA.CV.7247.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.CN.6994.01 2 0.0000 0.6459 0.00 1.00 0.00 0.00
#> TCGA.CV.6935.01 1 0.0000 0.9503 1.00 0.00 0.00 0.00
#> TCGA.BA.6868.01 2 0.0707 0.6322 0.00 0.98 0.00 0.02
#> TCGA.F7.A61W.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.T3.A92N.01 1 0.0000 0.9503 1.00 0.00 0.00 0.00
#> TCGA.IQ.A61G.01 2 0.3801 0.4070 0.00 0.78 0.00 0.22
#> TCGA.BB.8601.01 1 0.0000 0.9503 1.00 0.00 0.00 0.00
#> TCGA.H7.8502.01 2 0.5173 -0.2745 0.00 0.66 0.02 0.32
#> TCGA.DQ.7589.01 1 0.0000 0.9503 1.00 0.00 0.00 0.00
#> TCGA.CN.4725.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.BA.4076.01 2 0.0000 0.6459 0.00 1.00 0.00 0.00
#> TCGA.BB.4224.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.CV.7430.01 1 0.0000 0.9503 1.00 0.00 0.00 0.00
#> TCGA.UF.A7JC.01 4 0.6299 0.0000 0.00 0.42 0.06 0.52
#> TCGA.CV.7437.01 1 0.0000 0.9503 1.00 0.00 0.00 0.00
#> TCGA.P3.A6SX.01 2 0.6150 -0.0629 0.00 0.58 0.36 0.06
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CN.6011.01 2 0.4398 0.6021 0.00 0.72 0.00 0.24 0.04
#> TCGA.CV.5979.01 3 0.0000 0.9129 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.5434.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7423.01 3 0.0000 0.9129 0.00 0.00 1.00 0.00 0.00
#> TCGA.CN.6024.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.5323.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.7588.01 3 0.0000 0.9129 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.5440.01 5 0.1410 0.0000 0.06 0.00 0.00 0.00 0.94
#> TCGA.CV.7247.01 3 0.0609 0.8981 0.00 0.00 0.98 0.02 0.00
#> TCGA.CN.6994.01 2 0.0000 0.7705 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.6935.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.BA.6868.01 2 0.3319 0.7426 0.00 0.82 0.00 0.16 0.02
#> TCGA.F7.A61W.01 3 0.0000 0.9129 0.00 0.00 1.00 0.00 0.00
#> TCGA.T3.A92N.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.IQ.A61G.01 2 0.3109 0.6377 0.00 0.80 0.00 0.00 0.20
#> TCGA.BB.8601.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.H7.8502.01 4 0.5156 0.3030 0.00 0.32 0.00 0.62 0.06
#> TCGA.DQ.7589.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4725.01 3 0.0000 0.9129 0.00 0.00 1.00 0.00 0.00
#> TCGA.BA.4076.01 2 0.1410 0.7862 0.00 0.94 0.00 0.06 0.00
#> TCGA.BB.4224.01 3 0.0000 0.9129 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.7430.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A7JC.01 4 0.1820 0.4131 0.00 0.02 0.02 0.94 0.02
#> TCGA.CV.7437.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00
#> TCGA.P3.A6SX.01 3 0.6302 0.0637 0.00 0.42 0.48 0.04 0.06
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.CN.6011.01 2 0.1092 0.3898 0 0.96 0.00 0.02 0.00 0.02
#> TCGA.CV.5979.01 3 0.0547 0.9140 0 0.00 0.98 0.00 0.00 0.02
#> TCGA.CV.5434.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7423.01 3 0.0000 0.9172 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.CN.6024.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.5323.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.7588.01 3 0.0000 0.9172 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.5440.01 5 0.0000 0.0000 0 0.00 0.00 0.00 1.00 0.00
#> TCGA.CV.7247.01 3 0.0000 0.9172 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.CN.6994.01 2 0.4689 0.3716 0 0.58 0.00 0.02 0.02 0.38
#> TCGA.CV.6935.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.6868.01 2 0.3756 0.4518 0 0.60 0.00 0.00 0.00 0.40
#> TCGA.F7.A61W.01 3 0.0000 0.9172 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.T3.A92N.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.IQ.A61G.01 6 0.6803 0.0000 0 0.30 0.00 0.04 0.30 0.36
#> TCGA.BB.8601.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.H7.8502.01 4 0.4282 0.0835 0 0.42 0.00 0.56 0.00 0.02
#> TCGA.DQ.7589.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4725.01 3 0.0547 0.9140 0 0.00 0.98 0.00 0.00 0.02
#> TCGA.BA.4076.01 2 0.3916 0.4916 0 0.68 0.00 0.02 0.00 0.30
#> TCGA.BB.4224.01 3 0.0547 0.9140 0 0.00 0.98 0.00 0.00 0.02
#> TCGA.CV.7430.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A7JC.01 4 0.3797 0.1019 0 0.00 0.00 0.58 0.00 0.42
#> TCGA.CV.7437.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.P3.A6SX.01 3 0.6574 0.1816 0 0.24 0.52 0.08 0.00 0.16
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.CN.6011.01 2 0.6494 0.2228 0.20 0.44 0.00 0.26 0.00 0.10 0
#> TCGA.CV.5979.01 3 0.1006 0.9180 0.02 0.00 0.96 0.02 0.00 0.00 0
#> TCGA.CV.5434.01 7 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 0.00 1
#> TCGA.CV.7423.01 3 0.1363 0.9019 0.04 0.00 0.94 0.02 0.00 0.00 0
#> TCGA.CN.6024.01 7 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 0.00 1
#> TCGA.CQ.5323.01 7 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 0.00 1
#> TCGA.DQ.7588.01 3 0.2376 0.8427 0.12 0.00 0.86 0.02 0.00 0.00 0
#> TCGA.CV.5440.01 5 0.0000 0.0000 0.00 0.00 0.00 0.00 1.00 0.00 0
#> TCGA.CV.7247.01 3 0.2804 0.8391 0.06 0.00 0.86 0.06 0.02 0.00 0
#> TCGA.CN.6994.01 2 0.2422 0.5191 0.18 0.82 0.00 0.00 0.00 0.00 0
#> TCGA.CV.6935.01 7 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 0.00 1
#> TCGA.BA.6868.01 2 0.4127 0.4699 0.36 0.60 0.00 0.04 0.00 0.00 0
#> TCGA.F7.A61W.01 3 0.0504 0.9137 0.02 0.00 0.98 0.00 0.00 0.00 0
#> TCGA.T3.A92N.01 7 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 0.00 1
#> TCGA.IQ.A61G.01 2 0.4737 0.4069 0.34 0.56 0.00 0.00 0.10 0.00 0
#> TCGA.BB.8601.01 7 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 0.00 1
#> TCGA.H7.8502.01 4 0.1928 0.0558 0.00 0.02 0.00 0.90 0.00 0.08 0
#> TCGA.DQ.7589.01 7 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 0.00 1
#> TCGA.CN.4725.01 3 0.1006 0.9180 0.02 0.00 0.96 0.02 0.00 0.00 0
#> TCGA.BA.4076.01 2 0.1433 0.5622 0.00 0.92 0.00 0.08 0.00 0.00 0
#> TCGA.BB.4224.01 3 0.1006 0.9180 0.02 0.00 0.96 0.02 0.00 0.00 0
#> TCGA.CV.7430.01 7 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 0.00 1
#> TCGA.UF.A7JC.01 6 0.0000 0.0000 0.00 0.00 0.00 0.00 0.00 1.00 0
#> TCGA.CV.7437.01 7 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 0.00 1
#> TCGA.P3.A6SX.01 4 0.7011 0.1707 0.24 0.20 0.22 0.34 0.00 0.00 0
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.CN.6011.01 8 0.6274 0.109526 0.10 0.20 0.00 0.20 0.00 0.02 0.00 0.48
#> TCGA.CV.5979.01 3 0.0000 0.855166 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5434.01 7 0.0000 0.992374 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CV.7423.01 3 0.1947 0.835665 0.14 0.00 0.86 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.6024.01 7 0.0000 0.992374 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CQ.5323.01 7 0.0000 0.992374 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DQ.7588.01 3 0.3504 0.671458 0.26 0.00 0.70 0.04 0.00 0.00 0.00 0.00
#> TCGA.CV.5440.01 5 0.0000 0.000000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.7247.01 3 0.2756 0.733234 0.26 0.00 0.74 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.6994.01 2 0.2624 0.467704 0.06 0.86 0.00 0.00 0.02 0.00 0.00 0.06
#> TCGA.CV.6935.01 7 0.0000 0.992374 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BA.6868.01 8 0.3015 0.000352 0.00 0.32 0.00 0.00 0.00 0.00 0.00 0.68
#> TCGA.F7.A61W.01 3 0.1341 0.854106 0.08 0.00 0.92 0.00 0.00 0.00 0.00 0.00
#> TCGA.T3.A92N.01 7 0.1275 0.936306 0.04 0.02 0.00 0.00 0.00 0.00 0.94 0.00
#> TCGA.IQ.A61G.01 2 0.5098 0.409841 0.14 0.66 0.00 0.02 0.10 0.00 0.00 0.08
#> TCGA.BB.8601.01 7 0.0000 0.992374 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.H7.8502.01 4 0.0808 0.000000 0.00 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.DQ.7589.01 7 0.0000 0.992374 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CN.4725.01 3 0.0000 0.855166 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.4076.01 2 0.4138 0.311149 0.08 0.72 0.00 0.04 0.00 0.00 0.00 0.16
#> TCGA.BB.4224.01 3 0.0000 0.855166 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7430.01 7 0.0000 0.992374 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.UF.A7JC.01 6 0.0000 0.000000 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.7437.01 7 0.0000 0.992374 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.P3.A6SX.01 1 0.5606 0.000000 0.58 0.02 0.16 0.20 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: Node022. Child nodes: Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node02111-leaf , Node02112-leaf , Node02113-leaf , Node02114-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02124-leaf , Node02131-leaf , Node02132 , Node02133-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02231-leaf , Node02232-leaf , Node02233-leaf , Node02241-leaf , Node02242-leaf , Node02243-leaf , Node02321-leaf , Node02322-leaf , Node02323-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf , Node05114-leaf , Node05121 , Node05122-leaf , Node05123-leaf , Node05221-leaf , Node05222-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 28 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 1.000 1.000 1.000 0.4239 0.577 0.577
#> 3 3 1.000 0.986 0.991 0.4451 0.601 0.415
#> 4 4 0.863 0.939 0.969 0.1631 0.696 0.385
#> 5 5 0.938 0.947 0.961 0.1302 0.841 0.508
#> 6 6 0.865 0.871 0.919 0.0287 0.989 0.944
#> 7 7 0.868 0.839 0.907 0.0276 0.968 0.824
#> 8 8 0.837 0.740 0.881 0.0207 0.981 0.875
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
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.CQ.5325.01 1 0 1 1 0
#> TCGA.CV.5971.01 1 0 1 1 0
#> TCGA.CN.6017.01 2 0 1 0 1
#> TCGA.BB.4217.01 2 0 1 0 1
#> TCGA.CV.7410.01 2 0 1 0 1
#> TCGA.CR.7386.01 1 0 1 1 0
#> TCGA.CR.6474.01 1 0 1 1 0
#> TCGA.CR.7377.01 1 0 1 1 0
#> TCGA.CQ.6222.01 1 0 1 1 0
#> TCGA.DQ.5630.01 1 0 1 1 0
#> TCGA.CV.6943.01 1 0 1 1 0
#> TCGA.CN.4733.01 2 0 1 0 1
#> TCGA.CQ.6227.01 1 0 1 1 0
#> TCGA.CQ.6229.01 1 0 1 1 0
#> TCGA.CV.A45Y.01 1 0 1 1 0
#> TCGA.CV.A464.01 1 0 1 1 0
#> TCGA.QK.A652.01 1 0 1 1 0
#> TCGA.F7.8489.01 1 0 1 1 0
#> TCGA.CQ.A4CA.01 1 0 1 1 0
#> TCGA.CN.A63Y.01 2 0 1 0 1
#> TCGA.BA.A6DG.01 1 0 1 1 0
#> TCGA.CQ.A4CH.01 2 0 1 0 1
#> TCGA.CN.5359.01 1 0 1 1 0
#> TCGA.BB.7861.01 2 0 1 0 1
#> TCGA.CN.A6V1.01 2 0 1 0 1
#> TCGA.CV.7568.01 1 0 1 1 0
#> TCGA.CV.7433.01 1 0 1 1 0
#> TCGA.CR.7376.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CQ.5325.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.CV.5971.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.CN.6017.01 2 0.0892 0.981 0.00 0.98 0.02
#> TCGA.BB.4217.01 2 0.0892 0.981 0.00 0.98 0.02
#> TCGA.CV.7410.01 2 0.0892 0.981 0.00 0.98 0.02
#> TCGA.CR.7386.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.CR.6474.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.CR.7377.01 1 0.0892 0.985 0.98 0.02 0.00
#> TCGA.CQ.6222.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.DQ.5630.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.CV.6943.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.CN.4733.01 2 0.0892 0.981 0.00 0.98 0.02
#> TCGA.CQ.6227.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.CQ.6229.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.CV.A45Y.01 1 0.0892 0.985 0.98 0.02 0.00
#> TCGA.CV.A464.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.QK.A652.01 1 0.0000 0.989 1.00 0.00 0.00
#> TCGA.F7.8489.01 2 0.1529 0.944 0.04 0.96 0.00
#> TCGA.CQ.A4CA.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.CN.A63Y.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.BA.A6DG.01 1 0.0892 0.985 0.98 0.02 0.00
#> TCGA.CQ.A4CH.01 2 0.0892 0.981 0.00 0.98 0.02
#> TCGA.CN.5359.01 2 0.0000 0.986 0.00 1.00 0.00
#> TCGA.BB.7861.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.CN.A6V1.01 3 0.0000 1.000 0.00 0.00 1.00
#> TCGA.CV.7568.01 1 0.0892 0.985 0.98 0.02 0.00
#> TCGA.CV.7433.01 1 0.0892 0.985 0.98 0.02 0.00
#> TCGA.CR.7376.01 2 0.0000 0.986 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.CQ.5325.01 2 0.0000 0.917 0.00 1.00 0 0.00
#> TCGA.CV.5971.01 2 0.3172 0.773 0.00 0.84 0 0.16
#> TCGA.CN.6017.01 4 0.0000 1.000 0.00 0.00 0 1.00
#> TCGA.BB.4217.01 4 0.0000 1.000 0.00 0.00 0 1.00
#> TCGA.CV.7410.01 4 0.0000 1.000 0.00 0.00 0 1.00
#> TCGA.CR.7386.01 1 0.0000 1.000 1.00 0.00 0 0.00
#> TCGA.CR.6474.01 1 0.0000 1.000 1.00 0.00 0 0.00
#> TCGA.CR.7377.01 2 0.3975 0.737 0.24 0.76 0 0.00
#> TCGA.CQ.6222.01 2 0.0000 0.917 0.00 1.00 0 0.00
#> TCGA.DQ.5630.01 1 0.0000 1.000 1.00 0.00 0 0.00
#> TCGA.CV.6943.01 2 0.0000 0.917 0.00 1.00 0 0.00
#> TCGA.CN.4733.01 4 0.0000 1.000 0.00 0.00 0 1.00
#> TCGA.CQ.6227.01 1 0.0000 1.000 1.00 0.00 0 0.00
#> TCGA.CQ.6229.01 1 0.0000 1.000 1.00 0.00 0 0.00
#> TCGA.CV.A45Y.01 2 0.0000 0.917 0.00 1.00 0 0.00
#> TCGA.CV.A464.01 1 0.0000 1.000 1.00 0.00 0 0.00
#> TCGA.QK.A652.01 1 0.0000 1.000 1.00 0.00 0 0.00
#> TCGA.F7.8489.01 2 0.0000 0.917 0.00 1.00 0 0.00
#> TCGA.CQ.A4CA.01 2 0.0000 0.917 0.00 1.00 0 0.00
#> TCGA.CN.A63Y.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.BA.A6DG.01 2 0.0707 0.909 0.02 0.98 0 0.00
#> TCGA.CQ.A4CH.01 4 0.0000 1.000 0.00 0.00 0 1.00
#> TCGA.CN.5359.01 2 0.0000 0.917 0.00 1.00 0 0.00
#> TCGA.BB.7861.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.CN.A6V1.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.CV.7568.01 2 0.3801 0.762 0.22 0.78 0 0.00
#> TCGA.CV.7433.01 2 0.3801 0.762 0.22 0.78 0 0.00
#> TCGA.CR.7376.01 2 0.0000 0.917 0.00 1.00 0 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CQ.5325.01 2 0.000 0.950 0.00 1.00 0 0.00 0.00
#> TCGA.CV.5971.01 2 0.201 0.896 0.00 0.92 0 0.06 0.02
#> TCGA.CN.6017.01 4 0.000 0.992 0.00 0.00 0 1.00 0.00
#> TCGA.BB.4217.01 4 0.000 0.992 0.00 0.00 0 1.00 0.00
#> TCGA.CV.7410.01 4 0.000 0.992 0.00 0.00 0 1.00 0.00
#> TCGA.CR.7386.01 1 0.000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.CR.6474.01 1 0.000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.CR.7377.01 5 0.208 0.911 0.04 0.04 0 0.00 0.92
#> TCGA.CQ.6222.01 2 0.000 0.950 0.00 1.00 0 0.00 0.00
#> TCGA.DQ.5630.01 1 0.000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.CV.6943.01 2 0.000 0.950 0.00 1.00 0 0.00 0.00
#> TCGA.CN.4733.01 4 0.000 0.992 0.00 0.00 0 1.00 0.00
#> TCGA.CQ.6227.01 1 0.000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.CQ.6229.01 5 0.273 0.843 0.16 0.00 0 0.00 0.84
#> TCGA.CV.A45Y.01 5 0.228 0.885 0.00 0.12 0 0.00 0.88
#> TCGA.CV.A464.01 1 0.000 1.000 1.00 0.00 0 0.00 0.00
#> TCGA.QK.A652.01 5 0.293 0.824 0.18 0.00 0 0.00 0.82
#> TCGA.F7.8489.01 2 0.273 0.802 0.00 0.84 0 0.00 0.16
#> TCGA.CQ.A4CA.01 2 0.104 0.934 0.00 0.96 0 0.00 0.04
#> TCGA.CN.A63Y.01 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.BA.A6DG.01 5 0.141 0.918 0.00 0.06 0 0.00 0.94
#> TCGA.CQ.A4CH.01 4 0.104 0.967 0.00 0.00 0 0.96 0.04
#> TCGA.CN.5359.01 2 0.104 0.930 0.00 0.96 0 0.00 0.04
#> TCGA.BB.7861.01 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.CN.A6V1.01 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.CV.7568.01 5 0.141 0.918 0.00 0.06 0 0.00 0.94
#> TCGA.CV.7433.01 5 0.141 0.918 0.00 0.06 0 0.00 0.94
#> TCGA.CR.7376.01 2 0.000 0.950 0.00 1.00 0 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.CQ.5325.01 2 0.1556 0.883 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.CV.5971.01 2 0.2794 0.799 0.00 0.86 0.00 0.06 0.00 0.08
#> TCGA.CN.6017.01 4 0.0000 0.975 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BB.4217.01 4 0.0937 0.924 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.CV.7410.01 4 0.0000 0.975 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CR.7386.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.6474.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7377.01 5 0.3111 0.859 0.02 0.02 0.00 0.00 0.84 0.12
#> TCGA.CQ.6222.01 2 0.0000 0.885 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.5630.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6943.01 2 0.1556 0.883 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.CN.4733.01 4 0.0000 0.975 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CQ.6227.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.6229.01 5 0.3544 0.843 0.08 0.00 0.00 0.00 0.80 0.12
#> TCGA.CV.A45Y.01 5 0.3829 0.819 0.00 0.06 0.00 0.00 0.76 0.18
#> TCGA.CV.A464.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QK.A652.01 5 0.3787 0.830 0.10 0.00 0.00 0.00 0.78 0.12
#> TCGA.F7.8489.01 2 0.4377 0.706 0.00 0.72 0.00 0.00 0.12 0.16
#> TCGA.CQ.A4CA.01 2 0.2454 0.822 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.CN.A63Y.01 3 0.0547 0.984 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.BA.A6DG.01 5 0.2350 0.797 0.00 0.10 0.00 0.00 0.88 0.02
#> TCGA.CQ.A4CH.01 6 0.3797 0.000 0.00 0.00 0.00 0.42 0.00 0.58
#> TCGA.CN.5359.01 2 0.2190 0.871 0.00 0.90 0.00 0.00 0.04 0.06
#> TCGA.BB.7861.01 3 0.0000 0.992 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CN.A6V1.01 3 0.0000 0.992 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.7568.01 5 0.1480 0.840 0.00 0.02 0.00 0.00 0.94 0.04
#> TCGA.CV.7433.01 5 0.1480 0.840 0.00 0.02 0.00 0.00 0.94 0.04
#> TCGA.CR.7376.01 2 0.0000 0.885 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.CQ.5325.01 2 0.0504 0.850 0.00 0.98 0.0 0.00 0.02 0.00 0.00
#> TCGA.CV.5971.01 2 0.2569 0.751 0.00 0.84 0.0 0.02 0.00 0.14 0.00
#> TCGA.CN.6017.01 4 0.0000 0.985 0.00 0.00 0.0 1.00 0.00 0.00 0.00
#> TCGA.BB.4217.01 4 0.0863 0.954 0.00 0.00 0.0 0.96 0.00 0.04 0.00
#> TCGA.CV.7410.01 4 0.0000 0.985 0.00 0.00 0.0 1.00 0.00 0.00 0.00
#> TCGA.CR.7386.01 1 0.0000 1.000 1.00 0.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.CR.6474.01 1 0.0000 1.000 1.00 0.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.CR.7377.01 5 0.3139 0.872 0.00 0.00 0.0 0.00 0.70 0.00 0.30
#> TCGA.CQ.6222.01 2 0.0000 0.851 0.00 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.DQ.5630.01 1 0.0000 1.000 1.00 0.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.CV.6943.01 2 0.1363 0.842 0.00 0.94 0.0 0.00 0.04 0.02 0.00
#> TCGA.CN.4733.01 4 0.0000 0.985 0.00 0.00 0.0 1.00 0.00 0.00 0.00
#> TCGA.CQ.6227.01 1 0.0000 1.000 1.00 0.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.CQ.6229.01 5 0.3927 0.878 0.04 0.00 0.0 0.00 0.66 0.00 0.30
#> TCGA.CV.A45Y.01 5 0.3517 0.816 0.00 0.00 0.0 0.00 0.70 0.02 0.28
#> TCGA.CV.A464.01 1 0.0000 1.000 1.00 0.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.QK.A652.01 5 0.4003 0.868 0.04 0.00 0.0 0.00 0.64 0.00 0.32
#> TCGA.F7.8489.01 2 0.5304 0.502 0.00 0.60 0.0 0.00 0.24 0.04 0.12
#> TCGA.CQ.A4CA.01 2 0.3228 0.770 0.00 0.80 0.0 0.00 0.16 0.02 0.02
#> TCGA.CN.A63Y.01 3 0.1671 0.910 0.00 0.00 0.9 0.00 0.10 0.00 0.00
#> TCGA.BA.A6DG.01 7 0.4667 0.537 0.00 0.14 0.0 0.00 0.12 0.04 0.70
#> TCGA.CQ.A4CH.01 6 0.1671 0.000 0.00 0.00 0.0 0.10 0.00 0.90 0.00
#> TCGA.CN.5359.01 2 0.2864 0.787 0.00 0.84 0.0 0.00 0.02 0.02 0.12
#> TCGA.BB.7861.01 3 0.0000 0.956 0.00 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.CN.A6V1.01 3 0.0000 0.956 0.00 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.CV.7568.01 7 0.0000 0.798 0.00 0.00 0.0 0.00 0.00 0.00 1.00
#> TCGA.CV.7433.01 7 0.0000 0.798 0.00 0.00 0.0 0.00 0.00 0.00 1.00
#> TCGA.CR.7376.01 2 0.0000 0.851 0.00 1.00 0.0 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.CQ.5325.01 2 0.1887 0.718 0.00 0.90 0.00 0.00 0.04 0.00 0.00 0.06
#> TCGA.CV.5971.01 2 0.3720 0.549 0.00 0.80 0.00 0.06 0.04 0.04 0.00 0.06
#> TCGA.CN.6017.01 4 0.0000 0.942 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BB.4217.01 4 0.2407 0.842 0.00 0.00 0.00 0.86 0.06 0.08 0.00 0.00
#> TCGA.CV.7410.01 4 0.0471 0.932 0.00 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.CR.7386.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.6474.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7377.01 5 0.3015 0.828 0.00 0.00 0.00 0.00 0.68 0.00 0.32 0.00
#> TCGA.CQ.6222.01 2 0.0000 0.724 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.5630.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6943.01 2 0.2862 0.679 0.00 0.82 0.00 0.00 0.08 0.00 0.00 0.10
#> TCGA.CN.4733.01 4 0.0000 0.942 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.6227.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.6229.01 5 0.4050 0.823 0.06 0.00 0.00 0.00 0.60 0.00 0.34 0.00
#> TCGA.CV.A45Y.01 5 0.2981 0.747 0.00 0.00 0.00 0.00 0.76 0.00 0.22 0.02
#> TCGA.CV.A464.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QK.A652.01 5 0.4559 0.821 0.08 0.00 0.00 0.00 0.60 0.00 0.30 0.02
#> TCGA.F7.8489.01 2 0.5541 0.150 0.00 0.44 0.00 0.00 0.38 0.00 0.06 0.12
#> TCGA.CQ.A4CA.01 8 0.2534 0.000 0.00 0.22 0.00 0.00 0.00 0.00 0.00 0.78
#> TCGA.CN.A63Y.01 3 0.3523 0.784 0.00 0.00 0.78 0.00 0.10 0.02 0.00 0.10
#> TCGA.BA.A6DG.01 7 0.4593 0.506 0.00 0.10 0.00 0.00 0.20 0.00 0.66 0.04
#> TCGA.CQ.A4CH.01 6 0.1563 0.000 0.00 0.00 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.CN.5359.01 2 0.3002 0.649 0.00 0.82 0.00 0.00 0.04 0.00 0.12 0.02
#> TCGA.BB.7861.01 3 0.0000 0.891 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.A6V1.01 3 0.0471 0.887 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CV.7568.01 7 0.0000 0.796 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CV.7433.01 7 0.0000 0.796 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CR.7376.01 2 0.0471 0.717 0.00 0.98 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: Node022. Child nodes: Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node02111-leaf , Node02112-leaf , Node02113-leaf , Node02114-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02124-leaf , Node02131-leaf , Node02132 , Node02133-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02231-leaf , Node02232-leaf , Node02233-leaf , Node02241-leaf , Node02242-leaf , Node02243-leaf , Node02321-leaf , Node02322-leaf , Node02323-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf , Node05114-leaf , Node05121 , Node05122-leaf , Node05123-leaf , Node05221-leaf , Node05222-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0223"]
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 28 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 0.984 0.992 0.4576 0.548 0.548
#> 3 3 1.000 0.989 0.994 0.4749 0.778 0.594
#> 4 4 0.837 0.930 0.950 0.1192 0.899 0.701
#> 5 5 0.775 0.717 0.873 0.0433 0.960 0.844
#> 6 6 0.769 0.714 0.879 0.0441 0.926 0.682
#> 7 7 0.806 0.767 0.867 0.0351 0.923 0.608
#> 8 8 0.815 0.564 0.821 0.0232 0.984 0.891
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.CN.6016.01 2 0.000 0.988 0.00 1.00
#> TCGA.CN.6020.01 2 0.529 0.871 0.12 0.88
#> TCGA.CN.6023.01 2 0.000 0.988 0.00 1.00
#> TCGA.CV.7254.01 2 0.000 0.988 0.00 1.00
#> TCGA.CN.5370.01 1 0.000 1.000 1.00 0.00
#> TCGA.CR.7401.01 2 0.000 0.988 0.00 1.00
#> TCGA.CV.7090.01 1 0.000 1.000 1.00 0.00
#> TCGA.CX.7219.01 2 0.000 0.988 0.00 1.00
#> TCGA.D6.6825.01 2 0.469 0.894 0.10 0.90
#> TCGA.CV.6945.01 1 0.000 1.000 1.00 0.00
#> TCGA.CN.6989.01 2 0.000 0.988 0.00 1.00
#> TCGA.D6.6517.01 1 0.000 1.000 1.00 0.00
#> TCGA.CQ.6220.01 1 0.000 1.000 1.00 0.00
#> TCGA.BA.5152.01 1 0.000 1.000 1.00 0.00
#> TCGA.CQ.5326.01 2 0.000 0.988 0.00 1.00
#> TCGA.CR.6471.01 2 0.000 0.988 0.00 1.00
#> TCGA.D6.A4ZB.01 2 0.000 0.988 0.00 1.00
#> TCGA.BB.A5HU.01 1 0.000 1.000 1.00 0.00
#> TCGA.F7.A50G.01 2 0.000 0.988 0.00 1.00
#> TCGA.F7.A61S.01 2 0.000 0.988 0.00 1.00
#> TCGA.D6.8568.01 2 0.000 0.988 0.00 1.00
#> TCGA.CN.4729.01 2 0.000 0.988 0.00 1.00
#> TCGA.DQ.7590.01 2 0.000 0.988 0.00 1.00
#> TCGA.BB.7872.01 2 0.000 0.988 0.00 1.00
#> TCGA.CN.5365.01 1 0.000 1.000 1.00 0.00
#> TCGA.QK.A6IF.01 2 0.000 0.988 0.00 1.00
#> TCGA.CV.7429.01 1 0.000 1.000 1.00 0.00
#> TCGA.D6.A6EK.01 2 0.000 0.988 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CN.6016.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.CN.6020.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.CN.6023.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.CV.7254.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.CN.5370.01 1 0.000 0.989 1.00 0.00 0.00
#> TCGA.CR.7401.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.CV.7090.01 1 0.000 0.989 1.00 0.00 0.00
#> TCGA.CX.7219.01 2 0.153 0.960 0.00 0.96 0.04
#> TCGA.D6.6825.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.CV.6945.01 1 0.153 0.961 0.96 0.04 0.00
#> TCGA.CN.6989.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.D6.6517.01 1 0.153 0.961 0.96 0.04 0.00
#> TCGA.CQ.6220.01 1 0.000 0.989 1.00 0.00 0.00
#> TCGA.BA.5152.01 1 0.000 0.989 1.00 0.00 0.00
#> TCGA.CQ.5326.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.CR.6471.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.D6.A4ZB.01 2 0.153 0.960 0.00 0.96 0.04
#> TCGA.BB.A5HU.01 1 0.000 0.989 1.00 0.00 0.00
#> TCGA.F7.A50G.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.F7.A61S.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.D6.8568.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.CN.4729.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.DQ.7590.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.BB.7872.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.CN.5365.01 1 0.000 0.989 1.00 0.00 0.00
#> TCGA.QK.A6IF.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.CV.7429.01 1 0.000 0.989 1.00 0.00 0.00
#> TCGA.D6.A6EK.01 2 0.000 0.992 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.CN.6016.01 3 0.382 0.867 0.00 0.12 0.84 0.04
#> TCGA.CN.6020.01 4 0.121 0.879 0.00 0.04 0.00 0.96
#> TCGA.CN.6023.01 3 0.382 0.867 0.00 0.12 0.84 0.04
#> TCGA.CV.7254.01 3 0.000 0.940 0.00 0.00 1.00 0.00
#> TCGA.CN.5370.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CR.7401.01 2 0.000 0.915 0.00 1.00 0.00 0.00
#> TCGA.CV.7090.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CX.7219.01 2 0.121 0.893 0.00 0.96 0.00 0.04
#> TCGA.D6.6825.01 4 0.121 0.879 0.00 0.04 0.00 0.96
#> TCGA.CV.6945.01 4 0.292 0.868 0.14 0.00 0.00 0.86
#> TCGA.CN.6989.01 3 0.121 0.930 0.00 0.00 0.96 0.04
#> TCGA.D6.6517.01 4 0.292 0.868 0.14 0.00 0.00 0.86
#> TCGA.CQ.6220.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BA.5152.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CQ.5326.01 2 0.265 0.917 0.00 0.88 0.00 0.12
#> TCGA.CR.6471.01 3 0.000 0.940 0.00 0.00 1.00 0.00
#> TCGA.D6.A4ZB.01 2 0.121 0.893 0.00 0.96 0.00 0.04
#> TCGA.BB.A5HU.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.F7.A50G.01 2 0.265 0.917 0.00 0.88 0.00 0.12
#> TCGA.F7.A61S.01 2 0.265 0.917 0.00 0.88 0.00 0.12
#> TCGA.D6.8568.01 2 0.265 0.917 0.00 0.88 0.00 0.12
#> TCGA.CN.4729.01 2 0.000 0.915 0.00 1.00 0.00 0.00
#> TCGA.DQ.7590.01 3 0.000 0.940 0.00 0.00 1.00 0.00
#> TCGA.BB.7872.01 2 0.000 0.915 0.00 1.00 0.00 0.00
#> TCGA.CN.5365.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.QK.A6IF.01 3 0.000 0.940 0.00 0.00 1.00 0.00
#> TCGA.CV.7429.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.D6.A6EK.01 2 0.265 0.917 0.00 0.88 0.00 0.12
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CN.6016.01 3 0.646 0.478 0.00 0.24 0.50 0.26 0.00
#> TCGA.CN.6020.01 4 0.356 0.676 0.00 0.00 0.00 0.74 0.26
#> TCGA.CN.6023.01 3 0.646 0.478 0.00 0.24 0.50 0.26 0.00
#> TCGA.CV.7254.01 3 0.000 0.781 0.00 0.00 1.00 0.00 0.00
#> TCGA.CN.5370.01 1 0.141 0.962 0.94 0.00 0.00 0.00 0.06
#> TCGA.CR.7401.01 2 0.000 0.731 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.7090.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.CX.7219.01 2 0.356 0.550 0.00 0.74 0.00 0.26 0.00
#> TCGA.D6.6825.01 4 0.468 0.704 0.00 0.14 0.00 0.74 0.12
#> TCGA.CV.6945.01 5 0.141 0.000 0.00 0.00 0.00 0.06 0.94
#> TCGA.CN.6989.01 3 0.228 0.740 0.00 0.00 0.88 0.12 0.00
#> TCGA.D6.6517.01 4 0.356 0.676 0.00 0.00 0.00 0.74 0.26
#> TCGA.CQ.6220.01 1 0.141 0.962 0.94 0.00 0.00 0.00 0.06
#> TCGA.BA.5152.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.5326.01 2 0.342 0.654 0.00 0.76 0.00 0.24 0.00
#> TCGA.CR.6471.01 3 0.000 0.781 0.00 0.00 1.00 0.00 0.00
#> TCGA.D6.A4ZB.01 2 0.356 0.550 0.00 0.74 0.00 0.26 0.00
#> TCGA.BB.A5HU.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.F7.A50G.01 4 0.389 0.521 0.00 0.32 0.00 0.68 0.00
#> TCGA.F7.A61S.01 2 0.342 0.654 0.00 0.76 0.00 0.24 0.00
#> TCGA.D6.8568.01 2 0.342 0.654 0.00 0.76 0.00 0.24 0.00
#> TCGA.CN.4729.01 2 0.000 0.731 0.00 1.00 0.00 0.00 0.00
#> TCGA.DQ.7590.01 3 0.000 0.781 0.00 0.00 1.00 0.00 0.00
#> TCGA.BB.7872.01 2 0.000 0.731 0.00 1.00 0.00 0.00 0.00
#> TCGA.CN.5365.01 1 0.141 0.962 0.94 0.00 0.00 0.00 0.06
#> TCGA.QK.A6IF.01 3 0.000 0.781 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.7429.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.D6.A6EK.01 2 0.342 0.654 0.00 0.76 0.00 0.24 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.CN.6016.01 6 0.4503 0.603 0.00 0.08 0.24 0.00 0.00 0.68
#> TCGA.CN.6020.01 4 0.0937 0.799 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.CN.6023.01 6 0.2454 0.610 0.00 0.00 0.16 0.00 0.00 0.84
#> TCGA.CV.7254.01 3 0.0000 0.923 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CN.5370.01 1 0.3873 0.830 0.78 0.00 0.00 0.04 0.02 0.16
#> TCGA.CR.7401.01 2 0.2454 0.636 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.CV.7090.01 1 0.0000 0.935 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CX.7219.01 6 0.3851 0.119 0.00 0.46 0.00 0.00 0.00 0.54
#> TCGA.D6.6825.01 4 0.0937 0.799 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.CV.6945.01 5 0.0547 0.000 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.CN.6989.01 3 0.3198 0.636 0.00 0.00 0.74 0.00 0.00 0.26
#> TCGA.D6.6517.01 4 0.1807 0.714 0.00 0.00 0.00 0.92 0.02 0.06
#> TCGA.CQ.6220.01 1 0.2094 0.913 0.90 0.00 0.00 0.00 0.02 0.08
#> TCGA.BA.5152.01 1 0.0000 0.935 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.5326.01 2 0.1267 0.765 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.CR.6471.01 3 0.0000 0.923 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D6.A4ZB.01 6 0.2454 0.621 0.00 0.16 0.00 0.00 0.00 0.84
#> TCGA.BB.A5HU.01 1 0.0000 0.935 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F7.A50G.01 4 0.3647 0.509 0.00 0.36 0.00 0.64 0.00 0.00
#> TCGA.F7.A61S.01 2 0.1267 0.765 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.D6.8568.01 2 0.1267 0.765 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.CN.4729.01 2 0.3499 0.404 0.00 0.68 0.00 0.00 0.00 0.32
#> TCGA.DQ.7590.01 3 0.0000 0.923 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BB.7872.01 2 0.3499 0.404 0.00 0.68 0.00 0.00 0.00 0.32
#> TCGA.CN.5365.01 1 0.1807 0.921 0.92 0.00 0.00 0.00 0.02 0.06
#> TCGA.QK.A6IF.01 3 0.0000 0.923 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.7429.01 1 0.0937 0.924 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.D6.A6EK.01 2 0.1556 0.749 0.00 0.92 0.00 0.08 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.CN.6016.01 7 0.0504 0.362 0.00 0.00 0.02 0.00 0 0.00 0.98
#> TCGA.CN.6020.01 4 0.0504 0.876 0.00 0.02 0.00 0.98 0 0.00 0.00
#> TCGA.CN.6023.01 6 0.3558 1.000 0.00 0.00 0.00 0.00 0 0.52 0.48
#> TCGA.CV.7254.01 3 0.0504 0.866 0.00 0.00 0.98 0.00 0 0.00 0.02
#> TCGA.CN.5370.01 1 0.3755 0.662 0.64 0.00 0.00 0.02 0 0.34 0.00
#> TCGA.CR.7401.01 7 0.3459 0.656 0.00 0.40 0.00 0.00 0 0.00 0.60
#> TCGA.CV.7090.01 1 0.0000 0.902 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.CX.7219.01 7 0.2259 0.684 0.00 0.16 0.00 0.00 0 0.00 0.84
#> TCGA.D6.6825.01 4 0.0504 0.876 0.00 0.02 0.00 0.98 0 0.00 0.00
#> TCGA.CV.6945.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.CN.6989.01 3 0.5007 0.360 0.00 0.00 0.56 0.00 0 0.28 0.16
#> TCGA.D6.6517.01 4 0.2572 0.736 0.00 0.00 0.00 0.80 0 0.20 0.00
#> TCGA.CQ.6220.01 1 0.2259 0.849 0.84 0.00 0.00 0.00 0 0.16 0.00
#> TCGA.BA.5152.01 1 0.0000 0.902 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.CQ.5326.01 2 0.1671 0.817 0.00 0.90 0.00 0.00 0 0.10 0.00
#> TCGA.CR.6471.01 3 0.0000 0.874 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.D6.A4ZB.01 6 0.3558 1.000 0.00 0.00 0.00 0.00 0 0.52 0.48
#> TCGA.BB.A5HU.01 1 0.0000 0.902 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.F7.A50G.01 2 0.3221 0.489 0.00 0.68 0.00 0.32 0 0.00 0.00
#> TCGA.F7.A61S.01 2 0.0000 0.866 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.D6.8568.01 2 0.0000 0.866 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.CN.4729.01 7 0.3047 0.772 0.00 0.28 0.00 0.00 0 0.00 0.72
#> TCGA.DQ.7590.01 3 0.0000 0.874 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.BB.7872.01 7 0.3047 0.772 0.00 0.28 0.00 0.00 0 0.00 0.72
#> TCGA.CN.5365.01 1 0.1671 0.879 0.90 0.00 0.00 0.00 0 0.10 0.00
#> TCGA.QK.A6IF.01 3 0.0000 0.874 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.CV.7429.01 1 0.0504 0.898 0.98 0.00 0.00 0.00 0 0.02 0.00
#> TCGA.D6.A6EK.01 2 0.0000 0.866 0.00 1.00 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.CN.6016.01 7 0.2265 0.3145 0.00 0.00 0.02 0.00 0 0.08 0.88 0.02
#> TCGA.CN.6020.01 4 0.0000 0.7930 0.00 0.00 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CN.6023.01 6 0.3291 0.9565 0.00 0.00 0.02 0.00 0 0.70 0.28 0.00
#> TCGA.CV.7254.01 3 0.1947 0.7511 0.00 0.00 0.86 0.00 0 0.00 0.00 0.14
#> TCGA.CN.5370.01 8 0.2938 0.0000 0.30 0.00 0.00 0.00 0 0.00 0.00 0.70
#> TCGA.CR.7401.01 7 0.3272 0.6321 0.00 0.42 0.00 0.00 0 0.00 0.58 0.00
#> TCGA.CV.7090.01 1 0.0000 0.6818 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.CX.7219.01 7 0.3128 0.5326 0.00 0.10 0.00 0.00 0 0.04 0.82 0.04
#> TCGA.D6.6825.01 4 0.0000 0.7930 0.00 0.00 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CV.6945.01 5 0.0000 0.0000 0.00 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.CN.6989.01 3 0.6297 0.0698 0.00 0.00 0.40 0.00 0 0.28 0.16 0.16
#> TCGA.D6.6517.01 4 0.5009 0.5333 0.00 0.00 0.00 0.62 0 0.12 0.06 0.20
#> TCGA.CQ.6220.01 1 0.3318 -0.3282 0.54 0.00 0.00 0.00 0 0.00 0.00 0.46
#> TCGA.BA.5152.01 1 0.0000 0.6818 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.CQ.5326.01 2 0.3102 0.7017 0.00 0.82 0.00 0.00 0 0.08 0.02 0.08
#> TCGA.CR.6471.01 3 0.0000 0.8104 0.00 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.D6.A4ZB.01 6 0.3291 0.9564 0.00 0.02 0.00 0.00 0 0.70 0.28 0.00
#> TCGA.BB.A5HU.01 1 0.0000 0.6818 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.F7.A50G.01 2 0.3690 0.2809 0.00 0.56 0.00 0.42 0 0.02 0.00 0.00
#> TCGA.F7.A61S.01 2 0.0000 0.7844 0.00 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.D6.8568.01 2 0.0471 0.7776 0.00 0.98 0.00 0.00 0 0.00 0.02 0.00
#> TCGA.CN.4729.01 7 0.3193 0.6872 0.00 0.38 0.00 0.00 0 0.00 0.62 0.00
#> TCGA.DQ.7590.01 3 0.0000 0.8104 0.00 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.BB.7872.01 7 0.3083 0.7069 0.00 0.34 0.00 0.00 0 0.00 0.66 0.00
#> TCGA.CN.5365.01 1 0.3142 0.0302 0.64 0.00 0.00 0.00 0 0.00 0.00 0.36
#> TCGA.QK.A6IF.01 3 0.0000 0.8104 0.00 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CV.7429.01 1 0.2864 0.5572 0.84 0.00 0.00 0.00 0 0.08 0.02 0.06
#> TCGA.D6.A6EK.01 2 0.0941 0.7813 0.00 0.96 0.00 0.02 0 0.02 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: Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node02111-leaf , Node02112-leaf , Node02113-leaf , Node02114-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02124-leaf , Node02131-leaf , Node02132 , Node02133-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02231-leaf , Node02232-leaf , Node02233-leaf , Node02241-leaf , Node02242-leaf , Node02243-leaf , Node02321-leaf , Node02322-leaf , Node02323-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf , Node05114-leaf , Node05121 , Node05122-leaf , Node05123-leaf , Node05221-leaf , Node05222-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0224"]
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 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 0.4432 0.557 0.557
#> 3 3 1.000 0.985 0.993 0.5598 0.751 0.553
#> 4 4 0.857 0.787 0.908 0.0765 0.976 0.923
#> 5 5 0.818 0.629 0.852 0.0457 0.953 0.833
#> 6 6 0.748 0.559 0.756 0.0443 0.960 0.844
#> 7 7 0.762 0.573 0.792 0.0383 0.897 0.574
#> 8 8 0.738 0.588 0.723 0.0174 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] 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.HD.7753.01 2 0 1 0 1
#> TCGA.CV.7415.01 2 0 1 0 1
#> TCGA.DQ.7592.01 2 0 1 0 1
#> TCGA.CQ.6221.01 1 0 1 1 0
#> TCGA.CV.5970.01 2 0 1 0 1
#> TCGA.CV.7235.01 2 0 1 0 1
#> TCGA.CV.5439.01 2 0 1 0 1
#> TCGA.CV.7100.01 2 0 1 0 1
#> TCGA.CV.6950.01 2 0 1 0 1
#> TCGA.D6.6516.01 1 0 1 1 0
#> TCGA.CQ.6223.01 2 0 1 0 1
#> TCGA.CV.A45R.01 2 0 1 0 1
#> TCGA.CN.A49B.01 1 0 1 1 0
#> TCGA.P3.A5Q6.01 1 0 1 1 0
#> TCGA.F7.8298.01 2 0 1 0 1
#> TCGA.IQ.A61J.01 1 0 1 1 0
#> TCGA.D6.8569.01 2 0 1 0 1
#> TCGA.HL.7533.01 2 0 1 0 1
#> TCGA.CN.5361.01 1 0 1 1 0
#> TCGA.UF.A7JS.01 2 0 1 0 1
#> TCGA.MZ.A7D7.01 2 0 1 0 1
#> TCGA.CV.A6JN.01 2 0 1 0 1
#> TCGA.QK.A6II.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.HD.7753.01 2 0.0 1.000 0.00 1 0.00
#> TCGA.CV.7415.01 2 0.0 1.000 0.00 1 0.00
#> TCGA.DQ.7592.01 2 0.0 1.000 0.00 1 0.00
#> TCGA.CQ.6221.01 1 0.4 0.810 0.84 0 0.16
#> TCGA.CV.5970.01 3 0.0 1.000 0.00 0 1.00
#> TCGA.CV.7235.01 3 0.0 1.000 0.00 0 1.00
#> TCGA.CV.5439.01 2 0.0 1.000 0.00 1 0.00
#> TCGA.CV.7100.01 3 0.0 1.000 0.00 0 1.00
#> TCGA.CV.6950.01 2 0.0 1.000 0.00 1 0.00
#> TCGA.D6.6516.01 1 0.0 0.973 1.00 0 0.00
#> TCGA.CQ.6223.01 3 0.0 1.000 0.00 0 1.00
#> TCGA.CV.A45R.01 2 0.0 1.000 0.00 1 0.00
#> TCGA.CN.A49B.01 1 0.0 0.973 1.00 0 0.00
#> TCGA.P3.A5Q6.01 1 0.0 0.973 1.00 0 0.00
#> TCGA.F7.8298.01 2 0.0 1.000 0.00 1 0.00
#> TCGA.IQ.A61J.01 1 0.0 0.973 1.00 0 0.00
#> TCGA.D6.8569.01 3 0.0 1.000 0.00 0 1.00
#> TCGA.HL.7533.01 3 0.0 1.000 0.00 0 1.00
#> TCGA.CN.5361.01 1 0.0 0.973 1.00 0 0.00
#> TCGA.UF.A7JS.01 3 0.0 1.000 0.00 0 1.00
#> TCGA.MZ.A7D7.01 2 0.0 1.000 0.00 1 0.00
#> TCGA.CV.A6JN.01 2 0.0 1.000 0.00 1 0.00
#> TCGA.QK.A6II.01 1 0.0 0.973 1.00 0 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.HD.7753.01 2 0.2011 0.929 0.00 0.92 0.00 0.08
#> TCGA.CV.7415.01 2 0.0707 0.951 0.00 0.98 0.00 0.02
#> TCGA.DQ.7592.01 2 0.0707 0.951 0.00 0.98 0.00 0.02
#> TCGA.CQ.6221.01 4 0.4332 0.000 0.16 0.00 0.04 0.80
#> TCGA.CV.5970.01 3 0.0000 0.737 0.00 0.00 1.00 0.00
#> TCGA.CV.7235.01 3 0.4713 0.354 0.00 0.00 0.64 0.36
#> TCGA.CV.5439.01 2 0.1211 0.952 0.00 0.96 0.00 0.04
#> TCGA.CV.7100.01 3 0.4855 0.363 0.00 0.00 0.60 0.40
#> TCGA.CV.6950.01 2 0.2011 0.929 0.00 0.92 0.00 0.08
#> TCGA.D6.6516.01 1 0.0000 0.949 1.00 0.00 0.00 0.00
#> TCGA.CQ.6223.01 3 0.2706 0.691 0.00 0.02 0.90 0.08
#> TCGA.CV.A45R.01 2 0.1211 0.952 0.00 0.96 0.00 0.04
#> TCGA.CN.A49B.01 1 0.0000 0.949 1.00 0.00 0.00 0.00
#> TCGA.P3.A5Q6.01 1 0.0707 0.947 0.98 0.00 0.00 0.02
#> TCGA.F7.8298.01 2 0.1637 0.947 0.00 0.94 0.00 0.06
#> TCGA.IQ.A61J.01 1 0.2345 0.907 0.90 0.00 0.00 0.10
#> TCGA.D6.8569.01 3 0.0000 0.737 0.00 0.00 1.00 0.00
#> TCGA.HL.7533.01 3 0.4855 0.363 0.00 0.00 0.60 0.40
#> TCGA.CN.5361.01 1 0.2345 0.907 0.90 0.00 0.00 0.10
#> TCGA.UF.A7JS.01 3 0.0000 0.737 0.00 0.00 1.00 0.00
#> TCGA.MZ.A7D7.01 2 0.1211 0.952 0.00 0.96 0.00 0.04
#> TCGA.CV.A6JN.01 2 0.1637 0.944 0.00 0.94 0.00 0.06
#> TCGA.QK.A6II.01 1 0.0000 0.949 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.HD.7753.01 2 0.1648 0.8542 0.00 0.94 0.04 0.00 0.02
#> TCGA.CV.7415.01 2 0.2732 0.8888 0.00 0.84 0.16 0.00 0.00
#> TCGA.DQ.7592.01 2 0.0609 0.8712 0.00 0.98 0.00 0.00 0.02
#> TCGA.CQ.6221.01 4 0.1216 0.0000 0.02 0.00 0.00 0.96 0.02
#> TCGA.CV.5970.01 3 0.4287 -0.0651 0.00 0.00 0.54 0.00 0.46
#> TCGA.CV.7235.01 5 0.2280 0.4616 0.00 0.00 0.00 0.12 0.88
#> TCGA.CV.5439.01 2 0.2732 0.8897 0.00 0.84 0.16 0.00 0.00
#> TCGA.CV.7100.01 3 0.4613 0.2719 0.00 0.00 0.62 0.36 0.02
#> TCGA.CV.6950.01 2 0.1648 0.8542 0.00 0.94 0.04 0.00 0.02
#> TCGA.D6.6516.01 1 0.0000 0.9357 1.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.6223.01 5 0.2280 0.4798 0.00 0.00 0.12 0.00 0.88
#> TCGA.CV.A45R.01 2 0.2732 0.8897 0.00 0.84 0.16 0.00 0.00
#> TCGA.CN.A49B.01 1 0.0000 0.9357 1.00 0.00 0.00 0.00 0.00
#> TCGA.P3.A5Q6.01 1 0.0609 0.9328 0.98 0.00 0.00 0.02 0.00
#> TCGA.F7.8298.01 2 0.3109 0.8805 0.00 0.80 0.20 0.00 0.00
#> TCGA.IQ.A61J.01 1 0.2732 0.8599 0.84 0.00 0.00 0.16 0.00
#> TCGA.D6.8569.01 3 0.4287 -0.0651 0.00 0.00 0.54 0.00 0.46
#> TCGA.HL.7533.01 3 0.4540 0.2995 0.00 0.00 0.64 0.34 0.02
#> TCGA.CN.5361.01 1 0.2516 0.8760 0.86 0.00 0.00 0.14 0.00
#> TCGA.UF.A7JS.01 5 0.4767 -0.2663 0.00 0.00 0.42 0.02 0.56
#> TCGA.MZ.A7D7.01 2 0.3109 0.8805 0.00 0.80 0.20 0.00 0.00
#> TCGA.CV.A6JN.01 2 0.1216 0.8727 0.00 0.96 0.02 0.00 0.02
#> TCGA.QK.A6II.01 1 0.0000 0.9357 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.HD.7753.01 2 0.2474 0.6781 0.00 0.88 0.00 0.04 0.00 0.08
#> TCGA.CV.7415.01 2 0.5364 0.7023 0.00 0.56 0.00 0.00 0.14 0.30
#> TCGA.DQ.7592.01 2 0.0000 0.7265 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.6221.01 4 0.2094 0.0000 0.02 0.00 0.08 0.90 0.00 0.00
#> TCGA.CV.5970.01 5 0.6035 -0.2883 0.00 0.00 0.40 0.02 0.44 0.14
#> TCGA.CV.7235.01 5 0.5259 -0.0775 0.00 0.00 0.00 0.16 0.60 0.24
#> TCGA.CV.5439.01 2 0.3198 0.7564 0.00 0.74 0.00 0.00 0.00 0.26
#> TCGA.CV.7100.01 3 0.1092 0.9524 0.00 0.00 0.96 0.02 0.00 0.02
#> TCGA.CV.6950.01 2 0.2474 0.6781 0.00 0.88 0.00 0.04 0.00 0.08
#> TCGA.D6.6516.01 1 0.0000 0.8880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.6223.01 5 0.0547 0.0146 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.CV.A45R.01 2 0.3198 0.7564 0.00 0.74 0.00 0.00 0.00 0.26
#> TCGA.CN.A49B.01 1 0.0000 0.8880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P3.A5Q6.01 1 0.2474 0.8764 0.88 0.00 0.00 0.04 0.00 0.08
#> TCGA.F7.8298.01 2 0.5481 0.6905 0.00 0.52 0.00 0.00 0.14 0.34
#> TCGA.IQ.A61J.01 1 0.3928 0.8087 0.76 0.00 0.00 0.16 0.00 0.08
#> TCGA.D6.8569.01 5 0.6035 -0.2883 0.00 0.00 0.40 0.02 0.44 0.14
#> TCGA.HL.7533.01 3 0.0000 0.9520 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CN.5361.01 1 0.3544 0.8417 0.80 0.00 0.00 0.12 0.00 0.08
#> TCGA.UF.A7JS.01 6 0.6831 0.0000 0.00 0.00 0.20 0.06 0.34 0.40
#> TCGA.MZ.A7D7.01 2 0.3578 0.7345 0.00 0.66 0.00 0.00 0.00 0.34
#> TCGA.CV.A6JN.01 2 0.3318 0.6868 0.00 0.82 0.00 0.02 0.14 0.02
#> TCGA.QK.A6II.01 1 0.0000 0.8880 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.HD.7753.01 6 0.000 0.735 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CV.7415.01 2 0.472 0.672 0.00 0.60 0.00 0.00 0.06 0.32 0.02
#> TCGA.DQ.7592.01 6 0.398 0.365 0.00 0.28 0.00 0.00 0.02 0.68 0.02
#> TCGA.CQ.6221.01 4 0.000 0.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.5970.01 5 0.322 0.527 0.00 0.00 0.32 0.00 0.68 0.00 0.00
#> TCGA.CV.7235.01 7 0.202 0.000 0.00 0.00 0.00 0.04 0.06 0.00 0.90
#> TCGA.CV.5439.01 2 0.427 0.684 0.00 0.60 0.00 0.00 0.02 0.36 0.02
#> TCGA.CV.7100.01 3 0.117 0.947 0.00 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.CV.6950.01 6 0.000 0.735 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D6.6516.01 1 0.000 0.757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.6223.01 5 0.428 -0.274 0.00 0.04 0.00 0.00 0.50 0.00 0.46
#> TCGA.CV.A45R.01 2 0.427 0.684 0.00 0.60 0.00 0.00 0.02 0.36 0.02
#> TCGA.CN.A49B.01 1 0.000 0.757 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P3.A5Q6.01 1 0.433 0.725 0.72 0.18 0.00 0.04 0.06 0.00 0.00
#> TCGA.F7.8298.01 2 0.448 0.727 0.00 0.66 0.00 0.00 0.06 0.26 0.02
#> TCGA.IQ.A61J.01 1 0.578 0.632 0.56 0.18 0.00 0.20 0.06 0.00 0.00
#> TCGA.D6.8569.01 5 0.322 0.527 0.00 0.00 0.32 0.00 0.68 0.00 0.00
#> TCGA.HL.7533.01 3 0.000 0.947 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.5361.01 1 0.566 0.652 0.58 0.18 0.00 0.18 0.06 0.00 0.00
#> TCGA.UF.A7JS.01 5 0.481 0.251 0.00 0.02 0.10 0.00 0.64 0.00 0.24
#> TCGA.MZ.A7D7.01 2 0.283 0.754 0.00 0.76 0.00 0.00 0.00 0.24 0.00
#> TCGA.CV.A6JN.01 6 0.291 0.611 0.00 0.18 0.00 0.00 0.02 0.80 0.00
#> TCGA.QK.A6II.01 1 0.000 0.757 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.HD.7753.01 6 0.2981 0.7636 0.00 0.22 0.00 0.00 0.00 0.76 0.02 0.00
#> TCGA.CV.7415.01 2 0.3078 0.7066 0.00 0.82 0.00 0.02 0.00 0.06 0.10 0.00
#> TCGA.DQ.7592.01 6 0.4008 0.4538 0.00 0.48 0.00 0.00 0.00 0.48 0.04 0.00
#> TCGA.CQ.6221.01 4 0.0808 0.0000 0.04 0.00 0.00 0.96 0.00 0.00 0.00 0.00
#> TCGA.CV.5970.01 5 0.2114 0.5950 0.00 0.00 0.16 0.00 0.84 0.00 0.00 0.00
#> TCGA.CV.7235.01 8 0.0808 0.0000 0.00 0.00 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.CV.5439.01 2 0.2132 0.7633 0.00 0.88 0.00 0.00 0.00 0.08 0.04 0.00
#> TCGA.CV.7100.01 3 0.0471 0.8812 0.00 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.CV.6950.01 6 0.2534 0.7708 0.00 0.22 0.00 0.00 0.00 0.78 0.00 0.00
#> TCGA.D6.6516.01 1 0.3299 0.6744 0.56 0.00 0.00 0.00 0.00 0.00 0.44 0.00
#> TCGA.CQ.6223.01 5 0.5758 0.0431 0.00 0.00 0.00 0.02 0.42 0.02 0.36 0.18
#> TCGA.CV.A45R.01 2 0.2132 0.7633 0.00 0.88 0.00 0.00 0.00 0.08 0.04 0.00
#> TCGA.CN.A49B.01 1 0.3299 0.6744 0.56 0.00 0.00 0.00 0.00 0.00 0.44 0.00
#> TCGA.P3.A5Q6.01 1 0.0000 0.6364 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F7.8298.01 2 0.2025 0.7563 0.00 0.88 0.00 0.02 0.00 0.00 0.10 0.00
#> TCGA.IQ.A61J.01 1 0.1341 0.5955 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.D6.8569.01 5 0.2114 0.5950 0.00 0.00 0.16 0.00 0.84 0.00 0.00 0.00
#> TCGA.HL.7533.01 3 0.2348 0.8809 0.00 0.00 0.88 0.00 0.00 0.06 0.02 0.04
#> TCGA.CN.5361.01 1 0.2132 0.5926 0.88 0.00 0.00 0.08 0.00 0.04 0.00 0.00
#> TCGA.UF.A7JS.01 5 0.5133 0.2126 0.00 0.00 0.00 0.02 0.66 0.10 0.10 0.12
#> TCGA.MZ.A7D7.01 2 0.0000 0.7960 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A6JN.01 6 0.4415 0.6895 0.00 0.32 0.00 0.02 0.00 0.60 0.06 0.00
#> TCGA.QK.A6II.01 1 0.3299 0.6744 0.56 0.00 0.00 0.00 0.00 0.00 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: Node02. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0121 , Node0122 , Node0211 , Node0212 , Node0213 , Node0221 , Node0222 , Node0223 , Node0224 , Node0225-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0511 , Node0512 , Node0521-leaf , Node0522 , Node0523-leaf , Node0524-leaf .
