Date: 2021-07-22 20:34:32 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 375962 rows and 685 columns.
#> Performed in total 127400 partitions.
#> There are 62 groups under the following parameters:
#> - min_samples: 7
#> - 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, 685 cols
#> |-- 01, 243 cols, 18000 signatures
#> | |-- 011, 86 cols, 8024 signatures
#> | | |-- 0111, 39 cols, 3605 signatures
#> | | | |-- 01111, 21 cols, 120 signatures (c)
#> | | | `-- 01112, 18 cols, 322 signatures (c)
#> | | |-- 0112, 23 cols, 3846 signatures
#> | | | |-- 01121, 10 cols (b)
#> | | | |-- 01122, 4 cols (b)
#> | | | `-- 01123, 9 cols (b)
#> | | `-- 0113, 24 cols, 4199 signatures
#> | | |-- 01131, 7 cols (b)
#> | | |-- 01132, 11 cols (b)
#> | | `-- 01133, 6 cols (b)
#> | |-- 012, 74 cols, 5899 signatures
#> | | |-- 0121, 35 cols, 3806 signatures
#> | | | |-- 01211, 13 cols (b)
#> | | | |-- 01212, 8 cols (b)
#> | | | `-- 01213, 14 cols, 3621 signatures
#> | | | |-- 012131, 4 cols (b)
#> | | | |-- 012132, 4 cols (b)
#> | | | |-- 012133, 2 cols (b)
#> | | | `-- 012134, 4 cols (b)
#> | | |-- 0122, 34 cols, 21160 signatures
#> | | | |-- 01221, 10 cols (b)
#> | | | |-- 01222, 12 cols (b)
#> | | | |-- 01223, 2 cols (b)
#> | | | |-- 01224, 5 cols (b)
#> | | | `-- 01225, 5 cols (b)
#> | | `-- 0123, 5 cols (b)
#> | |-- 013, 41 cols, 9856 signatures
#> | | |-- 0131, 14 cols, 4915 signatures
#> | | | |-- 01311, 7 cols (b)
#> | | | |-- 01312, 4 cols (b)
#> | | | `-- 01313, 3 cols (b)
#> | | |-- 0132, 8 cols (b)
#> | | |-- 0133, 12 cols (b)
#> | | `-- 0134, 7 cols (b)
#> | `-- 014, 42 cols, 9621 signatures
#> | |-- 0141, 16 cols, 3477 signatures
#> | | |-- 01411, 11 cols (b)
#> | | `-- 01412, 5 cols (b)
#> | |-- 0142, 12 cols (b)
#> | `-- 0143, 14 cols, 3513 signatures
#> | |-- 01431, 11 cols (b)
#> | `-- 01432, 3 cols (b)
#> |-- 02, 328 cols, 7856 signatures
#> | |-- 021, 155 cols, 3958 signatures
#> | | |-- 0211, 89 cols, 281 signatures (c)
#> | | |-- 0212, 58 cols, 165 signatures (c)
#> | | |-- 0213, 5 cols (b)
#> | | `-- 0214, 3 cols (b)
#> | |-- 022, 133 cols, 3736 signatures
#> | | |-- 0221, 53 cols, 3669 signatures
#> | | | |-- 02211, 31 cols, 414 signatures (c)
#> | | | `-- 02212, 22 cols, 3544 signatures
#> | | | |-- 022121, 15 cols, 40 signatures (c)
#> | | | |-- 022122, 4 cols (b)
#> | | | `-- 022123, 3 cols (b)
#> | | |-- 0222, 33 cols, 6182 signatures
#> | | | |-- 02221, 19 cols, 3442 signatures
#> | | | | |-- 022211, 7 cols (b)
#> | | | | `-- 022212, 12 cols (b)
#> | | | |-- 02222, 10 cols (b)
#> | | | `-- 02223, 4 cols (b)
#> | | `-- 0223, 47 cols, 15681 signatures
#> | | |-- 02231, 21 cols, 4112 signatures
#> | | | |-- 022311, 11 cols (b)
#> | | | |-- 022312, 8 cols (b)
#> | | | `-- 022313, 2 cols (b)
#> | | |-- 02232, 8 cols (b)
#> | | |-- 02233, 5 cols (b)
#> | | `-- 02234, 13 cols (b)
#> | `-- 023, 40 cols, 18964 signatures
#> | |-- 0231, 19 cols, 3702 signatures
#> | | |-- 02311, 11 cols (b)
#> | | |-- 02312, 6 cols (b)
#> | | `-- 02313, 2 cols (b)
#> | |-- 0232, 10 cols (b)
#> | `-- 0233, 11 cols (b)
#> `-- 03, 114 cols, 20318 signatures
#> |-- 031, 78 cols, 5006 signatures
#> | |-- 0311, 24 cols, 115 signatures (c)
#> | |-- 0312, 21 cols, 714 signatures (c)
#> | |-- 0313, 21 cols, 32 signatures (c)
#> | `-- 0314, 12 cols (b)
#> |-- 032, 27 cols, 7999 signatures
#> | |-- 0321, 11 cols (b)
#> | |-- 0322, 13 cols (b)
#> | `-- 0323, 3 cols (b)
#> `-- 033, 9 cols (b)
#> Stop reason:
#> b) Subgroup had too few columns.
#> c) There were too few signatures.
#>
#> Following methods can be applied to this 'HierarchicalPartition' object:
#> [1] "all_leaves" "all_nodes" "cola_report" "collect_classes"
#> [5] "colnames" "compare_signatures" "dimension_reduction" "functional_enrichment"
#> [9] "get_anno_col" "get_anno" "get_children_nodes" "get_classes"
#> [13] "get_matrix" "get_signatures" "is_leaf_node" "max_depth"
#> [17] "merge_node" "ncol" "node_info" "node_level"
#> [21] "nrow" "rownames" "show" "split_node"
#> [25] "suggest_best_k" "test_to_known_factors" "top_rows_heatmap" "top_rows_overlap"
#>
#> You can get result for a single node by e.g. object["01"]
The call of hierarchical_partition() was:
#> hierarchical_partition(data = mat, top_n = 1000, top_value_method = c("SD", "ATC"),
#> partition_method = c("kmeans", "skmeans"), subset = 500, group_diff = 0.25, min_n_signatures = 1000,
#> filter_fun = function(mat) {
#> s = rowSds(mat)
#> order(-s)[1:30000]
#> }, max_k = 8, scale_rows = FALSE, cores = 4)
Dimension of the input matrix:
mat = get_matrix(res_rh)
dim(mat)
#> [1] 375962 685
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" "01111" "01112" "0112" "01121" "01122" "01123"
#> [11] "0113" "01131" "01132" "01133" "012" "0121" "01211" "01212" "01213" "012131"
#> [21] "012132" "012133" "012134" "0122" "01221" "01222" "01223" "01224" "01225" "0123"
#> [31] "013" "0131" "01311" "01312" "01313" "0132" "0133" "0134" "014" "0141"
#> [41] "01411" "01412" "0142" "0143" "01431" "01432" "02" "021" "0211" "0212"
#> [51] "0213" "0214" "022" "0221" "02211" "02212" "022121" "022122" "022123" "0222"
#> [61] "02221" "022211" "022212" "02222" "02223" "0223" "02231" "022311" "022312" "022313"
#> [71] "02232" "02233" "02234" "023" "0231" "02311" "02312" "02313" "0232" "0233"
#> [81] "03" "031" "0311" "0312" "0313" "0314" "032" "0321" "0322" "0323"
#> [91] "033"
all_leaves(res_rh)
#> [1] "01111" "01112" "01121" "01122" "01123" "01131" "01132" "01133" "01211" "01212"
#> [11] "012131" "012132" "012133" "012134" "01221" "01222" "01223" "01224" "01225" "0123"
#> [21] "01311" "01312" "01313" "0132" "0133" "0134" "01411" "01412" "0142" "01431"
#> [31] "01432" "0211" "0212" "0213" "0214" "02211" "022121" "022122" "022123" "022211"
#> [41] "022212" "02222" "02223" "022311" "022312" "022313" "02232" "02233" "02234" "02311"
#> [51] "02312" "02313" "0232" "0233" "0311" "0312" "0313" "0314" "0321" "0322"
#> [61] "0323" "033"
node_info(res_rh)
#> id best_method depth best_k n_columns n_signatures p_signatures is_leaf
#> 1 0 ATC:kmeans 1 3 685 39547 1.05e-01 FALSE
#> 2 01 ATC:skmeans 2 4 243 18000 4.79e-02 FALSE
#> 3 011 ATC:kmeans 3 3 86 8024 2.13e-02 FALSE
#> 4 0111 ATC:kmeans 4 2 39 3605 9.59e-03 FALSE
#> 5 01111 ATC:kmeans 5 2 21 120 3.19e-04 TRUE
#> 6 01112 ATC:skmeans 5 3 18 322 8.56e-04 TRUE
#> 7 0112 ATC:skmeans 4 3 23 3846 1.02e-02 FALSE
#> 8 01121 not applied 5 NA 10 NA NA TRUE
#> 9 01122 not applied 5 NA 4 NA NA TRUE
#> 10 01123 not applied 5 NA 9 NA NA TRUE
#> 11 0113 ATC:skmeans 4 3 24 4199 1.12e-02 FALSE
#> 12 01131 not applied 5 NA 7 NA NA TRUE
#> 13 01132 not applied 5 NA 11 NA NA TRUE
#> 14 01133 not applied 5 NA 6 NA NA TRUE
#> 15 012 SD:skmeans 3 3 74 5899 1.57e-02 FALSE
#> 16 0121 ATC:kmeans 4 3 35 3806 1.01e-02 FALSE
#> 17 01211 not applied 5 NA 13 NA NA TRUE
#> 18 01212 not applied 5 NA 8 NA NA TRUE
#> 19 01213 ATC:kmeans 5 4 14 3621 9.63e-03 FALSE
#> 20 012131 not applied 6 NA 4 NA NA TRUE
#> 21 012132 not applied 6 NA 4 NA NA TRUE
#> 22 012133 not applied 6 NA 2 NA NA TRUE
#> 23 012134 not applied 6 NA 4 NA NA TRUE
#> 24 0122 SD:kmeans 4 5 34 21160 5.63e-02 FALSE
#> 25 01221 not applied 5 NA 10 NA NA TRUE
#> 26 01222 not applied 5 NA 12 NA NA TRUE
#> 27 01223 not applied 5 NA 2 NA NA TRUE
#> 28 01224 not applied 5 NA 5 NA NA TRUE
#> 29 01225 not applied 5 NA 5 NA NA TRUE
#> 30 0123 not applied 4 NA 5 NA NA TRUE
#> 31 013 ATC:skmeans 3 4 41 9856 2.62e-02 FALSE
#> 32 0131 ATC:skmeans 4 3 14 4915 1.31e-02 FALSE
#> 33 01311 not applied 5 NA 7 NA NA TRUE
#> 34 01312 not applied 5 NA 4 NA NA TRUE
#> 35 01313 not applied 5 NA 3 NA NA TRUE
#> 36 0132 not applied 4 NA 8 NA NA TRUE
#> 37 0133 not applied 4 NA 12 NA NA TRUE
#> 38 0134 not applied 4 NA 7 NA NA TRUE
#> 39 014 ATC:kmeans 3 3 42 9621 2.56e-02 FALSE
#> 40 0141 ATC:kmeans 4 2 16 3477 9.25e-03 FALSE
#> 41 01411 not applied 5 NA 11 NA NA TRUE
#> 42 01412 not applied 5 NA 5 NA NA TRUE
#> 43 0142 not applied 4 NA 12 NA NA TRUE
#> 44 0143 ATC:kmeans 4 2 14 3513 9.34e-03 FALSE
#> 45 01431 not applied 5 NA 11 NA NA TRUE
#> 46 01432 not applied 5 NA 3 NA NA TRUE
#> 47 02 ATC:skmeans 2 3 328 7856 2.09e-02 FALSE
#> 48 021 ATC:skmeans 3 4 155 3958 1.05e-02 FALSE
#> 49 0211 ATC:skmeans 4 2 89 281 7.47e-04 TRUE
#> 50 0212 SD:skmeans 4 2 58 165 4.39e-04 TRUE
#> 51 0213 not applied 4 NA 5 NA NA TRUE
#> 52 0214 not applied 4 NA 3 NA NA TRUE
#> 53 022 ATC:kmeans 3 3 133 3736 9.94e-03 FALSE
#> 54 0221 ATC:kmeans 4 2 53 3669 9.76e-03 FALSE
#> 55 02211 ATC:skmeans 5 2 31 414 1.10e-03 TRUE
#> 56 02212 ATC:kmeans 5 3 22 3544 9.43e-03 FALSE
#> 57 022121 ATC:kmeans 6 2 15 40 1.06e-04 TRUE
#> 58 022122 not applied 6 NA 4 NA NA TRUE
#> 59 022123 not applied 6 NA 3 NA NA TRUE
#> 60 0222 ATC:kmeans 4 3 33 6182 1.64e-02 FALSE
#> 61 02221 ATC:kmeans 5 2 19 3442 9.16e-03 FALSE
#> 62 022211 not applied 6 NA 7 NA NA TRUE
#> 63 022212 not applied 6 NA 12 NA NA TRUE
#> 64 02222 not applied 5 NA 10 NA NA TRUE
#> 65 02223 not applied 5 NA 4 NA NA TRUE
#> 66 0223 ATC:kmeans 4 4 47 15681 4.17e-02 FALSE
#> 67 02231 ATC:skmeans 5 3 21 4112 1.09e-02 FALSE
#> 68 022311 not applied 6 NA 11 NA NA TRUE
#> 69 022312 not applied 6 NA 8 NA NA TRUE
#> 70 022313 not applied 6 NA 2 NA NA TRUE
#> 71 02232 not applied 5 NA 8 NA NA TRUE
#> 72 02233 not applied 5 NA 5 NA NA TRUE
#> 73 02234 not applied 5 NA 13 NA NA TRUE
#> 74 023 ATC:kmeans 3 3 40 18964 5.04e-02 FALSE
#> 75 0231 ATC:skmeans 4 3 19 3702 9.85e-03 FALSE
#> 76 02311 not applied 5 NA 11 NA NA TRUE
#> 77 02312 not applied 5 NA 6 NA NA TRUE
#> 78 02313 not applied 5 NA 2 NA NA TRUE
#> 79 0232 not applied 4 NA 10 NA NA TRUE
#> 80 0233 not applied 4 NA 11 NA NA TRUE
#> 81 03 ATC:kmeans 2 3 114 20318 5.40e-02 FALSE
#> 82 031 ATC:skmeans 3 4 78 5006 1.33e-02 FALSE
#> 83 0311 SD:kmeans 4 2 24 115 3.06e-04 TRUE
#> 84 0312 ATC:kmeans 4 2 21 714 1.90e-03 TRUE
#> 85 0313 ATC:kmeans 4 2 21 32 8.51e-05 TRUE
#> 86 0314 not applied 4 NA 12 NA NA TRUE
#> 87 032 ATC:skmeans 3 3 27 7999 2.13e-02 FALSE
#> 88 0321 not applied 4 NA 11 NA NA TRUE
#> 89 0322 not applied 4 NA 13 NA NA TRUE
#> 90 0323 not applied 4 NA 3 NA NA TRUE
#> 91 033 not applied 3 NA 9 NA NA TRUE
In the output from node_info(), there are the following columns:
id: The node id.best_method: The best method selected.depth: Depth of the node in the hierarchy.best_k: Best number of groups of the partition on that node.n_columns: Number of columns in the submatrix.n_signatures: Number of signatures with the best_k.p_signatures: Proportion of hte signatures in total number of rows in the matrix.is_leaf: Whether the node is a leaf.Labels of nodes are encoded in a special way. The number of digits correspond to the depth of the node in the hierarchy and the value of the digits correspond to the index of the subgroup in the current node, E.g. a label of “012” means the node is the second subgroup of the partition which is the first subgroup of the root node.