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 69 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 0.999 1.000 0.2526 0.749 0.749
#> 3 3 1.000 1.000 1.000 1.3941 0.647 0.528
#> 4 4 1.000 0.978 0.991 0.1806 0.808 0.561
#> 5 5 0.957 0.890 0.957 0.0250 0.980 0.930
#> 6 6 0.814 0.796 0.841 0.0354 0.980 0.931
#> 7 7 0.774 0.641 0.859 0.0258 0.980 0.928
#> 8 8 0.750 0.614 0.833 0.0220 0.975 0.904
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.CV.6436.01 2 0.000 1.00 0.00 1.00
#> TCGA.CV.6441.01 2 0.141 0.98 0.02 0.98
#> TCGA.IQ.7630.01 2 0.000 1.00 0.00 1.00
#> TCGA.CV.5977.01 2 0.000 1.00 0.00 1.00
#> TCGA.CQ.5324.01 2 0.000 1.00 0.00 1.00
#> TCGA.CR.7365.01 2 0.000 1.00 0.00 1.00
#> TCGA.CV.7089.01 2 0.000 1.00 0.00 1.00
#> TCGA.CV.5976.01 2 0.000 1.00 0.00 1.00
#> TCGA.CN.6995.01 2 0.000 1.00 0.00 1.00
#> TCGA.CQ.5334.01 2 0.000 1.00 0.00 1.00
#> TCGA.CV.5435.01 1 0.000 1.00 1.00 0.00
#> TCGA.CR.7373.01 2 0.000 1.00 0.00 1.00
#> TCGA.CN.6998.01 2 0.000 1.00 0.00 1.00
#> TCGA.CR.7380.01 2 0.000 1.00 0.00 1.00
#> TCGA.CV.7183.01 2 0.000 1.00 0.00 1.00
#> TCGA.HD.7229.01 2 0.000 1.00 0.00 1.00
#> TCGA.CV.7097.01 2 0.000 1.00 0.00 1.00
#> TCGA.CR.7367.01 2 0.000 1.00 0.00 1.00
#> TCGA.BA.5558.01 2 0.000 1.00 0.00 1.00
#> TCGA.CV.7243.01 2 0.000 1.00 0.00 1.00
#> TCGA.CR.6480.01 1 0.000 1.00 1.00 0.00
#> TCGA.CN.A49C.01 1 0.000 1.00 1.00 0.00
#> TCGA.CR.6491.01 2 0.000 1.00 0.00 1.00
#> TCGA.CR.6473.01 1 0.000 1.00 1.00 0.00
#> TCGA.CV.A45O.01 2 0.000 1.00 0.00 1.00
#> TCGA.CR.6493.01 2 0.000 1.00 0.00 1.00
#> TCGA.BA.6873.01 2 0.000 1.00 0.00 1.00
#> TCGA.CR.6467.01 1 0.000 1.00 1.00 0.00
#> TCGA.CV.6959.01 2 0.000 1.00 0.00 1.00
#> TCGA.CQ.6224.01 2 0.000 1.00 0.00 1.00
#> TCGA.CV.6938.01 2 0.000 1.00 0.00 1.00
#> TCGA.BA.6872.01 2 0.000 1.00 0.00 1.00
#> TCGA.CQ.A4C6.01 2 0.000 1.00 0.00 1.00
#> TCGA.HD.A633.01 2 0.000 1.00 0.00 1.00
#> TCGA.CQ.A4C7.01 2 0.000 1.00 0.00 1.00
#> TCGA.CQ.A4CD.01 2 0.000 1.00 0.00 1.00
#> TCGA.F7.A620.01 2 0.000 1.00 0.00 1.00
#> TCGA.QK.A8Z9.01 2 0.000 1.00 0.00 1.00
#> TCGA.BB.A5HY.01 2 0.000 1.00 0.00 1.00
#> TCGA.CQ.5333.01 2 0.000 1.00 0.00 1.00
#> TCGA.BA.A6DJ.01 2 0.000 1.00 0.00 1.00
#> TCGA.CQ.A4CB.01 2 0.000 1.00 0.00 1.00
#> TCGA.IQ.A61I.01 1 0.000 1.00 1.00 0.00
#> TCGA.D6.A4Z9.01 2 0.000 1.00 0.00 1.00
#> TCGA.H7.8501.01 2 0.000 1.00 0.00 1.00
#> TCGA.CN.A642.01 2 0.000 1.00 0.00 1.00
#> TCGA.P3.A6T2.01 2 0.000 1.00 0.00 1.00
#> TCGA.CN.A6V7.01 1 0.000 1.00 1.00 0.00
#> TCGA.CN.4734.01 2 0.000 1.00 0.00 1.00
#> TCGA.BA.4075.01 2 0.000 1.00 0.00 1.00
#> TCGA.CN.4726.01 2 0.000 1.00 0.00 1.00
#> TCGA.CN.5355.01 2 0.000 1.00 0.00 1.00
#> TCGA.BA.5151.01 2 0.000 1.00 0.00 1.00
#> TCGA.CN.5363.01 2 0.000 1.00 0.00 1.00
#> TCGA.T2.A6X2.01 2 0.000 1.00 0.00 1.00
#> TCGA.CN.4741.01 1 0.000 1.00 1.00 0.00
#> TCGA.CV.A6JO.01 2 0.000 1.00 0.00 1.00
#> TCGA.BB.7866.01 1 0.000 1.00 1.00 0.00
#> TCGA.CN.5366.01 2 0.000 1.00 0.00 1.00
#> TCGA.QK.A6V9.01 1 0.000 1.00 1.00 0.00
#> TCGA.CV.A6JZ.01 2 0.000 1.00 0.00 1.00
#> TCGA.HD.A6I0.01 2 0.000 1.00 0.00 1.00
#> TCGA.CV.A6JT.01 2 0.000 1.00 0.00 1.00
#> TCGA.D6.A6EN.01 2 0.000 1.00 0.00 1.00
#> TCGA.CV.7434.01 2 0.000 1.00 0.00 1.00
#> TCGA.HD.7832.01 2 0.000 1.00 0.00 1.00
#> TCGA.P3.A6T7.01 2 0.000 1.00 0.00 1.00
#> TCGA.CR.7382.01 2 0.000 1.00 0.00 1.00
#> TCGA.T2.A6WZ.01 2 0.000 1.00 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CV.6436.01 2 0 1 0 1 0
#> TCGA.CV.6441.01 2 0 1 0 1 0
#> TCGA.IQ.7630.01 3 0 1 0 0 1
#> TCGA.CV.5977.01 3 0 1 0 0 1
#> TCGA.CQ.5324.01 3 0 1 0 0 1
#> TCGA.CR.7365.01 3 0 1 0 0 1
#> TCGA.CV.7089.01 2 0 1 0 1 0
#> TCGA.CV.5976.01 2 0 1 0 1 0
#> TCGA.CN.6995.01 2 0 1 0 1 0
#> TCGA.CQ.5334.01 2 0 1 0 1 0
#> TCGA.CV.5435.01 1 0 1 1 0 0
#> TCGA.CR.7373.01 3 0 1 0 0 1
#> TCGA.CN.6998.01 3 0 1 0 0 1
#> TCGA.CR.7380.01 3 0 1 0 0 1
#> TCGA.CV.7183.01 3 0 1 0 0 1
#> TCGA.HD.7229.01 2 0 1 0 1 0
#> TCGA.CV.7097.01 2 0 1 0 1 0
#> TCGA.CR.7367.01 2 0 1 0 1 0
#> TCGA.BA.5558.01 3 0 1 0 0 1
#> TCGA.CV.7243.01 3 0 1 0 0 1
#> TCGA.CR.6480.01 1 0 1 1 0 0
#> TCGA.CN.A49C.01 1 0 1 1 0 0
#> TCGA.CR.6491.01 2 0 1 0 1 0
#> TCGA.CR.6473.01 1 0 1 1 0 0
#> TCGA.CV.A45O.01 2 0 1 0 1 0
#> TCGA.CR.6493.01 3 0 1 0 0 1
#> TCGA.BA.6873.01 3 0 1 0 0 1
#> TCGA.CR.6467.01 1 0 1 1 0 0
#> TCGA.CV.6959.01 3 0 1 0 0 1
#> TCGA.CQ.6224.01 2 0 1 0 1 0
#> TCGA.CV.6938.01 2 0 1 0 1 0
#> TCGA.BA.6872.01 3 0 1 0 0 1
#> TCGA.CQ.A4C6.01 2 0 1 0 1 0
#> TCGA.HD.A633.01 3 0 1 0 0 1
#> TCGA.CQ.A4C7.01 2 0 1 0 1 0
#> TCGA.CQ.A4CD.01 2 0 1 0 1 0
#> TCGA.F7.A620.01 2 0 1 0 1 0
#> TCGA.QK.A8Z9.01 2 0 1 0 1 0
#> TCGA.BB.A5HY.01 2 0 1 0 1 0
#> TCGA.CQ.5333.01 2 0 1 0 1 0
#> TCGA.BA.A6DJ.01 2 0 1 0 1 0
#> TCGA.CQ.A4CB.01 2 0 1 0 1 0
#> TCGA.IQ.A61I.01 1 0 1 1 0 0
#> TCGA.D6.A4Z9.01 2 0 1 0 1 0
#> TCGA.H7.8501.01 2 0 1 0 1 0
#> TCGA.CN.A642.01 3 0 1 0 0 1
#> TCGA.P3.A6T2.01 3 0 1 0 0 1
#> TCGA.CN.A6V7.01 1 0 1 1 0 0
#> TCGA.CN.4734.01 2 0 1 0 1 0
#> TCGA.BA.4075.01 3 0 1 0 0 1
#> TCGA.CN.4726.01 3 0 1 0 0 1
#> TCGA.CN.5355.01 2 0 1 0 1 0
#> TCGA.BA.5151.01 2 0 1 0 1 0
#> TCGA.CN.5363.01 2 0 1 0 1 0
#> TCGA.T2.A6X2.01 3 0 1 0 0 1
#> TCGA.CN.4741.01 1 0 1 1 0 0
#> TCGA.CV.A6JO.01 2 0 1 0 1 0
#> TCGA.BB.7866.01 1 0 1 1 0 0
#> TCGA.CN.5366.01 2 0 1 0 1 0
#> TCGA.QK.A6V9.01 1 0 1 1 0 0
#> TCGA.CV.A6JZ.01 2 0 1 0 1 0
#> TCGA.HD.A6I0.01 3 0 1 0 0 1
#> TCGA.CV.A6JT.01 3 0 1 0 0 1
#> TCGA.D6.A6EN.01 3 0 1 0 0 1
#> TCGA.CV.7434.01 2 0 1 0 1 0
#> TCGA.HD.7832.01 2 0 1 0 1 0
#> TCGA.P3.A6T7.01 2 0 1 0 1 0
#> TCGA.CR.7382.01 2 0 1 0 1 0
#> TCGA.T2.A6WZ.01 2 0 1 0 1 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.CV.6436.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.CV.6441.01 4 0.000 1.000 0 0.00 0.00 1.00
#> TCGA.IQ.7630.01 3 0.000 1.000 0 0.00 1.00 0.00
#> TCGA.CV.5977.01 3 0.000 1.000 0 0.00 1.00 0.00
#> TCGA.CQ.5324.01 3 0.000 1.000 0 0.00 1.00 0.00
#> TCGA.CR.7365.01 3 0.000 1.000 0 0.00 1.00 0.00
#> TCGA.CV.7089.01 4 0.000 1.000 0 0.00 0.00 1.00
#> TCGA.CV.5976.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.CN.6995.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.CQ.5334.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.CV.5435.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.CR.7373.01 3 0.000 1.000 0 0.00 1.00 0.00
#> TCGA.CN.6998.01 3 0.000 1.000 0 0.00 1.00 0.00
#> TCGA.CR.7380.01 3 0.000 1.000 0 0.00 1.00 0.00
#> TCGA.CV.7183.01 3 0.000 1.000 0 0.00 1.00 0.00
#> TCGA.HD.7229.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.CV.7097.01 4 0.000 1.000 0 0.00 0.00 1.00
#> TCGA.CR.7367.01 4 0.000 1.000 0 0.00 0.00 1.00
#> TCGA.BA.5558.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.CV.7243.01 3 0.000 1.000 0 0.00 1.00 0.00
#> TCGA.CR.6480.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.CN.A49C.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.CR.6491.01 4 0.000 1.000 0 0.00 0.00 1.00
#> TCGA.CR.6473.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.CV.A45O.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.CR.6493.01 3 0.000 1.000 0 0.00 1.00 0.00
#> TCGA.BA.6873.01 2 0.398 0.696 0 0.76 0.24 0.00
#> TCGA.CR.6467.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.CV.6959.01 3 0.000 1.000 0 0.00 1.00 0.00
#> TCGA.CQ.6224.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.CV.6938.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.BA.6872.01 3 0.000 1.000 0 0.00 1.00 0.00
#> TCGA.CQ.A4C6.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.HD.A633.01 3 0.000 1.000 0 0.00 1.00 0.00
#> TCGA.CQ.A4C7.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.CQ.A4CD.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.F7.A620.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.QK.A8Z9.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.BB.A5HY.01 4 0.000 1.000 0 0.00 0.00 1.00
#> TCGA.CQ.5333.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.BA.A6DJ.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.CQ.A4CB.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.IQ.A61I.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.D6.A4Z9.01 4 0.000 1.000 0 0.00 0.00 1.00
#> TCGA.H7.8501.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.CN.A642.01 3 0.000 1.000 0 0.00 1.00 0.00
#> TCGA.P3.A6T2.01 3 0.000 1.000 0 0.00 1.00 0.00
#> TCGA.CN.A6V7.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.CN.4734.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.BA.4075.01 3 0.000 1.000 0 0.00 1.00 0.00
#> TCGA.CN.4726.01 2 0.121 0.938 0 0.96 0.04 0.00
#> TCGA.CN.5355.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.BA.5151.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.CN.5363.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.T2.A6X2.01 3 0.000 1.000 0 0.00 1.00 0.00
#> TCGA.CN.4741.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.CV.A6JO.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.BB.7866.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.CN.5366.01 4 0.000 1.000 0 0.00 0.00 1.00
#> TCGA.QK.A6V9.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.CV.A6JZ.01 2 0.164 0.920 0 0.94 0.00 0.06
#> TCGA.HD.A6I0.01 3 0.000 1.000 0 0.00 1.00 0.00
#> TCGA.CV.A6JT.01 3 0.000 1.000 0 0.00 1.00 0.00
#> TCGA.D6.A6EN.01 2 0.441 0.591 0 0.70 0.30 0.00
#> TCGA.CV.7434.01 4 0.000 1.000 0 0.00 0.00 1.00
#> TCGA.HD.7832.01 4 0.000 1.000 0 0.00 0.00 1.00
#> TCGA.P3.A6T7.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.CR.7382.01 2 0.000 0.975 0 1.00 0.00 0.00
#> TCGA.T2.A6WZ.01 4 0.000 1.000 0 0.00 0.00 1.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CV.6436.01 2 0.0609 0.9191 0 0.98 0.00 0.00 0.02
#> TCGA.CV.6441.01 5 0.2280 0.0000 0 0.00 0.00 0.12 0.88
#> TCGA.IQ.7630.01 3 0.0000 0.9817 0 0.00 1.00 0.00 0.00
#> TCGA.CV.5977.01 3 0.0609 0.9760 0 0.00 0.98 0.00 0.02
#> TCGA.CQ.5324.01 3 0.0000 0.9817 0 0.00 1.00 0.00 0.00
#> TCGA.CR.7365.01 3 0.1410 0.9565 0 0.00 0.94 0.00 0.06
#> TCGA.CV.7089.01 4 0.1043 0.8771 0 0.00 0.00 0.96 0.04
#> TCGA.CV.5976.01 2 0.1216 0.9069 0 0.96 0.00 0.02 0.02
#> TCGA.CN.6995.01 2 0.0000 0.9194 0 1.00 0.00 0.00 0.00
#> TCGA.CQ.5334.01 2 0.0000 0.9194 0 1.00 0.00 0.00 0.00
#> TCGA.CV.5435.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00
#> TCGA.CR.7373.01 3 0.0000 0.9817 0 0.00 1.00 0.00 0.00
#> TCGA.CN.6998.01 3 0.0000 0.9817 0 0.00 1.00 0.00 0.00
#> TCGA.CR.7380.01 3 0.0000 0.9817 0 0.00 1.00 0.00 0.00
#> TCGA.CV.7183.01 3 0.0000 0.9817 0 0.00 1.00 0.00 0.00
#> TCGA.HD.7229.01 2 0.1043 0.9042 0 0.96 0.00 0.04 0.00
#> TCGA.CV.7097.01 4 0.0609 0.8859 0 0.00 0.00 0.98 0.02
#> TCGA.CR.7367.01 4 0.0609 0.8736 0 0.02 0.00 0.98 0.00
#> TCGA.BA.5558.01 2 0.2012 0.8822 0 0.92 0.06 0.00 0.02
#> TCGA.CV.7243.01 3 0.0000 0.9817 0 0.00 1.00 0.00 0.00
#> TCGA.CR.6480.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00
#> TCGA.CN.A49C.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00
#> TCGA.CR.6491.01 4 0.1043 0.8610 0 0.00 0.00 0.96 0.04
#> TCGA.CR.6473.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00
#> TCGA.CV.A45O.01 2 0.1043 0.9149 0 0.96 0.00 0.00 0.04
#> TCGA.CR.6493.01 3 0.0609 0.9760 0 0.00 0.98 0.00 0.02
#> TCGA.BA.6873.01 2 0.4252 0.5536 0 0.70 0.28 0.00 0.02
#> TCGA.CR.6467.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00
#> TCGA.CV.6959.01 3 0.0000 0.9817 0 0.00 1.00 0.00 0.00
#> TCGA.CQ.6224.01 2 0.0609 0.9150 0 0.98 0.00 0.00 0.02
#> TCGA.CV.6938.01 2 0.1043 0.9149 0 0.96 0.00 0.00 0.04
#> TCGA.BA.6872.01 3 0.1410 0.9565 0 0.00 0.94 0.00 0.06
#> TCGA.CQ.A4C6.01 2 0.0609 0.9191 0 0.98 0.00 0.00 0.02
#> TCGA.HD.A633.01 3 0.0000 0.9817 0 0.00 1.00 0.00 0.00
#> TCGA.CQ.A4C7.01 2 0.0609 0.9150 0 0.98 0.00 0.00 0.02
#> TCGA.CQ.A4CD.01 2 0.0000 0.9194 0 1.00 0.00 0.00 0.00
#> TCGA.F7.A620.01 2 0.1648 0.9047 0 0.94 0.00 0.02 0.04
#> TCGA.QK.A8Z9.01 2 0.0609 0.9150 0 0.98 0.00 0.00 0.02
#> TCGA.BB.A5HY.01 4 0.0609 0.8813 0 0.00 0.00 0.98 0.02
#> TCGA.CQ.5333.01 2 0.1043 0.9149 0 0.96 0.00 0.00 0.04
#> TCGA.BA.A6DJ.01 2 0.1216 0.9069 0 0.96 0.00 0.02 0.02
#> TCGA.CQ.A4CB.01 2 0.1043 0.9149 0 0.96 0.00 0.00 0.04
#> TCGA.IQ.A61I.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00
#> TCGA.D6.A4Z9.01 4 0.0000 0.8877 0 0.00 0.00 1.00 0.00
#> TCGA.H7.8501.01 2 0.0000 0.9194 0 1.00 0.00 0.00 0.00
#> TCGA.CN.A642.01 3 0.0609 0.9760 0 0.00 0.98 0.00 0.02
#> TCGA.P3.A6T2.01 3 0.1410 0.9565 0 0.00 0.94 0.00 0.06
#> TCGA.CN.A6V7.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00
#> TCGA.CN.4734.01 2 0.0609 0.9150 0 0.98 0.00 0.00 0.02
#> TCGA.BA.4075.01 3 0.0609 0.9760 0 0.00 0.98 0.00 0.02
#> TCGA.CN.4726.01 2 0.3513 0.7170 0 0.80 0.18 0.00 0.02
#> TCGA.CN.5355.01 2 0.0609 0.9191 0 0.98 0.00 0.00 0.02
#> TCGA.BA.5151.01 2 0.0609 0.9191 0 0.98 0.00 0.00 0.02
#> TCGA.CN.5363.01 2 0.0000 0.9194 0 1.00 0.00 0.00 0.00
#> TCGA.T2.A6X2.01 3 0.1648 0.9430 0 0.02 0.94 0.00 0.04
#> TCGA.CN.4741.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00
#> TCGA.CV.A6JO.01 2 0.1043 0.9149 0 0.96 0.00 0.00 0.04
#> TCGA.BB.7866.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00
#> TCGA.CN.5366.01 4 0.0609 0.8859 0 0.00 0.00 0.98 0.02
#> TCGA.QK.A6V9.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00
#> TCGA.CV.A6JZ.01 4 0.5048 0.1764 0 0.38 0.00 0.58 0.04
#> TCGA.HD.A6I0.01 3 0.0000 0.9817 0 0.00 1.00 0.00 0.00
#> TCGA.CV.A6JT.01 3 0.0609 0.9714 0 0.00 0.98 0.00 0.02
#> TCGA.D6.A6EN.01 2 0.4829 0.0907 0 0.50 0.48 0.00 0.02
#> TCGA.CV.7434.01 4 0.0000 0.8877 0 0.00 0.00 1.00 0.00
#> TCGA.HD.7832.01 4 0.0609 0.8832 0 0.00 0.00 0.98 0.02
#> TCGA.P3.A6T7.01 2 0.3274 0.6749 0 0.78 0.00 0.22 0.00
#> TCGA.CR.7382.01 2 0.1043 0.9149 0 0.96 0.00 0.00 0.04
#> TCGA.T2.A6WZ.01 4 0.1410 0.8610 0 0.00 0.00 0.94 0.06
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.CV.6436.01 2 0.0000 0.867 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6441.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.IQ.7630.01 3 0.0000 0.883 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.5977.01 3 0.1267 0.870 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.CQ.5324.01 3 0.0000 0.883 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CR.7365.01 3 0.3076 0.749 0.24 0.00 0.76 0.00 0.00 0.00
#> TCGA.CV.7089.01 4 0.0937 0.811 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.CV.5976.01 2 0.3499 0.699 0.32 0.68 0.00 0.00 0.00 0.00
#> TCGA.CN.6995.01 2 0.1480 0.864 0.04 0.94 0.02 0.00 0.00 0.00
#> TCGA.CQ.5334.01 2 0.1556 0.858 0.08 0.92 0.00 0.00 0.00 0.00
#> TCGA.CV.5435.01 6 0.3258 0.821 0.10 0.00 0.00 0.02 0.04 0.84
#> TCGA.CR.7373.01 3 0.0000 0.883 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CN.6998.01 3 0.1267 0.870 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.CR.7380.01 3 0.0000 0.883 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.7183.01 3 0.0000 0.883 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HD.7229.01 2 0.4475 0.691 0.20 0.70 0.00 0.10 0.00 0.00
#> TCGA.CV.7097.01 4 0.0000 0.823 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CR.7367.01 4 0.0937 0.822 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.BA.5558.01 2 0.1267 0.843 0.00 0.94 0.06 0.00 0.00 0.00
#> TCGA.CV.7243.01 3 0.0937 0.876 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.CR.6480.01 6 0.0000 0.983 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CN.A49C.01 6 0.0000 0.983 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CR.6491.01 4 0.4282 0.436 0.42 0.00 0.00 0.56 0.02 0.00
#> TCGA.CR.6473.01 6 0.0000 0.983 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CV.A45O.01 2 0.0547 0.864 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.CR.6493.01 3 0.1267 0.870 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.BA.6873.01 2 0.5655 0.244 0.16 0.48 0.36 0.00 0.00 0.00
#> TCGA.CR.6467.01 6 0.0000 0.983 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CV.6959.01 3 0.0000 0.883 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CQ.6224.01 2 0.2260 0.834 0.14 0.86 0.00 0.00 0.00 0.00
#> TCGA.CV.6938.01 2 0.0547 0.864 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.BA.6872.01 3 0.3647 0.633 0.36 0.00 0.64 0.00 0.00 0.00
#> TCGA.CQ.A4C6.01 2 0.0000 0.867 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HD.A633.01 3 0.0000 0.883 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CQ.A4C7.01 2 0.2260 0.834 0.14 0.86 0.00 0.00 0.00 0.00
#> TCGA.CQ.A4CD.01 2 0.0547 0.868 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.F7.A620.01 2 0.2094 0.819 0.02 0.90 0.00 0.08 0.00 0.00
#> TCGA.QK.A8Z9.01 2 0.2260 0.834 0.14 0.86 0.00 0.00 0.00 0.00
#> TCGA.BB.A5HY.01 4 0.2350 0.798 0.10 0.00 0.00 0.88 0.02 0.00
#> TCGA.CQ.5333.01 2 0.0547 0.864 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.BA.A6DJ.01 2 0.3309 0.740 0.28 0.72 0.00 0.00 0.00 0.00
#> TCGA.CQ.A4CB.01 2 0.0547 0.864 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.IQ.A61I.01 6 0.0000 0.983 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D6.A4Z9.01 4 0.0937 0.822 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.H7.8501.01 2 0.0937 0.866 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.CN.A642.01 3 0.1267 0.870 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.P3.A6T2.01 3 0.3578 0.656 0.34 0.00 0.66 0.00 0.00 0.00
#> TCGA.CN.A6V7.01 6 0.0000 0.983 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CN.4734.01 2 0.2941 0.788 0.22 0.78 0.00 0.00 0.00 0.00
#> TCGA.BA.4075.01 3 0.0937 0.877 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.CN.4726.01 2 0.4393 0.702 0.14 0.72 0.14 0.00 0.00 0.00
#> TCGA.CN.5355.01 2 0.0000 0.867 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BA.5151.01 2 0.0000 0.867 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.5363.01 2 0.1267 0.863 0.06 0.94 0.00 0.00 0.00 0.00
#> TCGA.T2.A6X2.01 3 0.2941 0.745 0.22 0.00 0.78 0.00 0.00 0.00
#> TCGA.CN.4741.01 6 0.0000 0.983 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CV.A6JO.01 2 0.0547 0.864 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.BB.7866.01 6 0.0000 0.983 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CN.5366.01 4 0.0000 0.823 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.QK.A6V9.01 6 0.0000 0.983 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CV.A6JZ.01 4 0.3819 0.445 0.02 0.28 0.00 0.70 0.00 0.00
#> TCGA.HD.A6I0.01 3 0.0547 0.877 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.CV.A6JT.01 3 0.2350 0.816 0.10 0.02 0.88 0.00 0.00 0.00
#> TCGA.D6.A6EN.01 3 0.5267 0.300 0.12 0.32 0.56 0.00 0.00 0.00
#> TCGA.CV.7434.01 4 0.2260 0.786 0.14 0.00 0.00 0.86 0.00 0.00
#> TCGA.HD.7832.01 4 0.4246 0.447 0.40 0.00 0.00 0.58 0.02 0.00
#> TCGA.P3.A6T7.01 2 0.5371 0.215 0.12 0.52 0.00 0.36 0.00 0.00
#> TCGA.CR.7382.01 2 0.0547 0.864 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.T2.A6WZ.01 4 0.0547 0.819 0.02 0.00 0.00 0.98 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.CV.6436.01 2 0.0000 0.7757 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6441.01 5 0.0000 0.0000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.IQ.7630.01 3 0.0504 0.8579 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.CV.5977.01 3 0.2278 0.8138 0.08 0.00 0.88 0.00 0.00 0.00 0.04
#> TCGA.CQ.5324.01 3 0.0000 0.8578 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7365.01 3 0.3606 0.6490 0.30 0.00 0.68 0.00 0.00 0.00 0.02
#> TCGA.CV.7089.01 4 0.2906 0.6486 0.00 0.00 0.00 0.80 0.02 0.00 0.18
#> TCGA.CV.5976.01 1 0.4487 -0.1644 0.52 0.42 0.06 0.00 0.00 0.00 0.00
#> TCGA.CN.6995.01 2 0.1433 0.7572 0.08 0.92 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.5334.01 2 0.1433 0.7551 0.08 0.92 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5435.01 6 0.4938 0.3854 0.02 0.00 0.00 0.00 0.08 0.58 0.32
#> TCGA.CR.7373.01 3 0.0504 0.8579 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.CN.6998.01 3 0.1006 0.8515 0.02 0.00 0.96 0.00 0.00 0.00 0.02
#> TCGA.CR.7380.01 3 0.0504 0.8579 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.CV.7183.01 3 0.0000 0.8578 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HD.7229.01 2 0.4714 0.2818 0.28 0.60 0.00 0.12 0.00 0.00 0.00
#> TCGA.CV.7097.01 4 0.1886 0.6994 0.00 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.CR.7367.01 4 0.0504 0.6852 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.BA.5558.01 2 0.3263 0.6047 0.08 0.80 0.12 0.00 0.00 0.00 0.00
#> TCGA.CV.7243.01 3 0.0504 0.8555 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CR.6480.01 6 0.0000 0.9536 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CN.A49C.01 6 0.0000 0.9536 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CR.6491.01 1 0.5480 -0.3982 0.52 0.02 0.00 0.36 0.02 0.00 0.08
#> TCGA.CR.6473.01 6 0.0000 0.9536 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CV.A45O.01 2 0.0504 0.7741 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.6493.01 3 0.1928 0.8224 0.08 0.00 0.90 0.00 0.00 0.00 0.02
#> TCGA.BA.6873.01 2 0.5644 -0.2335 0.32 0.34 0.34 0.00 0.00 0.00 0.00
#> TCGA.CR.6467.01 6 0.0000 0.9536 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CV.6959.01 3 0.0863 0.8524 0.04 0.00 0.96 0.00 0.00 0.00 0.00
#> TCGA.CQ.6224.01 2 0.1671 0.7453 0.10 0.90 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6938.01 2 0.0504 0.7741 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.6872.01 3 0.3606 0.6414 0.30 0.00 0.68 0.00 0.00 0.00 0.02
#> TCGA.CQ.A4C6.01 2 0.0504 0.7741 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.HD.A633.01 3 0.0504 0.8579 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.CQ.A4C7.01 2 0.2422 0.6835 0.18 0.82 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.A4CD.01 2 0.1006 0.7721 0.02 0.96 0.00 0.02 0.00 0.00 0.00
#> TCGA.F7.A620.01 2 0.3055 0.6105 0.02 0.82 0.00 0.14 0.00 0.00 0.02
#> TCGA.QK.A8Z9.01 2 0.2745 0.6821 0.16 0.82 0.00 0.02 0.00 0.00 0.00
#> TCGA.BB.A5HY.01 4 0.2803 0.5692 0.10 0.00 0.00 0.84 0.00 0.00 0.06
#> TCGA.CQ.5333.01 2 0.0504 0.7741 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A6DJ.01 2 0.4977 -0.0557 0.42 0.50 0.00 0.04 0.00 0.00 0.04
#> TCGA.CQ.A4CB.01 2 0.0504 0.7741 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.IQ.A61I.01 6 0.0000 0.9536 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D6.A4Z9.01 4 0.0000 0.6921 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.H7.8501.01 2 0.1166 0.7627 0.06 0.94 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.A642.01 3 0.1664 0.8299 0.06 0.00 0.92 0.00 0.00 0.00 0.02
#> TCGA.P3.A6T2.01 3 0.4505 0.3930 0.44 0.00 0.50 0.00 0.00 0.00 0.06
#> TCGA.CN.A6V7.01 6 0.0000 0.9536 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CN.4734.01 2 0.4070 0.4117 0.30 0.66 0.00 0.02 0.00 0.00 0.02
#> TCGA.BA.4075.01 3 0.1363 0.8486 0.04 0.00 0.94 0.00 0.00 0.00 0.02
#> TCGA.CN.4726.01 2 0.4970 0.2190 0.18 0.58 0.24 0.00 0.00 0.00 0.00
#> TCGA.CN.5355.01 2 0.0000 0.7757 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.5151.01 2 0.0000 0.7757 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.5363.01 2 0.1664 0.7562 0.06 0.92 0.00 0.02 0.00 0.00 0.00
#> TCGA.T2.A6X2.01 3 0.3186 0.7096 0.22 0.00 0.76 0.00 0.00 0.00 0.02
#> TCGA.CN.4741.01 6 0.0000 0.9536 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CV.A6JO.01 2 0.0504 0.7741 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.BB.7866.01 6 0.0000 0.9536 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CN.5366.01 4 0.2081 0.6915 0.00 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.QK.A6V9.01 6 0.0000 0.9536 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CV.A6JZ.01 4 0.4070 0.2379 0.02 0.30 0.00 0.66 0.00 0.00 0.02
#> TCGA.HD.A6I0.01 3 0.0504 0.8579 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.CV.A6JT.01 3 0.2512 0.7754 0.10 0.04 0.86 0.00 0.00 0.00 0.00
#> TCGA.D6.A6EN.01 3 0.4850 0.1778 0.12 0.32 0.56 0.00 0.00 0.00 0.00
#> TCGA.CV.7434.01 4 0.3199 0.5083 0.14 0.00 0.00 0.80 0.00 0.00 0.06
#> TCGA.HD.7832.01 7 0.5291 0.0000 0.20 0.00 0.00 0.30 0.00 0.00 0.50
#> TCGA.P3.A6T7.01 2 0.5888 -0.2411 0.22 0.40 0.00 0.36 0.00 0.00 0.02
#> TCGA.CR.7382.01 2 0.0504 0.7741 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.T2.A6WZ.01 4 0.3386 0.6396 0.02 0.00 0.00 0.78 0.02 0.00 0.18
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.CV.6436.01 2 0.0000 0.7600 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6441.01 5 0.0000 0.0000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.IQ.7630.01 3 0.0471 0.7884 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CV.5977.01 3 0.3444 0.7183 0.06 0.00 0.78 0.00 0.00 0.00 0.02 0.14
#> TCGA.CQ.5324.01 3 0.0808 0.7900 0.00 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.CR.7365.01 3 0.4538 0.4116 0.32 0.00 0.56 0.00 0.00 0.00 0.00 0.12
#> TCGA.CV.7089.01 4 0.0941 0.8091 0.00 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.CV.5976.01 1 0.4516 -0.1027 0.52 0.42 0.02 0.00 0.00 0.00 0.02 0.02
#> TCGA.CN.6995.01 2 0.1557 0.7437 0.06 0.92 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.CQ.5334.01 2 0.1275 0.7524 0.04 0.94 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.CV.5435.01 8 0.3083 0.0000 0.00 0.00 0.00 0.00 0.00 0.34 0.00 0.66
#> TCGA.CR.7373.01 3 0.0941 0.7824 0.02 0.00 0.96 0.00 0.00 0.00 0.00 0.02
#> TCGA.CN.6998.01 3 0.2132 0.7724 0.04 0.00 0.88 0.00 0.00 0.00 0.00 0.08
#> TCGA.CR.7380.01 3 0.0941 0.7824 0.02 0.00 0.96 0.00 0.00 0.00 0.00 0.02
#> TCGA.CV.7183.01 3 0.0000 0.7889 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HD.7229.01 2 0.4380 0.3372 0.32 0.58 0.00 0.10 0.00 0.00 0.00 0.00
#> TCGA.CV.7097.01 4 0.0000 0.8236 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7367.01 4 0.1557 0.8212 0.06 0.00 0.00 0.92 0.00 0.00 0.02 0.00
#> TCGA.BA.5558.01 2 0.4097 0.4446 0.08 0.70 0.20 0.00 0.00 0.00 0.00 0.02
#> TCGA.CV.7243.01 3 0.1887 0.7746 0.04 0.00 0.90 0.00 0.00 0.00 0.00 0.06
#> TCGA.CR.6480.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CN.A49C.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CR.6491.01 1 0.5390 -0.2327 0.54 0.00 0.00 0.28 0.02 0.00 0.02 0.14
#> TCGA.CR.6473.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.A45O.01 2 0.0941 0.7582 0.02 0.96 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.CR.6493.01 3 0.3444 0.7183 0.06 0.00 0.78 0.00 0.00 0.00 0.02 0.14
#> TCGA.BA.6873.01 1 0.5946 0.1697 0.38 0.34 0.22 0.00 0.00 0.00 0.00 0.06
#> TCGA.CR.6467.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.6959.01 3 0.1607 0.7667 0.04 0.00 0.92 0.00 0.00 0.00 0.00 0.04
#> TCGA.CQ.6224.01 2 0.4326 0.4879 0.28 0.64 0.00 0.00 0.00 0.00 0.04 0.04
#> TCGA.CV.6938.01 2 0.0941 0.7582 0.02 0.96 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.BA.6872.01 3 0.4562 0.1676 0.44 0.00 0.46 0.00 0.00 0.00 0.00 0.10
#> TCGA.CQ.A4C6.01 2 0.0471 0.7595 0.02 0.98 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HD.A633.01 3 0.0941 0.7870 0.00 0.00 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.CQ.A4C7.01 2 0.3637 0.5546 0.26 0.70 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.CQ.A4CD.01 2 0.1563 0.7369 0.10 0.90 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F7.A620.01 2 0.3169 0.5777 0.02 0.78 0.00 0.18 0.00 0.00 0.02 0.00
#> TCGA.QK.A8Z9.01 2 0.4241 0.5167 0.26 0.66 0.00 0.00 0.00 0.00 0.04 0.04
#> TCGA.BB.A5HY.01 4 0.3170 0.7301 0.20 0.00 0.00 0.76 0.00 0.00 0.04 0.00
#> TCGA.CQ.5333.01 2 0.0941 0.7582 0.02 0.96 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.BA.A6DJ.01 2 0.3729 0.1702 0.46 0.52 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.CQ.A4CB.01 2 0.0941 0.7582 0.02 0.96 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.IQ.A61I.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D6.A4Z9.01 4 0.1557 0.8212 0.06 0.00 0.00 0.92 0.00 0.00 0.02 0.00
#> TCGA.H7.8501.01 2 0.1947 0.7089 0.14 0.86 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.A642.01 3 0.2864 0.7502 0.06 0.00 0.84 0.00 0.00 0.00 0.02 0.08
#> TCGA.P3.A6T2.01 1 0.4898 -0.0717 0.56 0.00 0.30 0.00 0.00 0.00 0.02 0.12
#> TCGA.CN.A6V7.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CN.4734.01 2 0.3237 0.3756 0.40 0.60 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.4075.01 3 0.2132 0.7681 0.04 0.00 0.88 0.00 0.00 0.00 0.00 0.08
#> TCGA.CN.4726.01 2 0.6138 -0.0988 0.26 0.46 0.20 0.00 0.00 0.00 0.02 0.06
#> TCGA.CN.5355.01 2 0.0471 0.7598 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.BA.5151.01 2 0.0000 0.7600 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.5363.01 2 0.0471 0.7585 0.02 0.98 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.T2.A6X2.01 3 0.3318 0.3155 0.46 0.00 0.54 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4741.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.A6JO.01 2 0.0941 0.7582 0.02 0.96 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.BB.7866.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CN.5366.01 4 0.0000 0.8236 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QK.A6V9.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.A6JZ.01 4 0.3594 0.4409 0.04 0.28 0.00 0.68 0.00 0.00 0.00 0.00
#> TCGA.HD.A6I0.01 3 0.1275 0.7778 0.04 0.00 0.94 0.00 0.00 0.00 0.00 0.02
#> TCGA.CV.A6JT.01 3 0.2888 0.6592 0.16 0.00 0.80 0.00 0.00 0.00 0.00 0.04
#> TCGA.D6.A6EN.01 3 0.5725 -0.1988 0.26 0.26 0.44 0.00 0.00 0.00 0.00 0.04
#> TCGA.CV.7434.01 4 0.4276 0.6686 0.18 0.00 0.00 0.70 0.00 0.00 0.08 0.04
#> TCGA.HD.7832.01 7 0.1341 0.0000 0.00 0.00 0.00 0.08 0.00 0.00 0.92 0.00
#> TCGA.P3.A6T7.01 2 0.5273 0.0883 0.16 0.46 0.00 0.36 0.00 0.00 0.00 0.02
#> TCGA.CR.7382.01 2 0.0941 0.7582 0.02 0.96 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.T2.A6WZ.01 4 0.1741 0.7908 0.00 0.00 0.00 0.92 0.02 0.00 0.02 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: Node023. Child nodes: Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node02111-leaf , Node02112-leaf , Node02113-leaf , Node02114-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02124-leaf , Node02131-leaf , Node02132 , Node02133-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02231-leaf , Node02232-leaf , Node02233-leaf , Node02241-leaf , Node02242-leaf , Node02243-leaf , Node02321-leaf , Node02322-leaf , Node02323-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf , Node05114-leaf , Node05121 , Node05122-leaf , Node05123-leaf , Node05221-leaf , Node05222-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 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 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 0.3406 0.660 0.660
#> 3 3 1.000 0.994 0.997 0.7123 0.700 0.564
#> 4 4 0.683 0.682 0.862 0.1969 0.867 0.697
#> 5 5 0.803 0.860 0.907 0.1201 0.788 0.438
#> 6 6 0.872 0.779 0.901 0.0520 0.948 0.761
#> 7 7 0.843 0.632 0.798 0.0194 0.931 0.646
#> 8 8 0.821 0.584 0.846 0.0158 0.929 0.628
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.CV.6436.01 2 0 1 0 1
#> TCGA.CV.5976.01 2 0 1 0 1
#> TCGA.CN.6995.01 2 0 1 0 1
#> TCGA.CQ.5334.01 1 0 1 1 0
#> TCGA.HD.7229.01 2 0 1 0 1
#> TCGA.BA.5558.01 2 0 1 0 1
#> TCGA.CV.A45O.01 2 0 1 0 1
#> TCGA.BA.6873.01 2 0 1 0 1
#> TCGA.CQ.6224.01 2 0 1 0 1
#> TCGA.CV.6938.01 1 0 1 1 0
#> TCGA.CQ.A4C6.01 2 0 1 0 1
#> TCGA.CQ.A4C7.01 2 0 1 0 1
#> TCGA.CQ.A4CD.01 2 0 1 0 1
#> TCGA.F7.A620.01 2 0 1 0 1
#> TCGA.QK.A8Z9.01 2 0 1 0 1
#> TCGA.CQ.5333.01 1 0 1 1 0
#> TCGA.BA.A6DJ.01 1 0 1 1 0
#> TCGA.CQ.A4CB.01 2 0 1 0 1
#> TCGA.H7.8501.01 2 0 1 0 1
#> TCGA.CN.4734.01 1 0 1 1 0
#> TCGA.CN.4726.01 2 0 1 0 1
#> TCGA.CN.5355.01 2 0 1 0 1
#> TCGA.BA.5151.01 2 0 1 0 1
#> TCGA.CN.5363.01 1 0 1 1 0
#> TCGA.CV.A6JO.01 2 0 1 0 1
#> TCGA.CV.A6JZ.01 2 0 1 0 1
#> TCGA.D6.A6EN.01 2 0 1 0 1
#> TCGA.P3.A6T7.01 2 0 1 0 1
#> TCGA.CR.7382.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CV.6436.01 2 0.0000 0.995 0 1.00 0.00
#> TCGA.CV.5976.01 2 0.0000 0.995 0 1.00 0.00
#> TCGA.CN.6995.01 2 0.0000 0.995 0 1.00 0.00
#> TCGA.CQ.5334.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.HD.7229.01 2 0.0892 0.976 0 0.98 0.02
#> TCGA.BA.5558.01 2 0.0000 0.995 0 1.00 0.00
#> TCGA.CV.A45O.01 2 0.0000 0.995 0 1.00 0.00
#> TCGA.BA.6873.01 2 0.0000 0.995 0 1.00 0.00
#> TCGA.CQ.6224.01 2 0.0000 0.995 0 1.00 0.00
#> TCGA.CV.6938.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.CQ.A4C6.01 2 0.0000 0.995 0 1.00 0.00
#> TCGA.CQ.A4C7.01 2 0.0000 0.995 0 1.00 0.00
#> TCGA.CQ.A4CD.01 2 0.0000 0.995 0 1.00 0.00
#> TCGA.F7.A620.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.QK.A8Z9.01 2 0.0000 0.995 0 1.00 0.00
#> TCGA.CQ.5333.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.BA.A6DJ.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CQ.A4CB.01 2 0.0000 0.995 0 1.00 0.00
#> TCGA.H7.8501.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.CN.4734.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CN.4726.01 2 0.0000 0.995 0 1.00 0.00
#> TCGA.CN.5355.01 2 0.0000 0.995 0 1.00 0.00
#> TCGA.BA.5151.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.CN.5363.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.CV.A6JO.01 2 0.0000 0.995 0 1.00 0.00
#> TCGA.CV.A6JZ.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.D6.A6EN.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.P3.A6T7.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.CR.7382.01 2 0.2066 0.934 0 0.94 0.06
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.CV.6436.01 2 0.0000 0.8202 0 1.00 0.00 0.00
#> TCGA.CV.5976.01 2 0.2011 0.8035 0 0.92 0.08 0.00
#> TCGA.CN.6995.01 2 0.0000 0.8202 0 1.00 0.00 0.00
#> TCGA.CQ.5334.01 1 0.0000 1.0000 1 0.00 0.00 0.00
#> TCGA.HD.7229.01 2 0.7198 0.4559 0 0.52 0.32 0.16
#> TCGA.BA.5558.01 2 0.0000 0.8202 0 1.00 0.00 0.00
#> TCGA.CV.A45O.01 2 0.2647 0.7859 0 0.88 0.12 0.00
#> TCGA.BA.6873.01 2 0.0000 0.8202 0 1.00 0.00 0.00