Following table shows the best k (number of partitions) for each node in the
partition hierarchy. Clicking on the node name in the table goes to the
corresponding section for the partitioning on that node.
The cola vignette explains the definition of the metrics used for determining the best number of partitions.
suggest_best_k(res_rh)
| Node | Best method | Is leaf | Best k | 1-PAC | Mean silhouette | Concordance | #samples | |
|---|---|---|---|---|---|---|---|---|
| Node0 | ATC:kmeans | 3 | 1.00 | 0.99 | 0.99 | 685 | ** | |
| Node01 | ATC:skmeans | 5 | 0.97 | 0.94 | 0.97 | 243 | ** | |
| Node011 | ATC:kmeans | 3 | 1.00 | 0.96 | 0.99 | 86 | ** | |
| Node0111 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 39 | ** | |
| Node01111-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 21 | ** |
| Node01112-leaf | ATC:skmeans | ✓ (c) | 3 | 1.00 | 0.99 | 0.98 | 18 | ** |
| Node0112 | ATC:skmeans | 4 | 1.00 | 1.00 | 1.00 | 23 | ** | |
| Node01121-leaf | not applied | ✓ (b) | 10 | |||||
| Node01122-leaf | not applied | ✓ (b) | 4 | |||||
| Node01123-leaf | not applied | ✓ (b) | 9 | |||||
| Node0113 | ATC:skmeans | 4 | 1.00 | 0.93 | 0.97 | 24 | ** | |
| Node01131-leaf | not applied | ✓ (b) | 7 | |||||
| Node01132-leaf | not applied | ✓ (b) | 11 | |||||
| Node01133-leaf | not applied | ✓ (b) | 6 | |||||
| Node012 | SD:skmeans | 3 | 0.91 | 0.96 | 0.97 | 74 | * | |
| Node0121 | ATC:kmeans | 3 | 1.00 | 0.97 | 0.97 | 35 | ** | |
| Node01211-leaf | not applied | ✓ (b) | 13 | |||||
| Node01212-leaf | not applied | ✓ (b) | 8 | |||||
| Node01213 | ATC:kmeans | 4 | 1.00 | 0.99 | 0.99 | 14 | ** | |
| Node012131-leaf | not applied | ✓ (b) | 4 | |||||
| Node012132-leaf | not applied | ✓ (b) | 4 | |||||
| Node012133-leaf | not applied | ✓ (b) | 2 | |||||
| Node012134-leaf | not applied | ✓ (b) | 4 | |||||
| Node0122 | SD:kmeans | 5 | 0.95 | 0.96 | 0.96 | 34 | * | |
| Node01221-leaf | not applied | ✓ (b) | 10 | |||||
| Node01222-leaf | not applied | ✓ (b) | 12 | |||||
| Node01223-leaf | not applied | ✓ (b) | 2 | |||||
| Node01224-leaf | not applied | ✓ (b) | 5 | |||||
| Node01225-leaf | not applied | ✓ (b) | 5 | |||||
| Node0123-leaf | not applied | ✓ (b) | 5 | |||||
| Node013 | ATC:skmeans | 8 | 0.91 | 0.78 | 0.92 | 41 | * | |
| Node0131 | ATC:skmeans | 3 | 1.00 | 1.00 | 1.00 | 14 | ** | |
| Node01311-leaf | not applied | ✓ (b) | 7 | |||||
| Node01312-leaf | not applied | ✓ (b) | 4 | |||||
| Node01313-leaf | not applied | ✓ (b) | 3 | |||||
| Node0132-leaf | not applied | ✓ (b) | 8 | |||||
| Node0133-leaf | not applied | ✓ (b) | 12 | |||||
| Node0134-leaf | not applied | ✓ (b) | 7 | |||||
| Node014 | ATC:kmeans | 3 | 1.00 | 1.00 | 1.00 | 42 | ** | |
| Node0141 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 16 | ** | |
| Node01411-leaf | not applied | ✓ (b) | 11 | |||||
| Node01412-leaf | not applied | ✓ (b) | 5 | |||||
| Node0142-leaf | not applied | ✓ (b) | 12 | |||||
| Node0143 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 14 | ** | |
| Node01431-leaf | not applied | ✓ (b) | 11 | |||||
| Node01432-leaf | not applied | ✓ (b) | 3 | |||||
| Node02 | ATC:skmeans | 5 | 0.99 | 0.95 | 0.98 | 328 | ** | |
| Node021 | ATC:skmeans | 6 | 0.94 | 0.93 | 0.95 | 155 | * | |
| Node0211-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 0.98 | 0.99 | 89 | ** |
| Node0212-leaf | SD:skmeans | ✓ (c) | 2 | 1.00 | 0.99 | 1.00 | 58 | ** |
| Node0213-leaf | not applied | ✓ (b) | 5 | |||||
| Node0214-leaf | not applied | ✓ (b) | 3 | |||||
| Node022 | ATC:kmeans | 3 | 0.98 | 0.96 | 0.99 | 133 | ** | |
| Node0221 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 53 | ** | |
| Node02211-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 0.99 | 1.00 | 31 | ** |
| Node02212 | ATC:kmeans | 4 | 0.94 | 0.97 | 0.95 | 22 | * | |
| Node022121-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 15 | ** |
| Node022122-leaf | not applied | ✓ (b) | 4 | |||||
| Node022123-leaf | not applied | ✓ (b) | 3 | |||||
| Node0222 | ATC:kmeans | 3 | 1.00 | 0.99 | 1.00 | 33 | ** | |
| Node02221 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 19 | ** | |
| Node022211-leaf | not applied | ✓ (b) | 7 | |||||
| Node022212-leaf | not applied | ✓ (b) | 12 | |||||
| Node02222-leaf | not applied | ✓ (b) | 10 | |||||
| Node02223-leaf | not applied | ✓ (b) | 4 | |||||
| Node0223 | ATC:kmeans | 4 | 1.00 | 0.99 | 0.99 | 47 | ** | |
| Node02231 | ATC:skmeans | 3 | 0.96 | 0.97 | 0.98 | 21 | ** | |
| Node022311-leaf | not applied | ✓ (b) | 11 | |||||
| Node022312-leaf | not applied | ✓ (b) | 8 | |||||
| Node022313-leaf | not applied | ✓ (b) | 2 | |||||
| Node02232-leaf | not applied | ✓ (b) | 8 | |||||
| Node02233-leaf | not applied | ✓ (b) | 5 | |||||
| Node02234-leaf | not applied | ✓ (b) | 13 | |||||
| Node023 | ATC:kmeans | 3 | 1.00 | 1.00 | 1.00 | 40 | ** | |
| Node0231 | ATC:skmeans | 4 | 1.00 | 0.99 | 1.00 | 19 | ** | |
| Node02311-leaf | not applied | ✓ (b) | 11 | |||||
| Node02312-leaf | not applied | ✓ (b) | 6 | |||||
| Node02313-leaf | not applied | ✓ (b) | 2 | |||||
| Node0232-leaf | not applied | ✓ (b) | 10 | |||||
| Node0233-leaf | not applied | ✓ (b) | 11 | |||||
| Node03 | ATC:kmeans | 3 | 1.00 | 0.97 | 0.99 | 114 | ** | |
| Node031 | ATC:skmeans | 5 | 0.94 | 0.93 | 0.95 | 78 | * | |
| Node0311-leaf | SD:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 24 | ** |
| Node0312-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 21 | ** |
| Node0313-leaf | ATC:kmeans | ✓ (c) | 6 | 0.92 | 0.86 | 0.93 | 21 | * |
| Node0314-leaf | not applied | ✓ (b) | 12 | |||||
| Node032 | ATC:skmeans | 8 | 0.92 | 0.77 | 0.95 | 27 | * | |
| Node0321-leaf | not applied | ✓ (b) | 11 | |||||
| Node0322-leaf | not applied | ✓ (b) | 13 | |||||
| Node0323-leaf | not applied | ✓ (b) | 3 | |||||
| Node033-leaf | not applied | ✓ (b) | 9 |
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 = 3442))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3477))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3513))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3544))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3605))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3621))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3669))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3702))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3736))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3806))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3846))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3958))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4112))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4199))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4915))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5006))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5899))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6182))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7856))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7999))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8024))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 9621))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 9856))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 15681))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 18000))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 18964))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 20318))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 21160))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 39547))
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 = 3442))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "0312" "0212" "033" "02211" "033" "01222"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "02234" "0212" "0142" "0133" "01432" "022121"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "01132" "02311" "01131" "0313" "02312" "0312"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "01311" "022311" "01211" "0232" "02311" "0211"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "0312" "0212" "01112" "0313" "0212" "022311"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "0132" "0322" "01121" "0313" "033" "02234"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "022122" "01211" "02312" "022121" "0312" "0312"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "0313" "01112" "02211" "012134" "0311" "01132"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "01221" "01132" "033" "0212" "01212" "0312"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "01431" "01112" "0211" "0212" "0211" "022121"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "01111" "0211" "012134" "0211" "0123" "0132"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "01224" "02311" "01111" "0142" "0311" "0211"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "0211" "01431" "0313" "022121" "01221" "0314"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "0314" "01132" "0321" "02211" "033" "02311"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "02211" "022311" "0312" "0211" "0211" "0233"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "0322" "02211" "0211" "0311" "0321" "0232"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "0314" "022123" "02222" "01111" "01132" "01412"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "01411" "01112" "02311" "0212" "01431" "01111"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "01211" "02211" "0323" "0213" "0211" "0212"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "0322" "012134" "0311" "0232" "0212" "01211"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "0133" "02234" "01131" "02211" "0312" "01123"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "01121" "0212" "01412" "02211" "0212" "02211"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "0211" "0233" "02234" "01132" "0311" "0213"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "0212" "01311" "0211" "0322" "022121" "0313"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "0133" "0123" "0322" "0323" "02234" "0142"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "01411" "01221" "0211" "0211" "0312" "0132"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "01431" "0211" "0211" "0312" "01211" "0212"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "0212" "022122" "0133" "01111" "02232" "02232"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "02311" "01312" "02222" "0133" "0212" "0314"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "01111" "01131" "0322" "0212" "0313" "01411"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "0212" "012131" "01225" "0211" "022121" "0212"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "0212" "0233" "02223" "0211" "022212" "0211"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "02211" "022311" "01212" "02232" "01121" "0212"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "022121" "01121" "01431" "01111" "01121" "0211"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "02311" "02233" "0211" "01111" "01123" "0134"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "01131" "0211" "022312" "022121" "01112" "0123"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "0314" "02222" "022311" "0123" "0211" "0211"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "0212" "0132" "0232" "0311" "01212" "0321"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "01121" "0133" "0211" "02223" "0321" "0212"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "02234" "01224" "0313" "01311" "022121" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "01412" "02312" "02211" "0313" "01121" "02211"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "0211" "022212" "02234" "022311" "01313" "0311"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "0312" "012132" "01225" "0321" "0313" "0211"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "0142" "0211" "033" "0233" "022312" "01311"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "01111" "0212" "0212" "0212" "0313" "0211"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "01112" "022211" "02211" "01112" "022312" "022212"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "01222" "0211" "01132" "02312" "0212" "012133"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "0211" "0213" "01221" "0211" "022121" "022212"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "0313" "0211" "0211" "0321" "01112" "0142"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "0211" "012133" "0314" "0313" "0212" "0211"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "01411" "0313" "0211" "0211" "0311" "01111"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "02211" "0232" "0211" "01211" "01412" "0312"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "0212" "0134" "01212" "0311" "01111" "0133"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "012132" "0211" "0321" "0232" "02222" "0133"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "01311" "01221" "02232" "0212" "0132" "0133"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "0211" "0322" "01222" "022311" "01311" "022212"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "0211" "01312" "0211" "0211" "0133" "01212"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "02211" "0313" "02211" "0311" "0214" "02234"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "01211" "01112" "022312" "0212" "01313" "0212"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "0212" "0211" "0134" "02311" "0134" "022311"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "012134" "01211" "022212" "0211" "02232" "01225"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "01121" "01111" "01111" "0312" "022211" "01431"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "0142" "0233" "0211" "0214" "0212" "0213"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "01111" "01431" "0232" "0133" "01123" "0211"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "0313" "01111" "0211" "01411" "01123" "02211"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "01111" "01132" "01411" "022121" "02233" "0211"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "0311" "0211" "0142" "022212" "012132" "01211"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "022311" "0312" "0312" "0211" "01432" "0211"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "01133" "0211" "02311" "0212" "01112" "01131"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "0233" "0313" "01122" "02233" "02211" "02211"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "012131" "0212" "01133" "0211" "01221" "01123"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "01111" "0212" "02211" "022312" "01411" "01112"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "0322" "0233" "01111" "01112" "0313" "02211"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "0311" "02222" "0312" "022211" "0314" "01222"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "01411" "01224" "0321" "01221" "012132" "0312"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "022312" "01211" "01222" "0211" "01211" "01131"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "01123" "02311" "0212" "01131" "01432" "02313"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "01112" "0211" "0314" "0212" "0212" "02222"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "01221" "0212" "022313" "01223" "01223" "01121"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "0142" "0313" "022123" "0133" "0211" "02313"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "01133" "0312" "0214" "0212" "0311" "022212"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "022211" "022312" "0211" "01431" "022123" "02234"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "01112" "0211" "022212" "0311" "02312" "0211"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "01222" "02222" "0212" "01133" "01211" "0212"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "0321" "01222" "01222" "0211" "01212" "02234"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "0212" "0211" "0211" "0311" "0142" "01121"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "01222" "0211" "0123" "022121" "01122" "022212"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "022312" "01123" "0211" "02211" "02233" "02232"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "022122" "0211" "02211" "0213" "0134" "02234"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "01312" "0322" "02222" "0211" "01132" "0311"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "02211" "0211" "01222" "0322" "0232" "01221"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "0211" "022212" "0211" "01122" "022212" "01212"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "0211" "0212" "0233" "01222" "0313" "01133"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "0134" "0211" "022121" "0212" "0211" "022311"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "0311" "02211" "0142" "0311" "0134" "01112"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "0211" "022313" "022211" "01212" "0311" "0314"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "02234" "0312" "022211" "01431" "01222" "0212"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "01123" "01111" "0211" "01412" "02211" "02234"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "0314" "01211" "01431" "0211" "0211" "0321"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "01111" "022121" "0312" "0142" "01411" "02312"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "0212" "0314" "022121" "0211" "01311" "0212"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "0232" "0312" "0323" "01312" "01132" "0142"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "01112" "01411" "01132" "01411" "0211" "0211"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "0212" "01111" "0322" "0212" "0211" "0211"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "012131" "0313" "033" "0311" "01224" "0212"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "02222" "02233" "0132" "0233" "01112" "0211"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "0311" "02211" "02211" "01225" "01123" "012131"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "0211" "02211" "02311" "022122" "01133" "022311"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "0314" "0211" "0311" "0322" "0233"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "0212" "01225" "01224" "0311" "0233" "01112"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "02211" "02223" "02223" "0212" "0321" "0212"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "0212" "0322" "01122" "02211" "01221" "0132"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "0211" "02222" "02232" "0212" "0232" "022211"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0132" "0211" "0212" "01313" "0311" "02232"
#> TCGA.74.6578.01
#> "01431"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3477))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "0312" "0212" "033" "02211" "033" "01222"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "02234" "0212" "0142" "0133" "01432" "022121"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "01132" "02311" "01131" "0313" "02312" "0312"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "01311" "022311" "01211" "0232" "02311" "0211"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "0312" "0212" "01112" "0313" "0212" "022311"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "0132" "0322" "01121" "0313" "033" "02234"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "022122" "01211" "02312" "022121" "0312" "0312"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "0313" "01112" "02211" "012134" "0311" "01132"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "01221" "01132" "033" "0212" "01212" "0312"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "01431" "01112" "0211" "0212" "0211" "022121"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "01111" "0211" "012134" "0211" "0123" "0132"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "01224" "02311" "01111" "0142" "0311" "0211"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "0211" "01431" "0313" "022121" "01221" "0314"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "0314" "01132" "0321" "02211" "033" "02311"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "02211" "022311" "0312" "0211" "0211" "0233"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "0322" "02211" "0211" "0311" "0321" "0232"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "0314" "022123" "02222" "01111" "01132" "01412"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "01411" "01112" "02311" "0212" "01431" "01111"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "01211" "02211" "0323" "0213" "0211" "0212"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "0322" "012134" "0311" "0232" "0212" "01211"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "0133" "02234" "01131" "02211" "0312" "01123"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "01121" "0212" "01412" "02211" "0212" "02211"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "0211" "0233" "02234" "01132" "0311" "0213"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "0212" "01311" "0211" "0322" "022121" "0313"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "0133" "0123" "0322" "0323" "02234" "0142"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "01411" "01221" "0211" "0211" "0312" "0132"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "01431" "0211" "0211" "0312" "01211" "0212"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "0212" "022122" "0133" "01111" "02232" "02232"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "02311" "01312" "02222" "0133" "0212" "0314"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "01111" "01131" "0322" "0212" "0313" "01411"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "0212" "012131" "01225" "0211" "022121" "0212"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "0212" "0233" "02223" "0211" "02221" "0211"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "02211" "022311" "01212" "02232" "01121" "0212"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "022121" "01121" "01431" "01111" "01121" "0211"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "02311" "02233" "0211" "01111" "01123" "0134"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "01131" "0211" "022312" "022121" "01112" "0123"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "0314" "02222" "022311" "0123" "0211" "0211"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "0212" "0132" "0232" "0311" "01212" "0321"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "01121" "0133" "0211" "02223" "0321" "0212"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "02234" "01224" "0313" "01311" "022121" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "01412" "02312" "02211" "0313" "01121" "02211"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "0211" "02221" "02234" "022311" "01313" "0311"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "0312" "012132" "01225" "0321" "0313" "0211"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "0142" "0211" "033" "0233" "022312" "01311"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "01111" "0212" "0212" "0212" "0313" "0211"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "01112" "02221" "02211" "01112" "022312" "02221"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "01222" "0211" "01132" "02312" "0212" "012133"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "0211" "0213" "01221" "0211" "022121" "02221"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "0313" "0211" "0211" "0321" "01112" "0142"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "0211" "012133" "0314" "0313" "0212" "0211"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "01411" "0313" "0211" "0211" "0311" "01111"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "02211" "0232" "0211" "01211" "01412" "0312"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "0212" "0134" "01212" "0311" "01111" "0133"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "012132" "0211" "0321" "0232" "02222" "0133"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "01311" "01221" "02232" "0212" "0132" "0133"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "0211" "0322" "01222" "022311" "01311" "02221"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "0211" "01312" "0211" "0211" "0133" "01212"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "02211" "0313" "02211" "0311" "0214" "02234"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "01211" "01112" "022312" "0212" "01313" "0212"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "0212" "0211" "0134" "02311" "0134" "022311"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "012134" "01211" "02221" "0211" "02232" "01225"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "01121" "01111" "01111" "0312" "02221" "01431"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "0142" "0233" "0211" "0214" "0212" "0213"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "01111" "01431" "0232" "0133" "01123" "0211"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "0313" "01111" "0211" "01411" "01123" "02211"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "01111" "01132" "01411" "022121" "02233" "0211"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "0311" "0211" "0142" "02221" "012132" "01211"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "022311" "0312" "0312" "0211" "01432" "0211"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "01133" "0211" "02311" "0212" "01112" "01131"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "0233" "0313" "01122" "02233" "02211" "02211"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "012131" "0212" "01133" "0211" "01221" "01123"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "01111" "0212" "02211" "022312" "01411" "01112"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "0322" "0233" "01111" "01112" "0313" "02211"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "0311" "02222" "0312" "02221" "0314" "01222"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "01411" "01224" "0321" "01221" "012132" "0312"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "022312" "01211" "01222" "0211" "01211" "01131"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "01123" "02311" "0212" "01131" "01432" "02313"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "01112" "0211" "0314" "0212" "0212" "02222"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "01221" "0212" "022313" "01223" "01223" "01121"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "0142" "0313" "022123" "0133" "0211" "02313"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "01133" "0312" "0214" "0212" "0311" "02221"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "02221" "022312" "0211" "01431" "022123" "02234"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "01112" "0211" "02221" "0311" "02312" "0211"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "01222" "02222" "0212" "01133" "01211" "0212"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "0321" "01222" "01222" "0211" "01212" "02234"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "0212" "0211" "0211" "0311" "0142" "01121"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "01222" "0211" "0123" "022121" "01122" "02221"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "022312" "01123" "0211" "02211" "02233" "02232"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "022122" "0211" "02211" "0213" "0134" "02234"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "01312" "0322" "02222" "0211" "01132" "0311"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "02211" "0211" "01222" "0322" "0232" "01221"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "0211" "02221" "0211" "01122" "02221" "01212"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "0211" "0212" "0233" "01222" "0313" "01133"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "0134" "0211" "022121" "0212" "0211" "022311"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "0311" "02211" "0142" "0311" "0134" "01112"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "0211" "022313" "02221" "01212" "0311" "0314"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "02234" "0312" "02221" "01431" "01222" "0212"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "01123" "01111" "0211" "01412" "02211" "02234"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "0314" "01211" "01431" "0211" "0211" "0321"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "01111" "022121" "0312" "0142" "01411" "02312"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "0212" "0314" "022121" "0211" "01311" "0212"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "0232" "0312" "0323" "01312" "01132" "0142"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "01112" "01411" "01132" "01411" "0211" "0211"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "0212" "01111" "0322" "0212" "0211" "0211"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "012131" "0313" "033" "0311" "01224" "0212"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "02222" "02233" "0132" "0233" "01112" "0211"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "0311" "02211" "02211" "01225" "01123" "012131"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "0211" "02211" "02311" "022122" "01133" "022311"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "0314" "0211" "0311" "0322" "0233"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "0212" "01225" "01224" "0311" "0233" "01112"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "02211" "02223" "02223" "0212" "0321" "0212"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "0212" "0322" "01122" "02211" "01221" "0132"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "0211" "02222" "02232" "0212" "0232" "02221"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0132" "0211" "0212" "01313" "0311" "02232"
#> TCGA.74.6578.01
#> "01431"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3513))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "0312" "0212" "033" "02211" "033" "01222"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "02234" "0212" "0142" "0133" "01432" "022121"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "01132" "02311" "01131" "0313" "02312" "0312"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "01311" "022311" "01211" "0232" "02311" "0211"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "0312" "0212" "01112" "0313" "0212" "022311"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "0132" "0322" "01121" "0313" "033" "02234"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "022122" "01211" "02312" "022121" "0312" "0312"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "0313" "01112" "02211" "012134" "0311" "01132"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "01221" "01132" "033" "0212" "01212" "0312"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "01431" "01112" "0211" "0212" "0211" "022121"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "01111" "0211" "012134" "0211" "0123" "0132"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "01224" "02311" "01111" "0142" "0311" "0211"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "0211" "01431" "0313" "022121" "01221" "0314"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "0314" "01132" "0321" "02211" "033" "02311"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "02211" "022311" "0312" "0211" "0211" "0233"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "0322" "02211" "0211" "0311" "0321" "0232"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "0314" "022123" "02222" "01111" "01132" "0141"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "0141" "01112" "02311" "0212" "01431" "01111"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "01211" "02211" "0323" "0213" "0211" "0212"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "0322" "012134" "0311" "0232" "0212" "01211"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "0133" "02234" "01131" "02211" "0312" "01123"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "01121" "0212" "0141" "02211" "0212" "02211"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "0211" "0233" "02234" "01132" "0311" "0213"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "0212" "01311" "0211" "0322" "022121" "0313"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "0133" "0123" "0322" "0323" "02234" "0142"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "0141" "01221" "0211" "0211" "0312" "0132"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "01431" "0211" "0211" "0312" "01211" "0212"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "0212" "022122" "0133" "01111" "02232" "02232"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "02311" "01312" "02222" "0133" "0212" "0314"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "01111" "01131" "0322" "0212" "0313" "0141"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "0212" "012131" "01225" "0211" "022121" "0212"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "0212" "0233" "02223" "0211" "02221" "0211"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "02211" "022311" "01212" "02232" "01121" "0212"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "022121" "01121" "01431" "01111" "01121" "0211"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "02311" "02233" "0211" "01111" "01123" "0134"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "01131" "0211" "022312" "022121" "01112" "0123"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "0314" "02222" "022311" "0123" "0211" "0211"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "0212" "0132" "0232" "0311" "01212" "0321"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "01121" "0133" "0211" "02223" "0321" "0212"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "02234" "01224" "0313" "01311" "022121" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "0141" "02312" "02211" "0313" "01121" "02211"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "0211" "02221" "02234" "022311" "01313" "0311"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "0312" "012132" "01225" "0321" "0313" "0211"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "0142" "0211" "033" "0233" "022312" "01311"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "01111" "0212" "0212" "0212" "0313" "0211"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "01112" "02221" "02211" "01112" "022312" "02221"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "01222" "0211" "01132" "02312" "0212" "012133"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "0211" "0213" "01221" "0211" "022121" "02221"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "0313" "0211" "0211" "0321" "01112" "0142"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "0211" "012133" "0314" "0313" "0212" "0211"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "0141" "0313" "0211" "0211" "0311" "01111"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "02211" "0232" "0211" "01211" "0141" "0312"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "0212" "0134" "01212" "0311" "01111" "0133"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "012132" "0211" "0321" "0232" "02222" "0133"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "01311" "01221" "02232" "0212" "0132" "0133"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "0211" "0322" "01222" "022311" "01311" "02221"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "0211" "01312" "0211" "0211" "0133" "01212"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "02211" "0313" "02211" "0311" "0214" "02234"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "01211" "01112" "022312" "0212" "01313" "0212"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "0212" "0211" "0134" "02311" "0134" "022311"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "012134" "01211" "02221" "0211" "02232" "01225"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "01121" "01111" "01111" "0312" "02221" "01431"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "0142" "0233" "0211" "0214" "0212" "0213"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "01111" "01431" "0232" "0133" "01123" "0211"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "0313" "01111" "0211" "0141" "01123" "02211"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "01111" "01132" "0141" "022121" "02233" "0211"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "0311" "0211" "0142" "02221" "012132" "01211"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "022311" "0312" "0312" "0211" "01432" "0211"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "01133" "0211" "02311" "0212" "01112" "01131"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "0233" "0313" "01122" "02233" "02211" "02211"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "012131" "0212" "01133" "0211" "01221" "01123"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "01111" "0212" "02211" "022312" "0141" "01112"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "0322" "0233" "01111" "01112" "0313" "02211"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "0311" "02222" "0312" "02221" "0314" "01222"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "0141" "01224" "0321" "01221" "012132" "0312"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "022312" "01211" "01222" "0211" "01211" "01131"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "01123" "02311" "0212" "01131" "01432" "02313"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "01112" "0211" "0314" "0212" "0212" "02222"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "01221" "0212" "022313" "01223" "01223" "01121"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "0142" "0313" "022123" "0133" "0211" "02313"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "01133" "0312" "0214" "0212" "0311" "02221"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "02221" "022312" "0211" "01431" "022123" "02234"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "01112" "0211" "02221" "0311" "02312" "0211"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "01222" "02222" "0212" "01133" "01211" "0212"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "0321" "01222" "01222" "0211" "01212" "02234"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "0212" "0211" "0211" "0311" "0142" "01121"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "01222" "0211" "0123" "022121" "01122" "02221"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "022312" "01123" "0211" "02211" "02233" "02232"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "022122" "0211" "02211" "0213" "0134" "02234"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "01312" "0322" "02222" "0211" "01132" "0311"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "02211" "0211" "01222" "0322" "0232" "01221"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "0211" "02221" "0211" "01122" "02221" "01212"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "0211" "0212" "0233" "01222" "0313" "01133"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "0134" "0211" "022121" "0212" "0211" "022311"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "0311" "02211" "0142" "0311" "0134" "01112"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "0211" "022313" "02221" "01212" "0311" "0314"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "02234" "0312" "02221" "01431" "01222" "0212"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "01123" "01111" "0211" "0141" "02211" "02234"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "0314" "01211" "01431" "0211" "0211" "0321"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "01111" "022121" "0312" "0142" "0141" "02312"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "0212" "0314" "022121" "0211" "01311" "0212"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "0232" "0312" "0323" "01312" "01132" "0142"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "01112" "0141" "01132" "0141" "0211" "0211"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "0212" "01111" "0322" "0212" "0211" "0211"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "012131" "0313" "033" "0311" "01224" "0212"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "02222" "02233" "0132" "0233" "01112" "0211"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "0311" "02211" "02211" "01225" "01123" "012131"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "0211" "02211" "02311" "022122" "01133" "022311"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "0314" "0211" "0311" "0322" "0233"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "0212" "01225" "01224" "0311" "0233" "01112"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "02211" "02223" "02223" "0212" "0321" "0212"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "0212" "0322" "01122" "02211" "01221" "0132"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "0211" "02222" "02232" "0212" "0232" "02221"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0132" "0211" "0212" "01313" "0311" "02232"