#> TCGA.CQ.6224.01 2 0.0000 0.8202 0 1.00 0.00 0.00
#> TCGA.CV.6938.01 3 0.4977 -0.0523 0 0.00 0.54 0.46
#> TCGA.CQ.A4C6.01 2 0.0000 0.8202 0 1.00 0.00 0.00
#> TCGA.CQ.A4C7.01 2 0.4134 0.6860 0 0.74 0.26 0.00
#> TCGA.CQ.A4CD.01 2 0.0000 0.8202 0 1.00 0.00 0.00
#> TCGA.F7.A620.01 4 0.0707 0.9139 0 0.00 0.02 0.98
#> TCGA.QK.A8Z9.01 2 0.7135 0.5112 0 0.56 0.24 0.20
#> TCGA.CQ.5333.01 1 0.0000 1.0000 1 0.00 0.00 0.00
#> TCGA.BA.A6DJ.01 1 0.0000 1.0000 1 0.00 0.00 0.00
#> TCGA.CQ.A4CB.01 2 0.6720 0.5417 0 0.58 0.30 0.12
#> TCGA.H7.8501.01 3 0.2647 0.5389 0 0.00 0.88 0.12
#> TCGA.CN.4734.01 1 0.0000 1.0000 1 0.00 0.00 0.00
#> TCGA.CN.4726.01 3 0.4907 -0.1227 0 0.42 0.58 0.00
#> TCGA.CN.5355.01 2 0.1211 0.8147 0 0.96 0.04 0.00
#> TCGA.BA.5151.01 3 0.4977 -0.0523 0 0.00 0.54 0.46
#> TCGA.CN.5363.01 4 0.2647 0.7795 0 0.00 0.12 0.88
#> TCGA.CV.A6JO.01 2 0.6720 0.5417 0 0.58 0.30 0.12
#> TCGA.CV.A6JZ.01 4 0.0000 0.9124 0 0.00 0.00 1.00
#> TCGA.D6.A6EN.01 3 0.0707 0.5286 0 0.00 0.98 0.02
#> TCGA.P3.A6T7.01 4 0.0707 0.9139 0 0.00 0.02 0.98
#> TCGA.CR.7382.01 3 0.2647 0.5389 0 0.00 0.88 0.12
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CV.6436.01 2 0.0000 0.964 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.5976.01 3 0.3690 0.766 0.00 0.20 0.78 0.00 0.02
#> TCGA.CN.6995.01 2 0.0000 0.964 0.00 1.00 0.00 0.00 0.00
#> TCGA.CQ.5334.01 1 0.0609 0.990 0.98 0.00 0.02 0.00 0.00
#> TCGA.HD.7229.01 3 0.2077 0.824 0.00 0.04 0.92 0.04 0.00
#> TCGA.BA.5558.01 2 0.0000 0.964 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.A45O.01 3 0.4060 0.552 0.00 0.36 0.64 0.00 0.00
#> TCGA.BA.6873.01 2 0.0000 0.964 0.00 1.00 0.00 0.00 0.00
#> TCGA.CQ.6224.01 2 0.0000 0.964 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.6938.01 5 0.3684 0.762 0.00 0.00 0.00 0.28 0.72
#> TCGA.CQ.A4C6.01 2 0.0000 0.964 0.00 1.00 0.00 0.00 0.00
#> TCGA.CQ.A4C7.01 3 0.2616 0.825 0.00 0.10 0.88 0.00 0.02
#> TCGA.CQ.A4CD.01 2 0.0000 0.964 0.00 1.00 0.00 0.00 0.00
#> TCGA.F7.A620.01 4 0.0609 0.962 0.00 0.00 0.02 0.98 0.00
#> TCGA.QK.A8Z9.01 3 0.3037 0.799 0.00 0.04 0.86 0.10 0.00
#> TCGA.CQ.5333.01 1 0.0609 0.990 0.98 0.00 0.02 0.00 0.00
#> TCGA.BA.A6DJ.01 1 0.0000 0.990 1.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.A4CB.01 3 0.1732 0.832 0.00 0.08 0.92 0.00 0.00
#> TCGA.H7.8501.01 3 0.2929 0.753 0.00 0.00 0.82 0.00 0.18
#> TCGA.CN.4734.01 1 0.0000 0.990 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4726.01 3 0.4748 0.649 0.00 0.04 0.66 0.00 0.30
#> TCGA.CN.5355.01 2 0.3513 0.693 0.00 0.80 0.18 0.00 0.02
#> TCGA.BA.5151.01 5 0.3684 0.762 0.00 0.00 0.00 0.28 0.72
#> TCGA.CN.5363.01 4 0.1043 0.925 0.00 0.00 0.00 0.96 0.04
#> TCGA.CV.A6JO.01 3 0.1410 0.832 0.00 0.06 0.94 0.00 0.00
#> TCGA.CV.A6JZ.01 4 0.0000 0.958 0.00 0.00 0.00 1.00 0.00
#> TCGA.D6.A6EN.01 5 0.1410 0.617 0.00 0.00 0.06 0.00 0.94
#> TCGA.P3.A6T7.01 4 0.0609 0.962 0.00 0.00 0.02 0.98 0.00
#> TCGA.CR.7382.01 3 0.2929 0.753 0.00 0.00 0.82 0.00 0.18
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.CV.6436.01 2 0.0000 0.9634 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5976.01 3 0.3746 0.5399 0.00 0.14 0.78 0.00 0.00 0.08
#> TCGA.CN.6995.01 2 0.0000 0.9634 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.5334.01 1 0.0000 0.9788 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HD.7229.01 3 0.0000 0.6232 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BA.5558.01 2 0.0000 0.9634 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A45O.01 3 0.6016 -0.0554 0.00 0.38 0.38 0.00 0.00 0.24
#> TCGA.BA.6873.01 2 0.0000 0.9634 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.6224.01 2 0.0000 0.9634 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6938.01 5 0.0000 0.8902 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CQ.A4C6.01 2 0.0000 0.9634 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.A4C7.01 3 0.3916 0.3290 0.00 0.02 0.68 0.00 0.00 0.30
#> TCGA.CQ.A4CD.01 2 0.0000 0.9634 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.F7.A620.01 4 0.0547 0.9936 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.QK.A8Z9.01 3 0.0000 0.6232 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CQ.5333.01 1 0.0000 0.9788 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A6DJ.01 1 0.0937 0.9788 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.CQ.A4CB.01 3 0.0547 0.6304 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.H7.8501.01 6 0.3828 0.4850 0.00 0.00 0.44 0.00 0.00 0.56
#> TCGA.CN.4734.01 1 0.0937 0.9788 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.CN.4726.01 6 0.1267 0.4920 0.00 0.00 0.06 0.00 0.00 0.94
#> TCGA.CN.5355.01 2 0.3076 0.6810 0.00 0.76 0.00 0.00 0.00 0.24
#> TCGA.BA.5151.01 5 0.0547 0.8880 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.CN.5363.01 4 0.0000 0.9806 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.A6JO.01 3 0.3315 0.4942 0.00 0.02 0.78 0.00 0.00 0.20
#> TCGA.CV.A6JZ.01 4 0.0547 0.9936 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.D6.A6EN.01 5 0.2793 0.7641 0.00 0.00 0.00 0.00 0.80 0.20
#> TCGA.P3.A6T7.01 4 0.0547 0.9936 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.CR.7382.01 6 0.3647 0.5909 0.00 0.00 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.CV.6436.01 2 0.0000 0.8779 0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5976.01 3 0.5888 0.1067 0 0.22 0.40 0.00 0.00 0.36 0.02
#> TCGA.CN.6995.01 2 0.0000 0.8779 0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.5334.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HD.7229.01 3 0.2745 0.2406 0 0.00 0.82 0.00 0.00 0.16 0.02
#> TCGA.BA.5558.01 2 0.0000 0.8779 0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A45O.01 2 0.5221 0.0191 0 0.46 0.06 0.00 0.00 0.44 0.04
#> TCGA.BA.6873.01 2 0.0000 0.8779 0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.6224.01 2 0.0000 0.8779 0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6938.01 5 0.0000 0.8061 0 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CQ.A4C6.01 2 0.0000 0.8779 0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.A4C7.01 6 0.2945 0.3130 0 0.00 0.26 0.00 0.00 0.74 0.00
#> TCGA.CQ.A4CD.01 2 0.0000 0.8779 0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F7.A620.01 4 0.0000 0.9461 0 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.QK.A8Z9.01 3 0.5286 0.3351 0 0.00 0.62 0.06 0.00 0.22 0.10
#> TCGA.CQ.5333.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A6DJ.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.A4CB.01 3 0.3546 0.0827 0 0.00 0.54 0.00 0.00 0.46 0.00
#> TCGA.H7.8501.01 6 0.4015 0.1439 0 0.00 0.26 0.00 0.00 0.68 0.06
#> TCGA.CN.4734.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4726.01 7 0.3496 0.0000 0 0.00 0.00 0.00 0.00 0.42 0.58
#> TCGA.CN.5355.01 2 0.4211 0.5344 0 0.68 0.02 0.00 0.00 0.26 0.04
#> TCGA.BA.5151.01 5 0.2512 0.7709 0 0.00 0.04 0.00 0.86 0.00 0.10
#> TCGA.CN.5363.01 4 0.2722 0.8466 0 0.00 0.04 0.84 0.00 0.00 0.12
#> TCGA.CV.A6JO.01 6 0.3358 0.0803 0 0.00 0.36 0.00 0.00 0.64 0.00
#> TCGA.CV.A6JZ.01 4 0.0000 0.9461 0 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D6.A6EN.01 5 0.3617 0.6762 0 0.00 0.00 0.00 0.76 0.16 0.08
#> TCGA.P3.A6T7.01 4 0.0504 0.9394 0 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CR.7382.01 6 0.0504 0.3997 0 0.00 0.02 0.00 0.00 0.98 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.CV.6436.01 2 0.0000 0.929 0.0 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5976.01 3 0.3169 0.321 0.0 0.18 0.78 0.00 0.00 0.00 0.02 0.02
#> TCGA.CN.6995.01 2 0.0000 0.929 0.0 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.5334.01 1 0.0000 0.940 1.0 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HD.7229.01 3 0.4693 -0.217 0.0 0.00 0.46 0.00 0.00 0.42 0.00 0.12
#> TCGA.BA.5558.01 2 0.0000 0.929 0.0 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A45O.01 3 0.5122 0.180 0.0 0.32 0.56 0.00 0.00 0.02 0.06 0.04
#> TCGA.BA.6873.01 2 0.0000 0.929 0.0 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.6224.01 2 0.0000 0.929 0.0 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6938.01 5 0.0000 0.681 0.0 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CQ.A4C6.01 2 0.0000 0.929 0.0 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.A4C7.01 3 0.3494 0.268 0.0 0.00 0.78 0.00 0.00 0.04 0.14 0.04
#> TCGA.CQ.A4CD.01 2 0.0000 0.929 0.0 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F7.A620.01 4 0.0000 0.917 0.0 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QK.A8Z9.01 8 0.3991 0.000 0.0 0.00 0.32 0.06 0.00 0.00 0.00 0.62
#> TCGA.CQ.5333.01 1 0.0000 0.940 1.0 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A6DJ.01 1 0.1804 0.940 0.9 0.00 0.00 0.00 0.00 0.08 0.00 0.02
#> TCGA.CQ.A4CB.01 3 0.1804 0.332 0.0 0.00 0.90 0.00 0.00 0.08 0.00 0.02
#> TCGA.H7.8501.01 6 0.4873 0.000 0.0 0.00 0.36 0.00 0.00 0.48 0.16 0.00
#> TCGA.CN.4734.01 1 0.1804 0.940 0.9 0.00 0.00 0.00 0.00 0.08 0.00 0.02
#> TCGA.CN.4726.01 7 0.1341 0.000 0.0 0.00 0.08 0.00 0.00 0.00 0.92 0.00
#> TCGA.CN.5355.01 2 0.5491 0.245 0.0 0.56 0.20 0.00 0.00 0.00 0.16 0.08
#> TCGA.BA.5151.01 5 0.3630 0.641 0.0 0.00 0.00 0.00 0.78 0.10 0.04 0.08
#> TCGA.CN.5363.01 4 0.2888 0.795 0.0 0.00 0.00 0.80 0.00 0.04 0.00 0.16
#> TCGA.CV.A6JO.01 3 0.0941 0.380 0.0 0.00 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.CV.A6JZ.01 4 0.0000 0.917 0.0 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D6.A6EN.01 5 0.4953 0.442 0.0 0.00 0.00 0.00 0.58 0.24 0.16 0.02
#> TCGA.P3.A6T7.01 4 0.1275 0.892 0.0 0.00 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.CR.7382.01 3 0.5344 -0.116 0.0 0.00 0.56 0.00 0.00 0.14 0.24 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: Node0. Child nodes: Node011 , Node012 , Node013-leaf , Node021 , Node022 , Node023 , Node031-leaf , Node032-leaf , Node033 , Node034-leaf , Node041-leaf , Node042-leaf , Node043 , Node051 , Node052 , Node053-leaf .
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 55 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 '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 0.3481 0.653 0.653
#> 3 3 0.838 0.971 0.981 0.8539 0.702 0.544
#> 4 4 0.967 0.957 0.978 0.1466 0.895 0.708
#> 5 5 0.814 0.799 0.891 0.0770 0.901 0.644
#> 6 6 0.791 0.728 0.856 0.0264 0.977 0.888
#> 7 7 0.792 0.608 0.818 0.0263 0.978 0.885
#> 8 8 0.802 0.615 0.748 0.0155 0.958 0.782
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.CV.5435.11 1 0 1 1 0
#> TCGA.CV.5432.11 1 0 1 1 0
#> TCGA.CV.5430.11 1 0 1 1 0
#> TCGA.CV.5434.11 1 0 1 1 0
#> TCGA.CV.5970.11 1 0 1 1 0
#> TCGA.CV.5976.11 1 0 1 1 0
#> TCGA.CV.7103.11 1 0 1 1 0
#> TCGA.CV.6003.11 2 0 1 0 1
#> TCGA.CV.5439.11 1 0 1 1 0
#> TCGA.CV.5971.11 1 0 1 1 0
#> TCGA.CV.5966.11 2 0 1 0 1
#> TCGA.CV.5977.11 1 0 1 1 0
#> TCGA.CV.6441.11 1 0 1 1 0
#> TCGA.CV.5978.11 2 0 1 0 1
#> TCGA.CV.5973.11 2 0 1 0 1
#> TCGA.CV.6436.11 1 0 1 1 0
#> TCGA.CV.6433.11 1 0 1 1 0
#> TCGA.CV.5979.11 1 0 1 1 0
#> TCGA.CR.6492.01 1 0 1 1 0
#> TCGA.CV.6955.11 2 0 1 0 1
#> TCGA.CV.7238.11 2 0 1 0 1
#> TCGA.CV.7089.11 1 0 1 1 0
#> TCGA.CV.5431.11 1 0 1 1 0
#> TCGA.CV.7255.11 2 0 1 0 1
#> TCGA.CV.7236.01 2 0 1 0 1
#> TCGA.CV.7250.11 1 0 1 1 0
#> TCGA.CV.5442.11 2 0 1 0 1
#> TCGA.CV.5436.11 1 0 1 1 0
#> TCGA.CV.7245.11 1 0 1 1 0
#> TCGA.CV.7235.11 1 0 1 1 0
#> TCGA.CV.7263.11 1 0 1 1 0
#> TCGA.CV.6956.11 1 0 1 1 0
#> TCGA.CR.7393.01 1 0 1 1 0
#> TCGA.CV.5444.11 1 0 1 1 0
#> TCGA.CV.7178.11 2 0 1 0 1
#> TCGA.CV.5443.11 1 0 1 1 0
#> TCGA.CR.7397.01 1 0 1 1 0
#> TCGA.CV.5440.11 1 0 1 1 0
#> TCGA.CV.7101.11 1 0 1 1 0
#> TCGA.CV.6935.11 1 0 1 1 0
#> TCGA.CV.6959.11 1 0 1 1 0
#> TCGA.CV.6938.11 1 0 1 1 0
#> TCGA.CV.6952.11 2 0 1 0 1
#> TCGA.CV.6951.11 1 0 1 1 0
#> TCGA.CV.6939.11 1 0 1 1 0
#> TCGA.CV.6954.11 1 0 1 1 0
#> TCGA.CV.6962.11 1 0 1 1 0
#> TCGA.CV.6961.11 1 0 1 1 0
#> TCGA.CV.6934.11 2 0 1 0 1
#> TCGA.CV.6943.11 1 0 1 1 0
#> TCGA.CV.6936.11 1 0 1 1 0
#> TCGA.D6.6824.01 1 0 1 1 0
#> TCGA.CV.6933.11 1 0 1 1 0
#> TCGA.KU.A6H8.01 1 0 1 1 0
#> TCGA.CV.A6K0.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CV.5435.11 3 0.0000 0.997 0.00 0 1.00
#> TCGA.CV.5432.11 1 0.3340 0.907 0.88 0 0.12
#> TCGA.CV.5430.11 1 0.3340 0.907 0.88 0 0.12
#> TCGA.CV.5434.11 3 0.0000 0.997 0.00 0 1.00
#> TCGA.CV.5970.11 1 0.0000 0.957 1.00 0 0.00
#> TCGA.CV.5976.11 1 0.0000 0.957 1.00 0 0.00
#> TCGA.CV.7103.11 1 0.0000 0.957 1.00 0 0.00
#> TCGA.CV.6003.11 2 0.0000 1.000 0.00 1 0.00
#> TCGA.CV.5439.11 3 0.0000 0.997 0.00 0 1.00
#> TCGA.CV.5971.11 1 0.0892 0.953 0.98 0 0.02
#> TCGA.CV.5966.11 2 0.0000 1.000 0.00 1 0.00
#> TCGA.CV.5977.11 3 0.0000 0.997 0.00 0 1.00
#> TCGA.CV.6441.11 1 0.0000 0.957 1.00 0 0.00
#> TCGA.CV.5978.11 2 0.0000 1.000 0.00 1 0.00
#> TCGA.CV.5973.11 2 0.0000 1.000 0.00 1 0.00
#> TCGA.CV.6436.11 1 0.0000 0.957 1.00 0 0.00
#> TCGA.CV.6433.11 1 0.2066 0.938 0.94 0 0.06
#> TCGA.CV.5979.11 3 0.0000 0.997 0.00 0 1.00
#> TCGA.CR.6492.01 3 0.0000 0.997 0.00 0 1.00
#> TCGA.CV.6955.11 2 0.0000 1.000 0.00 1 0.00
#> TCGA.CV.7238.11 2 0.0000 1.000 0.00 1 0.00
#> TCGA.CV.7089.11 3 0.0000 0.997 0.00 0 1.00
#> TCGA.CV.5431.11 1 0.3340 0.907 0.88 0 0.12
#> TCGA.CV.7255.11 2 0.0000 1.000 0.00 1 0.00
#> TCGA.CV.7236.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.CV.7250.11 1 0.3340 0.907 0.88 0 0.12
#> TCGA.CV.5442.11 2 0.0000 1.000 0.00 1 0.00
#> TCGA.CV.5436.11 1 0.0000 0.957 1.00 0 0.00
#> TCGA.CV.7245.11 3 0.0000 0.997 0.00 0 1.00
#> TCGA.CV.7235.11 3 0.0000 0.997 0.00 0 1.00
#> TCGA.CV.7263.11 1 0.0000 0.957 1.00 0 0.00
#> TCGA.CV.6956.11 1 0.0000 0.957 1.00 0 0.00
#> TCGA.CR.7393.01 1 0.0892 0.953 0.98 0 0.02
#> TCGA.CV.5444.11 3 0.0000 0.997 0.00 0 1.00
#> TCGA.CV.7178.11 2 0.0000 1.000 0.00 1 0.00
#> TCGA.CV.5443.11 3 0.0000 0.997 0.00 0 1.00
#> TCGA.CR.7397.01 3 0.1529 0.950 0.04 0 0.96
#> TCGA.CV.5440.11 3 0.0000 0.997 0.00 0 1.00
#> TCGA.CV.7101.11 1 0.3340 0.907 0.88 0 0.12
#> TCGA.CV.6935.11 1 0.0000 0.957 1.00 0 0.00
#> TCGA.CV.6959.11 1 0.0000 0.957 1.00 0 0.00
#> TCGA.CV.6938.11 3 0.0000 0.997 0.00 0 1.00
#> TCGA.CV.6952.11 2 0.0000 1.000 0.00 1 0.00
#> TCGA.CV.6951.11 1 0.0000 0.957 1.00 0 0.00
#> TCGA.CV.6939.11 3 0.0000 0.997 0.00 0 1.00
#> TCGA.CV.6954.11 1 0.0000 0.957 1.00 0 0.00
#> TCGA.CV.6962.11 1 0.3340 0.907 0.88 0 0.12
#> TCGA.CV.6961.11 1 0.0000 0.957 1.00 0 0.00
#> TCGA.CV.6934.11 2 0.0000 1.000 0.00 1 0.00
#> TCGA.CV.6943.11 1 0.0000 0.957 1.00 0 0.00
#> TCGA.CV.6936.11 1 0.0000 0.957 1.00 0 0.00
#> TCGA.D6.6824.01 3 0.0000 0.997 0.00 0 1.00
#> TCGA.CV.6933.11 3 0.0000 0.997 0.00 0 1.00
#> TCGA.KU.A6H8.01 1 0.3340 0.907 0.88 0 0.12
#> TCGA.CV.A6K0.01 1 0.2537 0.930 0.92 0 0.08
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.CV.5435.11 3 0.0707 0.976 0.00 0 0.98 0.02
#> TCGA.CV.5432.11 4 0.0000 0.956 0.00 0 0.00 1.00
#> TCGA.CV.5430.11 4 0.0000 0.956 0.00 0 0.00 1.00
#> TCGA.CV.5434.11 3 0.0000 0.997 0.00 0 1.00 0.00
#> TCGA.CV.5970.11 1 0.1211 0.931 0.96 0 0.00 0.04
#> TCGA.CV.5976.11 1 0.0000 0.949 1.00 0 0.00 0.00
#> TCGA.CV.7103.11 1 0.0000 0.949 1.00 0 0.00 0.00
#> TCGA.CV.6003.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CV.5439.11 3 0.0000 0.997 0.00 0 1.00 0.00
#> TCGA.CV.5971.11 1 0.3198 0.883 0.88 0 0.08 0.04
#> TCGA.CV.5966.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CV.5977.11 3 0.0000 0.997 0.00 0 1.00 0.00
#> TCGA.CV.6441.11 1 0.0000 0.949 1.00 0 0.00 0.00
#> TCGA.CV.5978.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CV.5973.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CV.6436.11 1 0.0000 0.949 1.00 0 0.00 0.00
#> TCGA.CV.6433.11 1 0.3821 0.847 0.84 0 0.12 0.04
#> TCGA.CV.5979.11 3 0.0000 0.997 0.00 0 1.00 0.00
#> TCGA.CR.6492.01 3 0.0000 0.997 0.00 0 1.00 0.00
#> TCGA.CV.6955.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CV.7238.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CV.7089.11 3 0.0000 0.997 0.00 0 1.00 0.00
#> TCGA.CV.5431.11 4 0.0000 0.956 0.00 0 0.00 1.00
#> TCGA.CV.7255.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CV.7236.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CV.7250.11 4 0.0000 0.956 0.00 0 0.00 1.00
#> TCGA.CV.5442.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CV.5436.11 1 0.0000 0.949 1.00 0 0.00 0.00
#> TCGA.CV.7245.11 3 0.0000 0.997 0.00 0 1.00 0.00
#> TCGA.CV.7235.11 3 0.0000 0.997 0.00 0 1.00 0.00
#> TCGA.CV.7263.11 1 0.0000 0.949 1.00 0 0.00 0.00
#> TCGA.CV.6956.11 1 0.0000 0.949 1.00 0 0.00 0.00
#> TCGA.CR.7393.01 1 0.2411 0.912 0.92 0 0.04 0.04
#> TCGA.CV.5444.11 3 0.0000 0.997 0.00 0 1.00 0.00
#> TCGA.CV.7178.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CV.5443.11 4 0.4277 0.614 0.00 0 0.28 0.72
#> TCGA.CR.7397.01 3 0.0707 0.974 0.02 0 0.98 0.00
#> TCGA.CV.5440.11 3 0.0000 0.997 0.00 0 1.00 0.00
#> TCGA.CV.7101.11 4 0.0000 0.956 0.00 0 0.00 1.00
#> TCGA.CV.6935.11 4 0.0000 0.956 0.00 0 0.00 1.00
#> TCGA.CV.6959.11 1 0.0000 0.949 1.00 0 0.00 0.00
#> TCGA.CV.6938.11 3 0.0000 0.997 0.00 0 1.00 0.00
#> TCGA.CV.6952.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CV.6951.11 1 0.0000 0.949 1.00 0 0.00 0.00
#> TCGA.CV.6939.11 3 0.0000 0.997 0.00 0 1.00 0.00
#> TCGA.CV.6954.11 1 0.0000 0.949 1.00 0 0.00 0.00
#> TCGA.CV.6962.11 4 0.0000 0.956 0.00 0 0.00 1.00
#> TCGA.CV.6961.11 1 0.0000 0.949 1.00 0 0.00 0.00
#> TCGA.CV.6934.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CV.6943.11 1 0.0000 0.949 1.00 0 0.00 0.00
#> TCGA.CV.6936.11 1 0.1211 0.931 0.96 0 0.00 0.04
#> TCGA.D6.6824.01 3 0.0000 0.997 0.00 0 1.00 0.00
#> TCGA.CV.6933.11 3 0.0000 0.997 0.00 0 1.00 0.00
#> TCGA.KU.A6H8.01 1 0.5106 0.697 0.72 0 0.24 0.04
#> TCGA.CV.A6K0.01 1 0.4088 0.826 0.82 0 0.14 0.04
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CV.5435.11 3 0.5555 0.641 0.00 0 0.64 0.22 0.14
#> TCGA.CV.5432.11 4 0.0609 0.975 0.00 0 0.00 0.98 0.02
#> TCGA.CV.5430.11 4 0.0000 0.983 0.00 0 0.00 1.00 0.00
#> TCGA.CV.5434.11 3 0.1732 0.835 0.00 0 0.92 0.00 0.08
#> TCGA.CV.5970.11 5 0.4840 0.586 0.32 0 0.00 0.04 0.64
#> TCGA.CV.5976.11 1 0.4227 0.113 0.58 0 0.00 0.00 0.42
#> TCGA.CV.7103.11 1 0.0000 0.851 1.00 0 0.00 0.00 0.00
#> TCGA.CV.6003.11 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CV.5439.11 3 0.3796 0.583 0.00 0 0.70 0.00 0.30
#> TCGA.CV.5971.11 5 0.3852 0.745 0.22 0 0.02 0.00 0.76
#> TCGA.CV.5966.11 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CV.5977.11 3 0.1410 0.842 0.00 0 0.94 0.00 0.06
#> TCGA.CV.6441.11 1 0.0000 0.851 1.00 0 0.00 0.00 0.00
#> TCGA.CV.5978.11 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CV.5973.11 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CV.6436.11 1 0.1043 0.823 0.96 0 0.00 0.00 0.04
#> TCGA.CV.6433.11 5 0.3690 0.756 0.20 0 0.02 0.00 0.78
#> TCGA.CV.5979.11 3 0.0000 0.842 0.00 0 1.00 0.00 0.00
#> TCGA.CR.6492.01 3 0.3424 0.755 0.00 0 0.76 0.00 0.24
#> TCGA.CV.6955.11 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CV.7238.11 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CV.7089.11 3 0.1732 0.840 0.00 0 0.92 0.00 0.08
#> TCGA.CV.5431.11 4 0.0609 0.982 0.00 0 0.00 0.98 0.02
#> TCGA.CV.7255.11 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CV.7236.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CV.7250.11 4 0.0609 0.975 0.00 0 0.00 0.98 0.02
#> TCGA.CV.5442.11 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CV.5436.11 1 0.3796 0.464 0.70 0 0.00 0.00 0.30
#> TCGA.CV.7245.11 3 0.1732 0.840 0.00 0 0.92 0.00 0.08
#> TCGA.CV.7235.11 3 0.1410 0.827 0.00 0 0.94 0.00 0.06
#> TCGA.CV.7263.11 1 0.4307 -0.222 0.50 0 0.00 0.00 0.50
#> TCGA.CV.6956.11 1 0.0000 0.851 1.00 0 0.00 0.00 0.00
#> TCGA.CR.7393.01 5 0.3424 0.735 0.24 0 0.00 0.00 0.76
#> TCGA.CV.5444.11 3 0.0609 0.843 0.00 0 0.98 0.00 0.02
#> TCGA.CV.7178.11 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CV.5443.11 3 0.5927 0.288 0.00 0 0.54 0.34 0.12
#> TCGA.CR.7397.01 5 0.3561 0.486 0.00 0 0.26 0.00 0.74
#> TCGA.CV.5440.11 3 0.2929 0.775 0.00 0 0.82 0.00 0.18
#> TCGA.CV.7101.11 4 0.1043 0.972 0.00 0 0.00 0.96 0.04
#> TCGA.CV.6935.11 4 0.0000 0.983 0.00 0 0.00 1.00 0.00
#> TCGA.CV.6959.11 1 0.0000 0.851 1.00 0 0.00 0.00 0.00
#> TCGA.CV.6938.11 5 0.4126 0.265 0.00 0 0.38 0.00 0.62
#> TCGA.CV.6952.11 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CV.6951.11 1 0.0000 0.851 1.00 0 0.00 0.00 0.00
#> TCGA.CV.6939.11 3 0.1410 0.842 0.00 0 0.94 0.00 0.06
#> TCGA.CV.6954.11 1 0.0000 0.851 1.00 0 0.00 0.00 0.00
#> TCGA.CV.6962.11 4 0.0609 0.982 0.00 0 0.00 0.98 0.02
#> TCGA.CV.6961.11 1 0.0000 0.851 1.00 0 0.00 0.00 0.00
#> TCGA.CV.6934.11 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.CV.6943.11 1 0.0000 0.851 1.00 0 0.00 0.00 0.00
#> TCGA.CV.6936.11 5 0.3561 0.708 0.26 0 0.00 0.00 0.74
#> TCGA.D6.6824.01 3 0.4075 0.772 0.00 0 0.78 0.06 0.16
#> TCGA.CV.6933.11 3 0.1410 0.827 0.00 0 0.94 0.00 0.06
#> TCGA.KU.A6H8.01 5 0.4527 0.740 0.12 0 0.08 0.02 0.78
#> TCGA.CV.A6K0.01 5 0.3291 0.752 0.12 0 0.04 0.00 0.84
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.CV.5435.11 3 0.6290 0.2915 0.00 0.00 0.54 0.26 0.14 0.06
#> TCGA.CV.5432.11 4 0.3163 0.6757 0.00 0.00 0.00 0.82 0.14 0.04
#> TCGA.CV.5430.11 4 0.0547 0.8142 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.CV.5434.11 3 0.3523 0.6631 0.00 0.00 0.78 0.00 0.04 0.18
#> TCGA.CV.5970.11 5 0.3483 0.7446 0.12 0.00 0.00 0.04 0.82 0.02
#> TCGA.CV.5976.11 1 0.4337 -0.0243 0.50 0.00 0.02 0.00 0.48 0.00
#> TCGA.CV.7103.11 1 0.0547 0.8590 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CV.6003.11 2 0.0937 0.9788 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CV.5439.11 3 0.2793 0.6507 0.00 0.00 0.80 0.00 0.20 0.00
#> TCGA.CV.5971.11 5 0.2094 0.7782 0.08 0.00 0.02 0.00 0.90 0.00
#> TCGA.CV.5966.11 2 0.0937 0.9788 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CV.5977.11 3 0.0937 0.7337 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.CV.6441.11 1 0.0547 0.8565 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CV.5978.11 2 0.0547 0.9814 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CV.5973.11 2 0.0937 0.9788 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CV.6436.11 1 0.2981 0.7416 0.82 0.00 0.00 0.00 0.16 0.02
#> TCGA.CV.6433.11 5 0.2094 0.7782 0.08 0.00 0.02 0.00 0.90 0.00
#> TCGA.CV.5979.11 3 0.2793 0.6710 0.00 0.00 0.80 0.00 0.00 0.20
#> TCGA.CR.6492.01 3 0.6262 0.3565 0.00 0.00 0.46 0.02 0.32 0.20
#> TCGA.CV.6955.11 2 0.0000 0.9821 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7238.11 2 0.0937 0.9788 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CV.7089.11 3 0.2794 0.7089 0.00 0.00 0.86 0.00 0.06 0.08
#> TCGA.CV.5431.11 4 0.1480 0.8067 0.00 0.00 0.00 0.94 0.02 0.04
#> TCGA.CV.7255.11 2 0.0000 0.9821 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7236.01 2 0.0000 0.9821 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7250.11 4 0.2981 0.6655 0.00 0.00 0.00 0.82 0.16 0.02
#> TCGA.CV.5442.11 2 0.0000 0.9821 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5436.11 1 0.4002 0.4909 0.66 0.00 0.00 0.00 0.32 0.02
#> TCGA.CV.7245.11 3 0.0937 0.7337 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.CV.7235.11 3 0.3315 0.6515 0.00 0.00 0.78 0.00 0.02 0.20
#> TCGA.CV.7263.11 5 0.5071 0.2499 0.40 0.00 0.00 0.00 0.52 0.08
#> TCGA.CV.6956.11 1 0.0547 0.8565 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CR.7393.01 5 0.3572 0.7687 0.10 0.00 0.02 0.00 0.82 0.06
#> TCGA.CV.5444.11 3 0.0547 0.7323 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.CV.7178.11 2 0.0000 0.9821 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5443.11 6 0.5618 0.0000 0.00 0.00 0.16 0.34 0.00 0.50
#> TCGA.CR.7397.01 5 0.5292 0.4133 0.00 0.00 0.18 0.00 0.60 0.22
#> TCGA.CV.5440.11 3 0.4983 0.5969 0.00 0.00 0.68 0.04 0.22 0.06
#> TCGA.CV.7101.11 4 0.1267 0.8112 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.CV.6935.11 4 0.1267 0.8105 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.CV.6959.11 1 0.1556 0.8209 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.CV.6938.11 5 0.4199 0.2876 0.00 0.00 0.38 0.00 0.60 0.02
#> TCGA.CV.6952.11 2 0.0937 0.9788 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CV.6951.11 1 0.0000 0.8587 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6939.11 3 0.1092 0.7320 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.CV.6954.11 1 0.0547 0.8590 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CV.6962.11 4 0.1556 0.8026 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.CV.6961.11 1 0.0547 0.8590 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CV.6934.11 2 0.0000 0.9821 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6943.11 1 0.0547 0.8590 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CV.6936.11 5 0.2581 0.7559 0.12 0.00 0.00 0.02 0.86 0.00
#> TCGA.D6.6824.01 3 0.5693 0.4582 0.00 0.00 0.56 0.04 0.08 0.32
#> TCGA.CV.6933.11 3 0.3315 0.6515 0.00 0.00 0.78 0.00 0.02 0.20
#> TCGA.KU.A6H8.01 5 0.3697 0.6860 0.00 0.00 0.06 0.04 0.82 0.08
#> TCGA.CV.A6K0.01 5 0.1480 0.7646 0.04 0.00 0.02 0.00 0.94 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.CV.5435.11 3 0.7599 -0.3374 0.00 0.00 0.30 0.22 0.12 0.06 0.30
#> TCGA.CV.5432.11 4 0.1886 0.8269 0.00 0.00 0.00 0.88 0.12 0.00 0.00
#> TCGA.CV.5430.11 4 0.0504 0.8596 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.CV.5434.11 3 0.4108 0.2873 0.00 0.00 0.66 0.00 0.00 0.28 0.06
#> TCGA.CV.5970.11 5 0.5036 0.6129 0.18 0.00 0.00 0.04 0.68 0.02 0.08
#> TCGA.CV.5976.11 5 0.4127 0.3186 0.36 0.00 0.00 0.00 0.60 0.00 0.04
#> TCGA.CV.7103.11 1 0.0504 0.8629 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.CV.6003.11 2 0.0863 0.9757 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.CV.5439.11 3 0.3186 0.2356 0.00 0.00 0.76 0.00 0.22 0.02 0.00
#> TCGA.CV.5971.11 5 0.2769 0.6926 0.08 0.00 0.00 0.00 0.86 0.02 0.04
#> TCGA.CV.5966.11 2 0.0863 0.9757 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.CV.5977.11 3 0.0863 0.4480 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.CV.6441.11 1 0.1166 0.8601 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.CV.5978.11 2 0.0000 0.9827 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5973.11 2 0.0863 0.9757 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.CV.6436.11 1 0.3526 0.7088 0.76 0.00 0.00 0.00 0.18 0.00 0.06
#> TCGA.CV.6433.11 5 0.2421 0.7011 0.08 0.00 0.02 0.00 0.88 0.02 0.00
#> TCGA.CV.5979.11 3 0.4478 0.3719 0.00 0.00 0.66 0.00 0.00 0.20 0.14
#> TCGA.CR.6492.01 7 0.5776 0.0000 0.00 0.00 0.38 0.00 0.10 0.06 0.46
#> TCGA.CV.6955.11 2 0.0000 0.9827 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7238.11 2 0.0863 0.9757 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.CV.7089.11 3 0.4500 0.3082 0.00 0.00 0.68 0.00 0.02 0.08 0.22
#> TCGA.CV.5431.11 4 0.2376 0.8194 0.00 0.00 0.00 0.86 0.02 0.12 0.00
#> TCGA.CV.7255.11 2 0.0000 0.9827 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7236.01 2 0.0000 0.9827 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7250.11 4 0.3199 0.7868 0.00 0.00 0.00 0.80 0.14 0.00 0.06
#> TCGA.CV.5442.11 2 0.0000 0.9827 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5436.11 1 0.4514 -0.0761 0.48 0.00 0.00 0.00 0.46 0.00 0.06
#> TCGA.CV.7245.11 3 0.2278 0.4071 0.00 0.00 0.88 0.00 0.08 0.00 0.04
#> TCGA.CV.7235.11 3 0.4353 0.4035 0.00 0.00 0.66 0.00 0.00 0.24 0.10
#> TCGA.CV.7263.11 5 0.4338 0.5280 0.28 0.00 0.00 0.00 0.64 0.00 0.08
#> TCGA.CV.6956.11 1 0.1664 0.8571 0.92 0.00 0.00 0.00 0.02 0.00 0.06
#> TCGA.CR.7393.01 5 0.2159 0.6731 0.02 0.00 0.02 0.00 0.90 0.00 0.06
#> TCGA.CV.5444.11 3 0.3263 0.3994 0.00 0.00 0.80 0.00 0.00 0.12 0.08
#> TCGA.CV.7178.11 2 0.0000 0.9827 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5443.11 6 0.3680 0.0000 0.00 0.00 0.14 0.06 0.00 0.78 0.02
#> TCGA.CR.7397.01 5 0.5232 -0.1615 0.00 0.00 0.16 0.00 0.46 0.00 0.38
#> TCGA.CV.5440.11 3 0.6177 -0.1660 0.00 0.00 0.52 0.02 0.20 0.04 0.22
#> TCGA.CV.7101.11 4 0.3526 0.7433 0.00 0.00 0.00 0.76 0.00 0.18 0.06
#> TCGA.CV.6935.11 4 0.0863 0.8609 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.CV.6959.11 1 0.1928 0.8244 0.90 0.00 0.00 0.00 0.08 0.00 0.02
#> TCGA.CV.6938.11 5 0.4671 0.4396 0.00 0.00 0.16 0.00 0.68 0.02 0.14
#> TCGA.CV.6952.11 2 0.0863 0.9757 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.CV.6951.11 1 0.1664 0.8582 0.92 0.00 0.00 0.00 0.02 0.00 0.06
#> TCGA.CV.6939.11 3 0.1664 0.4674 0.00 0.00 0.92 0.00 0.00 0.02 0.06
#> TCGA.CV.6954.11 1 0.0504 0.8629 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.CV.6962.11 4 0.1664 0.8553 0.00 0.00 0.00 0.92 0.00 0.06 0.02
#> TCGA.CV.6961.11 1 0.0000 0.8651 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6934.11 2 0.0000 0.9827 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6943.11 1 0.1006 0.8595 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.CV.6936.11 5 0.3396 0.6871 0.14 0.00 0.00 0.00 0.80 0.04 0.02
#> TCGA.D6.6824.01 3 0.6150 -0.4523 0.00 0.00 0.42 0.00 0.04 0.24 0.30
#> TCGA.CV.6933.11 3 0.4353 0.4035 0.00 0.00 0.66 0.00 0.00 0.24 0.10
#> TCGA.KU.A6H8.01 5 0.4777 0.5146 0.00 0.00 0.10 0.02 0.70 0.02 0.16
#> TCGA.CV.A6K0.01 5 0.3257 0.6620 0.02 0.00 0.02 0.00 0.84 0.04 0.08
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.CV.5435.11 4 0.6936 -0.2179 0.00 0.00 0.22 0.38 0.06 0.10 0.24 0.00
#> TCGA.CV.5432.11 4 0.1741 0.7286 0.00 0.00 0.00 0.92 0.04 0.02 0.02 0.00
#> TCGA.CV.5430.11 4 0.0000 0.7469 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5434.11 3 0.4801 0.4396 0.00 0.04 0.64 0.00 0.00 0.18 0.14 0.00
#> TCGA.CV.5970.11 5 0.3637 0.6015 0.08 0.06 0.00 0.02 0.80 0.00 0.04 0.00
#> TCGA.CV.5976.11 1 0.5093 0.0383 0.46 0.06 0.00 0.00 0.42 0.00 0.06 0.00
#> TCGA.CV.7103.11 1 0.1557 0.7993 0.92 0.06 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.CV.6003.11 8 0.0941 0.9804 0.00 0.02 0.00 0.00 0.00 0.02 0.00 0.96
#> TCGA.CV.5439.11 3 0.4943 0.3823 0.00 0.04 0.64 0.00 0.22 0.02 0.08 0.00
#> TCGA.CV.5971.11 5 0.1741 0.6631 0.04 0.02 0.00 0.00 0.92 0.00 0.02 0.00
#> TCGA.CV.5966.11 8 0.0941 0.9804 0.00 0.02 0.00 0.00 0.00 0.02 0.00 0.96
#> TCGA.CV.5977.11 3 0.2204 0.5510 0.00 0.04 0.90 0.00 0.02 0.02 0.02 0.00
#> TCGA.CV.6441.11 1 0.1741 0.8055 0.92 0.02 0.00 0.00 0.02 0.00 0.04 0.00
#> TCGA.CV.5978.11 8 0.0471 0.9810 0.00 0.02 0.00 0.00 0.00 0.00 0.00 0.98
#> TCGA.CV.5973.11 8 0.0941 0.9804 0.00 0.02 0.00 0.00 0.00 0.02 0.00 0.96
#> TCGA.CV.6436.11 1 0.3586 0.7206 0.78 0.06 0.00 0.00 0.12 0.00 0.04 0.00
#> TCGA.CV.6433.11 5 0.1887 0.6762 0.04 0.00 0.00 0.00 0.90 0.00 0.06 0.00
#> TCGA.CV.5979.11 3 0.4460 0.4691 0.00 0.12 0.70 0.00 0.00 0.12 0.06 0.00
#> TCGA.CR.6492.01 7 0.5943 0.4367 0.00 0.00 0.30 0.02 0.14 0.06 0.48 0.00
#> TCGA.CV.6955.11 8 0.0000 0.9804 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CV.7238.11 8 0.0941 0.9804 0.00 0.02 0.00 0.00 0.00 0.02 0.00 0.96
#> TCGA.CV.7089.11 3 0.5435 0.2771 0.00 0.36 0.50 0.00 0.02 0.06 0.06 0.00
#> TCGA.CV.5431.11 4 0.2020 0.7296 0.00 0.02 0.00 0.90 0.02 0.06 0.00 0.00
#> TCGA.CV.7255.11 8 0.0471 0.9810 0.00 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.CV.7236.01 8 0.0000 0.9804 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CV.7250.11 4 0.1741 0.7273 0.00 0.00 0.00 0.92 0.02 0.02 0.04 0.00
#> TCGA.CV.5442.11 8 0.0000 0.9804 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CV.5436.11 1 0.4586 0.2390 0.52 0.02 0.00 0.00 0.40 0.00 0.06 0.00
#> TCGA.CV.7245.11 3 0.2020 0.5385 0.00 0.00 0.90 0.00 0.06 0.02 0.02 0.00
#> TCGA.CV.7235.11 3 0.5484 0.3361 0.00 0.28 0.50 0.00 0.00 0.18 0.04 0.00
#> TCGA.CV.7263.11 5 0.6317 0.4905 0.22 0.06 0.00 0.02 0.50 0.02 0.18 0.00
#> TCGA.CV.6956.11 1 0.0471 0.8132 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.CR.7393.01 5 0.4647 0.6097 0.12 0.02 0.00 0.00 0.68 0.02 0.16 0.00
#> TCGA.CV.5444.11 3 0.3421 0.5072 0.00 0.08 0.80 0.00 0.00 0.08 0.04 0.00
#> TCGA.CV.7178.11 8 0.0000 0.9804 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CV.5443.11 6 0.2132 0.0000 0.00 0.00 0.04 0.08 0.00 0.88 0.00 0.00
#> TCGA.CR.7397.01 7 0.3880 0.2530 0.00 0.00 0.08 0.00 0.24 0.00 0.68 0.00
#> TCGA.CV.5440.11 3 0.7586 -0.1398 0.00 0.02 0.38 0.16 0.14 0.12 0.18 0.00
#> TCGA.CV.7101.11 4 0.4528 0.5761 0.00 0.04 0.00 0.68 0.00 0.14 0.14 0.00
#> TCGA.CV.6935.11 4 0.2348 0.7245 0.00 0.02 0.00 0.88 0.00 0.04 0.06 0.00
#> TCGA.CV.6959.11 1 0.1887 0.7975 0.90 0.00 0.00 0.00 0.06 0.00 0.04 0.00
#> TCGA.CV.6938.11 5 0.5491 0.2285 0.00 0.08 0.20 0.00 0.56 0.00 0.16 0.00
#> TCGA.CV.6952.11 8 0.0941 0.9804 0.00 0.02 0.00 0.00 0.00 0.02 0.00 0.96
#> TCGA.CV.6951.11 1 0.0471 0.8097 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.CV.6939.11 3 0.3402 0.5365 0.00 0.04 0.82 0.00 0.02 0.06 0.06 0.00
#> TCGA.CV.6954.11 1 0.2025 0.7856 0.88 0.10 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.CV.6962.11 4 0.3078 0.6957 0.00 0.02 0.00 0.82 0.00 0.10 0.06 0.00
#> TCGA.CV.6961.11 1 0.1563 0.7835 0.90 0.10 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6934.11 8 0.0000 0.9804 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CV.6943.11 1 0.1091 0.7992 0.94 0.06 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6936.11 5 0.2674 0.6702 0.04 0.04 0.00 0.00 0.86 0.00 0.06 0.00
#> TCGA.D6.6824.01 7 0.7296 0.2070 0.00 0.06 0.26 0.10 0.02 0.20 0.36 0.00
#> TCGA.CV.6933.11 3 0.5484 0.3489 0.00 0.28 0.50 0.00 0.00 0.18 0.04 0.00
#> TCGA.KU.A6H8.01 5 0.5583 0.3587 0.00 0.02 0.04 0.06 0.52 0.02 0.34 0.00
#> TCGA.CV.A6K0.01 5 0.3808 0.5337 0.02 0.00 0.02 0.00 0.66 0.00 0.30 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 , Node0121 , Node0122 , Node0211 , Node0212 , Node0213 , Node0221 , Node0222 , Node0223 , Node0224 , Node0225-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0511 , Node0512 , Node0521-leaf , Node0522 , Node0523-leaf , Node0524-leaf .
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 16 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 0.4006 0.600 0.600
#> 3 3 1.000 1.000 1.000 0.6858 0.642 0.442
#> 4 4 1.000 0.938 1.000 0.0247 0.983 0.949
#> 5 5 0.783 0.789 0.960 0.0674 0.942 0.816
#> 6 6 0.700 0.391 0.718 0.0636 0.825 0.447
#> 7 7 0.742 0.455 0.828 0.0569 0.917 0.630
#> 8 8 0.800 0.368 0.769 0.0478 0.900 0.478
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.CV.5435.11 1 0 1 1 0
#> TCGA.CV.5434.11 1 0 1 1 0
#> TCGA.CV.5439.11 1 0 1 1 0
#> TCGA.CV.5977.11 1 0 1 1 0
#> TCGA.CV.5979.11 2 0 1 0 1
#> TCGA.CR.6492.01 1 0 1 1 0
#> TCGA.CV.7089.11 2 0 1 0 1
#> TCGA.CV.7245.11 1 0 1 1 0
#> TCGA.CV.7235.11 2 0 1 0 1
#> TCGA.CV.5444.11 1 0 1 1 0
#> TCGA.CR.7397.01 1 0 1 1 0
#> TCGA.CV.5440.11 1 0 1 1 0
#> TCGA.CV.6938.11 1 0 1 1 0
#> TCGA.CV.6939.11 1 0 1 1 0
#> TCGA.D6.6824.01 1 0 1 1 0
#> TCGA.CV.6933.11 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CV.5435.11 3 0 1 0 0 1
#> TCGA.CV.5434.11 3 0 1 0 0 1
#> TCGA.CV.5439.11 1 0 1 1 0 0
#> TCGA.CV.5977.11 1 0 1 1 0 0
#> TCGA.CV.5979.11 3 0 1 0 0 1
#> TCGA.CR.6492.01 3 0 1 0 0 1
#> TCGA.CV.7089.11 2 0 1 0 1 0
#> TCGA.CV.7245.11 1 0 1 1 0 0
#> TCGA.CV.7235.11 2 0 1 0 1 0
#> TCGA.CV.5444.11 1 0 1 1 0 0
#> TCGA.CR.7397.01 1 0 1 1 0 0
#> TCGA.CV.5440.11 1 0 1 1 0 0
#> TCGA.CV.6938.11 3 0 1 0 0 1
#> TCGA.CV.6939.11 1 0 1 1 0 0
#> TCGA.D6.6824.01 3 0 1 0 0 1
#> TCGA.CV.6933.11 2 0 1 0 1 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.CV.5435.11 3 0 1 0 0 1 0
#> TCGA.CV.5434.11 3 0 1 0 0 1 0
#> TCGA.CV.5439.11 1 0 1 1 0 0 0
#> TCGA.CV.5977.11 1 0 1 1 0 0 0
#> TCGA.CV.5979.11 3 0 1 0 0 1 0
#> TCGA.CR.6492.01 3 0 1 0 0 1 0
#> TCGA.CV.7089.11 4 0 0 0 0 0 1
#> TCGA.CV.7245.11 1 0 1 1 0 0 0
#> TCGA.CV.7235.11 2 0 1 0 1 0 0
#> TCGA.CV.5444.11 1 0 1 1 0 0 0
#> TCGA.CR.7397.01 1 0 1 1 0 0 0
#> TCGA.CV.5440.11 1 0 1 1 0 0 0
#> TCGA.CV.6938.11 3 0 1 0 0 1 0
#> TCGA.CV.6939.11 1 0 1 1 0 0 0
#> TCGA.D6.6824.01 3 0 1 0 0 1 0
#> TCGA.CV.6933.11 2 0 1 0 1 0 0
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CV.5435.11 3 0.000 0.941 0.00 0.00 1.00 0 0.0
#> TCGA.CV.5434.11 3 0.202 0.909 0.00 0.10 0.90 0 0.0
#> TCGA.CV.5439.11 1 0.000 0.947 1.00 0.00 0.00 0 0.0
#> TCGA.CV.5977.11 1 0.000 0.947 1.00 0.00 0.00 0 0.0
#> TCGA.CV.5979.11 2 0.141 0.783 0.00 0.94 0.06 0 0.0
#> TCGA.CR.6492.01 3 0.000 0.941 0.00 0.00 1.00 0 0.0
#> TCGA.CV.7089.11 4 0.000 0.000 0.00 0.00 0.00 1 0.0
#> TCGA.CV.7245.11 1 0.000 0.947 1.00 0.00 0.00 0 0.0
#> TCGA.CV.7235.11 2 0.202 0.770 0.00 0.90 0.00 0 0.1
#> TCGA.CV.5444.11 1 0.000 0.947 1.00 0.00 0.00 0 0.0
#> TCGA.CR.7397.01 1 0.273 0.830 0.84 0.00 0.16 0 0.0
#> TCGA.CV.5440.11 1 0.228 0.870 0.88 0.00 0.12 0 0.0
#> TCGA.CV.6938.11 3 0.000 0.941 0.00 0.00 1.00 0 0.0
#> TCGA.CV.6939.11 1 0.000 0.947 1.00 0.00 0.00 0 0.0
#> TCGA.D6.6824.01 3 0.202 0.909 0.00 0.10 0.90 0 0.0
#> TCGA.CV.6933.11 5 0.000 0.000 0.00 0.00 0.00 0 1.0
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.CV.5435.11 3 0.3797 0.2260 0.00 0.00 0.58 0 0.00 0.42
#> TCGA.CV.5434.11 3 0.0547 0.6018 0.00 0.00 0.98 0 0.00 0.02
#> TCGA.CV.5439.11 1 0.3864 0.9008 0.52 0.00 0.00 0 0.00 0.48
#> TCGA.CV.5977.11 1 0.3851 0.9150 0.54 0.00 0.00 0 0.00 0.46
#> TCGA.CV.5979.11 3 0.5569 0.0243 0.28 0.18 0.54 0 0.00 0.00
#> TCGA.CR.6492.01 3 0.3499 0.4065 0.00 0.00 0.68 0 0.00 0.32
#> TCGA.CV.7089.11 4 0.0000 0.0000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.CV.7245.11 1 0.3851 0.9150 0.54 0.00 0.00 0 0.00 0.46
#> TCGA.CV.7235.11 2 0.0547 0.0000 0.00 0.98 0.00 0 0.02 0.00
#> TCGA.CV.5444.11 1 0.3851 0.9150 0.54 0.00 0.00 0 0.00 0.46
#> TCGA.CR.7397.01 6 0.0000 0.3536 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.CV.5440.11 6 0.1814 0.1257 0.10 0.00 0.00 0 0.00 0.90
#> TCGA.CV.6938.11 6 0.4646 -0.3841 0.04 0.00 0.46 0 0.00 0.50
#> TCGA.CV.6939.11 1 0.3578 0.6613 0.66 0.00 0.00 0 0.00 0.34
#> TCGA.D6.6824.01 3 0.0547 0.5983 0.02 0.00 0.98 0 0.00 0.00
#> TCGA.CV.6933.11 5 0.0000 0.0000 0.00 0.00 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.CV.5435.11 3 0.1928 0.6415 0.02 0.00 0.90 0 0 0.08 0.00
#> TCGA.CV.5434.11 3 0.2572 0.5538 0.00 0.00 0.80 0 0 0.00 0.20
#> TCGA.CV.5439.11 1 0.3558 0.7429 0.52 0.00 0.00 0 0 0.48 0.00
#> TCGA.CV.5977.11 1 0.3546 0.7606 0.54 0.00 0.00 0 0 0.46 0.00
#> TCGA.CV.5979.11 7 0.2512 0.0000 0.00 0.04 0.10 0 0 0.00 0.86
#> TCGA.CR.6492.01 3 0.0504 0.6588 0.00 0.00 0.98 0 0 0.00 0.02
#> TCGA.CV.7089.11 4 0.0000 0.0000 0.00 0.00 0.00 1 0 0.00 0.00
#> TCGA.CV.7245.11 1 0.3546 0.7606 0.54 0.00 0.00 0 0 0.46 0.00
#> TCGA.CV.7235.11 2 0.0000 0.0000 0.00 1.00 0.00 0 0 0.00 0.00
#> TCGA.CV.5444.11 1 0.3546 0.7606 0.54 0.00 0.00 0 0 0.46 0.00
#> TCGA.CR.7397.01 6 0.2259 0.8351 0.00 0.00 0.16 0 0 0.84 0.00
#> TCGA.CV.5440.11 6 0.1928 0.8169 0.02 0.00 0.08 0 0 0.90 0.00
#> TCGA.CV.6938.11 3 0.3927 0.3517 0.04 0.00 0.66 0 0 0.30 0.00
#> TCGA.CV.6939.11 1 0.3199 0.0438 0.80 0.00 0.00 0 0 0.06 0.14
#> TCGA.D6.6824.01 3 0.3294 0.3493 0.00 0.00 0.66 0 0 0.00 0.34
#> TCGA.CV.6933.11 5 0.0000 0.0000 0.00 0.00 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.CV.5435.11 8 0.3333 -0.706 0.00 0 0.50 0 0 0.00 0.00 0.50
#> TCGA.CV.5434.11 3 0.4255 0.732 0.00 0 0.58 0 0 0.00 0.08 0.34
#> TCGA.CV.5439.11 1 0.2071 0.885 0.90 0 0.04 0 0 0.04 0.00 0.02
#> TCGA.CV.5977.11 1 0.0000 0.964 1.00 0 0.00 0 0 0.00 0.00 0.00
#> TCGA.CV.5979.11 7 0.0471 0.000 0.00 0 0.02 0 0 0.00 0.98 0.00
#> TCGA.CR.6492.01 3 0.3237 0.620 0.00 0 0.60 0 0 0.00 0.00 0.40
#> TCGA.CV.7089.11 4 0.0000 0.000 0.00 0 0.00 1 0 0.00 0.00 0.00
#> TCGA.CV.7245.11 1 0.0000 0.964 1.00 0 0.00 0 0 0.00 0.00 0.00
#> TCGA.CV.7235.11 2 0.0000 0.000 0.00 1 0.00 0 0 0.00 0.00 0.00
#> TCGA.CV.5444.11 1 0.0000 0.964 1.00 0 0.00 0 0 0.00 0.00 0.00
#> TCGA.CR.7397.01 6 0.4391 0.420 0.08 0 0.00 0 0 0.50 0.00 0.42
#> TCGA.CV.5440.11 6 0.4996 0.428 0.20 0 0.00 0 0 0.48 0.00 0.32
#> TCGA.CV.6938.11 8 0.0000 0.122 0.00 0 0.00 0 0 0.00 0.00 1.00
#> TCGA.CV.6939.11 6 0.4770 -0.156 0.02 0 0.40 0 0 0.52 0.02 0.04
#> TCGA.D6.6824.01 3 0.4560 0.657 0.00 0 0.60 0 0 0.00 0.18 0.22
#> TCGA.CV.6933.11 5 0.0000 0.000 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: Node0. Child nodes: Node011 , Node012 , Node013-leaf , Node021 , Node022 , Node023 , Node031-leaf , Node032-leaf , Node033 , Node034-leaf , Node041-leaf , Node042-leaf , Node043 , Node051 , Node052 , Node053-leaf .
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 68 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 0.813 0.962 0.979 0.4961 0.496 0.496
#> 3 3 0.981 0.967 0.984 0.3579 0.734 0.512
#> 4 4 0.694 0.725 0.841 0.1131 0.804 0.487
#> 5 5 0.750 0.686 0.822 0.0644 0.924 0.711
#> 6 6 0.752 0.608 0.766 0.0333 0.976 0.887
#> 7 7 0.832 0.733 0.827 0.0293 0.929 0.675
#> 8 8 0.813 0.625 0.789 0.0171 0.943 0.690
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.CR.5247.01 1 0.000 1.000 1.0 0.0
#> TCGA.CV.7263.01 1 0.000 1.000 1.0 0.0
#> TCGA.CV.6960.01 1 0.000 1.000 1.0 0.0
#> TCGA.CV.7245.01 1 0.000 1.000 1.0 0.0
#> TCGA.CN.4739.01 1 0.000 1.000 1.0 0.0
#> TCGA.CV.6956.01 2 0.000 0.952 0.0 1.0
#> TCGA.CV.7091.01 1 0.000 1.000 1.0 0.0
#> TCGA.CV.7242.01 1 0.000 1.000 1.0 0.0
#> TCGA.CR.7398.01 2 0.000 0.952 0.0 1.0
#> TCGA.CV.7253.01 2 0.000 0.952 0.0 1.0
#> TCGA.BA.5555.01 2 0.722 0.800 0.2 0.8
#> TCGA.CV.5441.01 1 0.000 1.000 1.0 0.0
#> TCGA.CV.7250.01 2 0.000 0.952 0.0 1.0
#> TCGA.CR.7364.01 2 0.000 0.952 0.0 1.0
#> TCGA.CR.7402.01 2 0.000 0.952 0.0 1.0
#> TCGA.CN.A49A.01 2 0.000 0.952 0.0 1.0
#> TCGA.CN.A497.01 2 0.722 0.800 0.2 0.8
#> TCGA.D6.6823.01 1 0.000 1.000 1.0 0.0
#> TCGA.BA.A4IF.01 1 0.000 1.000 1.0 0.0
#> TCGA.BA.6869.01 2 0.000 0.952 0.0 1.0
#> TCGA.CV.6941.01 2 0.000 0.952 0.0 1.0
#> TCGA.CV.6954.01 1 0.000 1.000 1.0 0.0
#> TCGA.CQ.6228.01 1 0.000 1.000 1.0 0.0
#> TCGA.CQ.6225.01 2 0.000 0.952 0.0 1.0
#> TCGA.CN.6988.01 1 0.000 1.000 1.0 0.0
#> TCGA.QK.A8Z8.01 2 0.000 0.952 0.0 1.0
#> TCGA.QK.A8Z7.01 2 0.000 0.952 0.0 1.0
#> TCGA.CQ.A4C9.01 1 0.000 1.000 1.0 0.0
#> TCGA.CQ.7072.01 2 0.722 0.800 0.2 0.8
#> TCGA.CN.A63T.01 2 0.722 0.800 0.2 0.8
#> TCGA.F7.A61V.01 1 0.000 1.000 1.0 0.0
#> TCGA.P3.A5QF.01 1 0.000 1.000 1.0 0.0
#> TCGA.BB.A5HZ.01 1 0.000 1.000 1.0 0.0
#> TCGA.CN.A641.01 2 0.000 0.952 0.0 1.0
#> TCGA.QK.AA3J.01 1 0.000 1.000 1.0 0.0
#> TCGA.KU.A66S.01 2 0.000 0.952 0.0 1.0
#> TCGA.BA.A6DL.01 1 0.000 1.000 1.0 0.0
#> TCGA.CV.A461.01 1 0.000 1.000 1.0 0.0
#> TCGA.P3.A6T6.01 1 0.000 1.000 1.0 0.0
#> TCGA.CN.4730.01 1 0.000 1.000 1.0 0.0
#> TCGA.BB.7864.01 1 0.000 1.000 1.0 0.0
#> TCGA.BA.4074.01 1 0.000 1.000 1.0 0.0
#> TCGA.QK.A6VB.01 2 0.000 0.952 0.0 1.0
#> TCGA.HD.7917.01 1 0.000 1.000 1.0 0.0
#> TCGA.CV.7409.01 1 0.000 1.000 1.0 0.0
#> TCGA.UF.A71D.01 1 0.000 1.000 1.0 0.0
#> TCGA.BB.7870.01 2 0.000 0.952 0.0 1.0
#> TCGA.CN.4727.01 2 0.000 0.952 0.0 1.0
#> TCGA.DQ.7595.01 2 0.722 0.800 0.2 0.8
#> TCGA.CN.5360.01 1 0.000 1.000 1.0 0.0
#> TCGA.CN.A6V3.01 2 0.000 0.952 0.0 1.0
#> TCGA.UF.A7JF.01 1 0.000 1.000 1.0 0.0
#> TCGA.CN.4731.01 1 0.000 1.000 1.0 0.0
#> TCGA.CN.A63W.01 2 0.000 0.952 0.0 1.0
#> TCGA.CN.A63U.01 2 0.000 0.952 0.0 1.0
#> TCGA.H7.A6C5.01 1 0.000 1.000 1.0 0.0
#> TCGA.CN.5356.01 2 0.000 0.952 0.0 1.0
#> TCGA.F7.7848.01 1 0.000 1.000 1.0 0.0
#> TCGA.CV.7428.01 1 0.000 1.000 1.0 0.0
#> TCGA.CV.7435.01 1 0.000 1.000 1.0 0.0
#> TCGA.UF.A719.01 2 0.000 0.952 0.0 1.0
#> TCGA.UF.A7JD.01 2 0.000 0.952 0.0 1.0
#> TCGA.UF.A7JH.01 1 0.000 1.000 1.0 0.0
#> TCGA.D6.A6EO.01 1 0.000 1.000 1.0 0.0
#> TCGA.D6.A74Q.01 1 0.000 1.000 1.0 0.0
#> TCGA.BA.A6DE.01 2 0.722 0.800 0.2 0.8
#> TCGA.CV.7440.01 2 0.000 0.952 0.0 1.0
#> TCGA.CV.A6JU.01 2 0.722 0.800 0.2 0.8
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CR.5247.01 1 0.0000 0.966 1.00 0.00 0.00
#> TCGA.CV.7263.01 1 0.0000 0.966 1.00 0.00 0.00
#> TCGA.CV.6960.01 1 0.0000 0.966 1.00 0.00 0.00
#> TCGA.CV.7245.01 3 0.3340 0.856 0.12 0.00 0.88
#> TCGA.CN.4739.01 1 0.0000 0.966 1.00 0.00 0.00
#> TCGA.CV.6956.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.CV.7091.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.CV.7242.01 1 0.0000 0.966 1.00 0.00 0.00
#> TCGA.CR.7398.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.CV.7253.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.BA.5555.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.CV.5441.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.CV.7250.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.CR.7364.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.CR.7402.01 3 0.1529 0.953 0.00 0.04 0.96
#> TCGA.CN.A49A.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.CN.A497.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.D6.6823.01 1 0.0000 0.966 1.00 0.00 0.00
#> TCGA.BA.A4IF.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.BA.6869.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.CV.6941.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.CV.6954.01 1 0.4291 0.798 0.82 0.00 0.18
#> TCGA.CQ.6228.01 1 0.0000 0.966 1.00 0.00 0.00
#> TCGA.CQ.6225.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.CN.6988.01 1 0.0000 0.966 1.00 0.00 0.00
#> TCGA.QK.A8Z8.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.QK.A8Z7.01 3 0.2066 0.933 0.00 0.06 0.94
#> TCGA.CQ.A4C9.01 1 0.5016 0.716 0.76 0.00 0.24
#> TCGA.CQ.7072.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.CN.A63T.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.F7.A61V.01 1 0.0000 0.966 1.00 0.00 0.00
#> TCGA.P3.A5QF.01 1 0.0000 0.966 1.00 0.00 0.00
#> TCGA.BB.A5HZ.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.CN.A641.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.QK.AA3J.01 1 0.5397 0.649 0.72 0.00 0.28
#> TCGA.KU.A66S.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.BA.A6DL.01 1 0.1529 0.937 0.96 0.00 0.04
#> TCGA.CV.A461.01 3 0.0892 0.971 0.02 0.00 0.98
#> TCGA.P3.A6T6.01 1 0.0000 0.966 1.00 0.00 0.00
#> TCGA.CN.4730.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.BB.7864.01 1 0.0000 0.966 1.00 0.00 0.00
#> TCGA.BA.4074.01 1 0.2959 0.885 0.90 0.00 0.10
#> TCGA.QK.A6VB.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HD.7917.01 1 0.0000 0.966 1.00 0.00 0.00
#> TCGA.CV.7409.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.UF.A71D.01 1 0.0000 0.966 1.00 0.00 0.00
#> TCGA.BB.7870.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.CN.4727.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DQ.7595.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.CN.5360.01 1 0.0000 0.966 1.00 0.00 0.00
#> TCGA.CN.A6V3.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.UF.A7JF.01 1 0.0000 0.966 1.00 0.00 0.00
#> TCGA.CN.4731.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.CN.A63W.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.CN.A63U.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.H7.A6C5.01 1 0.0000 0.966 1.00 0.00 0.00
#> TCGA.CN.5356.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.F7.7848.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.CV.7428.01 1 0.0000 0.966 1.00 0.00 0.00
#> TCGA.CV.7435.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.UF.A719.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.UF.A7JD.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.UF.A7JH.01 1 0.0000 0.966 1.00 0.00 0.00
#> TCGA.D6.A6EO.01 1 0.0000 0.966 1.00 0.00 0.00
#> TCGA.D6.A74Q.01 1 0.0000 0.966 1.00 0.00 0.00
#> TCGA.BA.A6DE.01 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.CV.7440.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.CV.A6JU.01 3 0.0000 0.987 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.CR.5247.01 1 0.485 0.2229 0.60 0.00 0.00 0.40
#> TCGA.CV.7263.01 1 0.000 0.9126 1.00 0.00 0.00 0.00
#> TCGA.CV.6960.01 1 0.000 0.9126 1.00 0.00 0.00 0.00
#> TCGA.CV.7245.01 4 0.234 0.7381 0.06 0.00 0.02 0.92
#> TCGA.CN.4739.01 4 0.452 0.5764 0.32 0.00 0.00 0.68
#> TCGA.CV.6956.01 2 0.317 0.8625 0.00 0.84 0.16 0.00
#> TCGA.CV.7091.01 4 0.398 0.5112 0.00 0.00 0.24 0.76
#> TCGA.CV.7242.01 1 0.000 0.9126 1.00 0.00 0.00 0.00
#> TCGA.CR.7398.01 2 0.000 0.8935 0.00 1.00 0.00 0.00
#> TCGA.CV.7253.01 2 0.317 0.8625 0.00 0.84 0.16 0.00
#> TCGA.BA.5555.01 3 0.413 0.7509 0.00 0.00 0.74 0.26
#> TCGA.CV.5441.01 4 0.398 0.5112 0.00 0.00 0.24 0.76
#> TCGA.CV.7250.01 2 0.317 0.8625 0.00 0.84 0.16 0.00
#> TCGA.CR.7364.01 2 0.000 0.8935 0.00 1.00 0.00 0.00
#> TCGA.CR.7402.01 3 0.433 0.7528 0.00 0.04 0.80 0.16
#> TCGA.CN.A49A.01 2 0.000 0.8935 0.00 1.00 0.00 0.00
#> TCGA.CN.A497.01 3 0.380 0.7514 0.00 0.00 0.78 0.22
#> TCGA.D6.6823.01 1 0.000 0.9126 1.00 0.00 0.00 0.00
#> TCGA.BA.A4IF.01 4 0.201 0.6964 0.00 0.00 0.08 0.92
#> TCGA.BA.6869.01 3 0.265 0.6032 0.00 0.12 0.88 0.00
#> TCGA.CV.6941.01 2 0.317 0.8625 0.00 0.84 0.16 0.00
#> TCGA.CV.6954.01 4 0.494 0.7067 0.22 0.00 0.04 0.74
#> TCGA.CQ.6228.01 1 0.000 0.9126 1.00 0.00 0.00 0.00
#> TCGA.CQ.6225.01 2 0.265 0.8734 0.00 0.88 0.12 0.00
#> TCGA.CN.6988.01 1 0.000 0.9126 1.00 0.00 0.00 0.00
#> TCGA.QK.A8Z8.01 2 0.000 0.8935 0.00 1.00 0.00 0.00
#> TCGA.QK.A8Z7.01 3 0.191 0.6961 0.00 0.04 0.94 0.02
#> TCGA.CQ.A4C9.01 4 0.494 0.7067 0.22 0.00 0.04 0.74
#> TCGA.CQ.7072.01 3 0.380 0.7514 0.00 0.00 0.78 0.22
#> TCGA.CN.A63T.01 3 0.413 0.7509 0.00 0.00 0.74 0.26
#> TCGA.F7.A61V.01 1 0.000 0.9126 1.00 0.00 0.00 0.00
#> TCGA.P3.A5QF.01 1 0.539 0.5239 0.68 0.00 0.04 0.28
#> TCGA.BB.A5HZ.01 4 0.398 0.5112 0.00 0.00 0.24 0.76
#> TCGA.CN.A641.01 2 0.000 0.8935 0.00 1.00 0.00 0.00
#> TCGA.QK.AA3J.01 4 0.361 0.7023 0.20 0.00 0.00 0.80
#> TCGA.KU.A66S.01 2 0.000 0.8935 0.00 1.00 0.00 0.00
#> TCGA.BA.A6DL.01 4 0.494 0.6678 0.22 0.00 0.04 0.74
#> TCGA.CV.A461.01 4 0.121 0.7090 0.00 0.00 0.04 0.96
#> TCGA.P3.A6T6.01 1 0.000 0.9126 1.00 0.00 0.00 0.00
#> TCGA.CN.4730.01 4 0.164 0.7084 0.00 0.00 0.06 0.94
#> TCGA.BB.7864.01 1 0.000 0.9126 1.00 0.00 0.00 0.00
#> TCGA.BA.4074.01 4 0.494 0.7067 0.22 0.00 0.04 0.74
#> TCGA.QK.A6VB.01 2 0.317 0.8625 0.00 0.84 0.16 0.00
#> TCGA.HD.7917.01 1 0.000 0.9126 1.00 0.00 0.00 0.00
#> TCGA.CV.7409.01 4 0.164 0.7003 0.00 0.00 0.06 0.94
#> TCGA.UF.A71D.01 4 0.428 0.6362 0.28 0.00 0.00 0.72
#> TCGA.BB.7870.01 2 0.000 0.8935 0.00 1.00 0.00 0.00
#> TCGA.CN.4727.01 3 0.495 0.2657 0.00 0.44 0.56 0.00
#> TCGA.DQ.7595.01 3 0.428 0.7193 0.00 0.00 0.72 0.28
#> TCGA.CN.5360.01 1 0.601 -0.0224 0.50 0.00 0.04 0.46
#> TCGA.CN.A6V3.01 3 0.380 0.7552 0.00 0.00 0.78 0.22
#> TCGA.UF.A7JF.01 1 0.000 0.9126 1.00 0.00 0.00 0.00
#> TCGA.CN.4731.01 4 0.380 0.5333 0.00 0.00 0.22 0.78
#> TCGA.CN.A63W.01 2 0.499 -0.1191 0.00 0.52 0.48 0.00
#> TCGA.CN.A63U.01 3 0.495 0.2657 0.00 0.44 0.56 0.00
#> TCGA.H7.A6C5.01 1 0.164 0.8595 0.94 0.00 0.00 0.06
#> TCGA.CN.5356.01 2 0.000 0.8935 0.00 1.00 0.00 0.00
#> TCGA.F7.7848.01 4 0.164 0.7084 0.00 0.00 0.06 0.94
#> TCGA.CV.7428.01 1 0.000 0.9126 1.00 0.00 0.00 0.00
#> TCGA.CV.7435.01 3 0.471 0.6361 0.00 0.00 0.64 0.36
#> TCGA.UF.A719.01 2 0.000 0.8935 0.00 1.00 0.00 0.00
#> TCGA.UF.A7JD.01 2 0.361 0.8388 0.00 0.80 0.20 0.00
#> TCGA.UF.A7JH.01 1 0.000 0.9126 1.00 0.00 0.00 0.00
#> TCGA.D6.A6EO.01 4 0.551 0.5436 0.30 0.00 0.04 0.66
#> TCGA.D6.A74Q.01 1 0.000 0.9126 1.00 0.00 0.00 0.00
#> TCGA.BA.A6DE.01 3 0.471 0.6397 0.00 0.00 0.64 0.36
#> TCGA.CV.7440.01 3 0.428 0.3184 0.00 0.28 0.72 0.00
#> TCGA.CV.A6JU.01 3 0.413 0.7509 0.00 0.00 0.74 0.26
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CR.5247.01 4 0.3895 0.227 0.32 0.00 0.00 0.68 0.00
#> TCGA.CV.7263.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6960.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7245.01 4 0.2516 0.485 0.00 0.00 0.00 0.86 0.14
#> TCGA.CN.4739.01 4 0.4458 0.391 0.12 0.00 0.00 0.76 0.12
#> TCGA.CV.6956.01 2 0.3852 0.845 0.00 0.76 0.02 0.00 0.22
#> TCGA.CV.7091.01 4 0.6133 0.276 0.00 0.00 0.16 0.54 0.30
#> TCGA.CV.7242.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7398.01 2 0.1216 0.876 0.00 0.96 0.02 0.00 0.02
#> TCGA.CV.7253.01 2 0.3852 0.845 0.00 0.76 0.02 0.00 0.22
#> TCGA.BA.5555.01 3 0.4398 0.721 0.00 0.00 0.72 0.04 0.24
#> TCGA.CV.5441.01 4 0.4818 0.475 0.00 0.00 0.10 0.72 0.18
#> TCGA.CV.7250.01 2 0.3852 0.845 0.00 0.76 0.02 0.00 0.22
#> TCGA.CR.7364.01 2 0.1216 0.876 0.00 0.96 0.02 0.00 0.02
#> TCGA.CR.7402.01 3 0.0609 0.739 0.00 0.00 0.98 0.00 0.02
#> TCGA.CN.A49A.01 2 0.0000 0.889 0.00 1.00 0.00 0.00 0.00
#> TCGA.CN.A497.01 3 0.4644 0.714 0.00 0.00 0.68 0.04 0.28
#> TCGA.D6.6823.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A4IF.01 5 0.5013 0.404 0.00 0.00 0.08 0.24 0.68
#> TCGA.BA.6869.01 3 0.2280 0.691 0.00 0.00 0.88 0.00 0.12
#> TCGA.CV.6941.01 2 0.3852 0.845 0.00 0.76 0.02 0.00 0.22
#> TCGA.CV.6954.01 4 0.1410 0.592 0.06 0.00 0.00 0.94 0.00
#> TCGA.CQ.6228.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.6225.01 2 0.2020 0.881 0.00 0.90 0.00 0.00 0.10
#> TCGA.CN.6988.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.QK.A8Z8.01 2 0.0000 0.889 0.00 1.00 0.00 0.00 0.00
#> TCGA.QK.A8Z7.01 3 0.1410 0.727 0.00 0.00 0.94 0.00 0.06
#> TCGA.CQ.A4C9.01 4 0.1410 0.592 0.06 0.00 0.00 0.94 0.00
#> TCGA.CQ.7072.01 3 0.4990 0.674 0.00 0.00 0.60 0.04 0.36
#> TCGA.CN.A63T.01 3 0.4644 0.702 0.00 0.00 0.68 0.04 0.28
#> TCGA.F7.A61V.01 1 0.2331 0.867 0.90 0.00 0.00 0.02 0.08
#> TCGA.P3.A5QF.01 5 0.6746 0.442 0.36 0.00 0.00 0.26 0.38
#> TCGA.BB.A5HZ.01 4 0.4818 0.475 0.00 0.00 0.10 0.72 0.18
#> TCGA.CN.A641.01 2 0.1648 0.876 0.00 0.94 0.04 0.00 0.02
#> TCGA.QK.AA3J.01 4 0.2331 0.534 0.02 0.00 0.00 0.90 0.08
#> TCGA.KU.A66S.01 2 0.0000 0.889 0.00 1.00 0.00 0.00 0.00
#> TCGA.BA.A6DL.01 4 0.6019 -0.396 0.12 0.00 0.00 0.50 0.38
#> TCGA.CV.A461.01 4 0.1043 0.565 0.00 0.00 0.00 0.96 0.04
#> TCGA.P3.A6T6.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4730.01 5 0.4990 0.453 0.00 0.00 0.04 0.36 0.60
#> TCGA.BB.7864.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.BA.4074.01 4 0.1410 0.592 0.06 0.00 0.00 0.94 0.00
#> TCGA.QK.A6VB.01 2 0.3852 0.845 0.00 0.76 0.02 0.00 0.22
#> TCGA.HD.7917.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7409.01 4 0.2012 0.572 0.00 0.00 0.02 0.92 0.06
#> TCGA.UF.A71D.01 4 0.1410 0.592 0.06 0.00 0.00 0.94 0.00
#> TCGA.BB.7870.01 2 0.0000 0.889 0.00 1.00 0.00 0.00 0.00
#> TCGA.CN.4727.01 3 0.3521 0.680 0.00 0.14 0.82 0.00 0.04
#> TCGA.DQ.7595.01 3 0.4990 0.646 0.00 0.00 0.60 0.04 0.36
#> TCGA.CN.5360.01 5 0.6794 0.456 0.32 0.00 0.00 0.30 0.38
#> TCGA.CN.A6V3.01 3 0.3106 0.739 0.00 0.00 0.84 0.02 0.14
#> TCGA.UF.A7JF.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4731.01 4 0.4373 0.502 0.00 0.00 0.08 0.76 0.16
#> TCGA.CN.A63W.01 3 0.3513 0.655 0.00 0.18 0.80 0.00 0.02
#> TCGA.CN.A63U.01 3 0.3521 0.680 0.00 0.14 0.82 0.00 0.04
#> TCGA.H7.A6C5.01 1 0.3521 0.721 0.82 0.00 0.00 0.14 0.04
#> TCGA.CN.5356.01 2 0.1043 0.889 0.00 0.96 0.00 0.00 0.04
#> TCGA.F7.7848.01 5 0.5173 0.382 0.00 0.00 0.04 0.46 0.50
#> TCGA.CV.7428.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7435.01 3 0.6254 0.492 0.00 0.00 0.50 0.16 0.34
#> TCGA.UF.A719.01 2 0.0000 0.889 0.00 1.00 0.00 0.00 0.00
#> TCGA.UF.A7JD.01 2 0.6157 0.652 0.00 0.56 0.22 0.00 0.22
#> TCGA.UF.A7JH.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.D6.A6EO.01 4 0.6447 -0.458 0.18 0.00 0.00 0.44 0.38
#> TCGA.D6.A74Q.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A6DE.01 4 0.6244 0.306 0.00 0.00 0.26 0.54 0.20
#> TCGA.CV.7440.01 3 0.3291 0.673 0.00 0.04 0.84 0.00 0.12
#> TCGA.CV.A6JU.01 3 0.4644 0.702 0.00 0.00 0.68 0.04 0.28
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.CR.5247.01 4 0.3679 0.509 0.20 0.00 0.00 0.76 0.00 0.04
#> TCGA.CV.7263.01 1 0.0937 0.949 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.CV.6960.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7245.01 4 0.1814 0.687 0.00 0.00 0.00 0.90 0.10 0.00
#> TCGA.CN.4739.01 4 0.4162 0.522 0.12 0.00 0.00 0.78 0.06 0.04
#> TCGA.CV.6956.01 2 0.3756 -0.127 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.CV.7091.01 4 0.5574 0.372 0.00 0.00 0.44 0.46 0.02 0.08
#> TCGA.CV.7242.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7398.01 2 0.1807 0.544 0.00 0.92 0.00 0.00 0.02 0.06
#> TCGA.CV.7253.01 2 0.3756 -0.127 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.BA.5555.01 3 0.0000 0.604 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.5441.01 4 0.4607 0.682 0.00 0.00 0.18 0.72 0.02 0.08
#> TCGA.CV.7250.01 2 0.3756 -0.127 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.CR.7364.01 2 0.1807 0.544 0.00 0.92 0.00 0.00 0.02 0.06
#> TCGA.CR.7402.01 3 0.5419 0.613 0.00 0.00 0.58 0.00 0.20 0.22
#> TCGA.CN.A49A.01 2 0.0000 0.623 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.A497.01 3 0.4566 0.527 0.00 0.00 0.70 0.00 0.14 0.16
#> TCGA.D6.6823.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A4IF.01 5 0.5825 0.416 0.00 0.00 0.22 0.04 0.60 0.14
#> TCGA.BA.6869.01 3 0.5798 0.570 0.00 0.00 0.48 0.00 0.20 0.32
#> TCGA.CV.6941.01 2 0.3756 -0.127 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.CV.6954.01 4 0.0000 0.753 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CQ.6228.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.6225.01 2 0.2454 0.493 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.CN.6988.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QK.A8Z8.01 2 0.0000 0.623 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QK.A8Z7.01 3 0.5963 0.576 0.00 0.00 0.44 0.00 0.24 0.32
#> TCGA.CQ.A4C9.01 4 0.0000 0.753 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CQ.7072.01 3 0.4536 0.484 0.00 0.00 0.70 0.00 0.12 0.18
#> TCGA.CN.A63T.01 3 0.1267 0.578 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.F7.A61V.01 1 0.3351 0.766 0.80 0.00 0.00 0.00 0.16 0.04
#> TCGA.P3.A5QF.01 5 0.5291 0.615 0.30 0.00 0.00 0.08 0.60 0.02
#> TCGA.BB.A5HZ.01 4 0.4607 0.682 0.00 0.00 0.18 0.72 0.02 0.08
#> TCGA.CN.A641.01 2 0.2094 0.534 0.00 0.90 0.00 0.00 0.02 0.08
#> TCGA.QK.AA3J.01 4 0.0937 0.734 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.KU.A66S.01 2 0.0000 0.623 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A6DL.01 5 0.5029 0.663 0.12 0.00 0.00 0.26 0.62 0.00
#> TCGA.CV.A461.01 4 0.3572 0.712 0.00 0.00 0.02 0.82 0.10 0.06
#> TCGA.P3.A6T6.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4730.01 5 0.5073 0.641 0.00 0.00 0.16 0.14 0.68 0.02
#> TCGA.BB.7864.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.4074.01 4 0.0000 0.753 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.QK.A6VB.01 2 0.3756 -0.127 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.HD.7917.01 1 0.0937 0.949 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.CV.7409.01 4 0.2629 0.742 0.00 0.00 0.02 0.88 0.02 0.08
#> TCGA.UF.A71D.01 4 0.0000 0.753 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BB.7870.01 2 0.0000 0.623 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4727.01 3 0.6750 0.559 0.00 0.06 0.46 0.00 0.22 0.26
#> TCGA.DQ.7595.01 3 0.5173 0.464 0.00 0.00 0.62 0.00 0.20 0.18
#> TCGA.CN.5360.01 5 0.4798 0.620 0.30 0.00 0.00 0.08 0.62 0.00
#> TCGA.CN.A6V3.01 3 0.2474 0.628 0.00 0.00 0.88 0.00 0.08 0.04
#> TCGA.UF.A7JF.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4731.01 4 0.4265 0.704 0.00 0.00 0.14 0.76 0.02 0.08
#> TCGA.CN.A63W.01 3 0.7320 0.472 0.00 0.12 0.38 0.00 0.22 0.28
#> TCGA.CN.A63U.01 3 0.7238 0.514 0.00 0.10 0.38 0.00 0.24 0.28
#> TCGA.H7.A6C5.01 1 0.3007 0.849 0.86 0.00 0.00 0.02 0.08 0.04
#> TCGA.CN.5356.01 2 0.2048 0.546 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.F7.7848.01 5 0.4926 0.618 0.00 0.00 0.12 0.24 0.64 0.00
#> TCGA.CV.7428.01 1 0.0937 0.949 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.CV.7435.01 3 0.4042 0.459 0.00 0.00 0.76 0.04 0.02 0.18
#> TCGA.UF.A719.01 2 0.0547 0.617 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.UF.A7JD.01 6 0.3756 0.000 0.00 0.40 0.00 0.00 0.00 0.60
#> TCGA.UF.A7JH.01 1 0.0937 0.949 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.D6.A6EO.01 5 0.5364 0.619 0.14 0.00 0.00 0.30 0.56 0.00
#> TCGA.D6.A74Q.01 1 0.0000 0.962 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A6DE.01 4 0.5564 0.380 0.00 0.00 0.42 0.48 0.02 0.08
#> TCGA.CV.7440.01 3 0.6262 0.553 0.00 0.02 0.46 0.00 0.20 0.32
#> TCGA.CV.A6JU.01 3 0.1267 0.578 0.00 0.00 0.94 0.00 0.00 0.06
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.CR.5247.01 4 0.2512 0.787 0.10 0.00 0.00 0.86 0.00 0.04 0.00
#> TCGA.CV.7263.01 6 0.0863 0.928 0.04 0.00 0.00 0.00 0.00 0.96 0.00
#> TCGA.CV.6960.01 6 0.0000 0.940 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CV.7245.01 4 0.3199 0.752 0.06 0.00 0.00 0.80 0.14 0.00 0.00
#> TCGA.CN.4739.01 4 0.2803 0.773 0.06 0.00 0.00 0.84 0.10 0.00 0.00
#> TCGA.CV.6956.01 2 0.4175 0.720 0.38 0.58 0.00 0.00 0.00 0.00 0.04
#> TCGA.CV.7091.01 3 0.4309 0.532 0.12 0.00 0.68 0.20 0.00 0.00 0.00
#> TCGA.CV.7242.01 6 0.0000 0.940 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CR.7398.01 2 0.1718 0.754 0.04 0.92 0.00 0.00 0.00 0.00 0.04
#> TCGA.CV.7253.01 2 0.4175 0.720 0.38 0.58 0.00 0.00 0.00 0.00 0.04
#> TCGA.BA.5555.01 3 0.2572 0.500 0.00 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.CV.5441.01 3 0.4945 0.332 0.12 0.00 0.52 0.36 0.00 0.00 0.00
#> TCGA.CV.7250.01 2 0.4175 0.720 0.38 0.58 0.00 0.00 0.00 0.00 0.04
#> TCGA.CR.7364.01 2 0.1718 0.754 0.04 0.92 0.00 0.00 0.00 0.00 0.04
#> TCGA.CR.7402.01 7 0.2376 0.876 0.02 0.00 0.12 0.00 0.00 0.00 0.86
#> TCGA.CN.A49A.01 2 0.0000 0.792 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.A497.01 3 0.5984 0.263 0.26 0.00 0.48 0.00 0.04 0.00 0.22
#> TCGA.D6.6823.01 6 0.0000 0.940 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BA.A4IF.01 5 0.4535 0.553 0.24 0.00 0.12 0.00 0.64 0.00 0.00
#> TCGA.BA.6869.01 7 0.1928 0.897 0.02 0.00 0.08 0.00 0.00 0.00 0.90
#> TCGA.CV.6941.01 2 0.4175 0.720 0.38 0.58 0.00 0.00 0.00 0.00 0.04
#> TCGA.CV.6954.01 4 0.0000 0.838 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CQ.6228.01 6 0.0000 0.940 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CQ.6225.01 2 0.3244 0.775 0.18 0.78 0.00 0.00 0.00 0.00 0.04
#> TCGA.CN.6988.01 6 0.0000 0.940 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.QK.A8Z8.01 2 0.0000 0.792 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QK.A8Z7.01 7 0.2857 0.845 0.06 0.00 0.04 0.00 0.04 0.00 0.86
#> TCGA.CQ.A4C9.01 4 0.0000 0.838 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CQ.7072.01 3 0.5861 0.318 0.28 0.00 0.50 0.00 0.04 0.00 0.18
#> TCGA.CN.A63T.01 3 0.1433 0.592 0.00 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.F7.A61V.01 6 0.4003 0.520 0.04 0.00 0.00 0.00 0.32 0.64 0.00
#> TCGA.P3.A5QF.01 5 0.2706 0.851 0.00 0.00 0.02 0.04 0.88 0.04 0.02
#> TCGA.BB.A5HZ.01 3 0.4945 0.332 0.12 0.00 0.52 0.36 0.00 0.00 0.00
#> TCGA.CN.A641.01 2 0.2016 0.758 0.04 0.90 0.00 0.00 0.00 0.00 0.06
#> TCGA.QK.AA3J.01 4 0.2278 0.807 0.08 0.00 0.00 0.88 0.04 0.00 0.00
#> TCGA.KU.A66S.01 2 0.0000 0.792 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A6DL.01 5 0.1433 0.856 0.00 0.00 0.00 0.08 0.92 0.00 0.00
#> TCGA.CV.A461.01 4 0.5393 0.435 0.04 0.00 0.12 0.58 0.26 0.00 0.00
#> TCGA.P3.A6T6.01 6 0.0000 0.940 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CN.4730.01 5 0.1363 0.846 0.02 0.00 0.00 0.04 0.94 0.00 0.00
#> TCGA.BB.7864.01 6 0.0000 0.940 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BA.4074.01 4 0.0000 0.838 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.QK.A6VB.01 2 0.4175 0.720 0.38 0.58 0.00 0.00 0.00 0.00 0.04
#> TCGA.HD.7917.01 6 0.0863 0.928 0.04 0.00 0.00 0.00 0.00 0.96 0.00
#> TCGA.CV.7409.01 4 0.4177 0.536 0.12 0.00 0.18 0.70 0.00 0.00 0.00
#> TCGA.UF.A71D.01 4 0.0000 0.838 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BB.7870.01 2 0.0000 0.792 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4727.01 7 0.2857 0.897 0.04 0.04 0.06 0.00 0.00 0.00 0.86
#> TCGA.DQ.7595.01 3 0.6814 0.140 0.28 0.00 0.38 0.00 0.16 0.00 0.18
#> TCGA.CN.5360.01 5 0.2706 0.851 0.00 0.00 0.02 0.04 0.88 0.04 0.02
#> TCGA.CN.A6V3.01 3 0.2708 0.485 0.00 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.UF.A7JF.01 6 0.0000 0.940 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CN.4731.01 3 0.4978 0.295 0.12 0.00 0.50 0.38 0.00 0.00 0.00
#> TCGA.CN.A63W.01 7 0.2563 0.901 0.04 0.04 0.04 0.00 0.00 0.00 0.88
#> TCGA.CN.A63U.01 7 0.2213 0.896 0.04 0.04 0.02 0.00 0.00 0.00 0.90
#> TCGA.H7.A6C5.01 6 0.4431 0.595 0.04 0.00 0.00 0.04 0.24 0.68 0.00
#> TCGA.CN.5356.01 2 0.2376 0.788 0.12 0.86 0.00 0.00 0.00 0.00 0.02
#> TCGA.F7.7848.01 5 0.1433 0.856 0.00 0.00 0.00 0.08 0.92 0.00 0.00
#> TCGA.CV.7428.01 6 0.0863 0.928 0.04 0.00 0.00 0.00 0.00 0.96 0.00
#> TCGA.CV.7435.01 3 0.1363 0.604 0.00 0.00 0.94 0.02 0.00 0.00 0.04
#> TCGA.UF.A719.01 2 0.0000 0.792 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A7JD.01 2 0.5539 0.470 0.38 0.38 0.00 0.00 0.00 0.00 0.24
#> TCGA.UF.A7JH.01 6 0.0863 0.928 0.04 0.00 0.00 0.00 0.00 0.96 0.00
#> TCGA.D6.A6EO.01 5 0.3526 0.706 0.06 0.00 0.00 0.18 0.76 0.00 0.00
#> TCGA.D6.A74Q.01 6 0.0000 0.940 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BA.A6DE.01 3 0.4309 0.531 0.12 0.00 0.68 0.20 0.00 0.00 0.00
#> TCGA.CV.7440.01 7 0.1664 0.907 0.00 0.02 0.06 0.00 0.00 0.00 0.92
#> TCGA.CV.A6JU.01 3 0.1433 0.592 0.00 0.00 0.92 0.00 0.00 0.00 0.08
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.CR.5247.01 4 0.4188 0.468 0.14 0.00 0.00 0.72 0.00 0.10 0.00 0.04
#> TCGA.CV.7263.01 6 0.2547 0.852 0.12 0.00 0.00 0.00 0.00 0.84 0.00 0.04
#> TCGA.CV.6960.01 6 0.0000 0.898 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.7245.01 4 0.5385 0.267 0.18 0.00 0.00 0.58 0.16 0.00 0.00 0.08
#> TCGA.CN.4739.01 4 0.4578 0.453 0.16 0.00 0.00 0.70 0.08 0.02 0.00 0.04
#> TCGA.CV.6956.01 2 0.0471 0.737 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.CV.7091.01 3 0.4917 0.282 0.04 0.00 0.62 0.26 0.00 0.00 0.02 0.06