#> TCGA.74.6578.01
#> "01431"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3544))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "0312" "0212" "033" "02211" "033" "01222"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "02234" "0212" "0142" "0133" "0143" "022121"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "01132" "02311" "01131" "0313" "02312" "0312"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "01311" "022311" "01211" "0232" "02311" "0211"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "0312" "0212" "01112" "0313" "0212" "022311"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "0132" "0322" "01121" "0313" "033" "02234"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "022122" "01211" "02312" "022121" "0312" "0312"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "0313" "01112" "02211" "012134" "0311" "01132"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "01221" "01132" "033" "0212" "01212" "0312"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0143" "01112" "0211" "0212" "0211" "022121"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "01111" "0211" "012134" "0211" "0123" "0132"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "01224" "02311" "01111" "0142" "0311" "0211"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "0211" "0143" "0313" "022121" "01221" "0314"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "0314" "01132" "0321" "02211" "033" "02311"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "02211" "022311" "0312" "0211" "0211" "0233"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "0322" "02211" "0211" "0311" "0321" "0232"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "0314" "022123" "02222" "01111" "01132" "0141"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "0141" "01112" "02311" "0212" "0143" "01111"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "01211" "02211" "0323" "0213" "0211" "0212"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "0322" "012134" "0311" "0232" "0212" "01211"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "0133" "02234" "01131" "02211" "0312" "01123"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "01121" "0212" "0141" "02211" "0212" "02211"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "0211" "0233" "02234" "01132" "0311" "0213"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "0212" "01311" "0211" "0322" "022121" "0313"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "0133" "0123" "0322" "0323" "02234" "0142"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "0141" "01221" "0211" "0211" "0312" "0132"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "0143" "0211" "0211" "0312" "01211" "0212"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "0212" "022122" "0133" "01111" "02232" "02232"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "02311" "01312" "02222" "0133" "0212" "0314"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "01111" "01131" "0322" "0212" "0313" "0141"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "0212" "012131" "01225" "0211" "022121" "0212"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "0212" "0233" "02223" "0211" "02221" "0211"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "02211" "022311" "01212" "02232" "01121" "0212"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "022121" "01121" "0143" "01111" "01121" "0211"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "02311" "02233" "0211" "01111" "01123" "0134"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "01131" "0211" "022312" "022121" "01112" "0123"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "0314" "02222" "022311" "0123" "0211" "0211"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "0212" "0132" "0232" "0311" "01212" "0321"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "01121" "0133" "0211" "02223" "0321" "0212"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "02234" "01224" "0313" "01311" "022121" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "0141" "02312" "02211" "0313" "01121" "02211"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "0211" "02221" "02234" "022311" "01313" "0311"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "0312" "012132" "01225" "0321" "0313" "0211"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "0142" "0211" "033" "0233" "022312" "01311"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "01111" "0212" "0212" "0212" "0313" "0211"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "01112" "02221" "02211" "01112" "022312" "02221"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "01222" "0211" "01132" "02312" "0212" "012133"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "0211" "0213" "01221" "0211" "022121" "02221"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "0313" "0211" "0211" "0321" "01112" "0142"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "0211" "012133" "0314" "0313" "0212" "0211"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "0141" "0313" "0211" "0211" "0311" "01111"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "02211" "0232" "0211" "01211" "0141" "0312"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "0212" "0134" "01212" "0311" "01111" "0133"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "012132" "0211" "0321" "0232" "02222" "0133"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "01311" "01221" "02232" "0212" "0132" "0133"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "0211" "0322" "01222" "022311" "01311" "02221"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "0211" "01312" "0211" "0211" "0133" "01212"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "02211" "0313" "02211" "0311" "0214" "02234"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "01211" "01112" "022312" "0212" "01313" "0212"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "0212" "0211" "0134" "02311" "0134" "022311"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "012134" "01211" "02221" "0211" "02232" "01225"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "01121" "01111" "01111" "0312" "02221" "0143"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "0142" "0233" "0211" "0214" "0212" "0213"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "01111" "0143" "0232" "0133" "01123" "0211"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "0313" "01111" "0211" "0141" "01123" "02211"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "01111" "01132" "0141" "022121" "02233" "0211"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "0311" "0211" "0142" "02221" "012132" "01211"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "022311" "0312" "0312" "0211" "0143" "0211"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "01133" "0211" "02311" "0212" "01112" "01131"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "0233" "0313" "01122" "02233" "02211" "02211"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "012131" "0212" "01133" "0211" "01221" "01123"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "01111" "0212" "02211" "022312" "0141" "01112"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "0322" "0233" "01111" "01112" "0313" "02211"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "0311" "02222" "0312" "02221" "0314" "01222"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "0141" "01224" "0321" "01221" "012132" "0312"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "022312" "01211" "01222" "0211" "01211" "01131"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "01123" "02311" "0212" "01131" "0143" "02313"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "01112" "0211" "0314" "0212" "0212" "02222"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "01221" "0212" "022313" "01223" "01223" "01121"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "0142" "0313" "022123" "0133" "0211" "02313"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "01133" "0312" "0214" "0212" "0311" "02221"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "02221" "022312" "0211" "0143" "022123" "02234"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "01112" "0211" "02221" "0311" "02312" "0211"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "01222" "02222" "0212" "01133" "01211" "0212"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "0321" "01222" "01222" "0211" "01212" "02234"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "0212" "0211" "0211" "0311" "0142" "01121"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "01222" "0211" "0123" "022121" "01122" "02221"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "022312" "01123" "0211" "02211" "02233" "02232"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "022122" "0211" "02211" "0213" "0134" "02234"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "01312" "0322" "02222" "0211" "01132" "0311"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "02211" "0211" "01222" "0322" "0232" "01221"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "0211" "02221" "0211" "01122" "02221" "01212"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "0211" "0212" "0233" "01222" "0313" "01133"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "0134" "0211" "022121" "0212" "0211" "022311"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "0311" "02211" "0142" "0311" "0134" "01112"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "0211" "022313" "02221" "01212" "0311" "0314"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "02234" "0312" "02221" "0143" "01222" "0212"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "01123" "01111" "0211" "0141" "02211" "02234"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "0314" "01211" "0143" "0211" "0211" "0321"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "01111" "022121" "0312" "0142" "0141" "02312"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "0212" "0314" "022121" "0211" "01311" "0212"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "0232" "0312" "0323" "01312" "01132" "0142"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "01112" "0141" "01132" "0141" "0211" "0211"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "0212" "01111" "0322" "0212" "0211" "0211"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "012131" "0313" "033" "0311" "01224" "0212"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "02222" "02233" "0132" "0233" "01112" "0211"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "0311" "02211" "02211" "01225" "01123" "012131"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "0211" "02211" "02311" "022122" "01133" "022311"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "0314" "0211" "0311" "0322" "0233"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "0212" "01225" "01224" "0311" "0233" "01112"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "02211" "02223" "02223" "0212" "0321" "0212"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "0212" "0322" "01122" "02211" "01221" "0132"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "0211" "02222" "02232" "0212" "0232" "02221"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0132" "0211" "0212" "01313" "0311" "02232"
#> TCGA.74.6578.01
#> "0143"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3605))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "0312" "0212" "033" "02211" "033" "01222"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "02234" "0212" "0142" "0133" "0143" "02212"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "01132" "02311" "01131" "0313" "02312" "0312"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "01311" "022311" "01211" "0232" "02311" "0211"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "0312" "0212" "01112" "0313" "0212" "022311"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "0132" "0322" "01121" "0313" "033" "02234"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "02212" "01211" "02312" "02212" "0312" "0312"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "0313" "01112" "02211" "012134" "0311" "01132"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "01221" "01132" "033" "0212" "01212" "0312"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0143" "01112" "0211" "0212" "0211" "02212"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "01111" "0211" "012134" "0211" "0123" "0132"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "01224" "02311" "01111" "0142" "0311" "0211"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "0211" "0143" "0313" "02212" "01221" "0314"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "0314" "01132" "0321" "02211" "033" "02311"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "02211" "022311" "0312" "0211" "0211" "0233"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "0322" "02211" "0211" "0311" "0321" "0232"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "0314" "02212" "02222" "01111" "01132" "0141"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "0141" "01112" "02311" "0212" "0143" "01111"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "01211" "02211" "0323" "0213" "0211" "0212"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "0322" "012134" "0311" "0232" "0212" "01211"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "0133" "02234" "01131" "02211" "0312" "01123"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "01121" "0212" "0141" "02211" "0212" "02211"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "0211" "0233" "02234" "01132" "0311" "0213"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "0212" "01311" "0211" "0322" "02212" "0313"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "0133" "0123" "0322" "0323" "02234" "0142"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "0141" "01221" "0211" "0211" "0312" "0132"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "0143" "0211" "0211" "0312" "01211" "0212"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "0212" "02212" "0133" "01111" "02232" "02232"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "02311" "01312" "02222" "0133" "0212" "0314"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "01111" "01131" "0322" "0212" "0313" "0141"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "0212" "012131" "01225" "0211" "02212" "0212"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "0212" "0233" "02223" "0211" "02221" "0211"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "02211" "022311" "01212" "02232" "01121" "0212"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "02212" "01121" "0143" "01111" "01121" "0211"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "02311" "02233" "0211" "01111" "01123" "0134"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "01131" "0211" "022312" "02212" "01112" "0123"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "0314" "02222" "022311" "0123" "0211" "0211"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "0212" "0132" "0232" "0311" "01212" "0321"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "01121" "0133" "0211" "02223" "0321" "0212"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "02234" "01224" "0313" "01311" "02212" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "0141" "02312" "02211" "0313" "01121" "02211"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "0211" "02221" "02234" "022311" "01313" "0311"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "0312" "012132" "01225" "0321" "0313" "0211"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "0142" "0211" "033" "0233" "022312" "01311"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "01111" "0212" "0212" "0212" "0313" "0211"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "01112" "02221" "02211" "01112" "022312" "02221"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "01222" "0211" "01132" "02312" "0212" "012133"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "0211" "0213" "01221" "0211" "02212" "02221"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "0313" "0211" "0211" "0321" "01112" "0142"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "0211" "012133" "0314" "0313" "0212" "0211"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "0141" "0313" "0211" "0211" "0311" "01111"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "02211" "0232" "0211" "01211" "0141" "0312"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "0212" "0134" "01212" "0311" "01111" "0133"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "012132" "0211" "0321" "0232" "02222" "0133"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "01311" "01221" "02232" "0212" "0132" "0133"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "0211" "0322" "01222" "022311" "01311" "02221"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "0211" "01312" "0211" "0211" "0133" "01212"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "02211" "0313" "02211" "0311" "0214" "02234"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "01211" "01112" "022312" "0212" "01313" "0212"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "0212" "0211" "0134" "02311" "0134" "022311"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "012134" "01211" "02221" "0211" "02232" "01225"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "01121" "01111" "01111" "0312" "02221" "0143"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "0142" "0233" "0211" "0214" "0212" "0213"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "01111" "0143" "0232" "0133" "01123" "0211"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "0313" "01111" "0211" "0141" "01123" "02211"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "01111" "01132" "0141" "02212" "02233" "0211"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "0311" "0211" "0142" "02221" "012132" "01211"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "022311" "0312" "0312" "0211" "0143" "0211"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "01133" "0211" "02311" "0212" "01112" "01131"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "0233" "0313" "01122" "02233" "02211" "02211"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "012131" "0212" "01133" "0211" "01221" "01123"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "01111" "0212" "02211" "022312" "0141" "01112"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "0322" "0233" "01111" "01112" "0313" "02211"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "0311" "02222" "0312" "02221" "0314" "01222"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "0141" "01224" "0321" "01221" "012132" "0312"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "022312" "01211" "01222" "0211" "01211" "01131"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "01123" "02311" "0212" "01131" "0143" "02313"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "01112" "0211" "0314" "0212" "0212" "02222"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "01221" "0212" "022313" "01223" "01223" "01121"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "0142" "0313" "02212" "0133" "0211" "02313"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "01133" "0312" "0214" "0212" "0311" "02221"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "02221" "022312" "0211" "0143" "02212" "02234"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "01112" "0211" "02221" "0311" "02312" "0211"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "01222" "02222" "0212" "01133" "01211" "0212"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "0321" "01222" "01222" "0211" "01212" "02234"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "0212" "0211" "0211" "0311" "0142" "01121"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "01222" "0211" "0123" "02212" "01122" "02221"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "022312" "01123" "0211" "02211" "02233" "02232"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "02212" "0211" "02211" "0213" "0134" "02234"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "01312" "0322" "02222" "0211" "01132" "0311"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "02211" "0211" "01222" "0322" "0232" "01221"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "0211" "02221" "0211" "01122" "02221" "01212"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "0211" "0212" "0233" "01222" "0313" "01133"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "0134" "0211" "02212" "0212" "0211" "022311"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "0311" "02211" "0142" "0311" "0134" "01112"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "0211" "022313" "02221" "01212" "0311" "0314"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "02234" "0312" "02221" "0143" "01222" "0212"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "01123" "01111" "0211" "0141" "02211" "02234"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "0314" "01211" "0143" "0211" "0211" "0321"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "01111" "02212" "0312" "0142" "0141" "02312"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "0212" "0314" "02212" "0211" "01311" "0212"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "0232" "0312" "0323" "01312" "01132" "0142"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "01112" "0141" "01132" "0141" "0211" "0211"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "0212" "01111" "0322" "0212" "0211" "0211"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "012131" "0313" "033" "0311" "01224" "0212"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "02222" "02233" "0132" "0233" "01112" "0211"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "0311" "02211" "02211" "01225" "01123" "012131"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "0211" "02211" "02311" "02212" "01133" "022311"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "0314" "0211" "0311" "0322" "0233"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "0212" "01225" "01224" "0311" "0233" "01112"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "02211" "02223" "02223" "0212" "0321" "0212"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "0212" "0322" "01122" "02211" "01221" "0132"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "0211" "02222" "02232" "0212" "0232" "02221"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0132" "0211" "0212" "01313" "0311" "02232"
#> TCGA.74.6578.01
#> "0143"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3621))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "0312" "0212" "033" "02211" "033" "01222"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "02234" "0212" "0142" "0133" "0143" "02212"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "01132" "02311" "01131" "0313" "02312" "0312"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "01311" "022311" "01211" "0232" "02311" "0211"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "0312" "0212" "0111" "0313" "0212" "022311"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "0132" "0322" "01121" "0313" "033" "02234"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "02212" "01211" "02312" "02212" "0312" "0312"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "0313" "0111" "02211" "012134" "0311" "01132"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "01221" "01132" "033" "0212" "01212" "0312"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0143" "0111" "0211" "0212" "0211" "02212"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "0111" "0211" "012134" "0211" "0123" "0132"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "01224" "02311" "0111" "0142" "0311" "0211"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "0211" "0143" "0313" "02212" "01221" "0314"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "0314" "01132" "0321" "02211" "033" "02311"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "02211" "022311" "0312" "0211" "0211" "0233"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "0322" "02211" "0211" "0311" "0321" "0232"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "0314" "02212" "02222" "0111" "01132" "0141"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "0141" "0111" "02311" "0212" "0143" "0111"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "01211" "02211" "0323" "0213" "0211" "0212"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "0322" "012134" "0311" "0232" "0212" "01211"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "0133" "02234" "01131" "02211" "0312" "01123"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "01121" "0212" "0141" "02211" "0212" "02211"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "0211" "0233" "02234" "01132" "0311" "0213"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "0212" "01311" "0211" "0322" "02212" "0313"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "0133" "0123" "0322" "0323" "02234" "0142"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "0141" "01221" "0211" "0211" "0312" "0132"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "0143" "0211" "0211" "0312" "01211" "0212"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "0212" "02212" "0133" "0111" "02232" "02232"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "02311" "01312" "02222" "0133" "0212" "0314"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "0111" "01131" "0322" "0212" "0313" "0141"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "0212" "012131" "01225" "0211" "02212" "0212"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "0212" "0233" "02223" "0211" "02221" "0211"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "02211" "022311" "01212" "02232" "01121" "0212"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "02212" "01121" "0143" "0111" "01121" "0211"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "02311" "02233" "0211" "0111" "01123" "0134"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "01131" "0211" "022312" "02212" "0111" "0123"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "0314" "02222" "022311" "0123" "0211" "0211"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "0212" "0132" "0232" "0311" "01212" "0321"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "01121" "0133" "0211" "02223" "0321" "0212"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "02234" "01224" "0313" "01311" "02212" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "0141" "02312" "02211" "0313" "01121" "02211"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "0211" "02221" "02234" "022311" "01313" "0311"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "0312" "012132" "01225" "0321" "0313" "0211"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "0142" "0211" "033" "0233" "022312" "01311"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "0111" "0212" "0212" "0212" "0313" "0211"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "0111" "02221" "02211" "0111" "022312" "02221"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "01222" "0211" "01132" "02312" "0212" "012133"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "0211" "0213" "01221" "0211" "02212" "02221"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "0313" "0211" "0211" "0321" "0111" "0142"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "0211" "012133" "0314" "0313" "0212" "0211"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "0141" "0313" "0211" "0211" "0311" "0111"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "02211" "0232" "0211" "01211" "0141" "0312"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "0212" "0134" "01212" "0311" "0111" "0133"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "012132" "0211" "0321" "0232" "02222" "0133"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "01311" "01221" "02232" "0212" "0132" "0133"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "0211" "0322" "01222" "022311" "01311" "02221"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "0211" "01312" "0211" "0211" "0133" "01212"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "02211" "0313" "02211" "0311" "0214" "02234"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "01211" "0111" "022312" "0212" "01313" "0212"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "0212" "0211" "0134" "02311" "0134" "022311"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "012134" "01211" "02221" "0211" "02232" "01225"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "01121" "0111" "0111" "0312" "02221" "0143"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "0142" "0233" "0211" "0214" "0212" "0213"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "0111" "0143" "0232" "0133" "01123" "0211"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "0313" "0111" "0211" "0141" "01123" "02211"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "0111" "01132" "0141" "02212" "02233" "0211"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "0311" "0211" "0142" "02221" "012132" "01211"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "022311" "0312" "0312" "0211" "0143" "0211"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "01133" "0211" "02311" "0212" "0111" "01131"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "0233" "0313" "01122" "02233" "02211" "02211"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "012131" "0212" "01133" "0211" "01221" "01123"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "0111" "0212" "02211" "022312" "0141" "0111"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "0322" "0233" "0111" "0111" "0313" "02211"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "0311" "02222" "0312" "02221" "0314" "01222"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "0141" "01224" "0321" "01221" "012132" "0312"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "022312" "01211" "01222" "0211" "01211" "01131"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "01123" "02311" "0212" "01131" "0143" "02313"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "0111" "0211" "0314" "0212" "0212" "02222"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "01221" "0212" "022313" "01223" "01223" "01121"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "0142" "0313" "02212" "0133" "0211" "02313"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "01133" "0312" "0214" "0212" "0311" "02221"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "02221" "022312" "0211" "0143" "02212" "02234"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "0111" "0211" "02221" "0311" "02312" "0211"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "01222" "02222" "0212" "01133" "01211" "0212"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "0321" "01222" "01222" "0211" "01212" "02234"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "0212" "0211" "0211" "0311" "0142" "01121"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "01222" "0211" "0123" "02212" "01122" "02221"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "022312" "01123" "0211" "02211" "02233" "02232"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "02212" "0211" "02211" "0213" "0134" "02234"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "01312" "0322" "02222" "0211" "01132" "0311"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "02211" "0211" "01222" "0322" "0232" "01221"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "0211" "02221" "0211" "01122" "02221" "01212"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "0211" "0212" "0233" "01222" "0313" "01133"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "0134" "0211" "02212" "0212" "0211" "022311"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "0311" "02211" "0142" "0311" "0134" "0111"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "0211" "022313" "02221" "01212" "0311" "0314"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "02234" "0312" "02221" "0143" "01222" "0212"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "01123" "0111" "0211" "0141" "02211" "02234"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "0314" "01211" "0143" "0211" "0211" "0321"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "0111" "02212" "0312" "0142" "0141" "02312"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "0212" "0314" "02212" "0211" "01311" "0212"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "0232" "0312" "0323" "01312" "01132" "0142"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "0111" "0141" "01132" "0141" "0211" "0211"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "0212" "0111" "0322" "0212" "0211" "0211"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "012131" "0313" "033" "0311" "01224" "0212"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "02222" "02233" "0132" "0233" "0111" "0211"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "0311" "02211" "02211" "01225" "01123" "012131"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "0211" "02211" "02311" "02212" "01133" "022311"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "0314" "0211" "0311" "0322" "0233"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "0212" "01225" "01224" "0311" "0233" "0111"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "02211" "02223" "02223" "0212" "0321" "0212"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "0212" "0322" "01122" "02211" "01221" "0132"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "0211" "02222" "02232" "0212" "0232" "02221"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0132" "0211" "0212" "01313" "0311" "02232"
#> TCGA.74.6578.01
#> "0143"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3669))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "0312" "0212" "033" "02211" "033" "01222"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "02234" "0212" "0142" "0133" "0143" "02212"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "01132" "02311" "01131" "0313" "02312" "0312"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "01311" "022311" "01211" "0232" "02311" "0211"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "0312" "0212" "0111" "0313" "0212" "022311"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "0132" "0322" "01121" "0313" "033" "02234"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "02212" "01211" "02312" "02212" "0312" "0312"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "0313" "0111" "02211" "01213" "0311" "01132"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "01221" "01132" "033" "0212" "01212" "0312"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0143" "0111" "0211" "0212" "0211" "02212"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "0111" "0211" "01213" "0211" "0123" "0132"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "01224" "02311" "0111" "0142" "0311" "0211"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "0211" "0143" "0313" "02212" "01221" "0314"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "0314" "01132" "0321" "02211" "033" "02311"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "02211" "022311" "0312" "0211" "0211" "0233"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "0322" "02211" "0211" "0311" "0321" "0232"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "0314" "02212" "02222" "0111" "01132" "0141"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "0141" "0111" "02311" "0212" "0143" "0111"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "01211" "02211" "0323" "0213" "0211" "0212"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "0322" "01213" "0311" "0232" "0212" "01211"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "0133" "02234" "01131" "02211" "0312" "01123"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "01121" "0212" "0141" "02211" "0212" "02211"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "0211" "0233" "02234" "01132" "0311" "0213"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "0212" "01311" "0211" "0322" "02212" "0313"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "0133" "0123" "0322" "0323" "02234" "0142"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "0141" "01221" "0211" "0211" "0312" "0132"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "0143" "0211" "0211" "0312" "01211" "0212"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "0212" "02212" "0133" "0111" "02232" "02232"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "02311" "01312" "02222" "0133" "0212" "0314"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "0111" "01131" "0322" "0212" "0313" "0141"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "0212" "01213" "01225" "0211" "02212" "0212"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "0212" "0233" "02223" "0211" "02221" "0211"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "02211" "022311" "01212" "02232" "01121" "0212"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "02212" "01121" "0143" "0111" "01121" "0211"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "02311" "02233" "0211" "0111" "01123" "0134"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "01131" "0211" "022312" "02212" "0111" "0123"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "0314" "02222" "022311" "0123" "0211" "0211"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "0212" "0132" "0232" "0311" "01212" "0321"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "01121" "0133" "0211" "02223" "0321" "0212"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "02234" "01224" "0313" "01311" "02212" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "0141" "02312" "02211" "0313" "01121" "02211"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "0211" "02221" "02234" "022311" "01313" "0311"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "0312" "01213" "01225" "0321" "0313" "0211"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "0142" "0211" "033" "0233" "022312" "01311"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "0111" "0212" "0212" "0212" "0313" "0211"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "0111" "02221" "02211" "0111" "022312" "02221"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "01222" "0211" "01132" "02312" "0212" "01213"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "0211" "0213" "01221" "0211" "02212" "02221"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "0313" "0211" "0211" "0321" "0111" "0142"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "0211" "01213" "0314" "0313" "0212" "0211"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "0141" "0313" "0211" "0211" "0311" "0111"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "02211" "0232" "0211" "01211" "0141" "0312"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "0212" "0134" "01212" "0311" "0111" "0133"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "01213" "0211" "0321" "0232" "02222" "0133"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "01311" "01221" "02232" "0212" "0132" "0133"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "0211" "0322" "01222" "022311" "01311" "02221"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "0211" "01312" "0211" "0211" "0133" "01212"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "02211" "0313" "02211" "0311" "0214" "02234"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "01211" "0111" "022312" "0212" "01313" "0212"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "0212" "0211" "0134" "02311" "0134" "022311"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "01213" "01211" "02221" "0211" "02232" "01225"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "01121" "0111" "0111" "0312" "02221" "0143"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "0142" "0233" "0211" "0214" "0212" "0213"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "0111" "0143" "0232" "0133" "01123" "0211"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "0313" "0111" "0211" "0141" "01123" "02211"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "0111" "01132" "0141" "02212" "02233" "0211"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "0311" "0211" "0142" "02221" "01213" "01211"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "022311" "0312" "0312" "0211" "0143" "0211"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "01133" "0211" "02311" "0212" "0111" "01131"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "0233" "0313" "01122" "02233" "02211" "02211"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "01213" "0212" "01133" "0211" "01221" "01123"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "0111" "0212" "02211" "022312" "0141" "0111"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "0322" "0233" "0111" "0111" "0313" "02211"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "0311" "02222" "0312" "02221" "0314" "01222"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "0141" "01224" "0321" "01221" "01213" "0312"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "022312" "01211" "01222" "0211" "01211" "01131"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "01123" "02311" "0212" "01131" "0143" "02313"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "0111" "0211" "0314" "0212" "0212" "02222"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "01221" "0212" "022313" "01223" "01223" "01121"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "0142" "0313" "02212" "0133" "0211" "02313"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "01133" "0312" "0214" "0212" "0311" "02221"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "02221" "022312" "0211" "0143" "02212" "02234"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "0111" "0211" "02221" "0311" "02312" "0211"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "01222" "02222" "0212" "01133" "01211" "0212"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "0321" "01222" "01222" "0211" "01212" "02234"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "0212" "0211" "0211" "0311" "0142" "01121"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "01222" "0211" "0123" "02212" "01122" "02221"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "022312" "01123" "0211" "02211" "02233" "02232"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "02212" "0211" "02211" "0213" "0134" "02234"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "01312" "0322" "02222" "0211" "01132" "0311"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "02211" "0211" "01222" "0322" "0232" "01221"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "0211" "02221" "0211" "01122" "02221" "01212"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "0211" "0212" "0233" "01222" "0313" "01133"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "0134" "0211" "02212" "0212" "0211" "022311"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "0311" "02211" "0142" "0311" "0134" "0111"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "0211" "022313" "02221" "01212" "0311" "0314"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "02234" "0312" "02221" "0143" "01222" "0212"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "01123" "0111" "0211" "0141" "02211" "02234"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "0314" "01211" "0143" "0211" "0211" "0321"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "0111" "02212" "0312" "0142" "0141" "02312"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "0212" "0314" "02212" "0211" "01311" "0212"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "0232" "0312" "0323" "01312" "01132" "0142"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "0111" "0141" "01132" "0141" "0211" "0211"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "0212" "0111" "0322" "0212" "0211" "0211"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "01213" "0313" "033" "0311" "01224" "0212"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "02222" "02233" "0132" "0233" "0111" "0211"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "0311" "02211" "02211" "01225" "01123" "01213"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "0211" "02211" "02311" "02212" "01133" "022311"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "0314" "0211" "0311" "0322" "0233"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "0212" "01225" "01224" "0311" "0233" "0111"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "02211" "02223" "02223" "0212" "0321" "0212"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "0212" "0322" "01122" "02211" "01221" "0132"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "0211" "02222" "02232" "0212" "0232" "02221"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0132" "0211" "0212" "01313" "0311" "02232"
#> TCGA.74.6578.01
#> "0143"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3702))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "0312" "0212" "033" "0221" "033" "01222"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "02234" "0212" "0142" "0133" "0143" "0221"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "01132" "02311" "01131" "0313" "02312" "0312"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "01311" "022311" "01211" "0232" "02311" "0211"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "0312" "0212" "0111" "0313" "0212" "022311"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "0132" "0322" "01121" "0313" "033" "02234"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "0221" "01211" "02312" "0221" "0312" "0312"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "0313" "0111" "0221" "01213" "0311" "01132"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "01221" "01132" "033" "0212" "01212" "0312"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0143" "0111" "0211" "0212" "0211" "0221"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "0111" "0211" "01213" "0211" "0123" "0132"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "01224" "02311" "0111" "0142" "0311" "0211"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "0211" "0143" "0313" "0221" "01221" "0314"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "0314" "01132" "0321" "0221" "033" "02311"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "0221" "022311" "0312" "0211" "0211" "0233"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "0322" "0221" "0211" "0311" "0321" "0232"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "0314" "0221" "02222" "0111" "01132" "0141"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "0141" "0111" "02311" "0212" "0143" "0111"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "01211" "0221" "0323" "0213" "0211" "0212"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "0322" "01213" "0311" "0232" "0212" "01211"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "0133" "02234" "01131" "0221" "0312" "01123"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "01121" "0212" "0141" "0221" "0212" "0221"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "0211" "0233" "02234" "01132" "0311" "0213"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "0212" "01311" "0211" "0322" "0221" "0313"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "0133" "0123" "0322" "0323" "02234" "0142"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "0141" "01221" "0211" "0211" "0312" "0132"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "0143" "0211" "0211" "0312" "01211" "0212"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "0212" "0221" "0133" "0111" "02232" "02232"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "02311" "01312" "02222" "0133" "0212" "0314"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "0111" "01131" "0322" "0212" "0313" "0141"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "0212" "01213" "01225" "0211" "0221" "0212"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "0212" "0233" "02223" "0211" "02221" "0211"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "0221" "022311" "01212" "02232" "01121" "0212"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "0221" "01121" "0143" "0111" "01121" "0211"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "02311" "02233" "0211" "0111" "01123" "0134"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "01131" "0211" "022312" "0221" "0111" "0123"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "0314" "02222" "022311" "0123" "0211" "0211"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "0212" "0132" "0232" "0311" "01212" "0321"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "01121" "0133" "0211" "02223" "0321" "0212"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "02234" "01224" "0313" "01311" "0221" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "0141" "02312" "0221" "0313" "01121" "0221"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "0211" "02221" "02234" "022311" "01313" "0311"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "0312" "01213" "01225" "0321" "0313" "0211"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "0142" "0211" "033" "0233" "022312" "01311"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "0111" "0212" "0212" "0212" "0313" "0211"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "0111" "02221" "0221" "0111" "022312" "02221"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "01222" "0211" "01132" "02312" "0212" "01213"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "0211" "0213" "01221" "0211" "0221" "02221"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "0313" "0211" "0211" "0321" "0111" "0142"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "0211" "01213" "0314" "0313" "0212" "0211"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "0141" "0313" "0211" "0211" "0311" "0111"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "0221" "0232" "0211" "01211" "0141" "0312"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "0212" "0134" "01212" "0311" "0111" "0133"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "01213" "0211" "0321" "0232" "02222" "0133"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "01311" "01221" "02232" "0212" "0132" "0133"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "0211" "0322" "01222" "022311" "01311" "02221"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "0211" "01312" "0211" "0211" "0133" "01212"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "0221" "0313" "0221" "0311" "0214" "02234"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "01211" "0111" "022312" "0212" "01313" "0212"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "0212" "0211" "0134" "02311" "0134" "022311"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "01213" "01211" "02221" "0211" "02232" "01225"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "01121" "0111" "0111" "0312" "02221" "0143"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "0142" "0233" "0211" "0214" "0212" "0213"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "0111" "0143" "0232" "0133" "01123" "0211"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "0313" "0111" "0211" "0141" "01123" "0221"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "0111" "01132" "0141" "0221" "02233" "0211"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "0311" "0211" "0142" "02221" "01213" "01211"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "022311" "0312" "0312" "0211" "0143" "0211"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "01133" "0211" "02311" "0212" "0111" "01131"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "0233" "0313" "01122" "02233" "0221" "0221"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "01213" "0212" "01133" "0211" "01221" "01123"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "0111" "0212" "0221" "022312" "0141" "0111"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "0322" "0233" "0111" "0111" "0313" "0221"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "0311" "02222" "0312" "02221" "0314" "01222"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "0141" "01224" "0321" "01221" "01213" "0312"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "022312" "01211" "01222" "0211" "01211" "01131"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "01123" "02311" "0212" "01131" "0143" "02313"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "0111" "0211" "0314" "0212" "0212" "02222"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "01221" "0212" "022313" "01223" "01223" "01121"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "0142" "0313" "0221" "0133" "0211" "02313"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "01133" "0312" "0214" "0212" "0311" "02221"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "02221" "022312" "0211" "0143" "0221" "02234"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "0111" "0211" "02221" "0311" "02312" "0211"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "01222" "02222" "0212" "01133" "01211" "0212"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "0321" "01222" "01222" "0211" "01212" "02234"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "0212" "0211" "0211" "0311" "0142" "01121"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "01222" "0211" "0123" "0221" "01122" "02221"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "022312" "01123" "0211" "0221" "02233" "02232"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "0221" "0211" "0221" "0213" "0134" "02234"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "01312" "0322" "02222" "0211" "01132" "0311"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "0221" "0211" "01222" "0322" "0232" "01221"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "0211" "02221" "0211" "01122" "02221" "01212"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "0211" "0212" "0233" "01222" "0313" "01133"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "0134" "0211" "0221" "0212" "0211" "022311"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "0311" "0221" "0142" "0311" "0134" "0111"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "0211" "022313" "02221" "01212" "0311" "0314"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "02234" "0312" "02221" "0143" "01222" "0212"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "01123" "0111" "0211" "0141" "0221" "02234"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "0314" "01211" "0143" "0211" "0211" "0321"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "0111" "0221" "0312" "0142" "0141" "02312"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "0212" "0314" "0221" "0211" "01311" "0212"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "0232" "0312" "0323" "01312" "01132" "0142"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "0111" "0141" "01132" "0141" "0211" "0211"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "0212" "0111" "0322" "0212" "0211" "0211"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "01213" "0313" "033" "0311" "01224" "0212"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "02222" "02233" "0132" "0233" "0111" "0211"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "0311" "0221" "0221" "01225" "01123" "01213"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "0211" "0221" "02311" "0221" "01133" "022311"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "0314" "0211" "0311" "0322" "0233"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "0212" "01225" "01224" "0311" "0233" "0111"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "0221" "02223" "02223" "0212" "0321" "0212"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "0212" "0322" "01122" "0221" "01221" "0132"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "0211" "02222" "02232" "0212" "0232" "02221"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0132" "0211" "0212" "01313" "0311" "02232"
#> TCGA.74.6578.01