#> TCGA.CV.7242.01 6 0.0000 0.898 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CR.7398.01 8 0.3922 0.873 0.00 0.30 0.00 0.00 0.00 0.00 0.06 0.64
#> TCGA.CV.7253.01 2 0.1408 0.719 0.00 0.94 0.00 0.00 0.02 0.00 0.02 0.02
#> TCGA.BA.5555.01 3 0.1557 0.676 0.02 0.00 0.92 0.00 0.00 0.00 0.06 0.00
#> TCGA.CV.5441.01 4 0.5430 0.227 0.04 0.00 0.38 0.48 0.00 0.00 0.02 0.08
#> TCGA.CV.7250.01 2 0.0000 0.737 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7364.01 8 0.3922 0.873 0.00 0.30 0.00 0.00 0.00 0.00 0.06 0.64
#> TCGA.CR.7402.01 7 0.2404 0.844 0.02 0.00 0.14 0.00 0.00 0.00 0.84 0.00
#> TCGA.CN.A49A.01 8 0.3193 0.920 0.00 0.38 0.00 0.00 0.00 0.00 0.00 0.62
#> TCGA.CN.A497.01 3 0.5256 0.488 0.10 0.00 0.54 0.00 0.30 0.00 0.06 0.00
#> TCGA.D6.6823.01 6 0.0000 0.898 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BA.A4IF.01 5 0.1557 0.111 0.00 0.00 0.06 0.00 0.92 0.00 0.02 0.00
#> TCGA.BA.6869.01 7 0.2807 0.874 0.02 0.04 0.06 0.00 0.00 0.00 0.86 0.02
#> TCGA.CV.6941.01 2 0.0000 0.737 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6954.01 4 0.0000 0.661 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.6228.01 6 0.0471 0.891 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.CQ.6225.01 2 0.3083 -0.151 0.00 0.66 0.00 0.00 0.00 0.00 0.00 0.34
#> TCGA.CN.6988.01 6 0.0000 0.898 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.QK.A8Z8.01 8 0.3193 0.920 0.00 0.38 0.00 0.00 0.00 0.00 0.00 0.62
#> TCGA.QK.A8Z7.01 7 0.5245 0.642 0.24 0.00 0.08 0.00 0.00 0.00 0.58 0.10
#> TCGA.CQ.A4C9.01 4 0.0000 0.661 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.7072.01 3 0.5080 0.501 0.10 0.00 0.54 0.00 0.32 0.00 0.04 0.00
#> TCGA.CN.A63T.01 3 0.0471 0.696 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.F7.A61V.01 6 0.3907 0.515 0.38 0.00 0.00 0.00 0.04 0.58 0.00 0.00
#> TCGA.P3.A5QF.01 5 0.4655 0.392 0.34 0.00 0.00 0.00 0.58 0.02 0.04 0.02
#> TCGA.BB.A5HZ.01 4 0.5430 0.227 0.04 0.00 0.38 0.48 0.00 0.00 0.02 0.08
#> TCGA.CN.A641.01 8 0.4318 0.825 0.00 0.30 0.00 0.00 0.00 0.00 0.10 0.60
#> TCGA.QK.AA3J.01 4 0.3663 0.513 0.06 0.00 0.00 0.78 0.10 0.00 0.00 0.06
#> TCGA.KU.A66S.01 8 0.3193 0.920 0.00 0.38 0.00 0.00 0.00 0.00 0.00 0.62
#> TCGA.BA.A6DL.01 5 0.3570 0.263 0.36 0.00 0.00 0.02 0.62 0.00 0.00 0.00
#> TCGA.CV.A461.01 4 0.4995 0.339 0.28 0.00 0.04 0.60 0.06 0.00 0.02 0.00
#> TCGA.P3.A6T6.01 6 0.0000 0.898 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CN.4730.01 5 0.3449 0.441 0.32 0.00 0.02 0.00 0.66 0.00 0.00 0.00
#> TCGA.BB.7864.01 6 0.0471 0.895 0.02 0.00 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.BA.4074.01 4 0.0000 0.661 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QK.A6VB.01 2 0.0471 0.737 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.HD.7917.01 6 0.2547 0.852 0.12 0.00 0.00 0.00 0.00 0.84 0.00 0.04
#> TCGA.CV.7409.01 4 0.3637 0.614 0.06 0.00 0.04 0.80 0.00 0.00 0.02 0.08
#> TCGA.UF.A71D.01 4 0.0000 0.661 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BB.7870.01 8 0.3193 0.920 0.00 0.38 0.00 0.00 0.00 0.00 0.00 0.62
#> TCGA.CN.4727.01 7 0.2025 0.878 0.00 0.00 0.10 0.00 0.00 0.00 0.88 0.02
#> TCGA.DQ.7595.01 3 0.5423 0.348 0.10 0.00 0.42 0.00 0.42 0.00 0.06 0.00
#> TCGA.CN.5360.01 5 0.3942 0.449 0.34 0.00 0.00 0.00 0.62 0.02 0.02 0.00
#> TCGA.CN.A6V3.01 3 0.1804 0.662 0.02 0.00 0.90 0.00 0.00 0.00 0.08 0.00
#> TCGA.UF.A7JF.01 6 0.0000 0.898 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CN.4731.01 4 0.5430 0.227 0.04 0.00 0.38 0.48 0.00 0.00 0.02 0.08
#> TCGA.CN.A63W.01 7 0.2591 0.866 0.02 0.00 0.04 0.00 0.00 0.00 0.86 0.08
#> TCGA.CN.A63U.01 7 0.2132 0.870 0.00 0.00 0.04 0.00 0.00 0.00 0.88 0.08
#> TCGA.H7.A6C5.01 6 0.4466 0.577 0.32 0.00 0.00 0.00 0.04 0.60 0.00 0.04
#> TCGA.CN.5356.01 2 0.3299 -0.530 0.00 0.56 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.F7.7848.01 5 0.3514 0.439 0.34 0.00 0.02 0.00 0.64 0.00 0.00 0.00
#> TCGA.CV.7428.01 6 0.2547 0.852 0.12 0.00 0.00 0.00 0.00 0.84 0.00 0.04
#> TCGA.CV.7435.01 3 0.0000 0.698 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A719.01 8 0.3193 0.920 0.00 0.38 0.00 0.00 0.00 0.00 0.00 0.62
#> TCGA.UF.A7JD.01 2 0.2534 0.519 0.00 0.78 0.00 0.00 0.00 0.00 0.22 0.00
#> TCGA.UF.A7JH.01 6 0.2547 0.852 0.12 0.00 0.00 0.00 0.00 0.84 0.00 0.04
#> TCGA.D6.A6EO.01 1 0.5216 0.000 0.44 0.00 0.00 0.10 0.42 0.00 0.00 0.04
#> TCGA.D6.A74Q.01 6 0.0000 0.898 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BA.A6DE.01 3 0.4917 0.286 0.06 0.00 0.62 0.26 0.00 0.00 0.02 0.04
#> TCGA.CV.7440.01 7 0.1887 0.880 0.00 0.04 0.06 0.00 0.00 0.00 0.90 0.00
#> TCGA.CV.A6JU.01 3 0.0471 0.696 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: Node04. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0121 , Node0122 , Node0211 , Node0212 , Node0213 , Node0221 , Node0222 , Node0223 , Node0224 , Node0225-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0511 , Node0512 , Node0521-leaf , Node0522 , Node0523-leaf , Node0524-leaf .
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 21 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 0.819 0.910 0.958 0.5156 0.476 0.476
#> 3 3 1.000 1.000 1.000 0.3214 0.652 0.392
#> 4 4 0.837 0.725 0.887 0.0980 0.962 0.881
#> 5 5 0.789 0.782 0.883 0.0570 0.857 0.538
#> 6 6 0.895 0.807 0.920 0.0517 0.952 0.762
#> 7 7 0.863 0.804 0.908 0.0285 1.000 1.000
#> 8 8 0.868 0.716 0.867 0.0274 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] 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.CV.7245.01 2 0.000 0.970 0.00 1.00
#> TCGA.CV.7091.01 2 0.000 0.970 0.00 1.00
#> TCGA.BA.5555.01 1 0.000 0.930 1.00 0.00
#> TCGA.CV.5441.01 2 0.000 0.970 0.00 1.00
#> TCGA.CR.7402.01 1 0.000 0.930 1.00 0.00
#> TCGA.CN.A497.01 1 0.904 0.552 0.68 0.32
#> TCGA.BA.A4IF.01 1 0.000 0.930 1.00 0.00
#> TCGA.QK.A8Z7.01 2 0.000 0.970 0.00 1.00
#> TCGA.CQ.7072.01 1 0.000 0.930 1.00 0.00
#> TCGA.CN.A63T.01 1 0.904 0.552 0.68 0.32
#> TCGA.BB.A5HZ.01 2 0.327 0.953 0.06 0.94
#> TCGA.CV.A461.01 1 0.000 0.930 1.00 0.00
#> TCGA.CN.4730.01 2 0.000 0.970 0.00 1.00
#> TCGA.CV.7409.01 1 0.000 0.930 1.00 0.00
#> TCGA.DQ.7595.01 2 0.000 0.970 0.00 1.00
#> TCGA.CN.A6V3.01 2 0.327 0.953 0.06 0.94
#> TCGA.CN.4731.01 2 0.327 0.953 0.06 0.94
#> TCGA.F7.7848.01 2 0.327 0.953 0.06 0.94
#> TCGA.CV.7435.01 1 0.000 0.930 1.00 0.00
#> TCGA.BA.A6DE.01 1 0.000 0.930 1.00 0.00
#> TCGA.CV.A6JU.01 1 0.000 0.930 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CV.7245.01 2 0 1 0 1 0
#> TCGA.CV.7091.01 3 0 1 0 0 1
#> TCGA.BA.5555.01 1 0 1 1 0 0
#> TCGA.CV.5441.01 2 0 1 0 1 0
#> TCGA.CR.7402.01 1 0 1 1 0 0
#> TCGA.CN.A497.01 3 0 1 0 0 1
#> TCGA.BA.A4IF.01 1 0 1 1 0 0
#> TCGA.QK.A8Z7.01 2 0 1 0 1 0
#> TCGA.CQ.7072.01 1 0 1 1 0 0
#> TCGA.CN.A63T.01 3 0 1 0 0 1
#> TCGA.BB.A5HZ.01 3 0 1 0 0 1
#> TCGA.CV.A461.01 1 0 1 1 0 0
#> TCGA.CN.4730.01 2 0 1 0 1 0
#> TCGA.CV.7409.01 1 0 1 1 0 0
#> TCGA.DQ.7595.01 2 0 1 0 1 0
#> TCGA.CN.A6V3.01 3 0 1 0 0 1
#> TCGA.CN.4731.01 3 0 1 0 0 1
#> TCGA.F7.7848.01 3 0 1 0 0 1
#> TCGA.CV.7435.01 3 0 1 0 0 1
#> TCGA.BA.A6DE.01 3 0 1 0 0 1
#> TCGA.CV.A6JU.01 1 0 1 1 0 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.CV.7245.01 2 0.000 1.0000 0.00 1 0.00 0.00
#> TCGA.CV.7091.01 3 0.000 0.8296 0.00 0 1.00 0.00
#> TCGA.BA.5555.01 1 0.479 0.7444 0.62 0 0.00 0.38
#> TCGA.CV.5441.01 2 0.000 1.0000 0.00 1 0.00 0.00
#> TCGA.CR.7402.01 1 0.479 0.7444 0.62 0 0.00 0.38
#> TCGA.CN.A497.01 4 0.698 0.0000 0.18 0 0.24 0.58
#> TCGA.BA.A4IF.01 1 0.201 0.5339 0.92 0 0.00 0.08
#> TCGA.QK.A8Z7.01 2 0.000 1.0000 0.00 1 0.00 0.00
#> TCGA.CQ.7072.01 1 0.000 0.5987 1.00 0 0.00 0.00
#> TCGA.CN.A63T.01 3 0.121 0.8154 0.00 0 0.96 0.04
#> TCGA.BB.A5HZ.01 3 0.000 0.8296 0.00 0 1.00 0.00
#> TCGA.CV.A461.01 1 0.479 0.7444 0.62 0 0.00 0.38
#> TCGA.CN.4730.01 2 0.000 1.0000 0.00 1 0.00 0.00
#> TCGA.CV.7409.01 1 0.479 0.7444 0.62 0 0.00 0.38
#> TCGA.DQ.7595.01 2 0.000 1.0000 0.00 1 0.00 0.00
#> TCGA.CN.A6V3.01 3 0.000 0.8296 0.00 0 1.00 0.00
#> TCGA.CN.4731.01 3 0.121 0.8075 0.00 0 0.96 0.04
#> TCGA.F7.7848.01 3 0.121 0.8154 0.00 0 0.96 0.04
#> TCGA.CV.7435.01 3 0.677 0.0503 0.38 0 0.52 0.10
#> TCGA.BA.A6DE.01 3 0.476 0.6011 0.20 0 0.76 0.04
#> TCGA.CV.A6JU.01 1 0.201 0.5339 0.92 0 0.00 0.08
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CV.7245.01 2 0.0000 0.953 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.7091.01 3 0.0000 0.932 0.00 0.00 1.00 0.00 0.00
#> TCGA.BA.5555.01 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5441.01 2 0.2873 0.858 0.00 0.86 0.02 0.00 0.12
#> TCGA.CR.7402.01 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.A497.01 4 0.3106 0.000 0.00 0.00 0.02 0.84 0.14
#> TCGA.BA.A4IF.01 5 0.3983 0.638 0.34 0.00 0.00 0.00 0.66
#> TCGA.QK.A8Z7.01 2 0.0000 0.953 0.00 1.00 0.00 0.00 0.00
#> TCGA.CQ.7072.01 5 0.4126 0.598 0.38 0.00 0.00 0.00 0.62
#> TCGA.CN.A63T.01 3 0.0609 0.927 0.00 0.00 0.98 0.02 0.00
#> TCGA.BB.A5HZ.01 3 0.0000 0.932 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.A461.01 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4730.01 2 0.0000 0.953 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.7409.01 1 0.1043 0.960 0.96 0.00 0.00 0.04 0.00
#> TCGA.DQ.7595.01 2 0.1410 0.922 0.00 0.94 0.00 0.00 0.06
#> TCGA.CN.A6V3.01 3 0.0000 0.932 0.00 0.00 1.00 0.00 0.00
#> TCGA.CN.4731.01 3 0.4872 0.656 0.00 0.00 0.72 0.12 0.16
#> TCGA.F7.7848.01 3 0.0609 0.927 0.00 0.00 0.98 0.02 0.00
#> TCGA.CV.7435.01 5 0.4456 0.377 0.00 0.00 0.32 0.02 0.66
#> TCGA.BA.A6DE.01 5 0.5355 0.309 0.00 0.00 0.22 0.12 0.66
#> TCGA.CV.A6JU.01 5 0.3983 0.638 0.34 0.00 0.00 0.00 0.66
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.CV.7245.01 2 0.0000 0.9232 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7091.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BA.5555.01 1 0.0000 0.9314 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5441.01 2 0.3483 0.8036 0.00 0.82 0.00 0.04 0.02 0.12
#> TCGA.CR.7402.01 1 0.0547 0.9242 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CN.A497.01 4 0.1267 0.0000 0.00 0.00 0.00 0.94 0.06 0.00
#> TCGA.BA.A4IF.01 5 0.0937 0.9563 0.04 0.00 0.00 0.00 0.96 0.00
#> TCGA.QK.A8Z7.01 2 0.0000 0.9232 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.7072.01 5 0.1556 0.9260 0.08 0.00 0.00 0.00 0.92 0.00
#> TCGA.CN.A63T.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BB.A5HZ.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.A461.01 1 0.0000 0.9314 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4730.01 2 0.0000 0.9232 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7409.01 1 0.3156 0.7959 0.80 0.00 0.00 0.02 0.00 0.18
#> TCGA.DQ.7595.01 2 0.2581 0.8388 0.00 0.86 0.00 0.00 0.02 0.12
#> TCGA.CN.A6V3.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CN.4731.01 6 0.3828 0.1089 0.00 0.00 0.44 0.00 0.00 0.56
#> TCGA.F7.7848.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.7435.01 5 0.0937 0.9125 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.BA.A6DE.01 6 0.4576 0.0817 0.00 0.00 0.04 0.00 0.40 0.56
#> TCGA.CV.A6JU.01 5 0.0937 0.9563 0.04 0.00 0.00 0.00 0.96 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.CV.7245.01 7 0.0000 0.827 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CV.7091.01 3 0.0863 0.940 0.00 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.BA.5555.01 1 0.0000 0.899 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5441.01 7 0.4850 0.478 0.00 0.32 0.00 0.00 0.00 0.12 0.56
#> TCGA.CR.7402.01 1 0.1363 0.875 0.94 0.04 0.00 0.00 0.00 0.02 0.00
#> TCGA.CN.A497.01 4 0.0504 0.000 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.BA.A4IF.01 5 0.1664 0.948 0.06 0.02 0.00 0.00 0.92 0.00 0.00
#> TCGA.QK.A8Z7.01 7 0.0000 0.827 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CQ.7072.01 5 0.1928 0.937 0.08 0.02 0.00 0.00 0.90 0.00 0.00
#> TCGA.CN.A63T.01 3 0.1718 0.922 0.00 0.04 0.92 0.00 0.04 0.00 0.00
#> TCGA.BB.A5HZ.01 3 0.0863 0.940 0.00 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.CV.A461.01 1 0.0000 0.899 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4730.01 7 0.1006 0.822 0.00 0.02 0.00 0.00 0.02 0.00 0.96
#> TCGA.CV.7409.01 1 0.2945 0.722 0.74 0.26 0.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.7595.01 7 0.3307 0.689 0.00 0.24 0.00 0.02 0.00 0.00 0.74
#> TCGA.CN.A6V3.01 3 0.0000 0.944 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4731.01 6 0.3449 0.726 0.00 0.08 0.14 0.00 0.00 0.78 0.00
#> TCGA.F7.7848.01 3 0.1363 0.933 0.00 0.02 0.94 0.00 0.04 0.00 0.00
#> TCGA.CV.7435.01 5 0.1006 0.881 0.00 0.02 0.02 0.00 0.96 0.00 0.00
#> TCGA.BA.A6DE.01 6 0.2376 0.724 0.00 0.00 0.02 0.00 0.12 0.86 0.00
#> TCGA.CV.A6JU.01 5 0.1166 0.946 0.06 0.00 0.00 0.00 0.94 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.CV.7245.01 7 0.0000 0.743 0.00 0.00 0.00 0 0.00 0.00 1.00 0.00
#> TCGA.CV.7091.01 3 0.2591 0.824 0.00 0.04 0.86 0 0.00 0.08 0.00 0.02
#> TCGA.BA.5555.01 1 0.0000 0.837 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CV.5441.01 7 0.5458 0.252 0.00 0.14 0.00 0 0.00 0.40 0.42 0.04
#> TCGA.CR.7402.01 1 0.1275 0.812 0.94 0.02 0.00 0 0.00 0.04 0.00 0.00
#> TCGA.CN.A497.01 4 0.0000 0.000 0.00 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.BA.A4IF.01 5 0.1765 0.889 0.00 0.12 0.00 0 0.88 0.00 0.00 0.00
#> TCGA.QK.A8Z7.01 7 0.0000 0.743 0.00 0.00 0.00 0 0.00 0.00 1.00 0.00
#> TCGA.CQ.7072.01 5 0.2224 0.882 0.02 0.12 0.00 0 0.86 0.00 0.00 0.00
#> TCGA.CN.A63T.01 3 0.2888 0.780 0.00 0.16 0.80 0 0.00 0.04 0.00 0.00
#> TCGA.BB.A5HZ.01 3 0.2591 0.824 0.00 0.04 0.86 0 0.00 0.08 0.00 0.02
#> TCGA.CV.A461.01 1 0.0000 0.837 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CN.4730.01 7 0.0941 0.737 0.00 0.02 0.00 0 0.00 0.00 0.96 0.02
#> TCGA.CV.7409.01 1 0.3299 0.479 0.56 0.00 0.00 0 0.00 0.44 0.00 0.00
#> TCGA.DQ.7595.01 7 0.3299 0.449 0.00 0.44 0.00 0 0.00 0.00 0.56 0.00
#> TCGA.CN.A6V3.01 3 0.0000 0.845 0.00 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.CN.4731.01 8 0.1091 0.791 0.00 0.00 0.06 0 0.00 0.00 0.00 0.94
#> TCGA.F7.7848.01 3 0.2350 0.816 0.00 0.10 0.86 0 0.00 0.04 0.00 0.00
#> TCGA.CV.7435.01 5 0.1804 0.827 0.00 0.08 0.02 0 0.90 0.00 0.00 0.00
#> TCGA.BA.A6DE.01 8 0.3454 0.791 0.00 0.08 0.00 0 0.06 0.06 0.00 0.80
#> TCGA.CV.A6JU.01 5 0.0000 0.882 0.00 0.00 0.00 0 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: Node0. Child nodes: Node011 , Node012 , Node013-leaf , Node021 , Node022 , Node023 , Node031-leaf , Node032-leaf , Node033 , Node034-leaf , Node041-leaf , Node042-leaf , Node043 , Node051 , Node052 , Node053-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["05"]
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 99 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 1.000 1.000 1.000 0.4940 0.506 0.506
#> 3 3 1.000 0.959 0.982 0.3139 0.835 0.677
#> 4 4 0.881 0.885 0.943 0.1079 0.888 0.696
#> 5 5 0.904 0.839 0.931 0.0353 0.953 0.837
#> 6 6 0.794 0.777 0.881 0.0307 0.969 0.885
#> 7 7 0.776 0.701 0.845 0.0221 0.989 0.957
#> 8 8 0.756 0.530 0.778 0.0300 0.978 0.913
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
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.CN.6022.01 2 0 1 0 1
#> TCGA.CV.5432.01 2 0 1 0 1
#> TCGA.IQ.7632.01 2 0 1 0 1
#> TCGA.CR.6488.01 2 0 1 0 1
#> TCGA.CV.6433.01 1 0 1 1 0
#> TCGA.HD.7754.01 1 0 1 1 0
#> TCGA.CV.7421.01 2 0 1 0 1
#> TCGA.CV.7406.01 1 0 1 1 0
#> TCGA.CX.7086.01 2 0 1 0 1
#> TCGA.CQ.7065.01 2 0 1 0 1
#> TCGA.IQ.7631.01 2 0 1 0 1
#> TCGA.CQ.5329.01 2 0 1 0 1
#> TCGA.BA.5559.01 1 0 1 1 0
#> TCGA.CX.7082.01 2 0 1 0 1
#> TCGA.CR.7379.01 2 0 1 0 1
#> TCGA.CR.5249.01 1 0 1 1 0
#> TCGA.CR.7399.01 2 0 1 0 1
#> TCGA.CV.7103.01 2 0 1 0 1
#> TCGA.CV.5443.01 1 0 1 1 0
#> TCGA.CV.5441.11 2 0 1 0 1
#> TCGA.CV.7255.01 2 0 1 0 1
#> TCGA.CR.7392.01 2 0 1 0 1
#> TCGA.CR.5248.01 1 0 1 1 0
#> TCGA.CR.5250.01 1 0 1 1 0
#> TCGA.BA.5149.01 2 0 1 0 1
#> TCGA.CV.5431.01 2 0 1 0 1
#> TCGA.CR.5243.01 1 0 1 1 0
#> TCGA.CV.5442.01 1 0 1 1 0
#> TCGA.CR.7385.01 1 0 1 1 0
#> TCGA.CV.7180.01 2 0 1 0 1
#> TCGA.CV.6939.01 1 0 1 1 0
#> TCGA.CR.6487.01 1 0 1 1 0
#> TCGA.CV.6936.01 2 0 1 0 1
#> TCGA.DQ.5631.01 2 0 1 0 1
#> TCGA.CR.6472.01 1 0 1 1 0
#> TCGA.CR.6481.01 1 0 1 1 0
#> TCGA.CR.6484.01 2 0 1 0 1
#> TCGA.CR.6470.01 1 0 1 1 0
#> TCGA.BA.A4IH.01 1 0 1 1 0
#> TCGA.CV.6951.01 2 0 1 0 1
#> TCGA.CR.6482.01 1 0 1 1 0
#> TCGA.P3.A5Q5.01 1 0 1 1 0
#> TCGA.CV.A45W.01 2 0 1 0 1
#> TCGA.F7.A624.01 2 0 1 0 1
#> TCGA.F7.A622.01 2 0 1 0 1
#> TCGA.BA.A4IG.01 1 0 1 1 0
#> TCGA.KU.A66T.01 2 0 1 0 1
#> TCGA.HD.8224.01 2 0 1 0 1
#> TCGA.BA.A8YP.01 2 0 1 0 1
#> TCGA.CQ.7069.01 2 0 1 0 1
#> TCGA.HD.A634.01 1 0 1 1 0
#> TCGA.CV.A465.01 2 0 1 0 1
#> TCGA.P3.A5QA.01 2 0 1 0 1
#> TCGA.MT.A67D.01 2 0 1 0 1
#> TCGA.CN.A63V.01 2 0 1 0 1
#> TCGA.QK.A8ZB.01 2 0 1 0 1
#> TCGA.MT.A51X.01 2 0 1 0 1
#> TCGA.CV.A45Z.01 2 0 1 0 1
#> TCGA.CN.4722.01 2 0 1 0 1
#> TCGA.P3.A6T8.01 2 0 1 0 1
#> TCGA.BA.5153.01 1 0 1 1 0
#> TCGA.DQ.7594.01 1 0 1 1 0
#> TCGA.DQ.7596.01 1 0 1 1 0
#> TCGA.P3.A6T3.01 2 0 1 0 1
#> TCGA.BB.4223.01 1 0 1 1 0
#> TCGA.UF.A71B.01 2 0 1 0 1
#> TCGA.CN.4737.01 2 0 1 0 1
#> TCGA.CN.5374.01 1 0 1 1 0
#> TCGA.TN.A7HJ.01 2 0 1 0 1
#> TCGA.BB.4228.01 1 0 1 1 0
#> TCGA.H7.A76A.01 1 0 1 1 0
#> TCGA.DQ.7593.01 1 0 1 1 0
#> TCGA.BB.4225.01 1 0 1 1 0
#> TCGA.CN.A6UY.01 1 0 1 1 0
#> TCGA.MZ.A5BI.01 1 0 1 1 0
#> TCGA.CN.5364.01 2 0 1 0 1
#> TCGA.BB.A6UM.01 1 0 1 1 0
#> TCGA.CN.4740.01 2 0 1 0 1
#> TCGA.CN.A6V6.01 1 0 1 1 0
#> TCGA.D6.A6ES.01 2 0 1 0 1
#> TCGA.RS.A6TP.01 1 0 1 1 0
#> TCGA.KU.A6H7.06 1 0 1 1 0
#> TCGA.UP.A6WW.01 1 0 1 1 0
#> TCGA.CV.A6JY.01 2 0 1 0 1
#> TCGA.CV.7432.01 2 0 1 0 1
#> TCGA.WA.A7H4.01 2 0 1 0 1
#> TCGA.MZ.A6I9.01 1 0 1 1 0
#> TCGA.QK.A6IG.01 2 0 1 0 1
#> TCGA.CV.A6JM.01 2 0 1 0 1
#> TCGA.CR.7404.01 1 0 1 1 0
#> TCGA.QK.A6IJ.01 2 0 1 0 1
#> TCGA.CV.A6JE.01 2 0 1 0 1
#> TCGA.BA.A6DD.01 2 0 1 0 1
#> TCGA.CR.7368.01 1 0 1 1 0
#> TCGA.UF.A718.01 2 0 1 0 1
#> TCGA.CR.7369.01 1 0 1 1 0
#> TCGA.QK.A6IH.01 2 0 1 0 1
#> TCGA.WA.A7GZ.01 2 0 1 0 1
#> TCGA.KU.A6H7.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CN.6022.01 2 0.0000 0.9868 0.00 1.00 0.00
#> TCGA.CV.5432.01 2 0.0892 0.9880 0.00 0.98 0.02
#> TCGA.IQ.7632.01 2 0.0892 0.9880 0.00 0.98 0.02
#> TCGA.CR.6488.01 3 0.0000 0.9520 0.00 0.00 1.00
#> TCGA.CV.6433.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.HD.7754.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.CV.7421.01 2 0.0892 0.9880 0.00 0.98 0.02
#> TCGA.CV.7406.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.CX.7086.01 2 0.0000 0.9868 0.00 1.00 0.00
#> TCGA.CQ.7065.01 3 0.0892 0.9365 0.00 0.02 0.98
#> TCGA.IQ.7631.01 2 0.0000 0.9868 0.00 1.00 0.00
#> TCGA.CQ.5329.01 3 0.0000 0.9520 0.00 0.00 1.00
#> TCGA.BA.5559.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.CX.7082.01 2 0.0892 0.9880 0.00 0.98 0.02
#> TCGA.CR.7379.01 2 0.0000 0.9868 0.00 1.00 0.00
#> TCGA.CR.5249.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.CR.7399.01 2 0.0892 0.9880 0.00 0.98 0.02
#> TCGA.CV.7103.01 2 0.0000 0.9868 0.00 1.00 0.00
#> TCGA.CV.5443.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.CV.5441.11 2 0.1529 0.9713 0.00 0.96 0.04
#> TCGA.CV.7255.01 2 0.0000 0.9868 0.00 1.00 0.00
#> TCGA.CR.7392.01 2 0.0892 0.9880 0.00 0.98 0.02
#> TCGA.CR.5248.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.CR.5250.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.BA.5149.01 3 0.0000 0.9520 0.00 0.00 1.00
#> TCGA.CV.5431.01 2 0.0892 0.9880 0.00 0.98 0.02
#> TCGA.CR.5243.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.CV.5442.01 1 0.6126 0.3416 0.60 0.00 0.40
#> TCGA.CR.7385.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.CV.7180.01 3 0.0000 0.9520 0.00 0.00 1.00
#> TCGA.CV.6939.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.CR.6487.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.CV.6936.01 3 0.0000 0.9520 0.00 0.00 1.00
#> TCGA.DQ.5631.01 3 0.0000 0.9520 0.00 0.00 1.00
#> TCGA.CR.6472.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.CR.6481.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.CR.6484.01 2 0.0892 0.9880 0.00 0.98 0.02
#> TCGA.CR.6470.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.BA.A4IH.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.CV.6951.01 3 0.0000 0.9520 0.00 0.00 1.00
#> TCGA.CR.6482.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.P3.A5Q5.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.CV.A45W.01 2 0.0892 0.9880 0.00 0.98 0.02
#> TCGA.F7.A624.01 3 0.6302 0.0816 0.00 0.48 0.52
#> TCGA.F7.A622.01 3 0.0000 0.9520 0.00 0.00 1.00
#> TCGA.BA.A4IG.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.KU.A66T.01 2 0.0000 0.9868 0.00 1.00 0.00
#> TCGA.HD.8224.01 3 0.0000 0.9520 0.00 0.00 1.00
#> TCGA.BA.A8YP.01 2 0.0000 0.9868 0.00 1.00 0.00
#> TCGA.CQ.7069.01 2 0.0000 0.9868 0.00 1.00 0.00
#> TCGA.HD.A634.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.CV.A465.01 3 0.0892 0.9363 0.00 0.02 0.98
#> TCGA.P3.A5QA.01 2 0.0000 0.9868 0.00 1.00 0.00
#> TCGA.MT.A67D.01 3 0.0000 0.9520 0.00 0.00 1.00
#> TCGA.CN.A63V.01 2 0.0892 0.9880 0.00 0.98 0.02
#> TCGA.QK.A8ZB.01 2 0.0892 0.9880 0.00 0.98 0.02
#> TCGA.MT.A51X.01 3 0.0000 0.9520 0.00 0.00 1.00
#> TCGA.CV.A45Z.01 2 0.0892 0.9880 0.00 0.98 0.02
#> TCGA.CN.4722.01 2 0.0892 0.9880 0.00 0.98 0.02
#> TCGA.P3.A6T8.01 3 0.0000 0.9520 0.00 0.00 1.00
#> TCGA.BA.5153.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.DQ.7594.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.DQ.7596.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.P3.A6T3.01 2 0.0000 0.9868 0.00 1.00 0.00
#> TCGA.BB.4223.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.UF.A71B.01 2 0.0892 0.9880 0.00 0.98 0.02
#> TCGA.CN.4737.01 2 0.0000 0.9868 0.00 1.00 0.00
#> TCGA.CN.5374.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.TN.A7HJ.01 2 0.0892 0.9880 0.00 0.98 0.02
#> TCGA.BB.4228.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.H7.A76A.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.DQ.7593.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.BB.4225.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.CN.A6UY.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.MZ.A5BI.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.CN.5364.01 3 0.0000 0.9520 0.00 0.00 1.00
#> TCGA.BB.A6UM.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.CN.4740.01 2 0.0892 0.9880 0.00 0.98 0.02
#> TCGA.CN.A6V6.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.D6.A6ES.01 2 0.0000 0.9868 0.00 1.00 0.00
#> TCGA.RS.A6TP.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.KU.A6H7.06 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.UP.A6WW.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.CV.A6JY.01 2 0.0892 0.9880 0.00 0.98 0.02
#> TCGA.CV.7432.01 3 0.0000 0.9520 0.00 0.00 1.00
#> TCGA.WA.A7H4.01 2 0.0892 0.9880 0.00 0.98 0.02
#> TCGA.MZ.A6I9.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.QK.A6IG.01 3 0.0000 0.9520 0.00 0.00 1.00
#> TCGA.CV.A6JM.01 2 0.0000 0.9868 0.00 1.00 0.00
#> TCGA.CR.7404.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.QK.A6IJ.01 2 0.2066 0.9504 0.00 0.94 0.06
#> TCGA.CV.A6JE.01 2 0.0000 0.9868 0.00 1.00 0.00
#> TCGA.BA.A6DD.01 3 0.0000 0.9520 0.00 0.00 1.00
#> TCGA.CR.7368.01 1 0.0000 0.9899 1.00 0.00 0.00
#> TCGA.UF.A718.01 3 0.6045 0.3856 0.00 0.38 0.62
#> TCGA.CR.7369.01 3 0.0892 0.9327 0.02 0.00 0.98
#> TCGA.QK.A6IH.01 2 0.0000 0.9868 0.00 1.00 0.00
#> TCGA.WA.A7GZ.01 2 0.0000 0.9868 0.00 1.00 0.00
#> TCGA.KU.A6H7.01 1 0.0000 0.9899 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.CN.6022.01 2 0.1211 0.926 0.00 0.96 0.00 0.04
#> TCGA.CV.5432.01 4 0.5619 0.555 0.00 0.32 0.04 0.64
#> TCGA.IQ.7632.01 2 0.0707 0.935 0.00 0.98 0.00 0.02
#> TCGA.CR.6488.01 3 0.0000 0.929 0.00 0.00 1.00 0.00
#> TCGA.CV.6433.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.HD.7754.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.CV.7421.01 4 0.4948 0.390 0.00 0.44 0.00 0.56
#> TCGA.CV.7406.01 1 0.3335 0.844 0.86 0.12 0.00 0.02
#> TCGA.CX.7086.01 4 0.0707 0.816 0.00 0.02 0.00 0.98
#> TCGA.CQ.7065.01 4 0.4713 0.277 0.00 0.00 0.36 0.64
#> TCGA.IQ.7631.01 4 0.2647 0.778 0.00 0.12 0.00 0.88
#> TCGA.CQ.5329.01 3 0.0000 0.929 0.00 0.00 1.00 0.00
#> TCGA.BA.5559.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.CX.7082.01 4 0.6808 0.514 0.00 0.32 0.12 0.56
#> TCGA.CR.7379.01 2 0.2921 0.811 0.00 0.86 0.00 0.14
#> TCGA.CR.5249.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.CR.7399.01 2 0.0707 0.916 0.00 0.98 0.00 0.02
#> TCGA.CV.7103.01 4 0.4977 0.363 0.00 0.46 0.00 0.54
#> TCGA.CV.5443.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.CV.5441.11 2 0.0000 0.927 0.00 1.00 0.00 0.00
#> TCGA.CV.7255.01 4 0.0707 0.816 0.00 0.02 0.00 0.98
#> TCGA.CR.7392.01 2 0.0707 0.935 0.00 0.98 0.00 0.02
#> TCGA.CR.5248.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.CR.5250.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.BA.5149.01 3 0.0000 0.929 0.00 0.00 1.00 0.00
#> TCGA.CV.5431.01 2 0.0707 0.916 0.00 0.98 0.00 0.02
#> TCGA.CR.5243.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.CV.5442.01 3 0.4277 0.553 0.28 0.00 0.72 0.00
#> TCGA.CR.7385.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.CV.7180.01 3 0.0000 0.929 0.00 0.00 1.00 0.00
#> TCGA.CV.6939.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.CR.6487.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.CV.6936.01 3 0.0000 0.929 0.00 0.00 1.00 0.00
#> TCGA.DQ.5631.01 3 0.0000 0.929 0.00 0.00 1.00 0.00
#> TCGA.CR.6472.01 1 0.2706 0.893 0.90 0.08 0.00 0.02
#> TCGA.CR.6481.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.CR.6484.01 2 0.0707 0.935 0.00 0.98 0.00 0.02
#> TCGA.CR.6470.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.BA.A4IH.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.CV.6951.01 3 0.4624 0.482 0.00 0.00 0.66 0.34
#> TCGA.CR.6482.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.P3.A5Q5.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.CV.A45W.01 2 0.0707 0.916 0.00 0.98 0.00 0.02
#> TCGA.F7.A624.01 2 0.2921 0.804 0.00 0.86 0.14 0.00
#> TCGA.F7.A622.01 3 0.0000 0.929 0.00 0.00 1.00 0.00
#> TCGA.BA.A4IG.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.KU.A66T.01 4 0.0707 0.816 0.00 0.02 0.00 0.98
#> TCGA.HD.8224.01 3 0.0000 0.929 0.00 0.00 1.00 0.00
#> TCGA.BA.A8YP.01 4 0.4977 0.363 0.00 0.46 0.00 0.54
#> TCGA.CQ.7069.01 2 0.1211 0.926 0.00 0.96 0.00 0.04
#> TCGA.HD.A634.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.CV.A465.01 3 0.3335 0.804 0.00 0.12 0.86 0.02
#> TCGA.P3.A5QA.01 4 0.0707 0.816 0.00 0.02 0.00 0.98
#> TCGA.MT.A67D.01 3 0.0000 0.929 0.00 0.00 1.00 0.00
#> TCGA.CN.A63V.01 2 0.1211 0.926 0.00 0.96 0.00 0.04
#> TCGA.QK.A8ZB.01 2 0.1211 0.926 0.00 0.96 0.00 0.04
#> TCGA.MT.A51X.01 3 0.2345 0.856 0.00 0.00 0.90 0.10
#> TCGA.CV.A45Z.01 2 0.0707 0.916 0.00 0.98 0.00 0.02
#> TCGA.CN.4722.01 2 0.0707 0.935 0.00 0.98 0.00 0.02
#> TCGA.P3.A6T8.01 3 0.0707 0.915 0.00 0.02 0.98 0.00
#> TCGA.BA.5153.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.DQ.7594.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.DQ.7596.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.P3.A6T3.01 4 0.0707 0.816 0.00 0.02 0.00 0.98
#> TCGA.BB.4223.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.UF.A71B.01 2 0.1637 0.904 0.00 0.94 0.00 0.06
#> TCGA.CN.4737.01 4 0.0707 0.816 0.00 0.02 0.00 0.98
#> TCGA.CN.5374.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.TN.A7HJ.01 2 0.0707 0.935 0.00 0.98 0.00 0.02
#> TCGA.BB.4228.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.H7.A76A.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.DQ.7593.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.BB.4225.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.CN.A6UY.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.MZ.A5BI.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.CN.5364.01 3 0.0000 0.929 0.00 0.00 1.00 0.00
#> TCGA.BB.A6UM.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.CN.4740.01 2 0.0707 0.935 0.00 0.98 0.00 0.02
#> TCGA.CN.A6V6.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.D6.A6ES.01 4 0.0707 0.816 0.00 0.02 0.00 0.98
#> TCGA.RS.A6TP.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.KU.A6H7.06 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.UP.A6WW.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.CV.A6JY.01 2 0.0707 0.935 0.00 0.98 0.00 0.02
#> TCGA.CV.7432.01 3 0.0000 0.929 0.00 0.00 1.00 0.00
#> TCGA.WA.A7H4.01 2 0.0707 0.935 0.00 0.98 0.00 0.02
#> TCGA.MZ.A6I9.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.QK.A6IG.01 3 0.2921 0.818 0.00 0.00 0.86 0.14
#> TCGA.CV.A6JM.01 4 0.0707 0.816 0.00 0.02 0.00 0.98
#> TCGA.CR.7404.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.QK.A6IJ.01 2 0.0707 0.935 0.00 0.98 0.00 0.02
#> TCGA.CV.A6JE.01 4 0.0707 0.816 0.00 0.02 0.00 0.98
#> TCGA.BA.A6DD.01 2 0.4713 0.457 0.00 0.64 0.36 0.00
#> TCGA.CR.7368.01 1 0.0000 0.994 1.00 0.00 0.00 0.00
#> TCGA.UF.A718.01 2 0.3400 0.755 0.00 0.82 0.18 0.00
#> TCGA.CR.7369.01 3 0.0000 0.929 0.00 0.00 1.00 0.00
#> TCGA.QK.A6IH.01 4 0.0707 0.816 0.00 0.02 0.00 0.98
#> TCGA.WA.A7GZ.01 4 0.4134 0.669 0.00 0.26 0.00 0.74
#> TCGA.KU.A6H7.01 1 0.0000 0.994 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.CN.6022.01 2 0.0000 0.9009 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.5432.01 4 0.7299 0.2793 0.00 0.22 0.12 0.54 0.12
#> TCGA.IQ.7632.01 2 0.0000 0.9009 0.00 1.00 0.00 0.00 0.00
#> TCGA.CR.6488.01 3 0.0000 0.9187 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.6433.01 1 0.0609 0.9697 0.98 0.00 0.00 0.00 0.02
#> TCGA.HD.7754.01 1 0.0609 0.9616 0.98 0.00 0.00 0.00 0.02
#> TCGA.CV.7421.01 2 0.5684 -0.0256 0.00 0.50 0.02 0.44 0.04
#> TCGA.CV.7406.01 5 0.1043 0.6472 0.04 0.00 0.00 0.00 0.96
#> TCGA.CX.7086.01 4 0.0000 0.8274 0.00 0.00 0.00 1.00 0.00
#> TCGA.CQ.7065.01 4 0.2732 0.6702 0.00 0.00 0.16 0.84 0.00
#> TCGA.IQ.7631.01 4 0.4132 0.5200 0.00 0.26 0.02 0.72 0.00
#> TCGA.CQ.5329.01 3 0.0000 0.9187 0.00 0.00 1.00 0.00 0.00
#> TCGA.BA.5559.01 1 0.0609 0.9697 0.98 0.00 0.00 0.00 0.02
#> TCGA.CX.7082.01 4 0.8172 -0.1154 0.00 0.16 0.16 0.38 0.30
#> TCGA.CR.7379.01 2 0.1732 0.8218 0.00 0.92 0.00 0.08 0.00
#> TCGA.CR.5249.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7399.01 2 0.3561 0.4998 0.00 0.74 0.00 0.00 0.26
#> TCGA.CV.7103.01 5 0.5791 0.6519 0.00 0.26 0.00 0.14 0.60
#> TCGA.CV.5443.01 1 0.0609 0.9697 0.98 0.00 0.00 0.00 0.02
#> TCGA.CV.5441.11 2 0.0000 0.9009 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.7255.01 4 0.0000 0.8274 0.00 0.00 0.00 1.00 0.00
#> TCGA.CR.7392.01 2 0.0000 0.9009 0.00 1.00 0.00 0.00 0.00
#> TCGA.CR.5248.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00
#> TCGA.CR.5250.01 1 0.0609 0.9697 0.98 0.00 0.00 0.00 0.02
#> TCGA.BA.5149.01 3 0.0000 0.9187 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.5431.01 2 0.0609 0.8868 0.00 0.98 0.00 0.00 0.02
#> TCGA.CR.5243.01 1 0.0609 0.9697 0.98 0.00 0.00 0.00 0.02
#> TCGA.CV.5442.01 1 0.5131 0.2413 0.54 0.00 0.42 0.00 0.04
#> TCGA.CR.7385.01 1 0.1410 0.9313 0.94 0.00 0.00 0.00 0.06
#> TCGA.CV.7180.01 3 0.0000 0.9187 0.00 0.00 1.00 0.00 0.00
#> TCGA.CV.6939.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00
#> TCGA.CR.6487.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6936.01 3 0.0000 0.9187 0.00 0.00 1.00 0.00 0.00
#> TCGA.DQ.5631.01 3 0.0000 0.9187 0.00 0.00 1.00 0.00 0.00
#> TCGA.CR.6472.01 5 0.1043 0.6472 0.04 0.00 0.00 0.00 0.96
#> TCGA.CR.6481.01 1 0.1410 0.9313 0.94 0.00 0.00 0.00 0.06
#> TCGA.CR.6484.01 2 0.0000 0.9009 0.00 1.00 0.00 0.00 0.00
#> TCGA.CR.6470.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A4IH.01 1 0.0609 0.9697 0.98 0.00 0.00 0.00 0.02