#> "0143"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3736))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "0312" "0212" "033" "0221" "033" "01222"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "02234" "0212" "0142" "0133" "0143" "0221"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "01132" "0231" "01131" "0313" "0231" "0312"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "01311" "022311" "01211" "0232" "0231" "0211"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "0312" "0212" "0111" "0313" "0212" "022311"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "0132" "0322" "01121" "0313" "033" "02234"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "0221" "01211" "0231" "0221" "0312" "0312"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "0313" "0111" "0221" "01213" "0311" "01132"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "01221" "01132" "033" "0212" "01212" "0312"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0143" "0111" "0211" "0212" "0211" "0221"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "0111" "0211" "01213" "0211" "0123" "0132"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "01224" "0231" "0111" "0142" "0311" "0211"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "0211" "0143" "0313" "0221" "01221" "0314"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "0314" "01132" "0321" "0221" "033" "0231"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "0221" "022311" "0312" "0211" "0211" "0233"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "0322" "0221" "0211" "0311" "0321" "0232"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "0314" "0221" "02222" "0111" "01132" "0141"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "0141" "0111" "0231" "0212" "0143" "0111"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "01211" "0221" "0323" "0213" "0211" "0212"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "0322" "01213" "0311" "0232" "0212" "01211"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "0133" "02234" "01131" "0221" "0312" "01123"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "01121" "0212" "0141" "0221" "0212" "0221"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "0211" "0233" "02234" "01132" "0311" "0213"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "0212" "01311" "0211" "0322" "0221" "0313"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "0133" "0123" "0322" "0323" "02234" "0142"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "0141" "01221" "0211" "0211" "0312" "0132"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "0143" "0211" "0211" "0312" "01211" "0212"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "0212" "0221" "0133" "0111" "02232" "02232"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "0231" "01312" "02222" "0133" "0212" "0314"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "0111" "01131" "0322" "0212" "0313" "0141"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "0212" "01213" "01225" "0211" "0221" "0212"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "0212" "0233" "02223" "0211" "02221" "0211"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "0221" "022311" "01212" "02232" "01121" "0212"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "0221" "01121" "0143" "0111" "01121" "0211"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "0231" "02233" "0211" "0111" "01123" "0134"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "01131" "0211" "022312" "0221" "0111" "0123"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "0314" "02222" "022311" "0123" "0211" "0211"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "0212" "0132" "0232" "0311" "01212" "0321"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "01121" "0133" "0211" "02223" "0321" "0212"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "02234" "01224" "0313" "01311" "0221" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "0141" "0231" "0221" "0313" "01121" "0221"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "0211" "02221" "02234" "022311" "01313" "0311"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "0312" "01213" "01225" "0321" "0313" "0211"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "0142" "0211" "033" "0233" "022312" "01311"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "0111" "0212" "0212" "0212" "0313" "0211"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "0111" "02221" "0221" "0111" "022312" "02221"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "01222" "0211" "01132" "0231" "0212" "01213"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "0211" "0213" "01221" "0211" "0221" "02221"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "0313" "0211" "0211" "0321" "0111" "0142"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "0211" "01213" "0314" "0313" "0212" "0211"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "0141" "0313" "0211" "0211" "0311" "0111"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "0221" "0232" "0211" "01211" "0141" "0312"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "0212" "0134" "01212" "0311" "0111" "0133"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "01213" "0211" "0321" "0232" "02222" "0133"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "01311" "01221" "02232" "0212" "0132" "0133"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "0211" "0322" "01222" "022311" "01311" "02221"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "0211" "01312" "0211" "0211" "0133" "01212"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "0221" "0313" "0221" "0311" "0214" "02234"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "01211" "0111" "022312" "0212" "01313" "0212"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "0212" "0211" "0134" "0231" "0134" "022311"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "01213" "01211" "02221" "0211" "02232" "01225"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "01121" "0111" "0111" "0312" "02221" "0143"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "0142" "0233" "0211" "0214" "0212" "0213"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "0111" "0143" "0232" "0133" "01123" "0211"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "0313" "0111" "0211" "0141" "01123" "0221"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "0111" "01132" "0141" "0221" "02233" "0211"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "0311" "0211" "0142" "02221" "01213" "01211"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "022311" "0312" "0312" "0211" "0143" "0211"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "01133" "0211" "0231" "0212" "0111" "01131"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "0233" "0313" "01122" "02233" "0221" "0221"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "01213" "0212" "01133" "0211" "01221" "01123"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "0111" "0212" "0221" "022312" "0141" "0111"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "0322" "0233" "0111" "0111" "0313" "0221"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "0311" "02222" "0312" "02221" "0314" "01222"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "0141" "01224" "0321" "01221" "01213" "0312"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "022312" "01211" "01222" "0211" "01211" "01131"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "01123" "0231" "0212" "01131" "0143" "0231"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "0111" "0211" "0314" "0212" "0212" "02222"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "01221" "0212" "022313" "01223" "01223" "01121"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "0142" "0313" "0221" "0133" "0211" "0231"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "01133" "0312" "0214" "0212" "0311" "02221"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "02221" "022312" "0211" "0143" "0221" "02234"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "0111" "0211" "02221" "0311" "0231" "0211"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "01222" "02222" "0212" "01133" "01211" "0212"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "0321" "01222" "01222" "0211" "01212" "02234"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "0212" "0211" "0211" "0311" "0142" "01121"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "01222" "0211" "0123" "0221" "01122" "02221"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "022312" "01123" "0211" "0221" "02233" "02232"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "0221" "0211" "0221" "0213" "0134" "02234"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "01312" "0322" "02222" "0211" "01132" "0311"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "0221" "0211" "01222" "0322" "0232" "01221"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "0211" "02221" "0211" "01122" "02221" "01212"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "0211" "0212" "0233" "01222" "0313" "01133"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "0134" "0211" "0221" "0212" "0211" "022311"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "0311" "0221" "0142" "0311" "0134" "0111"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "0211" "022313" "02221" "01212" "0311" "0314"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "02234" "0312" "02221" "0143" "01222" "0212"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "01123" "0111" "0211" "0141" "0221" "02234"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "0314" "01211" "0143" "0211" "0211" "0321"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "0111" "0221" "0312" "0142" "0141" "0231"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "0212" "0314" "0221" "0211" "01311" "0212"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "0232" "0312" "0323" "01312" "01132" "0142"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "0111" "0141" "01132" "0141" "0211" "0211"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "0212" "0111" "0322" "0212" "0211" "0211"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "01213" "0313" "033" "0311" "01224" "0212"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "02222" "02233" "0132" "0233" "0111" "0211"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "0311" "0221" "0221" "01225" "01123" "01213"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "0211" "0221" "0231" "0221" "01133" "022311"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "0314" "0211" "0311" "0322" "0233"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "0212" "01225" "01224" "0311" "0233" "0111"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "0221" "02223" "02223" "0212" "0321" "0212"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "0212" "0322" "01122" "0221" "01221" "0132"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "0211" "02222" "02232" "0212" "0232" "02221"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0132" "0211" "0212" "01313" "0311" "02232"
#> TCGA.74.6578.01
#> "0143"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3806))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "0312" "0212" "033" "022" "033" "01222"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "022" "0212" "0142" "0133" "0143" "022"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "01132" "0231" "01131" "0313" "0231" "0312"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "01311" "022311" "01211" "0232" "0231" "0211"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "0312" "0212" "0111" "0313" "0212" "022311"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "0132" "0322" "01121" "0313" "033" "022"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "022" "01211" "0231" "022" "0312" "0312"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "0313" "0111" "022" "01213" "0311" "01132"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "01221" "01132" "033" "0212" "01212" "0312"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0143" "0111" "0211" "0212" "0211" "022"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "0111" "0211" "01213" "0211" "0123" "0132"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "01224" "0231" "0111" "0142" "0311" "0211"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "0211" "0143" "0313" "022" "01221" "0314"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "0314" "01132" "0321" "022" "033" "0231"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "022" "022311" "0312" "0211" "0211" "0233"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "0322" "022" "0211" "0311" "0321" "0232"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "0314" "022" "022" "0111" "01132" "0141"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "0141" "0111" "0231" "0212" "0143" "0111"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "01211" "022" "0323" "0213" "0211" "0212"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "0322" "01213" "0311" "0232" "0212" "01211"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "0133" "022" "01131" "022" "0312" "01123"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "01121" "0212" "0141" "022" "0212" "022"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "0211" "0233" "022" "01132" "0311" "0213"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "0212" "01311" "0211" "0322" "022" "0313"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "0133" "0123" "0322" "0323" "022" "0142"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "0141" "01221" "0211" "0211" "0312" "0132"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "0143" "0211" "0211" "0312" "01211" "0212"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "0212" "022" "0133" "0111" "022" "022"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "0231" "01312" "022" "0133" "0212" "0314"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "0111" "01131" "0322" "0212" "0313" "0141"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "0212" "01213" "01225" "0211" "022" "0212"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "0212" "0233" "022" "0211" "022" "0211"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "022" "022311" "01212" "022" "01121" "0212"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "022" "01121" "0143" "0111" "01121" "0211"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "0231" "022" "0211" "0111" "01123" "0134"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "01131" "0211" "022312" "022" "0111" "0123"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "0314" "022" "022311" "0123" "0211" "0211"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "0212" "0132" "0232" "0311" "01212" "0321"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "01121" "0133" "0211" "022" "0321" "0212"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "022" "01224" "0313" "01311" "022" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "0141" "0231" "022" "0313" "01121" "022"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "0211" "022" "022" "022311" "01313" "0311"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "0312" "01213" "01225" "0321" "0313" "0211"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "0142" "0211" "033" "0233" "022312" "01311"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "0111" "0212" "0212" "0212" "0313" "0211"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "0111" "022" "022" "0111" "022312" "022"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "01222" "0211" "01132" "0231" "0212" "01213"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "0211" "0213" "01221" "0211" "022" "022"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "0313" "0211" "0211" "0321" "0111" "0142"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "0211" "01213" "0314" "0313" "0212" "0211"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "0141" "0313" "0211" "0211" "0311" "0111"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "022" "0232" "0211" "01211" "0141" "0312"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "0212" "0134" "01212" "0311" "0111" "0133"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "01213" "0211" "0321" "0232" "022" "0133"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "01311" "01221" "022" "0212" "0132" "0133"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "0211" "0322" "01222" "022311" "01311" "022"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "0211" "01312" "0211" "0211" "0133" "01212"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "022" "0313" "022" "0311" "0214" "022"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "01211" "0111" "022312" "0212" "01313" "0212"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "0212" "0211" "0134" "0231" "0134" "022311"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "01213" "01211" "022" "0211" "022" "01225"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "01121" "0111" "0111" "0312" "022" "0143"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "0142" "0233" "0211" "0214" "0212" "0213"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "0111" "0143" "0232" "0133" "01123" "0211"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "0313" "0111" "0211" "0141" "01123" "022"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "0111" "01132" "0141" "022" "022" "0211"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "0311" "0211" "0142" "022" "01213" "01211"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "022311" "0312" "0312" "0211" "0143" "0211"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "01133" "0211" "0231" "0212" "0111" "01131"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "0233" "0313" "01122" "022" "022" "022"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "01213" "0212" "01133" "0211" "01221" "01123"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "0111" "0212" "022" "022312" "0141" "0111"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "0322" "0233" "0111" "0111" "0313" "022"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "0311" "022" "0312" "022" "0314" "01222"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "0141" "01224" "0321" "01221" "01213" "0312"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "022312" "01211" "01222" "0211" "01211" "01131"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "01123" "0231" "0212" "01131" "0143" "0231"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "0111" "0211" "0314" "0212" "0212" "022"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "01221" "0212" "022313" "01223" "01223" "01121"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "0142" "0313" "022" "0133" "0211" "0231"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "01133" "0312" "0214" "0212" "0311" "022"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "022" "022312" "0211" "0143" "022" "022"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "0111" "0211" "022" "0311" "0231" "0211"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "01222" "022" "0212" "01133" "01211" "0212"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "0321" "01222" "01222" "0211" "01212" "022"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "0212" "0211" "0211" "0311" "0142" "01121"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "01222" "0211" "0123" "022" "01122" "022"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "022312" "01123" "0211" "022" "022" "022"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "022" "0211" "022" "0213" "0134" "022"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "01312" "0322" "022" "0211" "01132" "0311"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "022" "0211" "01222" "0322" "0232" "01221"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "0211" "022" "0211" "01122" "022" "01212"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "0211" "0212" "0233" "01222" "0313" "01133"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "0134" "0211" "022" "0212" "0211" "022311"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "0311" "022" "0142" "0311" "0134" "0111"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "0211" "022313" "022" "01212" "0311" "0314"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "022" "0312" "022" "0143" "01222" "0212"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "01123" "0111" "0211" "0141" "022" "022"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "0314" "01211" "0143" "0211" "0211" "0321"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "0111" "022" "0312" "0142" "0141" "0231"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "0212" "0314" "022" "0211" "01311" "0212"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "0232" "0312" "0323" "01312" "01132" "0142"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "0111" "0141" "01132" "0141" "0211" "0211"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "0212" "0111" "0322" "0212" "0211" "0211"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "01213" "0313" "033" "0311" "01224" "0212"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "022" "022" "0132" "0233" "0111" "0211"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "0311" "022" "022" "01225" "01123" "01213"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "0211" "022" "0231" "022" "01133" "022311"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "0314" "0211" "0311" "0322" "0233"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "0212" "01225" "01224" "0311" "0233" "0111"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "022" "022" "022" "0212" "0321" "0212"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "0212" "0322" "01122" "022" "01221" "0132"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "0211" "022" "022" "0212" "0232" "022"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0132" "0211" "0212" "01313" "0311" "022"