#> TCGA.CV.6951.01 3 0.3895 0.5548 0.00 0.00 0.68 0.32 0.00
#> TCGA.CR.6482.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00
#> TCGA.P3.A5Q5.01 1 0.1410 0.9313 0.94 0.00 0.00 0.00 0.06
#> TCGA.CV.A45W.01 5 0.4227 0.4470 0.00 0.42 0.00 0.00 0.58
#> TCGA.F7.A624.01 2 0.2020 0.7960 0.00 0.90 0.10 0.00 0.00
#> TCGA.F7.A622.01 3 0.0000 0.9187 0.00 0.00 1.00 0.00 0.00
#> TCGA.BA.A4IG.01 1 0.0609 0.9612 0.98 0.00 0.00 0.00 0.02
#> TCGA.KU.A66T.01 4 0.0000 0.8274 0.00 0.00 0.00 1.00 0.00
#> TCGA.HD.8224.01 3 0.0000 0.9187 0.00 0.00 1.00 0.00 0.00
#> TCGA.BA.A8YP.01 5 0.5263 0.6905 0.00 0.24 0.00 0.10 0.66
#> TCGA.CQ.7069.01 2 0.0000 0.9009 0.00 1.00 0.00 0.00 0.00
#> TCGA.HD.A634.01 1 0.1043 0.9476 0.96 0.00 0.00 0.00 0.04
#> TCGA.CV.A465.01 3 0.4373 0.6925 0.00 0.16 0.76 0.08 0.00
#> TCGA.P3.A5QA.01 4 0.0000 0.8274 0.00 0.00 0.00 1.00 0.00
#> TCGA.MT.A67D.01 3 0.0000 0.9187 0.00 0.00 1.00 0.00 0.00
#> TCGA.CN.A63V.01 2 0.0000 0.9009 0.00 1.00 0.00 0.00 0.00
#> TCGA.QK.A8ZB.01 2 0.0000 0.9009 0.00 1.00 0.00 0.00 0.00
#> TCGA.MT.A51X.01 3 0.2929 0.7731 0.00 0.00 0.82 0.18 0.00
#> TCGA.CV.A45Z.01 2 0.1043 0.8702 0.00 0.96 0.00 0.00 0.04
#> TCGA.CN.4722.01 2 0.0000 0.9009 0.00 1.00 0.00 0.00 0.00
#> TCGA.P3.A6T8.01 3 0.1410 0.8671 0.00 0.06 0.94 0.00 0.00
#> TCGA.BA.5153.01 1 0.0609 0.9697 0.98 0.00 0.00 0.00 0.02
#> TCGA.DQ.7594.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.7596.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00
#> TCGA.P3.A6T3.01 4 0.0000 0.8274 0.00 0.00 0.00 1.00 0.00
#> TCGA.BB.4223.01 1 0.0609 0.9697 0.98 0.00 0.00 0.00 0.02
#> TCGA.UF.A71B.01 2 0.2438 0.8073 0.00 0.90 0.00 0.06 0.04
#> TCGA.CN.4737.01 4 0.0000 0.8274 0.00 0.00 0.00 1.00 0.00
#> TCGA.CN.5374.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00
#> TCGA.TN.A7HJ.01 2 0.0000 0.9009 0.00 1.00 0.00 0.00 0.00
#> TCGA.BB.4228.01 1 0.0609 0.9697 0.98 0.00 0.00 0.00 0.02
#> TCGA.H7.A76A.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.7593.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00
#> TCGA.BB.4225.01 1 0.0609 0.9697 0.98 0.00 0.00 0.00 0.02
#> TCGA.CN.A6UY.01 1 0.0609 0.9697 0.98 0.00 0.00 0.00 0.02
#> TCGA.MZ.A5BI.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00
#> TCGA.CN.5364.01 3 0.0000 0.9187 0.00 0.00 1.00 0.00 0.00
#> TCGA.BB.A6UM.01 1 0.1043 0.9617 0.96 0.00 0.00 0.00 0.04
#> TCGA.CN.4740.01 2 0.0000 0.9009 0.00 1.00 0.00 0.00 0.00
#> TCGA.CN.A6V6.01 1 0.0609 0.9697 0.98 0.00 0.00 0.00 0.02
#> TCGA.D6.A6ES.01 4 0.0000 0.8274 0.00 0.00 0.00 1.00 0.00
#> TCGA.RS.A6TP.01 1 0.0609 0.9697 0.98 0.00 0.00 0.00 0.02
#> TCGA.KU.A6H7.06 1 0.0609 0.9697 0.98 0.00 0.00 0.00 0.02
#> TCGA.UP.A6WW.01 1 0.0609 0.9697 0.98 0.00 0.00 0.00 0.02
#> TCGA.CV.A6JY.01 2 0.0000 0.9009 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.7432.01 3 0.0000 0.9187 0.00 0.00 1.00 0.00 0.00
#> TCGA.WA.A7H4.01 2 0.0000 0.9009 0.00 1.00 0.00 0.00 0.00
#> TCGA.MZ.A6I9.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00
#> TCGA.QK.A6IG.01 3 0.3424 0.6965 0.00 0.00 0.76 0.24 0.00
#> TCGA.CV.A6JM.01 4 0.0000 0.8274 0.00 0.00 0.00 1.00 0.00
#> TCGA.CR.7404.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00
#> TCGA.QK.A6IJ.01 2 0.0000 0.9009 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.A6JE.01 4 0.0000 0.8274 0.00 0.00 0.00 1.00 0.00
#> TCGA.BA.A6DD.01 2 0.3274 0.6102 0.00 0.78 0.22 0.00 0.00
#> TCGA.CR.7368.01 1 0.1216 0.9458 0.96 0.00 0.02 0.00 0.02
#> TCGA.UF.A718.01 2 0.2929 0.6850 0.00 0.82 0.18 0.00 0.00
#> TCGA.CR.7369.01 3 0.1216 0.8854 0.02 0.00 0.96 0.00 0.02
#> TCGA.QK.A6IH.01 4 0.0000 0.8274 0.00 0.00 0.00 1.00 0.00
#> TCGA.WA.A7GZ.01 4 0.4182 0.2674 0.00 0.40 0.00 0.60 0.00
#> TCGA.KU.A6H7.01 1 0.0000 0.9706 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.CN.6022.01 2 0.0937 0.8572 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CV.5432.01 6 0.5778 0.7254 0.00 0.12 0.08 0.16 0.00 0.64
#> TCGA.IQ.7632.01 2 0.0000 0.8658 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CR.6488.01 3 0.0000 0.8098 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.6433.01 1 0.3045 0.8934 0.84 0.00 0.00 0.00 0.06 0.10
#> TCGA.HD.7754.01 1 0.3321 0.8573 0.82 0.00 0.00 0.00 0.08 0.10
#> TCGA.CV.7421.01 4 0.6540 -0.3527 0.00 0.30 0.00 0.36 0.02 0.32
#> TCGA.CV.7406.01 5 0.2094 0.9526 0.08 0.02 0.00 0.00 0.90 0.00
#> TCGA.CX.7086.01 4 0.0000 0.8192 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CQ.7065.01 4 0.4608 0.4166 0.00 0.00 0.22 0.68 0.00 0.10
#> TCGA.IQ.7631.01 4 0.5742 0.4756 0.00 0.12 0.02 0.66 0.04 0.16
#> TCGA.CQ.5329.01 3 0.0547 0.8089 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.BA.5559.01 1 0.3045 0.8934 0.84 0.00 0.00 0.00 0.06 0.10
#> TCGA.CX.7082.01 6 0.6156 0.7095 0.00 0.12 0.10 0.12 0.02 0.64
#> TCGA.CR.7379.01 2 0.3163 0.6956 0.00 0.82 0.00 0.14 0.00 0.04
#> TCGA.CR.5249.01 1 0.0000 0.9139 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7399.01 2 0.3985 0.6304 0.00 0.76 0.00 0.00 0.14 0.10
#> TCGA.CV.7103.01 6 0.6793 0.6929 0.00 0.14 0.00 0.16 0.18 0.52
#> TCGA.CV.5443.01 1 0.3045 0.8934 0.84 0.00 0.00 0.00 0.06 0.10
#> TCGA.CV.5441.11 2 0.0000 0.8658 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7255.01 4 0.0000 0.8192 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CR.7392.01 2 0.0000 0.8658 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CR.5248.01 1 0.0000 0.9139 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.5250.01 1 0.3045 0.8934 0.84 0.00 0.00 0.00 0.06 0.10
#> TCGA.BA.5149.01 3 0.1267 0.8088 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.CV.5431.01 2 0.1267 0.8377 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.CR.5243.01 1 0.3045 0.8934 0.84 0.00 0.00 0.00 0.06 0.10
#> TCGA.CV.5442.01 3 0.7010 -0.0159 0.28 0.00 0.42 0.00 0.08 0.22
#> TCGA.CR.7385.01 1 0.0547 0.9042 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.CV.7180.01 3 0.0000 0.8098 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.6939.01 1 0.0000 0.9139 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.6487.01 1 0.0000 0.9139 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6936.01 3 0.2260 0.7920 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.DQ.5631.01 3 0.2048 0.7879 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.CR.6472.01 5 0.2345 0.9516 0.06 0.02 0.00 0.00 0.90 0.02
#> TCGA.CR.6481.01 1 0.0547 0.9042 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.CR.6484.01 2 0.0000 0.8658 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CR.6470.01 1 0.0000 0.9139 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A4IH.01 1 0.3045 0.8934 0.84 0.00 0.00 0.00 0.06 0.10
#> TCGA.CV.6951.01 3 0.5447 0.1288 0.00 0.00 0.46 0.12 0.00 0.42
#> TCGA.CR.6482.01 1 0.0000 0.9139 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P3.A5Q5.01 1 0.0547 0.9042 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.CV.A45W.01 2 0.5520 0.1630 0.00 0.56 0.00 0.00 0.20 0.24
#> TCGA.F7.A624.01 2 0.3315 0.6479 0.00 0.78 0.20 0.00 0.00 0.02
#> TCGA.F7.A622.01 3 0.1267 0.8027 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.BA.A4IG.01 1 0.0547 0.9042 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.KU.A66T.01 4 0.0000 0.8192 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HD.8224.01 3 0.2048 0.7775 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.BA.A8YP.01 6 0.6678 0.6745 0.00 0.10 0.00 0.16 0.22 0.52
#> TCGA.CQ.7069.01 2 0.0937 0.8572 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.HD.A634.01 1 0.0547 0.9042 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.CV.A465.01 3 0.5636 0.4482 0.00 0.24 0.62 0.06 0.00 0.08
#> TCGA.P3.A5QA.01 4 0.0547 0.8071 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.MT.A67D.01 3 0.0000 0.8098 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CN.A63V.01 2 0.0937 0.8572 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.QK.A8ZB.01 2 0.0937 0.8572 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.MT.A51X.01 3 0.4328 0.6348 0.00 0.00 0.72 0.18 0.00 0.10
#> TCGA.CV.A45Z.01 2 0.0547 0.8591 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.CN.4722.01 2 0.0000 0.8658 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.P3.A6T8.01 3 0.1267 0.7792 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.BA.5153.01 1 0.3045 0.8934 0.84 0.00 0.00 0.00 0.06 0.10
#> TCGA.DQ.7594.01 1 0.0000 0.9139 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.7596.01 1 0.0000 0.9139 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P3.A6T3.01 4 0.0000 0.8192 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BB.4223.01 1 0.3045 0.8934 0.84 0.00 0.00 0.00 0.06 0.10
#> TCGA.UF.A71B.01 2 0.5087 -0.1178 0.00 0.52 0.02 0.04 0.00 0.42
#> TCGA.CN.4737.01 4 0.0937 0.7923 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.CN.5374.01 1 0.0000 0.9139 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TN.A7HJ.01 2 0.0000 0.8658 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BB.4228.01 1 0.3045 0.8934 0.84 0.00 0.00 0.00 0.06 0.10
#> TCGA.H7.A76A.01 1 0.0000 0.9139 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.7593.01 1 0.0000 0.9139 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BB.4225.01 1 0.3045 0.8934 0.84 0.00 0.00 0.00 0.06 0.10
#> TCGA.CN.A6UY.01 1 0.3045 0.8934 0.84 0.00 0.00 0.00 0.06 0.10
#> TCGA.MZ.A5BI.01 1 0.0000 0.9139 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.5364.01 3 0.0000 0.8098 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BB.A6UM.01 1 0.3045 0.8934 0.84 0.00 0.00 0.00 0.06 0.10
#> TCGA.CN.4740.01 2 0.0547 0.8642 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CN.A6V6.01 1 0.3045 0.8934 0.84 0.00 0.00 0.00 0.06 0.10
#> TCGA.D6.A6ES.01 4 0.0000 0.8192 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.RS.A6TP.01 1 0.3544 0.8651 0.80 0.00 0.00 0.00 0.08 0.12
#> TCGA.KU.A6H7.06 1 0.3045 0.8934 0.84 0.00 0.00 0.00 0.06 0.10
#> TCGA.UP.A6WW.01 1 0.3045 0.8934 0.84 0.00 0.00 0.00 0.06 0.10
#> TCGA.CV.A6JY.01 2 0.0547 0.8642 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CV.7432.01 3 0.1556 0.7820 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.WA.A7H4.01 2 0.0547 0.8642 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.MZ.A6I9.01 1 0.0000 0.9139 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QK.A6IG.01 3 0.4834 0.5264 0.00 0.00 0.64 0.26 0.00 0.10
#> TCGA.CV.A6JM.01 4 0.0000 0.8192 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CR.7404.01 1 0.0000 0.9139 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QK.A6IJ.01 2 0.0000 0.8658 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A6JE.01 4 0.0000 0.8192 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BA.A6DD.01 2 0.2941 0.6474 0.00 0.78 0.22 0.00 0.00 0.00
#> TCGA.CR.7368.01 1 0.1480 0.8765 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.UF.A718.01 2 0.3679 0.6199 0.00 0.76 0.20 0.00 0.00 0.04
#> TCGA.CR.7369.01 3 0.2956 0.7272 0.00 0.00 0.84 0.00 0.04 0.12
#> TCGA.QK.A6IH.01 4 0.0000 0.8192 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.WA.A7GZ.01 4 0.4420 0.2372 0.00 0.34 0.00 0.62 0.00 0.04
#> TCGA.KU.A6H7.01 1 0.0000 0.9139 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.CN.6022.01 2 0.3114 0.73927 0.00 0.84 0.00 0.04 0.00 0.04 0.08
#> TCGA.CV.5432.01 6 0.4181 0.77341 0.00 0.16 0.04 0.06 0.00 0.74 0.00
#> TCGA.IQ.7632.01 2 0.0000 0.79856 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.6488.01 3 0.0863 0.66075 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CV.6433.01 1 0.2708 0.82620 0.78 0.00 0.00 0.00 0.00 0.00 0.22
#> TCGA.HD.7754.01 1 0.3417 0.72614 0.72 0.00 0.00 0.00 0.02 0.00 0.26
#> TCGA.CV.7421.01 2 0.6865 0.00287 0.00 0.44 0.02 0.22 0.00 0.22 0.10
#> TCGA.CV.7406.01 5 0.0504 1.00000 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.CX.7086.01 4 0.0863 0.80925 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.CQ.7065.01 4 0.4139 0.52970 0.00 0.00 0.20 0.72 0.00 0.06 0.02
#> TCGA.IQ.7631.01 4 0.7511 0.25528 0.00 0.08 0.10 0.42 0.02 0.10 0.28
#> TCGA.CQ.5329.01 3 0.1006 0.66870 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.BA.5559.01 1 0.2708 0.82620 0.78 0.00 0.00 0.00 0.00 0.00 0.22
#> TCGA.CX.7082.01 6 0.4405 0.73436 0.00 0.08 0.08 0.10 0.00 0.74 0.00
#> TCGA.CR.7379.01 2 0.4702 0.54192 0.00 0.68 0.00 0.20 0.00 0.04 0.08
#> TCGA.CR.5249.01 1 0.0000 0.85514 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7399.01 2 0.4479 0.41173 0.00 0.66 0.00 0.00 0.06 0.26 0.02
#> TCGA.CV.7103.01 6 0.4696 0.76850 0.00 0.16 0.00 0.06 0.08 0.70 0.00
#> TCGA.CV.5443.01 1 0.2708 0.82620 0.78 0.00 0.00 0.00 0.00 0.00 0.22
#> TCGA.CV.5441.11 2 0.1006 0.78864 0.00 0.96 0.02 0.00 0.02 0.00 0.00
#> TCGA.CV.7255.01 4 0.0000 0.82087 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CR.7392.01 2 0.0000 0.79856 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.5248.01 1 0.0000 0.85514 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.5250.01 1 0.2708 0.82620 0.78 0.00 0.00 0.00 0.00 0.00 0.22
#> TCGA.BA.5149.01 3 0.2278 0.64703 0.00 0.00 0.88 0.00 0.00 0.04 0.08
#> TCGA.CV.5431.01 2 0.1505 0.77974 0.00 0.94 0.00 0.00 0.02 0.02 0.02
#> TCGA.CR.5243.01 1 0.2708 0.82620 0.78 0.00 0.00 0.00 0.00 0.00 0.22
#> TCGA.CV.5442.01 7 0.5370 0.00000 0.10 0.00 0.30 0.00 0.00 0.04 0.56
#> TCGA.CR.7385.01 1 0.0863 0.83511 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.CV.7180.01 3 0.0863 0.66075 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CV.6939.01 1 0.0504 0.84657 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.CR.6487.01 1 0.0000 0.85514 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6936.01 3 0.4033 0.49524 0.00 0.00 0.70 0.00 0.00 0.08 0.22
#> TCGA.DQ.5631.01 3 0.4594 0.41324 0.00 0.00 0.64 0.00 0.00 0.14 0.22
#> TCGA.CR.6472.01 5 0.0504 1.00000 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.CR.6481.01 1 0.0863 0.83511 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.CR.6484.01 2 0.0000 0.79856 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.6470.01 1 0.0000 0.85514 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A4IH.01 1 0.2708 0.82620 0.78 0.00 0.00 0.00 0.00 0.00 0.22
#> TCGA.CV.6951.01 3 0.5822 0.22108 0.00 0.00 0.44 0.14 0.00 0.38 0.04
#> TCGA.CR.6482.01 1 0.0000 0.85514 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P3.A5Q5.01 1 0.1166 0.81974 0.94 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.CV.A45W.01 2 0.4869 0.04161 0.00 0.54 0.00 0.00 0.06 0.38 0.02
#> TCGA.F7.A624.01 2 0.3386 0.64493 0.00 0.78 0.18 0.00 0.02 0.02 0.00
#> TCGA.F7.A622.01 3 0.3617 0.59118 0.00 0.00 0.76 0.00 0.00 0.08 0.16
#> TCGA.BA.A4IG.01 1 0.0504 0.84794 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.KU.A66T.01 4 0.0863 0.80360 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.HD.8224.01 3 0.0504 0.66890 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BA.A8YP.01 6 0.4937 0.76092 0.00 0.12 0.00 0.06 0.14 0.68 0.00
#> TCGA.CQ.7069.01 2 0.3404 0.72189 0.00 0.82 0.00 0.06 0.00 0.04 0.08
#> TCGA.HD.A634.01 1 0.1671 0.84749 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.CV.A465.01 3 0.4473 0.43405 0.00 0.18 0.72 0.02 0.00 0.02 0.06
#> TCGA.P3.A5QA.01 4 0.2421 0.77636 0.00 0.02 0.00 0.88 0.00 0.02 0.08
#> TCGA.MT.A67D.01 3 0.0863 0.66075 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CN.A63V.01 2 0.3114 0.73927 0.00 0.84 0.00 0.04 0.00 0.04 0.08
#> TCGA.QK.A8ZB.01 2 0.1166 0.78993 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.MT.A51X.01 3 0.5201 0.50438 0.00 0.02 0.66 0.20 0.00 0.06 0.06
#> TCGA.CV.A45Z.01 2 0.1363 0.77887 0.00 0.94 0.00 0.00 0.02 0.04 0.00
#> TCGA.CN.4722.01 2 0.0000 0.79856 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P3.A6T8.01 3 0.2803 0.57573 0.00 0.10 0.84 0.00 0.00 0.00 0.06
#> TCGA.BA.5153.01 1 0.2708 0.82620 0.78 0.00 0.00 0.00 0.00 0.00 0.22
#> TCGA.DQ.7594.01 1 0.1006 0.83584 0.96 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.DQ.7596.01 1 0.0000 0.85514 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P3.A6T3.01 4 0.0000 0.82087 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BB.4223.01 1 0.2708 0.82620 0.78 0.00 0.00 0.00 0.00 0.00 0.22
#> TCGA.UF.A71B.01 2 0.3546 -0.03622 0.00 0.54 0.00 0.00 0.00 0.46 0.00
#> TCGA.CN.4737.01 4 0.2857 0.75874 0.00 0.04 0.00 0.86 0.00 0.04 0.06
#> TCGA.CN.5374.01 1 0.0504 0.84657 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.TN.A7HJ.01 2 0.0000 0.79856 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BB.4228.01 1 0.2708 0.82620 0.78 0.00 0.00 0.00 0.00 0.00 0.22
#> TCGA.H7.A76A.01 1 0.0504 0.84657 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.DQ.7593.01 1 0.0000 0.85514 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BB.4225.01 1 0.2708 0.82620 0.78 0.00 0.00 0.00 0.00 0.00 0.22
#> TCGA.CN.A6UY.01 1 0.2708 0.82620 0.78 0.00 0.00 0.00 0.00 0.00 0.22
#> TCGA.MZ.A5BI.01 1 0.0000 0.85514 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.5364.01 3 0.0863 0.66075 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.BB.A6UM.01 1 0.2708 0.82344 0.78 0.00 0.00 0.00 0.00 0.00 0.22
#> TCGA.CN.4740.01 2 0.1928 0.77319 0.00 0.90 0.00 0.00 0.00 0.02 0.08
#> TCGA.CN.A6V6.01 1 0.2708 0.82620 0.78 0.00 0.00 0.00 0.00 0.00 0.22
#> TCGA.D6.A6ES.01 4 0.1006 0.81520 0.00 0.02 0.00 0.96 0.00 0.02 0.00
#> TCGA.RS.A6TP.01 1 0.2832 0.81226 0.76 0.00 0.00 0.00 0.00 0.00 0.24
#> TCGA.KU.A6H7.06 1 0.2708 0.82620 0.78 0.00 0.00 0.00 0.00 0.00 0.22
#> TCGA.UP.A6WW.01 1 0.2708 0.82620 0.78 0.00 0.00 0.00 0.00 0.00 0.22
#> TCGA.CV.A6JY.01 2 0.0504 0.79798 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CV.7432.01 3 0.4033 0.45457 0.00 0.00 0.70 0.00 0.00 0.08 0.22
#> TCGA.WA.A7H4.01 2 0.1166 0.78999 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.MZ.A6I9.01 1 0.0000 0.85514 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QK.A6IG.01 3 0.5189 0.45550 0.00 0.00 0.62 0.24 0.00 0.08 0.06
#> TCGA.CV.A6JM.01 4 0.1664 0.80490 0.00 0.00 0.00 0.92 0.00 0.06 0.02
#> TCGA.CR.7404.01 1 0.0000 0.85514 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QK.A6IJ.01 2 0.0504 0.79443 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.CV.A6JE.01 4 0.0504 0.81526 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.BA.A6DD.01 2 0.3047 0.55490 0.00 0.72 0.28 0.00 0.00 0.00 0.00
#> TCGA.CR.7368.01 1 0.3637 0.46521 0.72 0.00 0.00 0.00 0.04 0.00 0.24
#> TCGA.UF.A718.01 2 0.2572 0.65125 0.00 0.80 0.20 0.00 0.00 0.00 0.00
#> TCGA.CR.7369.01 3 0.4684 -0.11297 0.02 0.00 0.52 0.00 0.00 0.04 0.42
#> TCGA.QK.A6IH.01 4 0.0000 0.82087 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.WA.A7GZ.01 4 0.5577 0.18563 0.00 0.36 0.00 0.50 0.00 0.06 0.08
#> TCGA.KU.A6H7.01 1 0.0000 0.85514 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.CN.6022.01 2 0.2267 0.67466 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.CV.5432.01 6 0.4960 0.63244 0.00 0.06 0.08 0.02 0.00 0.70 0.02 0.12
#> TCGA.IQ.7632.01 2 0.0941 0.71940 0.00 0.96 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.CR.6488.01 3 0.1607 0.69576 0.00 0.00 0.92 0.00 0.00 0.04 0.04 0.00
#> TCGA.CV.6433.01 1 0.0000 0.62520 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HD.7754.01 1 0.4998 0.21762 0.50 0.00 0.00 0.00 0.26 0.00 0.24 0.00
#> TCGA.CV.7421.01 2 0.7047 -0.21341 0.00 0.38 0.06 0.24 0.00 0.16 0.00 0.16
#> TCGA.CV.7406.01 5 0.5040 -0.27660 0.00 0.00 0.00 0.00 0.60 0.10 0.24 0.06
#> TCGA.CX.7086.01 4 0.0000 0.80834 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CQ.7065.01 4 0.5201 0.19656 0.00 0.00 0.28 0.58 0.00 0.02 0.04 0.08
#> TCGA.IQ.7631.01 8 0.6531 0.00000 0.00 0.10 0.06 0.14 0.00 0.10 0.04 0.56
#> TCGA.CQ.5329.01 3 0.2071 0.70028 0.00 0.00 0.90 0.00 0.00 0.04 0.02 0.04
#> TCGA.BA.5559.01 1 0.0000 0.62520 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CX.7082.01 6 0.4868 0.59773 0.00 0.04 0.08 0.02 0.00 0.70 0.02 0.14
#> TCGA.CR.7379.01 2 0.3729 0.56808 0.00 0.72 0.00 0.10 0.00 0.00 0.00 0.18
#> TCGA.CR.5249.01 1 0.3272 0.58012 0.58 0.00 0.00 0.00 0.42 0.00 0.00 0.00
#> TCGA.CR.7399.01 2 0.4917 0.39807 0.00 0.62 0.00 0.00 0.02 0.26 0.06 0.04
#> TCGA.CV.7103.01 6 0.4521 0.61760 0.00 0.12 0.00 0.08 0.06 0.72 0.00 0.02
#> TCGA.CV.5443.01 1 0.0000 0.62520 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5441.11 2 0.1275 0.70526 0.00 0.94 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.CV.7255.01 4 0.0000 0.80834 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7392.01 2 0.0471 0.71632 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.CR.5248.01 1 0.3272 0.58012 0.58 0.00 0.00 0.00 0.42 0.00 0.00 0.00
#> TCGA.CR.5250.01 1 0.0000 0.62520 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.5149.01 3 0.1275 0.69744 0.00 0.00 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.CV.5431.01 2 0.4339 0.57957 0.00 0.74 0.00 0.00 0.02 0.10 0.06 0.08
#> TCGA.CR.5243.01 1 0.0000 0.62520 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5442.01 7 0.5051 0.43767 0.20 0.00 0.16 0.00 0.04 0.00 0.60 0.00
#> TCGA.CR.7385.01 1 0.3329 0.49268 0.52 0.00 0.00 0.00 0.48 0.00 0.00 0.00
#> TCGA.CV.7180.01 3 0.1275 0.69909 0.00 0.00 0.94 0.00 0.00 0.04 0.02 0.00
#> TCGA.CV.6939.01 1 0.3272 0.58012 0.58 0.00 0.00 0.00 0.42 0.00 0.00 0.00
#> TCGA.CR.6487.01 1 0.3272 0.58012 0.58 0.00 0.00 0.00 0.42 0.00 0.00 0.00
#> TCGA.CV.6936.01 3 0.3036 0.57266 0.00 0.00 0.78 0.00 0.00 0.00 0.18 0.04
#> TCGA.DQ.5631.01 3 0.3504 0.43742 0.00 0.00 0.70 0.00 0.00 0.00 0.26 0.04
#> TCGA.CR.6472.01 5 0.5040 -0.27660 0.00 0.00 0.00 0.00 0.60 0.10 0.24 0.06
#> TCGA.CR.6481.01 1 0.3299 0.55233 0.56 0.00 0.00 0.00 0.44 0.00 0.00 0.00
#> TCGA.CR.6484.01 2 0.1341 0.71407 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.CR.6470.01 1 0.3272 0.58012 0.58 0.00 0.00 0.00 0.42 0.00 0.00 0.00
#> TCGA.BA.A4IH.01 1 0.0000 0.62520 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.6951.01 3 0.6821 0.12404 0.00 0.00 0.42 0.06 0.00 0.22 0.10 0.20
#> TCGA.CR.6482.01 1 0.3272 0.58012 0.58 0.00 0.00 0.00 0.42 0.00 0.00 0.00
#> TCGA.P3.A5Q5.01 5 0.3737 -0.56419 0.48 0.00 0.00 0.00 0.50 0.00 0.02 0.00
#> TCGA.CV.A45W.01 2 0.5742 -0.16785 0.00 0.44 0.00 0.00 0.06 0.40 0.06 0.04
#> TCGA.F7.A624.01 2 0.5269 0.44485 0.00 0.64 0.12 0.00 0.00 0.08 0.02 0.14
#> TCGA.F7.A622.01 3 0.3299 0.56793 0.00 0.00 0.76 0.00 0.00 0.00 0.18 0.06
#> TCGA.BA.A4IG.01 1 0.3318 0.52814 0.54 0.00 0.00 0.00 0.46 0.00 0.00 0.00
#> TCGA.KU.A66T.01 4 0.1741 0.77032 0.00 0.00 0.00 0.92 0.00 0.02 0.02 0.04
#> TCGA.HD.8224.01 3 0.2020 0.67614 0.00 0.00 0.90 0.00 0.00 0.02 0.06 0.02
#> TCGA.BA.A8YP.01 6 0.3663 0.63093 0.00 0.10 0.00 0.06 0.06 0.78 0.00 0.00
#> TCGA.CQ.7069.01 2 0.2719 0.65816 0.00 0.80 0.00 0.02 0.00 0.00 0.00 0.18
#> TCGA.HD.A634.01 1 0.3142 0.56478 0.64 0.00 0.00 0.00 0.36 0.00 0.00 0.00
#> TCGA.CV.A465.01 3 0.4276 0.53223 0.00 0.18 0.70 0.00 0.00 0.08 0.00 0.04
#> TCGA.P3.A5QA.01 4 0.2348 0.74490 0.00 0.04 0.00 0.88 0.00 0.02 0.00 0.06
#> TCGA.MT.A67D.01 3 0.1607 0.69576 0.00 0.00 0.92 0.00 0.00 0.04 0.04 0.00
#> TCGA.CN.A63V.01 2 0.2267 0.67466 0.00 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.QK.A8ZB.01 2 0.1765 0.70464 0.00 0.88 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.MT.A51X.01 3 0.3941 0.58877 0.00 0.00 0.76 0.14 0.00 0.04 0.02 0.04
#> TCGA.CV.A45Z.01 2 0.2888 0.62794 0.00 0.80 0.00 0.00 0.00 0.16 0.00 0.04
#> TCGA.CN.4722.01 2 0.0471 0.71632 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.P3.A6T8.01 3 0.3036 0.54892 0.00 0.18 0.78 0.00 0.00 0.04 0.00 0.00
#> TCGA.BA.5153.01 1 0.0000 0.62520 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.7594.01 1 0.3272 0.58012 0.58 0.00 0.00 0.00 0.42 0.00 0.00 0.00
#> TCGA.DQ.7596.01 1 0.3272 0.58012 0.58 0.00 0.00 0.00 0.42 0.00 0.00 0.00
#> TCGA.P3.A6T3.01 4 0.0000 0.80834 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BB.4223.01 1 0.0000 0.62520 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UF.A71B.01 2 0.5456 -0.15686 0.00 0.44 0.04 0.00 0.00 0.42 0.02 0.08
#> TCGA.CN.4737.01 4 0.2623 0.66378 0.00 0.06 0.00 0.84 0.00 0.00 0.00 0.10
#> TCGA.CN.5374.01 1 0.3272 0.58012 0.58 0.00 0.00 0.00 0.42 0.00 0.00 0.00
#> TCGA.TN.A7HJ.01 2 0.0000 0.71920 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BB.4228.01 1 0.0000 0.62520 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.H7.A76A.01 1 0.3272 0.58012 0.58 0.00 0.00 0.00 0.42 0.00 0.00 0.00
#> TCGA.DQ.7593.01 1 0.3272 0.58012 0.58 0.00 0.00 0.00 0.42 0.00 0.00 0.00
#> TCGA.BB.4225.01 1 0.0000 0.62520 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.A6UY.01 1 0.0000 0.62520 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MZ.A5BI.01 1 0.3272 0.58012 0.58 0.00 0.00 0.00 0.42 0.00 0.00 0.00
#> TCGA.CN.5364.01 3 0.1607 0.69576 0.00 0.00 0.92 0.00 0.00 0.04 0.04 0.00
#> TCGA.BB.A6UM.01 1 0.0808 0.59162 0.96 0.00 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.CN.4740.01 2 0.1947 0.69598 0.00 0.86 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.CN.A6V6.01 1 0.0000 0.62520 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D6.A6ES.01 4 0.2020 0.74930 0.00 0.02 0.00 0.90 0.00 0.02 0.00 0.06
#> TCGA.RS.A6TP.01 1 0.1275 0.57210 0.94 0.00 0.00 0.00 0.02 0.00 0.04 0.00
#> TCGA.KU.A6H7.06 1 0.0000 0.62520 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.UP.A6WW.01 1 0.0000 0.62520 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A6JY.01 2 0.1563 0.71152 0.00 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.CV.7432.01 3 0.3015 0.33716 0.00 0.00 0.68 0.00 0.00 0.00 0.32 0.00
#> TCGA.WA.A7H4.01 2 0.1947 0.69598 0.00 0.86 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.MZ.A6I9.01 1 0.3299 0.55727 0.56 0.00 0.00 0.00 0.44 0.00 0.00 0.00
#> TCGA.QK.A6IG.01 3 0.3941 0.58877 0.00 0.00 0.76 0.14 0.00 0.04 0.02 0.04
#> TCGA.CV.A6JM.01 4 0.0941 0.79461 0.00 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.CR.7404.01 1 0.3237 0.58359 0.60 0.00 0.00 0.00 0.40 0.00 0.00 0.00
#> TCGA.QK.A6IJ.01 2 0.1275 0.70592 0.00 0.94 0.02 0.00 0.00 0.04 0.00 0.00
#> TCGA.CV.A6JE.01 4 0.0941 0.79502 0.00 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.BA.A6DD.01 2 0.4642 0.30613 0.00 0.60 0.30 0.00 0.00 0.06 0.00 0.04
#> TCGA.CR.7368.01 5 0.5698 -0.29955 0.36 0.00 0.04 0.00 0.40 0.00 0.20 0.00
#> TCGA.UF.A718.01 2 0.4728 0.41990 0.00 0.66 0.22 0.00 0.00 0.06 0.02 0.04
#> TCGA.CR.7369.01 7 0.3658 0.32593 0.00 0.00 0.40 0.00 0.02 0.00 0.58 0.00
#> TCGA.QK.A6IH.01 4 0.0000 0.80834 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.WA.A7GZ.01 4 0.4747 -0.00824 0.00 0.30 0.00 0.54 0.00 0.00 0.00 0.16
#> TCGA.KU.A6H7.01 1 0.3083 0.59015 0.66 0.00 0.00 0.00 0.34 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: Node05. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0121 , Node0122 , Node0211 , Node0212 , Node0213 , Node0221 , Node0222 , Node0223 , Node0224 , Node0225-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0511 , Node0512 , Node0521-leaf , Node0522 , Node0523-leaf , Node0524-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["051"]
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 '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 0.4761 0.524 0.524
#> 3 3 0.632 0.576 0.758 0.3173 0.799 0.616
#> 4 4 0.737 0.810 0.885 0.1484 0.890 0.682
#> 5 5 0.672 0.617 0.737 0.0559 0.979 0.924
#> 6 6 0.656 0.609 0.762 0.0463 0.876 0.575
#> 7 7 0.725 0.676 0.706 0.0314 0.948 0.758
#> 8 8 0.731 0.770 0.821 0.0256 0.956 0.768
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.CV.6433.01 1 0 1 1 0
#> TCGA.HD.7754.01 2 0 1 0 1
#> TCGA.CV.7406.01 2 0 1 0 1
#> TCGA.BA.5559.01 1 0 1 1 0
#> TCGA.CR.5249.01 2 0 1 0 1
#> TCGA.CV.5443.01 1 0 1 1 0
#> TCGA.CR.5248.01 2 0 1 0 1
#> TCGA.CR.5250.01 1 0 1 1 0
#> TCGA.CR.5243.01 1 0 1 1 0
#> TCGA.CV.5442.01 1 0 1 1 0
#> TCGA.CR.7385.01 2 0 1 0 1
#> TCGA.CV.6939.01 2 0 1 0 1
#> TCGA.CR.6487.01 2 0 1 0 1
#> TCGA.CR.6472.01 2 0 1 0 1
#> TCGA.CR.6481.01 2 0 1 0 1
#> TCGA.CR.6470.01 2 0 1 0 1
#> TCGA.BA.A4IH.01 2 0 1 0 1
#> TCGA.CR.6482.01 2 0 1 0 1
#> TCGA.P3.A5Q5.01 2 0 1 0 1
#> TCGA.BA.A4IG.01 2 0 1 0 1
#> TCGA.HD.A634.01 2 0 1 0 1
#> TCGA.BA.5153.01 1 0 1 1 0
#> TCGA.DQ.7594.01 2 0 1 0 1
#> TCGA.DQ.7596.01 2 0 1 0 1
#> TCGA.BB.4223.01 1 0 1 1 0
#> TCGA.CN.5374.01 2 0 1 0 1
#> TCGA.BB.4228.01 1 0 1 1 0
#> TCGA.H7.A76A.01 2 0 1 0 1
#> TCGA.DQ.7593.01 2 0 1 0 1
#> TCGA.BB.4225.01 1 0 1 1 0
#> TCGA.CN.A6UY.01 1 0 1 1 0
#> TCGA.MZ.A5BI.01 2 0 1 0 1
#> TCGA.BB.A6UM.01 2 0 1 0 1
#> TCGA.CN.A6V6.01 1 0 1 1 0
#> TCGA.RS.A6TP.01 1 0 1 1 0
#> TCGA.KU.A6H7.06 1 0 1 1 0
#> TCGA.UP.A6WW.01 1 0 1 1 0
#> TCGA.MZ.A6I9.01 2 0 1 0 1
#> TCGA.CR.7404.01 2 0 1 0 1
#> TCGA.CR.7368.01 2 0 1 0 1
#> TCGA.KU.A6H7.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CV.6433.01 1 0.000 0.9611 1.00 0.00 0.00
#> TCGA.HD.7754.01 2 0.624 -0.1929 0.00 0.56 0.44
#> TCGA.CV.7406.01 3 0.000 0.5205 0.00 0.00 1.00
#> TCGA.BA.5559.01 1 0.000 0.9611 1.00 0.00 0.00
#> TCGA.CR.5249.01 3 0.624 0.1349 0.00 0.44 0.56
#> TCGA.CV.5443.01 1 0.000 0.9611 1.00 0.00 0.00
#> TCGA.CR.5248.01 2 0.571 0.4901 0.00 0.68 0.32
#> TCGA.CR.5250.01 1 0.000 0.9611 1.00 0.00 0.00
#> TCGA.CR.5243.01 1 0.000 0.9611 1.00 0.00 0.00
#> TCGA.CV.5442.01 1 0.502 0.7791 0.76 0.24 0.00
#> TCGA.CR.7385.01 3 0.254 0.5724 0.00 0.08 0.92
#> TCGA.CV.6939.01 2 0.630 0.4384 0.00 0.52 0.48
#> TCGA.CR.6487.01 2 0.571 0.4901 0.00 0.68 0.32
#> TCGA.CR.6472.01 3 0.000 0.5205 0.00 0.00 1.00
#> TCGA.CR.6481.01 3 0.480 0.4296 0.00 0.22 0.78
#> TCGA.CR.6470.01 2 0.630 0.4384 0.00 0.52 0.48
#> TCGA.BA.A4IH.01 2 0.630 0.4384 0.00 0.52 0.48
#> TCGA.CR.6482.01 2 0.604 0.4950 0.00 0.62 0.38
#> TCGA.P3.A5Q5.01 3 0.254 0.5724 0.00 0.08 0.92
#> TCGA.BA.A4IG.01 3 0.624 0.2764 0.00 0.44 0.56
#> TCGA.HD.A634.01 3 0.613 0.2805 0.00 0.40 0.60
#> TCGA.BA.5153.01 1 0.000 0.9611 1.00 0.00 0.00
#> TCGA.DQ.7594.01 3 0.207 0.5658 0.00 0.06 0.94
#> TCGA.DQ.7596.01 2 0.604 0.4950 0.00 0.62 0.38
#> TCGA.BB.4223.01 1 0.000 0.9611 1.00 0.00 0.00
#> TCGA.CN.5374.01 3 0.604 0.3251 0.00 0.38 0.62
#> TCGA.BB.4228.01 1 0.000 0.9611 1.00 0.00 0.00
#> TCGA.H7.A76A.01 2 0.630 0.4384 0.00 0.52 0.48
#> TCGA.DQ.7593.01 2 0.604 0.4950 0.00 0.62 0.38
#> TCGA.BB.4225.01 1 0.000 0.9611 1.00 0.00 0.00
#> TCGA.CN.A6UY.01 1 0.000 0.9611 1.00 0.00 0.00
#> TCGA.MZ.A5BI.01 2 0.630 0.4384 0.00 0.52 0.48
#> TCGA.BB.A6UM.01 2 0.502 -0.0745 0.00 0.76 0.24
#> TCGA.CN.A6V6.01 1 0.000 0.9611 1.00 0.00 0.00
#> TCGA.RS.A6TP.01 1 0.619 0.5834 0.58 0.42 0.00
#> TCGA.KU.A6H7.06 1 0.000 0.9611 1.00 0.00 0.00
#> TCGA.UP.A6WW.01 1 0.000 0.9611 1.00 0.00 0.00
#> TCGA.MZ.A6I9.01 3 0.624 0.2764 0.00 0.44 0.56
#> TCGA.CR.7404.01 2 0.571 0.4901 0.00 0.68 0.32
#> TCGA.CR.7368.01 2 0.502 -0.0745 0.00 0.76 0.24
#> TCGA.KU.A6H7.01 2 0.571 0.4901 0.00 0.68 0.32
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.CV.6433.01 1 0.0000 0.984 1.00 0.00 0.00 0.00
#> TCGA.HD.7754.01 4 0.5355 0.146 0.00 0.02 0.36 0.62
#> TCGA.CV.7406.01 3 0.1637 0.713 0.00 0.06 0.94 0.00
#> TCGA.BA.5559.01 1 0.0000 0.984 1.00 0.00 0.00 0.00
#> TCGA.CR.5249.01 2 0.4731 0.668 0.00 0.78 0.06 0.16
#> TCGA.CV.5443.01 1 0.0000 0.984 1.00 0.00 0.00 0.00
#> TCGA.CR.5248.01 2 0.0000 0.926 0.00 1.00 0.00 0.00
#> TCGA.CR.5250.01 1 0.0000 0.984 1.00 0.00 0.00 0.00
#> TCGA.CR.5243.01 1 0.1913 0.944 0.94 0.00 0.04 0.02
#> TCGA.CV.5442.01 4 0.5915 0.224 0.40 0.00 0.04 0.56
#> TCGA.CR.7385.01 3 0.3972 0.733 0.00 0.08 0.84 0.08
#> TCGA.CV.6939.01 2 0.1211 0.918 0.00 0.96 0.04 0.00
#> TCGA.CR.6487.01 2 0.0000 0.926 0.00 1.00 0.00 0.00
#> TCGA.CR.6472.01 3 0.1637 0.713 0.00 0.06 0.94 0.00
#> TCGA.CR.6481.01 3 0.3172 0.707 0.00 0.16 0.84 0.00
#> TCGA.CR.6470.01 2 0.1211 0.918 0.00 0.96 0.04 0.00
#> TCGA.BA.A4IH.01 2 0.3935 0.837 0.00 0.84 0.06 0.10
#> TCGA.CR.6482.01 2 0.0000 0.926 0.00 1.00 0.00 0.00
#> TCGA.P3.A5Q5.01 3 0.3972 0.733 0.00 0.08 0.84 0.08
#> TCGA.BA.A4IG.01 3 0.7198 0.641 0.00 0.28 0.54 0.18
#> TCGA.HD.A634.01 3 0.7198 0.641 0.00 0.28 0.54 0.18
#> TCGA.BA.5153.01 1 0.0000 0.984 1.00 0.00 0.00 0.00
#> TCGA.DQ.7594.01 3 0.2335 0.720 0.00 0.06 0.92 0.02
#> TCGA.DQ.7596.01 2 0.0000 0.926 0.00 1.00 0.00 0.00
#> TCGA.BB.4223.01 1 0.0000 0.984 1.00 0.00 0.00 0.00
#> TCGA.CN.5374.01 3 0.7198 0.641 0.00 0.28 0.54 0.18
#> TCGA.BB.4228.01 1 0.0000 0.984 1.00 0.00 0.00 0.00
#> TCGA.H7.A76A.01 2 0.1211 0.918 0.00 0.96 0.04 0.00
#> TCGA.DQ.7593.01 2 0.0000 0.926 0.00 1.00 0.00 0.00
#> TCGA.BB.4225.01 1 0.0000 0.984 1.00 0.00 0.00 0.00
#> TCGA.CN.A6UY.01 1 0.0000 0.984 1.00 0.00 0.00 0.00
#> TCGA.MZ.A5BI.01 2 0.3247 0.863 0.00 0.88 0.06 0.06
#> TCGA.BB.A6UM.01 4 0.3247 0.634 0.00 0.06 0.06 0.88
#> TCGA.CN.A6V6.01 1 0.1913 0.944 0.94 0.00 0.04 0.02
#> TCGA.RS.A6TP.01 4 0.4088 0.628 0.14 0.00 0.04 0.82
#> TCGA.KU.A6H7.06 1 0.1913 0.944 0.94 0.00 0.04 0.02
#> TCGA.UP.A6WW.01 1 0.0000 0.984 1.00 0.00 0.00 0.00
#> TCGA.MZ.A6I9.01 3 0.7414 0.567 0.00 0.34 0.48 0.18
#> TCGA.CR.7404.01 2 0.2647 0.815 0.00 0.88 0.00 0.12
#> TCGA.CR.7368.01 4 0.3247 0.634 0.00 0.06 0.06 0.88
#> TCGA.KU.A6H7.01 2 0.0707 0.915 0.00 0.98 0.02 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CV.6433.01 1 0.430 0.8099 0.52 0.00 0.00 0.48 0.00
#> TCGA.HD.7754.01 5 0.273 0.5529 0.00 0.00 0.16 0.00 0.84
#> TCGA.CV.7406.01 3 0.407 0.4502 0.00 0.06 0.78 0.16 0.00
#> TCGA.BA.5559.01 1 0.423 0.7894 0.58 0.00 0.00 0.42 0.00
#> TCGA.CR.5249.01 2 0.701 0.0889 0.00 0.52 0.18 0.04 0.26
#> TCGA.CV.5443.01 1 0.423 0.7894 0.58 0.00 0.00 0.42 0.00
#> TCGA.CR.5248.01 2 0.000 0.7886 0.00 1.00 0.00 0.00 0.00
#> TCGA.CR.5250.01 1 0.430 0.8099 0.52 0.00 0.00 0.48 0.00
#> TCGA.CR.5243.01 1 0.000 0.4602 1.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5442.01 1 0.625 -0.4402 0.52 0.00 0.04 0.06 0.38
#> TCGA.CR.7385.01 3 0.364 0.5839 0.00 0.06 0.82 0.00 0.12
#> TCGA.CV.6939.01 2 0.482 0.7006 0.00 0.72 0.18 0.10 0.00
#> TCGA.CR.6487.01 2 0.000 0.7886 0.00 1.00 0.00 0.00 0.00
#> TCGA.CR.6472.01 3 0.407 0.4502 0.00 0.06 0.78 0.16 0.00
#> TCGA.CR.6481.01 3 0.385 0.5391 0.00 0.22 0.76 0.02 0.00
#> TCGA.CR.6470.01 2 0.482 0.7006 0.00 0.72 0.18 0.10 0.00
#> TCGA.BA.A4IH.01 2 0.558 0.6087 0.00 0.60 0.10 0.30 0.00
#> TCGA.CR.6482.01 2 0.000 0.7886 0.00 1.00 0.00 0.00 0.00
#> TCGA.P3.A5Q5.01 3 0.364 0.5839 0.00 0.06 0.82 0.00 0.12
#> TCGA.BA.A4IG.01 3 0.678 0.4616 0.00 0.34 0.38 0.00 0.28
#> TCGA.HD.A634.01 3 0.678 0.4616 0.00 0.34 0.38 0.00 0.28
#> TCGA.BA.5153.01 1 0.430 0.8099 0.52 0.00 0.00 0.48 0.00
#> TCGA.DQ.7594.01 3 0.280 0.5806 0.00 0.06 0.88 0.00 0.06
#> TCGA.DQ.7596.01 2 0.304 0.7862 0.00 0.86 0.04 0.10 0.00
#> TCGA.BB.4223.01 1 0.430 0.8099 0.52 0.00 0.00 0.48 0.00
#> TCGA.CN.5374.01 3 0.678 0.4616 0.00 0.34 0.38 0.00 0.28
#> TCGA.BB.4228.01 1 0.430 0.8099 0.52 0.00 0.00 0.48 0.00
#> TCGA.H7.A76A.01 2 0.370 0.7715 0.00 0.82 0.08 0.10 0.00
#> TCGA.DQ.7593.01 2 0.141 0.7925 0.00 0.94 0.00 0.06 0.00
#> TCGA.BB.4225.01 1 0.430 0.8099 0.52 0.00 0.00 0.48 0.00
#> TCGA.CN.A6UY.01 1 0.430 0.8099 0.52 0.00 0.00 0.48 0.00
#> TCGA.MZ.A5BI.01 2 0.482 0.7201 0.00 0.72 0.10 0.18 0.00
#> TCGA.BB.A6UM.01 5 0.000 0.7297 0.00 0.00 0.00 0.00 1.00
#> TCGA.CN.A6V6.01 1 0.202 0.3306 0.90 0.10 0.00 0.00 0.00
#> TCGA.RS.A6TP.01 5 0.630 0.4343 0.42 0.00 0.04 0.06 0.48
#> TCGA.KU.A6H7.06 1 0.000 0.4602 1.00 0.00 0.00 0.00 0.00
#> TCGA.UP.A6WW.01 1 0.430 0.8099 0.52 0.00 0.00 0.48 0.00
#> TCGA.MZ.A6I9.01 3 0.679 0.4202 0.00 0.36 0.36 0.00 0.28
#> TCGA.CR.7404.01 2 0.228 0.6867 0.00 0.88 0.00 0.00 0.12
#> TCGA.CR.7368.01 5 0.000 0.7297 0.00 0.00 0.00 0.00 1.00
#> TCGA.KU.A6H7.01 2 0.104 0.7650 0.04 0.96 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.CV.6433.01 1 0.0547 0.9134 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.HD.7754.01 5 0.4803 0.2169 0.00 0.00 0.04 0.16 0.72 0.08
#> TCGA.CV.7406.01 3 0.1480 0.5725 0.00 0.04 0.94 0.00 0.02 0.00
#> TCGA.BA.5559.01 1 0.3156 0.6584 0.80 0.00 0.02 0.00 0.00 0.18
#> TCGA.CR.5249.01 5 0.4631 0.3140 0.00 0.32 0.06 0.00 0.62 0.00
#> TCGA.CV.5443.01 1 0.3315 0.6137 0.78 0.00 0.02 0.00 0.00 0.20
#> TCGA.CR.5248.01 2 0.4873 0.6187 0.00 0.60 0.00 0.00 0.08 0.32
#> TCGA.CR.5250.01 1 0.0547 0.9134 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.CR.5243.01 6 0.5574 0.6170 0.44 0.00 0.02 0.04 0.02 0.48
#> TCGA.CV.5442.01 4 0.3592 0.9861 0.00 0.00 0.02 0.74 0.00 0.24
#> TCGA.CR.7385.01 3 0.4845 0.6286 0.00 0.06 0.54 0.00 0.40 0.00
#> TCGA.CV.6939.01 2 0.3045 0.6024 0.00 0.84 0.06 0.00 0.10 0.00
#> TCGA.CR.6487.01 2 0.4613 0.6506 0.00 0.66 0.00 0.00 0.08 0.26
#> TCGA.CR.6472.01 3 0.1480 0.5725 0.00 0.04 0.94 0.00 0.02 0.00
#> TCGA.CR.6481.01 3 0.5636 0.5686 0.00 0.18 0.52 0.00 0.30 0.00
#> TCGA.CR.6470.01 2 0.3045 0.6024 0.00 0.84 0.06 0.00 0.10 0.00
#> TCGA.BA.A4IH.01 2 0.4626 0.5729 0.00 0.74 0.04 0.14 0.00 0.08
#> TCGA.CR.6482.01 2 0.4613 0.6506 0.00 0.66 0.00 0.00 0.08 0.26
#> TCGA.P3.A5Q5.01 3 0.4845 0.6286 0.00 0.06 0.54 0.00 0.40 0.00
#> TCGA.BA.A4IG.01 5 0.5039 0.3093 0.00 0.18 0.18 0.00 0.64 0.00
#> TCGA.HD.A634.01 5 0.5524 0.3270 0.00 0.20 0.16 0.02 0.62 0.00
#> TCGA.BA.5153.01 1 0.0000 0.9233 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.7594.01 3 0.4631 0.6720 0.00 0.06 0.62 0.00 0.32 0.00
#> TCGA.DQ.7596.01 2 0.0000 0.6952 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BB.4223.01 1 0.0000 0.9233 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.5374.01 5 0.5027 0.3401 0.00 0.20 0.16 0.00 0.64 0.00
#> TCGA.BB.4228.01 1 0.0000 0.9233 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.H7.A76A.01 2 0.1865 0.6693 0.00 0.92 0.04 0.00 0.04 0.00
#> TCGA.DQ.7593.01 2 0.1556 0.6991 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.BB.4225.01 1 0.0000 0.9233 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.A6UY.01 1 0.0000 0.9233 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MZ.A5BI.01 2 0.3103 0.6511 0.00 0.86 0.04 0.04 0.00 0.06
#> TCGA.BB.A6UM.01 5 0.4938 -0.0317 0.00 0.00 0.00 0.34 0.58 0.08
#> TCGA.CN.A6V6.01 6 0.3854 0.1758 0.12 0.04 0.00 0.04 0.00 0.80
#> TCGA.RS.A6TP.01 4 0.3076 0.9861 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.KU.A6H7.06 6 0.5574 0.6170 0.44 0.00 0.02 0.04 0.02 0.48
#> TCGA.UP.A6WW.01 1 0.0000 0.9233 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MZ.A6I9.01 5 0.4989 0.3528 0.00 0.22 0.14 0.00 0.64 0.00
#> TCGA.CR.7404.01 2 0.5428 0.5574 0.00 0.54 0.00 0.00 0.14 0.32
#> TCGA.CR.7368.01 5 0.4938 -0.0317 0.00 0.00 0.00 0.34 0.58 0.08
#> TCGA.KU.A6H7.01 2 0.5071 0.5561 0.00 0.52 0.00 0.00 0.08 0.40
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.CV.6433.01 1 0.0504 0.885 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.HD.7754.01 7 0.3413 0.719 0.00 0.00 0.00 0.00 0.38 0.00 0.62
#> TCGA.CV.7406.01 3 0.1433 0.987 0.00 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.BA.5559.01 1 0.4211 0.382 0.68 0.00 0.04 0.02 0.00 0.26 0.00
#> TCGA.CR.5249.01 5 0.1433 0.572 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.CV.5443.01 1 0.4211 0.382 0.68 0.00 0.04 0.02 0.00 0.26 0.00
#> TCGA.CR.5248.01 2 0.7728 0.595 0.00 0.38 0.00 0.10 0.18 0.20 0.14
#> TCGA.CR.5250.01 1 0.0504 0.885 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.CR.5243.01 6 0.3294 0.742 0.34 0.00 0.00 0.00 0.00 0.66 0.00
#> TCGA.CV.5442.01 4 0.4242 0.956 0.02 0.00 0.00 0.72 0.00 0.08 0.18
#> TCGA.CR.7385.01 5 0.3358 0.475 0.00 0.00 0.36 0.00 0.64 0.00 0.00
#> TCGA.CV.6939.01 2 0.2945 0.545 0.00 0.74 0.00 0.00 0.26 0.00 0.00
#> TCGA.CR.6487.01 2 0.7728 0.595 0.00 0.38 0.00 0.10 0.18 0.20 0.14
#> TCGA.CR.6472.01 3 0.1928 0.987 0.00 0.00 0.90 0.00 0.08 0.02 0.00
#> TCGA.CR.6481.01 5 0.4902 0.343 0.00 0.12 0.34 0.00 0.54 0.00 0.00
#> TCGA.CR.6470.01 2 0.2945 0.545 0.00 0.74 0.00 0.00 0.26 0.00 0.00
#> TCGA.BA.A4IH.01 2 0.4171 0.388 0.00 0.78 0.04 0.12 0.02 0.02 0.02
#> TCGA.CR.6482.01 2 0.7728 0.595 0.00 0.38 0.00 0.10 0.18 0.20 0.14
#> TCGA.P3.A5Q5.01 5 0.3358 0.475 0.00 0.00 0.36 0.00 0.64 0.00 0.00
#> TCGA.BA.A4IG.01 5 0.0000 0.658 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HD.A634.01 5 0.2213 0.605 0.00 0.00 0.00 0.04 0.90 0.04 0.02
#> TCGA.BA.5153.01 1 0.0000 0.889 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.7594.01 5 0.3496 0.366 0.00 0.00 0.42 0.00 0.58 0.00 0.00
#> TCGA.DQ.7596.01 2 0.2569 0.620 0.00 0.84 0.00 0.00 0.14 0.02 0.00
#> TCGA.BB.4223.01 1 0.0504 0.885 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.CN.5374.01 5 0.0000 0.658 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BB.4228.01 1 0.0000 0.889 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.H7.A76A.01 2 0.2572 0.600 0.00 0.80 0.00 0.00 0.20 0.00 0.00
#> TCGA.DQ.7593.01 2 0.5090 0.627 0.00 0.70 0.00 0.02 0.10 0.08 0.10
#> TCGA.BB.4225.01 1 0.0000 0.889 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.A6UY.01 1 0.0000 0.889 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MZ.A5BI.01 2 0.1718 0.540 0.00 0.92 0.00 0.04 0.04 0.00 0.00
#> TCGA.BB.A6UM.01 7 0.3519 0.821 0.00 0.00 0.00 0.00 0.22 0.04 0.74
#> TCGA.CN.A6V6.01 6 0.2722 0.532 0.12 0.00 0.04 0.00 0.00 0.84 0.00
#> TCGA.RS.A6TP.01 4 0.3908 0.956 0.00 0.00 0.00 0.72 0.00 0.08 0.20
#> TCGA.KU.A6H7.06 6 0.4070 0.742 0.34 0.00 0.00 0.00 0.00 0.62 0.04
#> TCGA.UP.A6WW.01 1 0.0000 0.889 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MZ.A6I9.01 5 0.0504 0.646 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.CR.7404.01 2 0.7849 0.561 0.00 0.34 0.00 0.10 0.22 0.20 0.14
#> TCGA.CR.7368.01 7 0.2708 0.826 0.00 0.00 0.00 0.00 0.22 0.00 0.78
#> TCGA.KU.A6H7.01 2 0.7640 0.594 0.00 0.38 0.00 0.08 0.18 0.22 0.14
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.CV.6433.01 1 0.2204 0.8357 0.90 0.00 0.04 0.02 0.00 0.00 0.02 0.02
#> TCGA.HD.7754.01 7 0.1563 0.8813 0.00 0.00 0.00 0.00 0.10 0.00 0.90 0.00
#> TCGA.CV.7406.01 3 0.2756 1.0000 0.00 0.00 0.74 0.00 0.26 0.00 0.00 0.00
#> TCGA.BA.5559.01 1 0.5117 0.3707 0.54 0.00 0.04 0.02 0.00 0.36 0.02 0.02
#> TCGA.CR.5249.01 5 0.3744 0.7663 0.00 0.18 0.00 0.00 0.74 0.00 0.06 0.02
#> TCGA.CV.5443.01 1 0.5117 0.3707 0.54 0.00 0.04 0.02 0.00 0.36 0.02 0.02
#> TCGA.CR.5248.01 2 0.0471 0.8691 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.CR.5250.01 1 0.2204 0.8357 0.90 0.00 0.04 0.02 0.00 0.00 0.02 0.02
#> TCGA.CR.5243.01 6 0.5490 0.7967 0.12 0.00 0.04 0.16 0.00 0.62 0.00 0.06
#> TCGA.CV.5442.01 4 0.2807 0.9314 0.00 0.00 0.04 0.86 0.00 0.02 0.06 0.02
#> TCGA.CR.7385.01 5 0.0000 0.7538 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.6939.01 8 0.4437 0.7424 0.00 0.22 0.00 0.00 0.16 0.00 0.00 0.62
#> TCGA.CR.6487.01 2 0.0000 0.8677 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.6472.01 3 0.2756 1.0000 0.00 0.00 0.74 0.00 0.26 0.00 0.00 0.00
#> TCGA.CR.6481.01 5 0.1804 0.7320 0.00 0.02 0.00 0.00 0.90 0.00 0.00 0.08
#> TCGA.CR.6470.01 8 0.4458 0.7239 0.00 0.20 0.00 0.00 0.18 0.00 0.00 0.62
#> TCGA.BA.A4IH.01 8 0.5452 0.3965 0.00 0.10 0.02 0.02 0.04 0.20 0.00 0.62
#> TCGA.CR.6482.01 2 0.0000 0.8677 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P3.A5Q5.01 5 0.0000 0.7538 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BA.A4IG.01 5 0.3450 0.8055 0.00 0.12 0.00 0.00 0.76 0.00 0.12 0.00
#> TCGA.HD.A634.01 5 0.5533 0.7416 0.00 0.10 0.06 0.02 0.66 0.06 0.10 0.00
#> TCGA.BA.5153.01 1 0.0000 0.8638 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DQ.7594.01 5 0.0471 0.7360 0.00 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.DQ.7596.01 8 0.3808 0.7066 0.00 0.34 0.00 0.00 0.04 0.00 0.00 0.62
#> TCGA.BB.4223.01 1 0.0941 0.8566 0.96 0.00 0.02 0.00 0.00 0.00 0.02 0.00
#> TCGA.CN.5374.01 5 0.3450 0.8055 0.00 0.12 0.00 0.00 0.76 0.00 0.12 0.00
#> TCGA.BB.4228.01 1 0.0000 0.8638 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.H7.A76A.01 8 0.4134 0.7493 0.00 0.30 0.00 0.00 0.08 0.00 0.00 0.62
#> TCGA.DQ.7593.01 2 0.3193 -0.0535 0.00 0.62 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.BB.4225.01 1 0.0000 0.8638 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.A6UY.01 1 0.0000 0.8638 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MZ.A5BI.01 8 0.3504 0.7277 0.00 0.26 0.00 0.00 0.04 0.00 0.00 0.70
#> TCGA.BB.A6UM.01 7 0.1408 0.8990 0.00 0.00 0.00 0.02 0.02 0.00 0.94 0.02
#> TCGA.CN.A6V6.01 6 0.3589 0.6504 0.00 0.10 0.00 0.16 0.00 0.74 0.00 0.00
#> TCGA.RS.A6TP.01 4 0.1091 0.9324 0.00 0.00 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.KU.A6H7.06 6 0.6313 0.7776 0.12 0.00 0.10 0.16 0.00 0.54 0.00 0.08
#> TCGA.UP.A6WW.01 1 0.0000 0.8638 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MZ.A6I9.01 5 0.3619 0.7936 0.00 0.14 0.00 0.00 0.74 0.00 0.12 0.00
#> TCGA.CR.7404.01 2 0.0471 0.8691 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.CR.7368.01 7 0.0808 0.9195 0.00 0.00 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.KU.A6H7.01 2 0.0808 0.8493 0.00 0.96 0.00 0.00 0.00 0.04 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: Node051. Child nodes: Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node02111-leaf , Node02112-leaf , Node02113-leaf , Node02114-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02124-leaf , Node02131-leaf , Node02132 , Node02133-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02231-leaf , Node02232-leaf , Node02233-leaf , Node02241-leaf , Node02242-leaf , Node02243-leaf , Node02321-leaf , Node02322-leaf , Node02323-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf , Node05114-leaf , Node05121 , Node05122-leaf , Node05123-leaf , Node05221-leaf , Node05222-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0511"]
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 15 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 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 0.867 0.942 0.977 0.2807 0.752 0.752
#> 3 3 1.000 1.000 1.000 1.1051 0.657 0.544
#> 4 4 1.000 0.956 0.968 0.0823 0.962 0.907
#> 5 5 0.762 0.943 0.896 0.2031 0.810 0.487
#> 6 6 0.743 0.820 0.851 0.0664 0.962 0.789
#> 7 7 0.905 0.760 0.876 0.0578 1.000 1.000
#> 8 8 0.905 0.730 0.848 0.0252 0.962 0.733
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] 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.CV.6433.01 2 0.000 0.971 0.00 1.00
#> TCGA.BA.5559.01 2 0.000 0.971 0.00 1.00
#> TCGA.CV.5443.01 2 0.000 0.971 0.00 1.00
#> TCGA.CR.5250.01 2 0.000 0.971 0.00 1.00
#> TCGA.CR.5243.01 2 0.925 0.485 0.34 0.66
#> TCGA.CV.5442.01 1 0.000 1.000 1.00 0.00
#> TCGA.BA.5153.01 2 0.000 0.971 0.00 1.00
#> TCGA.BB.4223.01 2 0.000 0.971 0.00 1.00
#> TCGA.BB.4228.01 2 0.000 0.971 0.00 1.00
#> TCGA.BB.4225.01 2 0.000 0.971 0.00 1.00
#> TCGA.CN.A6UY.01 2 0.000 0.971 0.00 1.00
#> TCGA.CN.A6V6.01 2 0.000 0.971 0.00 1.00
#> TCGA.RS.A6TP.01 1 0.000 1.000 1.00 0.00
#> TCGA.KU.A6H7.06 2 0.000 0.971 0.00 1.00
#> TCGA.UP.A6WW.01 2 0.000 0.971 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CV.6433.01 2 0 1 0 1 0
#> TCGA.BA.5559.01 2 0 1 0 1 0
#> TCGA.CV.5443.01 3 0 1 0 0 1
#> TCGA.CR.5250.01 2 0 1 0 1 0
#> TCGA.CR.5243.01 3 0 1 0 0 1
#> TCGA.CV.5442.01 1 0 1 1 0 0
#> TCGA.BA.5153.01 2 0 1 0 1 0
#> TCGA.BB.4223.01 2 0 1 0 1 0
#> TCGA.BB.4228.01 2 0 1 0 1 0
#> TCGA.BB.4225.01 2 0 1 0 1 0
#> TCGA.CN.A6UY.01 2 0 1 0 1 0
#> TCGA.CN.A6V6.01 3 0 1 0 0 1
#> TCGA.RS.A6TP.01 1 0 1 1 0 0
#> TCGA.KU.A6H7.06 3 0 1 0 0 1
#> TCGA.UP.A6WW.01 2 0 1 0 1 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.CV.6433.01 2 0.201 0.959 0 0.92 0.08 0.00
#> TCGA.BA.5559.01 2 0.201 0.959 0 0.92 0.08 0.00
#> TCGA.CV.5443.01 3 0.000 0.876 0 0.00 1.00 0.00
#> TCGA.CR.5250.01 2 0.000 0.949 0 1.00 0.00 0.00
#> TCGA.CR.5243.01 4 0.000 1.000 0 0.00 0.00 1.00
#> TCGA.CV.5442.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.BA.5153.01 2 0.000 0.949 0 1.00 0.00 0.00
#> TCGA.BB.4223.01 2 0.000 0.949 0 1.00 0.00 0.00
#> TCGA.BB.4228.01 2 0.201 0.959 0 0.92 0.08 0.00
#> TCGA.BB.4225.01 2 0.201 0.959 0 0.92 0.08 0.00
#> TCGA.CN.A6UY.01 2 0.201 0.959 0 0.92 0.08 0.00
#> TCGA.CN.A6V6.01 3 0.201 0.870 0 0.00 0.92 0.08
#> TCGA.RS.A6TP.01 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.KU.A6H7.06 4 0.000 1.000 0 0.00 0.00 1.00
#> TCGA.UP.A6WW.01 2 0.000 0.949 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.CV.6433.01 2 0.0609 0.909 0.0 0.98 0.00 0 0.02
#> TCGA.BA.5559.01 2 0.0609 0.909 0.0 0.98 0.00 0 0.02
#> TCGA.CV.5443.01 3 0.1410 0.956 0.0 0.00 0.94 0 0.06
#> TCGA.CR.5250.01 5 0.3983 1.000 0.0 0.34 0.00 0 0.66
#> TCGA.CR.5243.01 4 0.0000 1.000 0.0 0.00 0.00 1 0.00
#> TCGA.CV.5442.01 1 0.0000 0.926 1.0 0.00 0.00 0 0.00
#> TCGA.BA.5153.01 5 0.3983 1.000 0.0 0.34 0.00 0 0.66
#> TCGA.BB.4223.01 5 0.3983 1.000 0.0 0.34 0.00 0 0.66
#> TCGA.BB.4228.01 2 0.0000 0.916 0.0 1.00 0.00 0 0.00
#> TCGA.BB.4225.01 2 0.2929 0.733 0.0 0.82 0.00 0 0.18
#> TCGA.CN.A6UY.01 2 0.0000 0.916 0.0 1.00 0.00 0 0.00
#> TCGA.CN.A6V6.01 3 0.0000 0.956 0.0 0.00 1.00 0 0.00
#> TCGA.RS.A6TP.01 1 0.2020 0.926 0.9 0.00 0.00 0 0.10
#> TCGA.KU.A6H7.06 4 0.0000 1.000 0.0 0.00 0.00 1 0.00
#> TCGA.UP.A6WW.01 5 0.3983 1.000 0.0 0.34 0.00 0 0.66
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.CV.6433.01 2 0.486 0.785 0.00 0.66 0.00 0.00 0.20 0.14
#> TCGA.BA.5559.01 2 0.486 0.785 0.00 0.66 0.00 0.00 0.20 0.14
#> TCGA.CV.5443.01 3 0.379 0.828 0.00 0.10 0.78 0.00 0.00 0.12
#> TCGA.CR.5250.01 5 0.000 1.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CR.5243.01 4 0.263 0.859 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.CV.5442.01 1 0.000 0.876 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.5153.01 5 0.000 1.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BB.4223.01 5 0.000 1.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BB.4228.01 2 0.263 0.803 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.BB.4225.01 6 0.484 0.000 0.00 0.40 0.00 0.00 0.06 0.54
#> TCGA.CN.A6UY.01 2 0.263 0.803 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.CN.A6V6.01 3 0.000 0.828 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.RS.A6TP.01 1 0.245 0.876 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.KU.A6H7.06 4 0.000 0.859 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.UP.A6WW.01 5 0.000 1.000 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.CV.6433.01 2 0.449 0.681 0.0 0.60 0.00 0.00 0.08 0.32 0.00
#> TCGA.BA.5559.01 2 0.449 0.681 0.0 0.60 0.00 0.00 0.08 0.32 0.00
#> TCGA.CV.5443.01 3 0.336 0.676 0.0 0.00 0.64 0.00 0.00 0.00 0.36
#> TCGA.CR.5250.01 5 0.000 1.000 0.0 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CR.5243.01 4 0.000 0.899 0.0 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.5442.01 1 0.000 0.828 1.0 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.5153.01 5 0.000 1.000 0.0 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BB.4223.01 5 0.000 1.000 0.0 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BB.4228.01 2 0.353 0.581 0.0 0.76 0.00 0.00 0.06 0.00 0.18
#> TCGA.BB.4225.01 6 0.339 0.000 0.0 0.04 0.00 0.00 0.00 0.76 0.20
#> TCGA.CN.A6UY.01 2 0.202 0.647 0.0 0.90 0.00 0.00 0.06 0.00 0.04
#> TCGA.CN.A6V6.01 3 0.000 0.676 0.0 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RS.A6TP.01 1 0.340 0.828 0.8 0.02 0.00 0.00 0.00 0.04 0.14
#> TCGA.KU.A6H7.06 4 0.228 0.899 0.0 0.04 0.00 0.88 0.00 0.00 0.08
#> TCGA.UP.A6WW.01 5 0.000 1.000 0.0 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.CV.6433.01 2 0.0808 1.000 0.00 0.96 0.00 0.00 0.04 0.00 0.0 0.00
#> TCGA.BA.5559.01 2 0.0808 1.000 0.00 0.96 0.00 0.00 0.04 0.00 0.0 0.00
#> TCGA.CV.5443.01 3 0.2114 0.554 0.16 0.00 0.84 0.00 0.00 0.00 0.0 0.00
#> TCGA.CR.5250.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00 0.0 0.00
#> TCGA.CR.5243.01 4 0.0000 0.695 0.00 0.00 0.00 1.00 0.00 0.00 0.0 0.00
#> TCGA.CV.5442.01 7 0.0000 0.734 0.00 0.00 0.00 0.00 0.00 0.00 1.0 0.00
#> TCGA.BA.5153.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00 0.0 0.00
#> TCGA.BB.4223.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00 0.0 0.00
#> TCGA.BB.4228.01 8 0.3293 0.517 0.00 0.22 0.00 0.00 0.04 0.00 0.0 0.74
#> TCGA.BB.4225.01 6 0.2114 0.000 0.00 0.16 0.00 0.00 0.00 0.84 0.0 0.00
#> TCGA.CN.A6UY.01 8 0.6239 0.470 0.32 0.30 0.00 0.00 0.04 0.02 0.0 0.32
#> TCGA.CN.A6V6.01 3 0.3970 0.554 0.00 0.00 0.68 0.00 0.00 0.10 0.0 0.22
#> TCGA.RS.A6TP.01 7 0.4543 0.734 0.18 0.04 0.00 0.00 0.00 0.04 0.7 0.04
#> TCGA.KU.A6H7.06 4 0.3083 0.695 0.34 0.00 0.00 0.66 0.00 0.00 0.0 0.00
#> TCGA.UP.A6WW.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00 0.0 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: Node051. Child nodes: Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node02111-leaf , Node02112-leaf , Node02113-leaf , Node02114-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02124-leaf , Node02131-leaf , Node02132 , Node02133-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02231-leaf , Node02232-leaf , Node02233-leaf , Node02241-leaf , Node02242-leaf , Node02243-leaf , Node02321-leaf , Node02322-leaf , Node02323-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf , Node05114-leaf , Node05121 , Node05122-leaf , Node05123-leaf , Node05221-leaf , Node05222-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0512"]
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 26 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 1.000 1.000 0.4713 0.529 0.529
#> 3 3 1.000 1.000 1.000 0.3913 0.692 0.479
#> 4 4 0.717 0.791 0.856 0.1297 0.818 0.516
#> 5 5 0.906 0.870 0.941 0.0687 0.982 0.918
#> 6 6 0.819 0.683 0.868 0.0407 0.960 0.824
#> 7 7 0.797 0.656 0.812 0.0312 0.945 0.735
#> 8 8 0.818 0.593 0.822 0.0216 0.975 0.846
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.HD.7754.01 2 0 1 0 1
#> TCGA.CV.7406.01 2 0 1 0 1
#> TCGA.CR.5249.01 1 0 1 1 0
#> TCGA.CR.5248.01 1 0 1 1 0
#> TCGA.CR.7385.01 1 0 1 1 0
#> TCGA.CV.6939.01 1 0 1 1 0
#> TCGA.CR.6487.01 1 0 1 1 0
#> TCGA.CR.6472.01 2 0 1 0 1
#> TCGA.CR.6481.01 1 0 1 1 0
#> TCGA.CR.6470.01 1 0 1 1 0
#> TCGA.BA.A4IH.01 1 0 1 1 0
#> TCGA.CR.6482.01 1 0 1 1 0
#> TCGA.P3.A5Q5.01 2 0 1 0 1
#> TCGA.BA.A4IG.01 2 0 1 0 1
#> TCGA.HD.A634.01 1 0 1 1 0
#> TCGA.DQ.7594.01 2 0 1 0 1
#> TCGA.DQ.7596.01 1 0 1 1 0
#> TCGA.CN.5374.01 1 0 1 1 0
#> TCGA.H7.A76A.01 1 0 1 1 0
#> TCGA.DQ.7593.01 1 0 1 1 0
#> TCGA.MZ.A5BI.01 1 0 1 1 0
#> TCGA.BB.A6UM.01 2 0 1 0 1
#> TCGA.MZ.A6I9.01 2 0 1 0 1
#> TCGA.CR.7404.01 1 0 1 1 0
#> TCGA.CR.7368.01 2 0 1 0 1
#> TCGA.KU.A6H7.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.HD.7754.01 2 0 1 0 1 0
#> TCGA.CV.7406.01 2 0 1 0 1 0
#> TCGA.CR.5249.01 3 0 1 0 0 1
#> TCGA.CR.5248.01 1 0 1 1 0 0
#> TCGA.CR.7385.01 3 0 1 0 0 1
#> TCGA.CV.6939.01 3 0 1 0 0 1
#> TCGA.CR.6487.01 1 0 1 1 0 0
#> TCGA.CR.6472.01 2 0 1 0 1 0
#> TCGA.CR.6481.01 1 0 1 1 0 0
#> TCGA.CR.6470.01 1 0 1 1 0 0
#> TCGA.BA.A4IH.01 1 0 1 1 0 0
#> TCGA.CR.6482.01 1 0 1 1 0 0
#> TCGA.P3.A5Q5.01 3 0 1 0 0 1
#> TCGA.BA.A4IG.01 3 0 1 0 0 1
#> TCGA.HD.A634.01 3 0 1 0 0 1
#> TCGA.DQ.7594.01 3 0 1 0 0 1
#> TCGA.DQ.7596.01 1 0 1 1 0 0
#> TCGA.CN.5374.01 3 0 1 0 0 1
#> TCGA.H7.A76A.01 1 0 1 1 0 0
#> TCGA.DQ.7593.01 1 0 1 1 0 0
#> TCGA.MZ.A5BI.01 1 0 1 1 0 0
#> TCGA.BB.A6UM.01 2 0 1 0 1 0
#> TCGA.MZ.A6I9.01 3 0 1 0 0 1
#> TCGA.CR.7404.01 1 0 1 1 0 0
#> TCGA.CR.7368.01 2 0 1 0 1 0
#> TCGA.KU.A6H7.01 1 0 1 1 0 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.HD.7754.01 2 0.000 0.944 0.00 1.00 0.00 0.00
#> TCGA.CV.7406.01 2 0.000 0.944 0.00 1.00 0.00 0.00
#> TCGA.CR.5249.01 4 0.462 0.316 0.00 0.00 0.34 0.66
#> TCGA.CR.5248.01 4 0.265 0.579 0.12 0.00 0.00 0.88
#> TCGA.CR.7385.01 3 0.265 0.814 0.00 0.00 0.88 0.12
#> TCGA.CV.6939.01 4 0.462 0.316 0.00 0.00 0.34 0.66
#> TCGA.CR.6487.01 1 0.452 0.982 0.68 0.00 0.00 0.32
#> TCGA.CR.6472.01 2 0.000 0.944 0.00 1.00 0.00 0.00
#> TCGA.CR.6481.01 1 0.479 0.917 0.62 0.00 0.00 0.38
#> TCGA.CR.6470.01 4 0.000 0.721 0.00 0.00 0.00 1.00
#> TCGA.BA.A4IH.01 1 0.452 0.982 0.68 0.00 0.00 0.32
#> TCGA.CR.6482.01 1 0.452 0.982 0.68 0.00 0.00 0.32
#> TCGA.P3.A5Q5.01 3 0.000 0.862 0.00 0.00 1.00 0.00
#> TCGA.BA.A4IG.01 3 0.000 0.862 0.00 0.00 1.00 0.00
#> TCGA.HD.A634.01 3 0.777 0.177 0.24 0.00 0.40 0.36
#> TCGA.DQ.7594.01 3 0.000 0.862 0.00 0.00 1.00 0.00
#> TCGA.DQ.7596.01 4 0.265 0.579 0.12 0.00 0.00 0.88
#> TCGA.CN.5374.01 3 0.265 0.814 0.00 0.00 0.88 0.12
#> TCGA.H7.A76A.01 1 0.462 0.967 0.66 0.00 0.00 0.34
#> TCGA.DQ.7593.01 1 0.452 0.982 0.68 0.00 0.00 0.32
#> TCGA.MZ.A5BI.01 1 0.452 0.982 0.68 0.00 0.00 0.32
#> TCGA.BB.A6UM.01 2 0.201 0.923 0.08 0.92 0.00 0.00
#> TCGA.MZ.A6I9.01 3 0.000 0.862 0.00 0.00 1.00 0.00
#> TCGA.CR.7404.01 4 0.000 0.721 0.00 0.00 0.00 1.00
#> TCGA.CR.7368.01 2 0.484 0.822 0.08 0.78 0.14 0.00
#> TCGA.KU.A6H7.01 4 0.000 0.721 0.00 0.00 0.00 1.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.HD.7754.01 2 0.0000 0.854 0.00 1.00 0.00 0.00 0.00
#> TCGA.CV.7406.01 2 0.0000 0.854 0.00 1.00 0.00 0.00 0.00
#> TCGA.CR.5249.01 4 0.2077 0.896 0.00 0.00 0.04 0.92 0.04
#> TCGA.CR.5248.01 4 0.1043 0.940 0.04 0.00 0.00 0.96 0.00
#> TCGA.CR.7385.01 3 0.2077 0.896 0.00 0.00 0.92 0.04 0.04
#> TCGA.CV.6939.01 4 0.2077 0.896 0.00 0.00 0.04 0.92 0.04
#> TCGA.CR.6487.01 1 0.0000 0.963 1.00 0.00 0.00 0.00 0.00
#> TCGA.CR.6472.01 2 0.0000 0.854 0.00 1.00 0.00 0.00 0.00
#> TCGA.CR.6481.01 1 0.2732 0.784 0.84 0.00 0.00 0.16 0.00
#> TCGA.CR.6470.01 4 0.0609 0.952 0.02 0.00 0.00 0.98 0.00
#> TCGA.BA.A4IH.01 1 0.0000 0.963 1.00 0.00 0.00 0.00 0.00
#> TCGA.CR.6482.01 1 0.0000 0.963 1.00 0.00 0.00 0.00 0.00
#> TCGA.P3.A5Q5.01 3 0.0000 0.946 0.00 0.00 1.00 0.00 0.00
#> TCGA.BA.A4IG.01 3 0.0609 0.928 0.00 0.00 0.98 0.00 0.02
#> TCGA.HD.A634.01 5 0.4637 0.000 0.00 0.00 0.16 0.10 0.74
#> TCGA.DQ.7594.01 3 0.0000 0.946 0.00 0.00 1.00 0.00 0.00
#> TCGA.DQ.7596.01 4 0.1043 0.940 0.04 0.00 0.00 0.96 0.00
#> TCGA.CN.5374.01 3 0.2077 0.896 0.00 0.00 0.92 0.04 0.04
#> TCGA.H7.A76A.01 1 0.0609 0.949 0.98 0.00 0.00 0.02 0.00
#> TCGA.DQ.7593.01 1 0.0000 0.963 1.00 0.00 0.00 0.00 0.00
#> TCGA.MZ.A5BI.01 1 0.0000 0.963 1.00 0.00 0.00 0.00 0.00
#> TCGA.BB.A6UM.01 2 0.3999 0.761 0.00 0.74 0.00 0.02 0.24
#> TCGA.MZ.A6I9.01 3 0.0000 0.946 0.00 0.00 1.00 0.00 0.00
#> TCGA.CR.7404.01 4 0.0609 0.952 0.02 0.00 0.00 0.98 0.00
#> TCGA.CR.7368.01 2 0.5484 0.669 0.00 0.64 0.12 0.00 0.24
#> TCGA.KU.A6H7.01 4 0.0609 0.952 0.02 0.00 0.00 0.98 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.HD.7754.01 2 0.3647 0.763 0.00 0.64 0.00 0.00 0.00 0.36
#> TCGA.CV.7406.01 2 0.3647 0.763 0.00 0.64 0.00 0.00 0.00 0.36
#> TCGA.CR.5249.01 4 0.3864 0.444 0.00 0.00 0.00 0.52 0.00 0.48
#> TCGA.CR.5248.01 4 0.0000 0.696 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CR.7385.01 3 0.2793 0.792 0.00 0.00 0.80 0.00 0.00 0.20
#> TCGA.CV.6939.01 4 0.3864 0.444 0.00 0.00 0.00 0.52 0.00 0.48
#> TCGA.CR.6487.01 1 0.0000 0.921 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.6472.01 2 0.3647 0.763 0.00 0.64 0.00 0.00 0.00 0.36
#> TCGA.CR.6481.01 4 0.3864 -0.169 0.48 0.00 0.00 0.52 0.00 0.00
#> TCGA.CR.6470.01 4 0.3198 0.592 0.00 0.00 0.00 0.74 0.00 0.26
#> TCGA.BA.A4IH.01 1 0.2454 0.794 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.CR.6482.01 1 0.0000 0.921 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P3.A5Q5.01 3 0.0000 0.901 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BA.A4IG.01 3 0.0000 0.901 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HD.A634.01 5 0.0937 0.000 0.00 0.00 0.00 0.04 0.96 0.00
#> TCGA.DQ.7594.01 3 0.0000 0.901 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DQ.7596.01 4 0.0000 0.696 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CN.5374.01 3 0.2941 0.776 0.00 0.00 0.78 0.00 0.00 0.22
#> TCGA.H7.A76A.01 1 0.2631 0.741 0.82 0.00 0.00 0.18 0.00 0.00
#> TCGA.DQ.7593.01 1 0.0000 0.921 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MZ.A5BI.01 1 0.0000 0.921 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BB.A6UM.01 2 0.0000 0.608 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.MZ.A6I9.01 3 0.0000 0.901 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CR.7404.01 4 0.0000 0.696 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CR.7368.01 2 0.3821 0.390 0.00 0.74 0.22 0.00 0.04 0.00
#> TCGA.KU.A6H7.01 4 0.0000 0.696 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.HD.7754.01 2 0.0000 0.9846 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.CV.7406.01 2 0.0504 0.9689 0.00 0.98 0.00 0.00 0 0.02 0.00
#> TCGA.CR.5249.01 7 0.4248 0.8849 0.00 0.00 0.00 0.26 0 0.08 0.66
#> TCGA.CR.5248.01 4 0.0000 0.6577 0.00 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.CR.7385.01 3 0.3617 0.7211 0.00 0.00 0.76 0.00 0 0.08 0.16
#> TCGA.CV.6939.01 7 0.2945 0.8808 0.00 0.00 0.00 0.26 0 0.00 0.74
#> TCGA.CR.6487.01 1 0.0000 0.8355 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.CR.6472.01 2 0.0000 0.9846 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.CR.6481.01 4 0.3943 0.0638 0.42 0.00 0.00 0.56 0 0.02 0.00
#> TCGA.CR.6470.01 4 0.3968 -0.2138 0.00 0.00 0.00 0.54 0 0.02 0.44
#> TCGA.BA.A4IH.01 1 0.5233 0.3008 0.52 0.00 0.00 0.00 0 0.28 0.20
#> TCGA.CR.6482.01 1 0.0000 0.8355 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.P3.A5Q5.01 3 0.0000 0.8573 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.BA.A4IG.01 3 0.0000 0.8573 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.HD.A634.01 5 0.0000 0.0000 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.DQ.7594.01 3 0.0000 0.8573 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.DQ.7596.01 4 0.2803 0.5985 0.00 0.00 0.00 0.84 0 0.06 0.10
#> TCGA.CN.5374.01 3 0.4418 0.5544 0.00 0.00 0.62 0.00 0 0.08 0.30
#> TCGA.H7.A76A.01 1 0.3186 0.6114 0.76 0.00 0.00 0.22 0 0.02 0.00
#> TCGA.DQ.7593.01 1 0.0000 0.8355 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.MZ.A5BI.01 1 0.0504 0.8280 0.98 0.00 0.00 0.00 0 0.00 0.02
#> TCGA.BB.A6UM.01 6 0.4266 0.4230 0.00 0.44 0.00 0.00 0 0.52 0.04
#> TCGA.MZ.A6I9.01 3 0.0000 0.8573 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.CR.7404.01 4 0.1718 0.6407 0.00 0.00 0.00 0.92 0 0.04 0.04
#> TCGA.CR.7368.01 6 0.4990 0.5714 0.00 0.20 0.22 0.00 0 0.58 0.00
#> TCGA.KU.A6H7.01 4 0.0000 0.6577 0.00 0.00 0.00 1.00 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.HD.7754.01 2 0.0000 0.970 0.00 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.CV.7406.01 2 0.0941 0.940 0.00 0.96 0.00 0.00 0 0.02 0.02 0.00
#> TCGA.CR.5249.01 7 0.4487 0.502 0.00 0.00 0.02 0.08 0 0.00 0.62 0.28
#> TCGA.CR.5248.01 4 0.0000 0.727 0.00 0.00 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CR.7385.01 3 0.2938 0.592 0.00 0.00 0.70 0.00 0 0.00 0.00 0.30
#> TCGA.CV.6939.01 7 0.1804 0.629 0.00 0.00 0.02 0.08 0 0.00 0.90 0.00
#> TCGA.CR.6487.01 1 0.0000 0.807 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.CR.6472.01 2 0.0000 0.970 0.00 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.CR.6481.01 4 0.3991 0.368 0.32 0.00 0.00 0.62 0 0.06 0.00 0.00
#> TCGA.CR.6470.01 7 0.4299 0.446 0.00 0.00 0.00 0.22 0 0.14 0.64 0.00
#> TCGA.BA.A4IH.01 1 0.5816 0.137 0.42 0.00 0.00 0.00 0 0.36 0.08 0.14
#> TCGA.CR.6482.01 1 0.0000 0.807 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.P3.A5Q5.01 3 0.0000 0.778 0.00 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.BA.A4IG.01 3 0.0000 0.778 0.00 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.HD.A634.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.DQ.7594.01 3 0.0000 0.778 0.00 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.DQ.7596.01 4 0.4211 0.562 0.00 0.00 0.00 0.70 0 0.12 0.16 0.02
#> TCGA.CN.5374.01 3 0.5102 0.282 0.00 0.00 0.46 0.00 0 0.00 0.24 0.30
#> TCGA.H7.A76A.01 1 0.3431 0.574 0.74 0.00 0.00 0.20 0 0.06 0.00 0.00
#> TCGA.DQ.7593.01 1 0.1091 0.787 0.94 0.00 0.00 0.00 0 0.06 0.00 0.00
#> TCGA.MZ.A5BI.01 1 0.0000 0.807 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.BB.A6UM.01 6 0.5183 0.000 0.00 0.38 0.00 0.00 0 0.38 0.00 0.24
#> TCGA.MZ.A6I9.01 3 0.0000 0.778 0.00 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CR.7404.01 4 0.1557 0.715 0.00 0.00 0.00 0.92 0 0.06 0.00 0.02
#> TCGA.CR.7368.01 8 0.5469 0.000 0.00 0.16 0.24 0.00 0 0.06 0.00 0.54
#> TCGA.KU.A6H7.01 4 0.1765 0.683 0.00 0.00 0.00 0.88 0 0.12 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: Node0512. Child nodes: Node021321-leaf , Node021322-leaf , Node051211-leaf , Node051212-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["05121"]
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 12 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 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 0.3037 0.697 0.697
#> 3 3 1.000 0.903 0.980 0.9876 0.561 0.420
#> 4 4 1.000 0.833 1.000 0.1550 0.803 0.552
#> 5 5 0.788 0.714 0.922 0.1642 0.818 0.455
#> 6 6 0.833 0.317 0.817 0.0612 0.818 0.294
#> 7 7 0.909 0.648 0.942 0.0401 0.909 0.455
#> 8 8 0.970 0.541 0.957 0.0297 0.985 0.833
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 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.CR.5248.01 1 0 1 1 0
#> TCGA.CR.6487.01 1 0 1 1 0
#> TCGA.CR.6481.01 1 0 1 1 0
#> TCGA.CR.6470.01 1 0 1 1 0
#> TCGA.BA.A4IH.01 2 0 1 0 1
#> TCGA.CR.6482.01 1 0 1 1 0
#> TCGA.DQ.7596.01 1 0 1 1 0
#> TCGA.H7.A76A.01 1 0 1 1 0
#> TCGA.DQ.7593.01 1 0 1 1 0
#> TCGA.MZ.A5BI.01 2 0 1 0 1
#> TCGA.CR.7404.01 1 0 1 1 0
#> TCGA.KU.A6H7.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CR.5248.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.CR.6487.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.CR.6481.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.CR.6470.01 3 0.207 0.980 0.06 0 0.94
#> TCGA.BA.A4IH.01 2 0.000 0.000 0.00 1 0.00
#> TCGA.CR.6482.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.DQ.7596.01 3 0.207 0.980 0.06 0 0.94
#> TCGA.H7.A76A.01 3 0.207 0.980 0.06 0 0.94
#> TCGA.DQ.7593.01 3 0.207 0.980 0.06 0 0.94
#> TCGA.MZ.A5BI.01 3 0.000 0.915 0.00 0 1.00
#> TCGA.CR.7404.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.KU.A6H7.01 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.CR.5248.01 1 0 1 1 0 0 0
#> TCGA.CR.6487.01 1 0 1 1 0 0 0
#> TCGA.CR.6481.01 1 0 1 1 0 0 0
#> TCGA.CR.6470.01 3 0 1 0 0 1 0
#> TCGA.BA.A4IH.01 2 0 0 0 1 0 0
#> TCGA.CR.6482.01 3 0 1 0 0 1 0
#> TCGA.DQ.7596.01 3 0 1 0 0 1 0
#> TCGA.H7.A76A.01 3 0 1 0 0 1 0
#> TCGA.DQ.7593.01 3 0 1 0 0 1 0
#> TCGA.MZ.A5BI.01 4 0 0 0 0 0 1
#> TCGA.CR.7404.01 1 0 1 1 0 0 0
#> TCGA.KU.A6H7.01 1 0 1 1 0 0 0
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CR.5248.01 1 0.327 1.000 0.78 0 0.00 0 0.22
#> TCGA.CR.6487.01 1 0.327 1.000 0.78 0 0.00 0 0.22
#> TCGA.CR.6481.01 5 0.000 0.837 0.00 0 0.00 0 1.00
#> TCGA.CR.6470.01 3 0.327 0.823 0.22 0 0.78 0 0.00
#> TCGA.BA.A4IH.01 2 0.000 0.000 0.00 1 0.00 0 0.00
#> TCGA.CR.6482.01 5 0.327 0.660 0.00 0 0.22 0 0.78
#> TCGA.DQ.7596.01 3 0.327 0.823 0.22 0 0.78 0 0.00
#> TCGA.H7.A76A.01 3 0.141 0.778 0.00 0 0.94 0 0.06
#> TCGA.DQ.7593.01 3 0.000 0.813 0.00 0 1.00 0 0.00
#> TCGA.MZ.A5BI.01 4 0.000 0.000 0.00 0 0.00 1 0.00
#> TCGA.CR.7404.01 1 0.327 1.000 0.78 0 0.00 0 0.22
#> TCGA.KU.A6H7.01 5 0.000 0.837 0.00 0 0.00 0 1.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.CR.5248.01 1 0.000 0.7589 1.00 0 0.00 0 0.00 0.00
#> TCGA.CR.6487.01 1 0.000 0.7589 1.00 0 0.00 0 0.00 0.00
#> TCGA.CR.6481.01 1 0.609 -0.0707 0.36 0 0.00 0 0.36 0.28
#> TCGA.CR.6470.01 3 0.000 0.9162 0.00 0 1.00 0 0.00 0.00
#> TCGA.BA.A4IH.01 2 0.000 0.0000 0.00 1 0.00 0 0.00 0.00
#> TCGA.CR.6482.01 5 0.000 0.0000 0.00 0 0.00 0 1.00 0.00
#> TCGA.DQ.7596.01 3 0.156 0.9163 0.00 0 0.92 0 0.00 0.08
#> TCGA.H7.A76A.01 6 0.386 0.0610 0.00 0 0.00 0 0.48 0.52
#> TCGA.DQ.7593.01 6 0.386 0.0610 0.00 0 0.00 0 0.48 0.52
#> TCGA.MZ.A5BI.01 4 0.000 0.0000 0.00 0 0.00 1 0.00 0.00
#> TCGA.CR.7404.01 1 0.000 0.7589 1.00 0 0.00 0 0.00 0.00
#> TCGA.KU.A6H7.01 6 0.577 -0.3523 0.18 0 0.00 0 0.36 0.46
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.CR.5248.01 1 0.0000 1.000 1.00 0 0.00 0 0.00 0.00 0.00
#> TCGA.CR.6487.01 1 0.0000 1.000 1.00 0 0.00 0 0.00 0.00 0.00
#> TCGA.CR.6481.01 7 0.4615 0.578 0.30 0 0.00 0 0.10 0.00 0.60
#> TCGA.CR.6470.01 3 0.2016 0.833 0.00 0 0.90 0 0.04 0.00 0.06
#> TCGA.BA.A4IH.01 2 0.0000 0.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.CR.6482.01 5 0.0863 0.000 0.00 0 0.00 0 0.96 0.04 0.00
#> TCGA.DQ.7596.01 3 0.1433 0.833 0.00 0 0.92 0 0.00 0.08 0.00
#> TCGA.H7.A76A.01 6 0.0504 0.975 0.00 0 0.00 0 0.02 0.98 0.00
#> TCGA.DQ.7593.01 6 0.0000 0.976 0.00 0 0.00 0 0.00 1.00 0.00
#> TCGA.MZ.A5BI.01 4 0.0000 0.000 0.00 0 0.00 1 0.00 0.00 0.00
#> TCGA.CR.7404.01 1 0.0000 1.000 1.00 0 0.00 0 0.00 0.00 0.00
#> TCGA.KU.A6H7.01 7 0.1166 0.578 0.06 0 0.00 0 0.00 0.00 0.94
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.CR.5248.01 1 0.0000 1.000 1.00 0 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CR.6487.01 1 0.0000 1.000 1.00 0 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CR.6481.01 7 0.0808 0.000 0.04 0 0.00 0 0.00 0.00 0.96 0.00
#> TCGA.CR.6470.01 3 0.0000 0.748 0.00 0 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.BA.A4IH.01 2 0.0000 0.000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.CR.6482.01 5 0.1091 0.000 0.00 0 0.00 0 0.94 0.00 0.06 0.00
#> TCGA.DQ.7596.01 3 0.4511 0.748 0.00 0 0.72 0 0.06 0.04 0.04 0.14
#> TCGA.H7.A76A.01 6 0.0000 1.000 0.00 0 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.DQ.7593.01 6 0.0000 1.000 0.00 0 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.MZ.A5BI.01 4 0.0000 0.000 0.00 0 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.CR.7404.01 1 0.0000 1.000 1.00 0 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.KU.A6H7.01 8 0.1947 0.000 0.00 0 0.00 0 0.00 0.00 0.14 0.86
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: Node05. Child nodes: Node0111-leaf , Node0112-leaf , Node0113-leaf , Node0121 , Node0122 , Node0211 , Node0212 , Node0213 , Node0221 , Node0222 , Node0223 , Node0224 , Node0225-leaf , Node0231-leaf , Node0232 , Node0233-leaf , Node0234-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0511 , Node0512 , Node0521-leaf , Node0522 , Node0523-leaf , Node0524-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["052"]
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 37 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 0.4510 0.550 0.550
#> 3 3 0.783 0.741 0.909 0.2173 0.964 0.934
#> 4 4 1.000 0.951 0.989 0.1832 0.794 0.616
#> 5 5 0.821 0.786 0.911 0.0632 0.989 0.970
#> 6 6 0.760 0.613 0.845 0.0719 0.917 0.760
#> 7 7 0.743 0.458 0.793 0.0381 0.985 0.943
#> 8 8 0.736 0.591 0.814 0.0305 0.875 0.546
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.CN.6022.01 2 0 1 0 1
#> TCGA.CV.5432.01 1 0 1 1 0
#> TCGA.IQ.7632.01 2 0 1 0 1
#> TCGA.CV.7421.01 2 0 1 0 1
#> TCGA.CX.7086.01 1 0 1 1 0
#> TCGA.IQ.7631.01 2 0 1 0 1
#> TCGA.CX.7082.01 1 0 1 1 0
#> TCGA.CR.7379.01 2 0 1 0 1
#> TCGA.CR.7399.01 2 0 1 0 1
#> TCGA.CV.7103.01 1 0 1 1 0
#> TCGA.CV.5441.11 2 0 1 0 1
#> TCGA.CV.7255.01 1 0 1 1 0
#> TCGA.CR.7392.01 2 0 1 0 1
#> TCGA.CV.5431.01 2 0 1 0 1
#> TCGA.CR.6484.01 2 0 1 0 1
#> TCGA.CV.A45W.01 2 0 1 0 1
#> TCGA.KU.A66T.01 1 0 1 1 0
#> TCGA.BA.A8YP.01 1 0 1 1 0
#> TCGA.CQ.7069.01 2 0 1 0 1
#> TCGA.P3.A5QA.01 2 0 1 0 1
#> TCGA.CN.A63V.01 2 0 1 0 1
#> TCGA.QK.A8ZB.01 2 0 1 0 1
#> TCGA.CV.A45Z.01 2 0 1 0 1
#> TCGA.CN.4722.01 2 0 1 0 1
#> TCGA.P3.A6T3.01 1 0 1 1 0
#> TCGA.UF.A71B.01 2 0 1 0 1
#> TCGA.CN.4737.01 2 0 1 0 1
#> TCGA.TN.A7HJ.01 2 0 1 0 1
#> TCGA.CN.4740.01 2 0 1 0 1
#> TCGA.D6.A6ES.01 1 0 1 1 0
#> TCGA.CV.A6JY.01 2 0 1 0 1
#> TCGA.WA.A7H4.01 2 0 1 0 1
#> TCGA.CV.A6JM.01 1 0 1 1 0
#> TCGA.QK.A6IJ.01 2 0 1 0 1
#> TCGA.CV.A6JE.01 1 0 1 1 0
#> TCGA.QK.A6IH.01 1 0 1 1 0
#> TCGA.WA.A7GZ.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CN.6022.01 2 0.0000 0.892 0.00 1.00 0.00
#> TCGA.CV.5432.01 1 0.0000 0.856 1.00 0.00 0.00
#> TCGA.IQ.7632.01 2 0.0000 0.892 0.00 1.00 0.00
#> TCGA.CV.7421.01 2 0.6192 0.359 0.00 0.58 0.42
#> TCGA.CX.7086.01 1 0.0000 0.856 1.00 0.00 0.00
#> TCGA.IQ.7631.01 3 0.0892 0.000 0.00 0.02 0.98
#> TCGA.CX.7082.01 1 0.0000 0.856 1.00 0.00 0.00
#> TCGA.CR.7379.01 2 0.0000 0.892 0.00 1.00 0.00
#> TCGA.CR.7399.01 2 0.0000 0.892 0.00 1.00 0.00
#> TCGA.CV.7103.01 1 0.6126 0.353 0.60 0.00 0.40
#> TCGA.CV.5441.11 2 0.0000 0.892 0.00 1.00 0.00
#> TCGA.CV.7255.01 1 0.0000 0.856 1.00 0.00 0.00
#> TCGA.CR.7392.01 2 0.0000 0.892 0.00 1.00 0.00
#> TCGA.CV.5431.01 2 0.0000 0.892 0.00 1.00 0.00
#> TCGA.CR.6484.01 2 0.0000 0.892 0.00 1.00 0.00
#> TCGA.CV.A45W.01 2 0.0000 0.892 0.00 1.00 0.00
#> TCGA.KU.A66T.01 1 0.0000 0.856 1.00 0.00 0.00
#> TCGA.BA.A8YP.01 1 0.0000 0.856 1.00 0.00 0.00
#> TCGA.CQ.7069.01 2 0.0000 0.892 0.00 1.00 0.00
#> TCGA.P3.A5QA.01 2 0.6192 0.359 0.00 0.58 0.42
#> TCGA.CN.A63V.01 2 0.0000 0.892 0.00 1.00 0.00
#> TCGA.QK.A8ZB.01 2 0.0000 0.892 0.00 1.00 0.00
#> TCGA.CV.A45Z.01 2 0.0000 0.892 0.00 1.00 0.00
#> TCGA.CN.4722.01 2 0.0000 0.892 0.00 1.00 0.00
#> TCGA.P3.A6T3.01 1 0.0000 0.856 1.00 0.00 0.00
#> TCGA.UF.A71B.01 2 0.6192 0.359 0.00 0.58 0.42
#> TCGA.CN.4737.01 2 0.6192 0.359 0.00 0.58 0.42
#> TCGA.TN.A7HJ.01 2 0.0000 0.892 0.00 1.00 0.00
#> TCGA.CN.4740.01 2 0.0000 0.892 0.00 1.00 0.00
#> TCGA.D6.A6ES.01 1 0.0000 0.856 1.00 0.00 0.00
#> TCGA.CV.A6JY.01 2 0.0000 0.892 0.00 1.00 0.00
#> TCGA.WA.A7H4.01 2 0.0000 0.892 0.00 1.00 0.00
#> TCGA.CV.A6JM.01 1 0.6192 0.313 0.58 0.00 0.42
#> TCGA.QK.A6IJ.01 2 0.0000 0.892 0.00 1.00 0.00
#> TCGA.CV.A6JE.01 1 0.6192 0.313 0.58 0.00 0.42
#> TCGA.QK.A6IH.01 1 0.0000 0.856 1.00 0.00 0.00
#> TCGA.WA.A7GZ.01 2 0.6192 0.359 0.00 0.58 0.42
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.CN.6022.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.CV.5432.01 1 0.0000 0.995 1.00 0.00 0.00 0.00
#> TCGA.IQ.7632.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.CV.7421.01 4 0.0000 0.963 0.00 0.00 0.00 1.00
#> TCGA.CX.7086.01 1 0.0000 0.995 1.00 0.00 0.00 0.00
#> TCGA.IQ.7631.01 3 0.0707 0.000 0.00 0.00 0.98 0.02
#> TCGA.CX.7082.01 1 0.0000 0.995 1.00 0.00 0.00 0.00
#> TCGA.CR.7379.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.CR.7399.01 2 0.1411 0.968 0.00 0.96 0.02 0.02
#> TCGA.CV.7103.01 4 0.2647 0.831 0.12 0.00 0.00 0.88
#> TCGA.CV.5441.11 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.CV.7255.01 1 0.0000 0.995 1.00 0.00 0.00 0.00
#> TCGA.CR.7392.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.CV.5431.01 2 0.1411 0.968 0.00 0.96 0.02 0.02
#> TCGA.CR.6484.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.CV.A45W.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.KU.A66T.01 1 0.0000 0.995 1.00 0.00 0.00 0.00
#> TCGA.BA.A8YP.01 1 0.0000 0.995 1.00 0.00 0.00 0.00
#> TCGA.CQ.7069.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.P3.A5QA.01 4 0.0000 0.963 0.00 0.00 0.00 1.00
#> TCGA.CN.A63V.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.QK.A8ZB.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.CV.A45Z.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.CN.4722.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.P3.A6T3.01 1 0.0707 0.982 0.98 0.00 0.02 0.00
#> TCGA.UF.A71B.01 4 0.0000 0.963 0.00 0.00 0.00 1.00
#> TCGA.CN.4737.01 4 0.0000 0.963 0.00 0.00 0.00 1.00
#> TCGA.TN.A7HJ.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.CN.4740.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.D6.A6ES.01 1 0.0707 0.982 0.98 0.00 0.02 0.00
#> TCGA.CV.A6JY.01 2 0.0707 0.981 0.00 0.98 0.00 0.02
#> TCGA.WA.A7H4.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.CV.A6JM.01 4 0.1411 0.942 0.02 0.00 0.02 0.96
#> TCGA.QK.A6IJ.01 2 0.0000 0.991 0.00 1.00 0.00 0.00
#> TCGA.CV.A6JE.01 4 0.1411 0.938 0.02 0.00 0.02 0.96
#> TCGA.QK.A6IH.01 1 0.0000 0.995 1.00 0.00 0.00 0.00
#> TCGA.WA.A7GZ.01 4 0.0000 0.963 0.00 0.00 0.00 1.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CN.6022.01 2 0.0000 0.908 0.00 1.00 0 0.00 0.00
#> TCGA.CV.5432.01 1 0.1732 0.924 0.92 0.00 0 0.00 0.08
#> TCGA.IQ.7632.01 2 0.0000 0.908 0.00 1.00 0 0.00 0.00
#> TCGA.CV.7421.01 4 0.0000 0.767 0.00 0.00 0 1.00 0.00
#> TCGA.CX.7086.01 1 0.0000 0.947 1.00 0.00 0 0.00 0.00
#> TCGA.IQ.7631.01 3 0.0000 0.000 0.00 0.00 1 0.00 0.00
#> TCGA.CX.7082.01 1 0.1732 0.924 0.92 0.00 0 0.00 0.08
#> TCGA.CR.7379.01 2 0.2012 0.888 0.00 0.92 0 0.02 0.06
#> TCGA.CR.7399.01 2 0.4132 0.788 0.00 0.72 0 0.02 0.26
#> TCGA.CV.7103.01 4 0.5828 -0.321 0.10 0.00 0 0.52 0.38
#> TCGA.CV.5441.11 2 0.0000 0.908 0.00 1.00 0 0.00 0.00
#> TCGA.CV.7255.01 1 0.0000 0.947 1.00 0.00 0 0.00 0.00
#> TCGA.CR.7392.01 2 0.0000 0.908 0.00 1.00 0 0.00 0.00
#> TCGA.CV.5431.01 2 0.4132 0.788 0.00 0.72 0 0.02 0.26
#> TCGA.CR.6484.01 2 0.0000 0.908 0.00 1.00 0 0.00 0.00
#> TCGA.CV.A45W.01 2 0.4132 0.788 0.00 0.72 0 0.02 0.26
#> TCGA.KU.A66T.01 1 0.0000 0.947 1.00 0.00 0 0.00 0.00
#> TCGA.BA.A8YP.01 1 0.2280 0.897 0.88 0.00 0 0.00 0.12
#> TCGA.CQ.7069.01 2 0.0000 0.908 0.00 1.00 0 0.00 0.00
#> TCGA.P3.A5QA.01 4 0.0609 0.770 0.00 0.00 0 0.98 0.02
#> TCGA.CN.A63V.01 2 0.0000 0.908 0.00 1.00 0 0.00 0.00
#> TCGA.QK.A8ZB.01 2 0.3319 0.853 0.00 0.82 0 0.02 0.16
#> TCGA.CV.A45Z.01 2 0.3274 0.830 0.00 0.78 0 0.00 0.22
#> TCGA.CN.4722.01 2 0.0000 0.908 0.00 1.00 0 0.00 0.00
#> TCGA.P3.A6T3.01 1 0.1410 0.921 0.94 0.00 0 0.00 0.06
#> TCGA.UF.A71B.01 4 0.1043 0.724 0.00 0.00 0 0.96 0.04
#> TCGA.CN.4737.01 4 0.0609 0.770 0.00 0.00 0 0.98 0.02
#> TCGA.TN.A7HJ.01 2 0.3690 0.831 0.00 0.78 0 0.02 0.20
#> TCGA.CN.4740.01 2 0.0000 0.908 0.00 1.00 0 0.00 0.00
#> TCGA.D6.A6ES.01 1 0.2012 0.906 0.92 0.00 0 0.02 0.06
#> TCGA.CV.A6JY.01 2 0.3106 0.861 0.00 0.84 0 0.02 0.14
#> TCGA.WA.A7H4.01 2 0.0000 0.908 0.00 1.00 0 0.00 0.00
#> TCGA.CV.A6JM.01 5 0.4302 0.000 0.00 0.00 0 0.48 0.52
#> TCGA.QK.A6IJ.01 2 0.0000 0.908 0.00 1.00 0 0.00 0.00
#> TCGA.CV.A6JE.01 4 0.2754 0.639 0.04 0.00 0 0.88 0.08
#> TCGA.QK.A6IH.01 1 0.0000 0.947 1.00 0.00 0 0.00 0.00
#> TCGA.WA.A7GZ.01 4 0.0000 0.767 0.00 0.00 0 1.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.CN.6022.01 2 0.0000 0.778 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CV.5432.01 1 0.4328 0.724 0.72 0.00 0 0.00 0.18 0.10
#> TCGA.IQ.7632.01 2 0.0000 0.778 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CV.7421.01 4 0.1865 0.818 0.00 0.00 0 0.92 0.04 0.04
#> TCGA.CX.7086.01 1 0.0000 0.852 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.IQ.7631.01 3 0.0000 0.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.CX.7082.01 1 0.3045 0.808 0.84 0.00 0 0.00 0.10 0.06
#> TCGA.CR.7379.01 2 0.3198 0.273 0.00 0.74 0 0.00 0.00 0.26
#> TCGA.CR.7399.01 6 0.3706 0.935 0.00 0.38 0 0.00 0.00 0.62
#> TCGA.CV.7103.01 5 0.7013 0.298 0.06 0.00 0 0.32 0.34 0.28
#> TCGA.CV.5441.11 2 0.0000 0.778 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CV.7255.01 1 0.0000 0.852 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CR.7392.01 2 0.0000 0.778 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CV.5431.01 6 0.3797 0.902 0.00 0.42 0 0.00 0.00 0.58
#> TCGA.CR.6484.01 2 0.0000 0.778 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CV.A45W.01 6 0.4199 0.933 0.00 0.38 0 0.02 0.00 0.60
#> TCGA.KU.A66T.01 1 0.0000 0.852 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.BA.A8YP.01 1 0.4890 0.657 0.66 0.00 0 0.00 0.18 0.16
#> TCGA.CQ.7069.01 2 0.0000 0.778 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.P3.A5QA.01 4 0.0547 0.840 0.00 0.00 0 0.98 0.02 0.00
#> TCGA.CN.A63V.01 2 0.0000 0.778 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.QK.A8ZB.01 2 0.4144 -0.243 0.00 0.62 0 0.00 0.02 0.36
#> TCGA.CV.A45Z.01 2 0.3706 -0.264 0.00 0.62 0 0.00 0.00 0.38
#> TCGA.CN.4722.01 2 0.0000 0.778 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.P3.A6T3.01 1 0.3321 0.788 0.82 0.00 0 0.00 0.10 0.08
#> TCGA.UF.A71B.01 4 0.2260 0.735 0.00 0.00 0 0.86 0.00 0.14
#> TCGA.CN.4737.01 4 0.1480 0.841 0.00 0.00 0 0.94 0.04 0.02
#> TCGA.TN.A7HJ.01 2 0.4282 -0.493 0.00 0.56 0 0.00 0.02 0.42
#> TCGA.CN.4740.01 2 0.0000 0.778 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.D6.A6ES.01 1 0.3787 0.773 0.78 0.00 0 0.00 0.10 0.12
#> TCGA.CV.A6JY.01 2 0.3756 -0.348 0.00 0.60 0 0.00 0.00 0.40
#> TCGA.WA.A7H4.01 2 0.0000 0.778 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CV.A6JM.01 5 0.3592 0.236 0.00 0.00 0 0.24 0.74 0.02
#> TCGA.QK.A6IJ.01 2 0.0000 0.778 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CV.A6JE.01 4 0.3846 0.686 0.02 0.00 0 0.80 0.10 0.08
#> TCGA.QK.A6IH.01 1 0.0547 0.848 0.98 0.00 0 0.00 0.02 0.00
#> TCGA.WA.A7GZ.01 4 0.1865 0.819 0.00 0.00 0 0.92 0.04 0.04
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.CN.6022.01 2 0.0504 0.7430 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.CV.5432.01 1 0.5385 0.4652 0.56 0.00 0.08 0.00 0.32 0.02 0.02
#> TCGA.IQ.7632.01 2 0.0504 0.7395 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CV.7421.01 4 0.3833 0.6463 0.00 0.00 0.00 0.78 0.12 0.04 0.06
#> TCGA.CX.7086.01 1 0.0000 0.7035 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IQ.7631.01 3 0.5324 -0.2494 0.00 0.00 0.58 0.00 0.02 0.22 0.18
#> TCGA.CX.7082.01 1 0.2422 0.6503 0.82 0.00 0.00 0.00 0.18 0.00 0.00
#> TCGA.CR.7379.01 2 0.4698 0.0879 0.00 0.62 0.00 0.14 0.00 0.24 0.00
#> TCGA.CR.7399.01 6 0.3911 0.8762 0.00 0.24 0.00 0.06 0.00 0.70 0.00
#> TCGA.CV.7103.01 5 0.1166 0.0000 0.00 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.CV.5441.11 2 0.0504 0.7395 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CV.7255.01 1 0.0000 0.7035 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7392.01 2 0.0504 0.7395 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CV.5431.01 6 0.4070 0.8523 0.00 0.34 0.00 0.04 0.00 0.62 0.00
#> TCGA.CR.6484.01 2 0.0000 0.7454 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A45W.01 6 0.4338 0.8876 0.00 0.28 0.00 0.08 0.00 0.64 0.00
#> TCGA.KU.A66T.01 1 0.0000 0.7035 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A8YP.01 1 0.3943 0.3904 0.56 0.00 0.00 0.00 0.42 0.02 0.00
#> TCGA.CQ.7069.01 2 0.0504 0.7430 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.P3.A5QA.01 4 0.0863 0.7371 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.CN.A63V.01 2 0.0000 0.7454 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QK.A8ZB.01 2 0.4669 -0.3359 0.00 0.52 0.00 0.08 0.00 0.40 0.00
#> TCGA.CV.A45Z.01 2 0.4244 -0.2803 0.00 0.54 0.00 0.04 0.00 0.42 0.00
#> TCGA.CN.4722.01 2 0.0504 0.7430 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.P3.A6T3.01 1 0.4487 0.0456 0.52 0.00 0.42 0.00 0.06 0.00 0.00
#> TCGA.UF.A71B.01 4 0.3530 0.6196 0.00 0.00 0.00 0.76 0.02 0.20 0.02
#> TCGA.CN.4737.01 4 0.0504 0.7374 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.TN.A7HJ.01 2 0.5016 -0.4938 0.00 0.46 0.00 0.12 0.00 0.42 0.00
#> TCGA.CN.4740.01 2 0.0000 0.7454 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D6.A6ES.01 3 0.6474 -0.3209 0.38 0.00 0.42 0.00 0.10 0.06 0.04
#> TCGA.CV.A6JY.01 2 0.5086 -0.3501 0.00 0.50 0.00 0.14 0.00 0.36 0.00
#> TCGA.WA.A7H4.01 2 0.0504 0.7395 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CV.A6JM.01 7 0.3908 0.0000 0.00 0.00 0.00 0.08 0.20 0.00 0.72
#> TCGA.QK.A6IJ.01 2 0.0504 0.7430 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.CV.A6JE.01 4 0.4264 0.3627 0.00 0.00 0.32 0.62 0.06 0.00 0.00
#> TCGA.QK.A6IH.01 1 0.1886 0.6351 0.88 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.WA.A7GZ.01 4 0.3541 0.6990 0.00 0.00 0.00 0.80 0.02 0.08 0.10
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.CN.6022.01 2 0.0941 0.8896 0.00 0.96 0 0.00 0.02 0.02 0.00 0.00
#> TCGA.CV.5432.01 1 0.4476 0.1152 0.54 0.00 0 0.00 0.36 0.00 0.00 0.10
#> TCGA.IQ.7632.01 2 0.0000 0.9236 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7421.01 4 0.4511 0.5571 0.00 0.00 0 0.72 0.14 0.04 0.04 0.06
#> TCGA.CX.7086.01 1 0.0000 0.7615 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.IQ.7631.01 3 0.0000 0.0000 0.00 0.00 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.CX.7082.01 1 0.4073 0.4390 0.66 0.00 0 0.00 0.24 0.00 0.00 0.10
#> TCGA.CR.7379.01 2 0.4586 -0.4700 0.00 0.52 0 0.06 0.02 0.40 0.00 0.00
#> TCGA.CR.7399.01 6 0.2807 0.5314 0.00 0.10 0 0.00 0.00 0.84 0.02 0.04
#> TCGA.CV.7103.01 5 0.2407 0.0814 0.00 0.00 0 0.06 0.86 0.00 0.08 0.00
#> TCGA.CV.5441.11 2 0.0000 0.9236 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.7255.01 1 0.0000 0.7615 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7392.01 2 0.0000 0.9236 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.5431.01 6 0.3977 0.7473 0.00 0.24 0 0.02 0.00 0.70 0.02 0.02
#> TCGA.CR.6484.01 2 0.0000 0.9236 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A45W.01 6 0.3170 0.7219 0.00 0.20 0 0.04 0.00 0.76 0.00 0.00
#> TCGA.KU.A66T.01 1 0.0000 0.7615 1.00 0.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.BA.A8YP.01 5 0.5162 -0.0873 0.36 0.00 0 0.00 0.50 0.04 0.00 0.10
#> TCGA.CQ.7069.01 2 0.0471 0.9100 0.00 0.98 0 0.00 0.02 0.00 0.00 0.00
#> TCGA.P3.A5QA.01 4 0.1275 0.7078 0.00 0.00 0 0.94 0.00 0.04 0.00 0.02
#> TCGA.CN.A63V.01 2 0.0000 0.9236 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.QK.A8ZB.01 6 0.4399 0.6657 0.00 0.44 0 0.04 0.02 0.50 0.00 0.00
#> TCGA.CV.A45Z.01 6 0.3690 0.6709 0.00 0.42 0 0.00 0.02 0.56 0.00 0.00
#> TCGA.CN.4722.01 2 0.0471 0.9100 0.00 0.98 0 0.00 0.02 0.00 0.00 0.00
#> TCGA.P3.A6T3.01 8 0.3907 0.3173 0.38 0.00 0 0.04 0.00 0.00 0.00 0.58
#> TCGA.UF.A71B.01 4 0.4397 0.6196 0.00 0.00 0 0.66 0.06 0.24 0.00 0.04
#> TCGA.CN.4737.01 4 0.2224 0.6628 0.00 0.00 0 0.86 0.00 0.02 0.00 0.12
#> TCGA.TN.A7HJ.01 6 0.4471 0.7606 0.00 0.34 0 0.06 0.02 0.58 0.00 0.00
#> TCGA.CN.4740.01 2 0.0000 0.9236 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.D6.A6ES.01 8 0.3169 0.4126 0.18 0.00 0 0.00 0.02 0.00 0.02 0.78
#> TCGA.CV.A6JY.01 6 0.4777 0.7077 0.00 0.40 0 0.08 0.02 0.50 0.00 0.00
#> TCGA.WA.A7H4.01 2 0.0471 0.9074 0.00 0.98 0 0.00 0.02 0.00 0.00 0.00
#> TCGA.CV.A6JM.01 7 0.0471 0.0000 0.00 0.00 0 0.02 0.00 0.00 0.98 0.00
#> TCGA.QK.A6IJ.01 2 0.0000 0.9236 0.00 1.00 0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CV.A6JE.01 8 0.4125 -0.0445 0.00 0.00 0 0.44 0.02 0.02 0.00 0.52
#> TCGA.QK.A6IH.01 1 0.1563 0.7078 0.90 0.00 0 0.00 0.00 0.00 0.00 0.10
#> TCGA.WA.A7GZ.01 4 0.4409 0.6636 0.00 0.00 0 0.70 0.02 0.18 0.02 0.08
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: Node052. Child nodes: Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node02111-leaf , Node02112-leaf , Node02113-leaf , Node02114-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node02124-leaf , Node02131-leaf , Node02132 , Node02133-leaf , Node02211-leaf , Node02212-leaf , Node02213-leaf , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02231-leaf , Node02232-leaf , Node02233-leaf , Node02241-leaf , Node02242-leaf , Node02243-leaf , Node02321-leaf , Node02322-leaf , Node02323-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf , Node05114-leaf , Node05121 , Node05122-leaf , Node05123-leaf , Node05221-leaf , Node05222-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0522"]
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 '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 1.000 1.000 0.5151 0.485 0.485
#> 3 3 0.725 0.562 0.721 0.2068 0.836 0.663
#> 4 4 0.690 0.919 0.833 0.1489 0.930 0.782
#> 5 5 0.678 0.783 0.831 0.0744 0.959 0.837
#> 6 6 0.649 0.726 0.818 0.0474 1.000 1.000
#> 7 7 0.743 0.717 0.805 0.0447 0.977 0.889
#> 8 8 0.813 0.636 0.817 0.0352 0.965 0.812
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.CN.6022.01 2 0 1 0 1
#> TCGA.IQ.7632.01 1 0 1 1 0
#> TCGA.CR.7379.01 1 0 1 1 0
#> TCGA.CR.7399.01 1 0 1 1 0
#> TCGA.CV.5441.11 2 0 1 0 1
#> TCGA.CR.7392.01 1 0 1 1 0
#> TCGA.CV.5431.01 2 0 1 0 1
#> TCGA.CR.6484.01 1 0 1 1 0
#> TCGA.CV.A45W.01 2 0 1 0 1
#> TCGA.CQ.7069.01 1 0 1 1 0
#> TCGA.CN.A63V.01 2 0 1 0 1
#> TCGA.QK.A8ZB.01 2 0 1 0 1
#> TCGA.CV.A45Z.01 2 0 1 0 1
#> TCGA.CN.4722.01 1 0 1 1 0
#> TCGA.TN.A7HJ.01 2 0 1 0 1
#> TCGA.CN.4740.01 1 0 1 1 0
#> TCGA.CV.A6JY.01 2 0 1 0 1
#> TCGA.WA.A7H4.01 2 0 1 0 1
#> TCGA.QK.A6IJ.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CN.6022.01 3 0.613 0.910 0.00 0.40 0.60
#> TCGA.IQ.7632.01 1 0.000 0.958 1.00 0.00 0.00
#> TCGA.CR.7379.01 1 0.153 0.938 0.96 0.00 0.04
#> TCGA.CR.7399.01 1 0.583 0.702 0.66 0.00 0.34
#> TCGA.CV.5441.11 3 0.624 0.906 0.00 0.44 0.56
#> TCGA.CR.7392.01 1 0.000 0.958 1.00 0.00 0.00
#> TCGA.CV.5431.01 2 0.000 0.409 0.00 1.00 0.00
#> TCGA.CR.6484.01 1 0.000 0.958 1.00 0.00 0.00
#> TCGA.CV.A45W.01 2 0.000 0.409 0.00 1.00 0.00
#> TCGA.CQ.7069.01 1 0.000 0.958 1.00 0.00 0.00
#> TCGA.CN.A63V.01 2 0.628 -0.396 0.00 0.54 0.46
#> TCGA.QK.A8ZB.01 3 0.613 0.910 0.00 0.40 0.60
#> TCGA.CV.A45Z.01 2 0.000 0.409 0.00 1.00 0.00
#> TCGA.CN.4722.01 1 0.000 0.958 1.00 0.00 0.00
#> TCGA.TN.A7HJ.01 2 0.619 -0.289 0.00 0.58 0.42
#> TCGA.CN.4740.01 1 0.000 0.958 1.00 0.00 0.00
#> TCGA.CV.A6JY.01 2 0.631 -0.493 0.00 0.50 0.50
#> TCGA.WA.A7H4.01 3 0.624 0.906 0.00 0.44 0.56
#> TCGA.QK.A6IJ.01 2 0.628 -0.396 0.00 0.54 0.46
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.CN.6022.01 3 0.4624 0.956 0.00 0.34 0.66 0.00
#> TCGA.IQ.7632.01 1 0.0707 0.906 0.98 0.00 0.00 0.02
#> TCGA.CR.7379.01 1 0.2647 0.864 0.88 0.00 0.00 0.12
#> TCGA.CR.7399.01 1 0.7198 0.525 0.52 0.00 0.32 0.16
#> TCGA.CV.5441.11 3 0.4790 0.955 0.00 0.38 0.62 0.00
#> TCGA.CR.7392.01 1 0.1211 0.908 0.96 0.00 0.00 0.04
#> TCGA.CV.5431.01 4 0.4406 1.000 0.00 0.30 0.00 0.70
#> TCGA.CR.6484.01 1 0.0707 0.906 0.98 0.00 0.00 0.02
#> TCGA.CV.A45W.01 4 0.4406 1.000 0.00 0.30 0.00 0.70
#> TCGA.CQ.7069.01 1 0.1411 0.902 0.96 0.00 0.02 0.02
#> TCGA.CN.A63V.01 2 0.0000 0.966 0.00 1.00 0.00 0.00
#> TCGA.QK.A8ZB.01 3 0.4624 0.956 0.00 0.34 0.66 0.00
#> TCGA.CV.A45Z.01 4 0.4406 1.000 0.00 0.30 0.00 0.70
#> TCGA.CN.4722.01 1 0.1211 0.908 0.96 0.00 0.00 0.04
#> TCGA.TN.A7HJ.01 2 0.0707 0.949 0.00 0.98 0.00 0.02
#> TCGA.CN.4740.01 1 0.1211 0.908 0.96 0.00 0.00 0.04
#> TCGA.CV.A6JY.01 2 0.1211 0.928 0.00 0.96 0.04 0.00
#> TCGA.WA.A7H4.01 3 0.4790 0.955 0.00 0.38 0.62 0.00
#> TCGA.QK.A6IJ.01 2 0.0000 0.966 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.CN.6022.01 3 0.5444 0.788 0.00 0.16 0.66 0.00 0.18
#> TCGA.IQ.7632.01 1 0.1216 0.828 0.96 0.00 0.00 0.02 0.02
#> TCGA.CR.7379.01 1 0.5440 0.393 0.70 0.16 0.12 0.00 0.02
#> TCGA.CR.7399.01 5 0.3796 0.000 0.30 0.00 0.00 0.00 0.70
#> TCGA.CV.5441.11 3 0.3684 0.775 0.00 0.28 0.72 0.00 0.00
#> TCGA.CR.7392.01 1 0.2331 0.829 0.90 0.00 0.00 0.02 0.08
#> TCGA.CV.5431.01 4 0.2077 0.964 0.00 0.04 0.00 0.92 0.04
#> TCGA.CR.6484.01 1 0.0609 0.832 0.98 0.00 0.02 0.00 0.00
#> TCGA.CV.A45W.01 4 0.1043 0.982 0.00 0.04 0.00 0.96 0.00
#> TCGA.CQ.7069.01 1 0.3271 0.795 0.88 0.04 0.02 0.04 0.02
#> TCGA.CN.A63V.01 2 0.3109 0.915 0.00 0.80 0.00 0.20 0.00
#> TCGA.QK.A8ZB.01 3 0.5444 0.788 0.00 0.16 0.66 0.00 0.18
#> TCGA.CV.A45Z.01 4 0.1043 0.982 0.00 0.04 0.00 0.96 0.00
#> TCGA.CN.4722.01 1 0.2012 0.830 0.92 0.00 0.02 0.00 0.06
#> TCGA.TN.A7HJ.01 2 0.3274 0.900 0.00 0.78 0.00 0.22 0.00
#> TCGA.CN.4740.01 1 0.2012 0.830 0.92 0.00 0.02 0.00 0.06
#> TCGA.CV.A6JY.01 2 0.6471 0.762 0.00 0.62 0.12 0.20 0.06
#> TCGA.WA.A7H4.01 3 0.3684 0.775 0.00 0.28 0.72 0.00 0.00
#> TCGA.QK.A6IJ.01 2 0.3109 0.915 0.00 0.80 0.00 0.20 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.CN.6022.01 3 0.181 0.775 0.00 0.02 0.92 0.00 0.00 0.06
#> TCGA.IQ.7632.01 1 0.348 0.738 0.82 0.00 0.02 0.12 0.04 0.00
#> TCGA.CR.7379.01 1 0.386 0.366 0.52 0.00 0.00 0.48 0.00 0.00
#> TCGA.CR.7399.01 5 0.294 0.000 0.22 0.00 0.00 0.00 0.78 0.00
#> TCGA.CV.5441.11 3 0.595 0.775 0.00 0.06 0.58 0.26 0.00 0.10
#> TCGA.CR.7392.01 1 0.357 0.736 0.82 0.00 0.02 0.10 0.06 0.00
#> TCGA.CV.5431.01 6 0.347 0.821 0.00 0.00 0.00 0.06 0.14 0.80
#> TCGA.CR.6484.01 1 0.181 0.730 0.92 0.06 0.00 0.02 0.00 0.00
#> TCGA.CV.A45W.01 6 0.000 0.915 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CQ.7069.01 1 0.590 0.648 0.68 0.06 0.08 0.12 0.06 0.00
#> TCGA.CN.A63V.01 2 0.400 0.871 0.00 0.78 0.00 0.06 0.02 0.14
#> TCGA.QK.A8ZB.01 3 0.181 0.775 0.00 0.02 0.92 0.00 0.00 0.06
#> TCGA.CV.A45Z.01 6 0.000 0.915 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CN.4722.01 1 0.181 0.724 0.92 0.06 0.00 0.00 0.02 0.00
#> TCGA.TN.A7HJ.01 2 0.226 0.884 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.CN.4740.01 1 0.109 0.736 0.96 0.02 0.00 0.00 0.02 0.00
#> TCGA.CV.A6JY.01 2 0.656 0.722 0.00 0.60 0.08 0.18 0.04 0.10
#> TCGA.WA.A7H4.01 3 0.595 0.775 0.00 0.06 0.58 0.26 0.00 0.10
#> TCGA.QK.A6IJ.01 2 0.226 0.884 0.00 0.86 0.00 0.00 0.00 0.14
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.CN.6022.01 3 0.1860 0.926 0.00 0.02 0.92 0.02 0.04 0.00 0.00
#> TCGA.IQ.7632.01 1 0.0000 0.752 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CR.7379.01 1 0.3413 0.400 0.62 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.CR.7399.01 5 0.2081 0.000 0.14 0.00 0.00 0.00 0.86 0.00 0.00
#> TCGA.CV.5441.11 4 0.5207 1.000 0.00 0.16 0.36 0.48 0.00 0.00 0.00
#> TCGA.CR.7392.01 1 0.0863 0.753 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.CV.5431.01 6 0.5551 0.558 0.00 0.00 0.00 0.06 0.10 0.56 0.28
#> TCGA.CR.6484.01 1 0.3244 0.739 0.78 0.00 0.00 0.18 0.00 0.00 0.04
#> TCGA.CV.A45W.01 6 0.0863 0.784 0.00 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.CQ.7069.01 1 0.3744 0.601 0.78 0.00 0.02 0.12 0.00 0.00 0.08
#> TCGA.CN.A63V.01 2 0.3058 0.768 0.00 0.82 0.00 0.10 0.00 0.00 0.08
#> TCGA.QK.A8ZB.01 3 0.0504 0.928 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.CV.A45Z.01 6 0.0000 0.784 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CN.4722.01 1 0.4055 0.727 0.74 0.00 0.00 0.18 0.04 0.00 0.04
#> TCGA.TN.A7HJ.01 2 0.0000 0.794 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4740.01 1 0.3343 0.750 0.82 0.00 0.00 0.10 0.04 0.00 0.04
#> TCGA.CV.A6JY.01 2 0.6020 0.569 0.00 0.54 0.14 0.10 0.00 0.00 0.22
#> TCGA.WA.A7H4.01 4 0.5207 1.000 0.00 0.16 0.36 0.48 0.00 0.00 0.00
#> TCGA.QK.A6IJ.01 2 0.0000 0.794 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.CN.6022.01 7 0.207 0.880 0.00 0.00 0.00 0.02 0.04 0.00 0.90 0.04
#> TCGA.IQ.7632.01 1 0.248 0.645 0.86 0.00 0.02 0.00 0.02 0.00 0.00 0.10
#> TCGA.CR.7379.01 8 0.265 0.000 0.24 0.00 0.00 0.00 0.00 0.00 0.00 0.76
#> TCGA.CR.7399.01 5 0.134 0.000 0.08 0.00 0.00 0.00 0.92 0.00 0.00 0.00
#> TCGA.CV.5441.11 4 0.357 1.000 0.00 0.02 0.00 0.62 0.00 0.00 0.36 0.00
#> TCGA.CR.7392.01 1 0.227 0.651 0.88 0.00 0.02 0.00 0.02 0.00 0.00 0.08
#> TCGA.CV.5431.01 6 0.332 0.508 0.00 0.00 0.46 0.00 0.00 0.54 0.00 0.00
#> TCGA.CR.6484.01 1 0.318 0.600 0.80 0.00 0.14 0.04 0.00 0.00 0.00 0.02
#> TCGA.CV.A45W.01 6 0.000 0.782 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CQ.7069.01 1 0.619 0.170 0.50 0.00 0.12 0.22 0.02 0.00 0.00 0.14
#> TCGA.CN.A63V.01 2 0.281 0.788 0.00 0.86 0.04 0.02 0.02 0.00 0.00 0.06
#> TCGA.QK.A8ZB.01 7 0.000 0.882 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CV.A45Z.01 6 0.000 0.782 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CN.4722.01 1 0.289 0.600 0.80 0.00 0.16 0.04 0.00 0.00 0.00 0.00
#> TCGA.TN.A7HJ.01 2 0.000 0.813 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CN.4740.01 1 0.128 0.655 0.94 0.00 0.04 0.02 0.00 0.00 0.00 0.00
#> TCGA.CV.A6JY.01 2 0.625 0.517 0.00 0.52 0.24 0.10 0.02 0.00 0.02 0.10
#> TCGA.WA.A7H4.01 4 0.357 1.000 0.00 0.02 0.00 0.62 0.00 0.00 0.36 0.00
#> TCGA.QK.A6IJ.01 2 0.000 0.813 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.
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
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#> [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