#> TCGA.74.6578.01
#> "0143"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3846))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "0312" "0212" "033" "022" "033" "01222"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "022" "0212" "0142" "0133" "0143" "022"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "01132" "0231" "01131" "0313" "0231" "0312"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "01311" "022311" "0121" "0232" "0231" "0211"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "0312" "0212" "0111" "0313" "0212" "022311"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "0132" "0322" "01121" "0313" "033" "022"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "022" "0121" "0231" "022" "0312" "0312"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "0313" "0111" "022" "0121" "0311" "01132"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "01221" "01132" "033" "0212" "0121" "0312"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0143" "0111" "0211" "0212" "0211" "022"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "0111" "0211" "0121" "0211" "0123" "0132"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "01224" "0231" "0111" "0142" "0311" "0211"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "0211" "0143" "0313" "022" "01221" "0314"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "0314" "01132" "0321" "022" "033" "0231"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "022" "022311" "0312" "0211" "0211" "0233"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "0322" "022" "0211" "0311" "0321" "0232"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "0314" "022" "022" "0111" "01132" "0141"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "0141" "0111" "0231" "0212" "0143" "0111"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "0121" "022" "0323" "0213" "0211" "0212"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "0322" "0121" "0311" "0232" "0212" "0121"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "0133" "022" "01131" "022" "0312" "01123"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "01121" "0212" "0141" "022" "0212" "022"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "0211" "0233" "022" "01132" "0311" "0213"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "0212" "01311" "0211" "0322" "022" "0313"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "0133" "0123" "0322" "0323" "022" "0142"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "0141" "01221" "0211" "0211" "0312" "0132"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "0143" "0211" "0211" "0312" "0121" "0212"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "0212" "022" "0133" "0111" "022" "022"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "0231" "01312" "022" "0133" "0212" "0314"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "0111" "01131" "0322" "0212" "0313" "0141"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "0212" "0121" "01225" "0211" "022" "0212"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "0212" "0233" "022" "0211" "022" "0211"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "022" "022311" "0121" "022" "01121" "0212"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "022" "01121" "0143" "0111" "01121" "0211"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "0231" "022" "0211" "0111" "01123" "0134"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "01131" "0211" "022312" "022" "0111" "0123"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "0314" "022" "022311" "0123" "0211" "0211"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "0212" "0132" "0232" "0311" "0121" "0321"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "01121" "0133" "0211" "022" "0321" "0212"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "022" "01224" "0313" "01311" "022" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "0141" "0231" "022" "0313" "01121" "022"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "0211" "022" "022" "022311" "01313" "0311"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "0312" "0121" "01225" "0321" "0313" "0211"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "0142" "0211" "033" "0233" "022312" "01311"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "0111" "0212" "0212" "0212" "0313" "0211"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "0111" "022" "022" "0111" "022312" "022"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "01222" "0211" "01132" "0231" "0212" "0121"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "0211" "0213" "01221" "0211" "022" "022"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "0313" "0211" "0211" "0321" "0111" "0142"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "0211" "0121" "0314" "0313" "0212" "0211"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "0141" "0313" "0211" "0211" "0311" "0111"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "022" "0232" "0211" "0121" "0141" "0312"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "0212" "0134" "0121" "0311" "0111" "0133"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "0121" "0211" "0321" "0232" "022" "0133"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "01311" "01221" "022" "0212" "0132" "0133"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "0211" "0322" "01222" "022311" "01311" "022"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "0211" "01312" "0211" "0211" "0133" "0121"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "022" "0313" "022" "0311" "0214" "022"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "0121" "0111" "022312" "0212" "01313" "0212"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "0212" "0211" "0134" "0231" "0134" "022311"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "0121" "0121" "022" "0211" "022" "01225"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "01121" "0111" "0111" "0312" "022" "0143"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "0142" "0233" "0211" "0214" "0212" "0213"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "0111" "0143" "0232" "0133" "01123" "0211"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "0313" "0111" "0211" "0141" "01123" "022"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "0111" "01132" "0141" "022" "022" "0211"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "0311" "0211" "0142" "022" "0121" "0121"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "022311" "0312" "0312" "0211" "0143" "0211"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "01133" "0211" "0231" "0212" "0111" "01131"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "0233" "0313" "01122" "022" "022" "022"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "0121" "0212" "01133" "0211" "01221" "01123"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "0111" "0212" "022" "022312" "0141" "0111"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "0322" "0233" "0111" "0111" "0313" "022"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "0311" "022" "0312" "022" "0314" "01222"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "0141" "01224" "0321" "01221" "0121" "0312"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "022312" "0121" "01222" "0211" "0121" "01131"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "01123" "0231" "0212" "01131" "0143" "0231"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "0111" "0211" "0314" "0212" "0212" "022"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "01221" "0212" "022313" "01223" "01223" "01121"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "0142" "0313" "022" "0133" "0211" "0231"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "01133" "0312" "0214" "0212" "0311" "022"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "022" "022312" "0211" "0143" "022" "022"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "0111" "0211" "022" "0311" "0231" "0211"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "01222" "022" "0212" "01133" "0121" "0212"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "0321" "01222" "01222" "0211" "0121" "022"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "0212" "0211" "0211" "0311" "0142" "01121"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "01222" "0211" "0123" "022" "01122" "022"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "022312" "01123" "0211" "022" "022" "022"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "022" "0211" "022" "0213" "0134" "022"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "01312" "0322" "022" "0211" "01132" "0311"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "022" "0211" "01222" "0322" "0232" "01221"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "0211" "022" "0211" "01122" "022" "0121"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "0211" "0212" "0233" "01222" "0313" "01133"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "0134" "0211" "022" "0212" "0211" "022311"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "0311" "022" "0142" "0311" "0134" "0111"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "0211" "022313" "022" "0121" "0311" "0314"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "022" "0312" "022" "0143" "01222" "0212"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "01123" "0111" "0211" "0141" "022" "022"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "0314" "0121" "0143" "0211" "0211" "0321"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "0111" "022" "0312" "0142" "0141" "0231"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "0212" "0314" "022" "0211" "01311" "0212"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "0232" "0312" "0323" "01312" "01132" "0142"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "0111" "0141" "01132" "0141" "0211" "0211"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "0212" "0111" "0322" "0212" "0211" "0211"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "0121" "0313" "033" "0311" "01224" "0212"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "022" "022" "0132" "0233" "0111" "0211"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "0311" "022" "022" "01225" "01123" "0121"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "0211" "022" "0231" "022" "01133" "022311"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "0314" "0211" "0311" "0322" "0233"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "0212" "01225" "01224" "0311" "0233" "0111"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "022" "022" "022" "0212" "0321" "0212"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "0212" "0322" "01122" "022" "01221" "0132"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "0211" "022" "022" "0212" "0232" "022"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0132" "0211" "0212" "01313" "0311" "022"
#> TCGA.74.6578.01
#> "0143"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3958))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "0312" "0212" "033" "022" "033" "01222"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "022" "0212" "0142" "0133" "0143" "022"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "01132" "0231" "01131" "0313" "0231" "0312"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "01311" "022311" "0121" "0232" "0231" "0211"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "0312" "0212" "0111" "0313" "0212" "022311"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "0132" "0322" "0112" "0313" "033" "022"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "022" "0121" "0231" "022" "0312" "0312"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "0313" "0111" "022" "0121" "0311" "01132"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "01221" "01132" "033" "0212" "0121" "0312"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0143" "0111" "0211" "0212" "0211" "022"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "0111" "0211" "0121" "0211" "0123" "0132"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "01224" "0231" "0111" "0142" "0311" "0211"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "0211" "0143" "0313" "022" "01221" "0314"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "0314" "01132" "0321" "022" "033" "0231"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "022" "022311" "0312" "0211" "0211" "0233"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "0322" "022" "0211" "0311" "0321" "0232"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "0314" "022" "022" "0111" "01132" "0141"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "0141" "0111" "0231" "0212" "0143" "0111"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "0121" "022" "0323" "0213" "0211" "0212"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "0322" "0121" "0311" "0232" "0212" "0121"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "0133" "022" "01131" "022" "0312" "0112"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "0112" "0212" "0141" "022" "0212" "022"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "0211" "0233" "022" "01132" "0311" "0213"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "0212" "01311" "0211" "0322" "022" "0313"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "0133" "0123" "0322" "0323" "022" "0142"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "0141" "01221" "0211" "0211" "0312" "0132"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "0143" "0211" "0211" "0312" "0121" "0212"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "0212" "022" "0133" "0111" "022" "022"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "0231" "01312" "022" "0133" "0212" "0314"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "0111" "01131" "0322" "0212" "0313" "0141"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "0212" "0121" "01225" "0211" "022" "0212"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "0212" "0233" "022" "0211" "022" "0211"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "022" "022311" "0121" "022" "0112" "0212"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "022" "0112" "0143" "0111" "0112" "0211"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "0231" "022" "0211" "0111" "0112" "0134"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "01131" "0211" "022312" "022" "0111" "0123"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "0314" "022" "022311" "0123" "0211" "0211"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "0212" "0132" "0232" "0311" "0121" "0321"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "0112" "0133" "0211" "022" "0321" "0212"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "022" "01224" "0313" "01311" "022" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "0141" "0231" "022" "0313" "0112" "022"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "0211" "022" "022" "022311" "01313" "0311"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "0312" "0121" "01225" "0321" "0313" "0211"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "0142" "0211" "033" "0233" "022312" "01311"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "0111" "0212" "0212" "0212" "0313" "0211"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "0111" "022" "022" "0111" "022312" "022"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "01222" "0211" "01132" "0231" "0212" "0121"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "0211" "0213" "01221" "0211" "022" "022"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "0313" "0211" "0211" "0321" "0111" "0142"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "0211" "0121" "0314" "0313" "0212" "0211"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "0141" "0313" "0211" "0211" "0311" "0111"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "022" "0232" "0211" "0121" "0141" "0312"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "0212" "0134" "0121" "0311" "0111" "0133"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "0121" "0211" "0321" "0232" "022" "0133"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "01311" "01221" "022" "0212" "0132" "0133"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "0211" "0322" "01222" "022311" "01311" "022"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "0211" "01312" "0211" "0211" "0133" "0121"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "022" "0313" "022" "0311" "0214" "022"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "0121" "0111" "022312" "0212" "01313" "0212"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "0212" "0211" "0134" "0231" "0134" "022311"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "0121" "0121" "022" "0211" "022" "01225"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "0112" "0111" "0111" "0312" "022" "0143"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "0142" "0233" "0211" "0214" "0212" "0213"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "0111" "0143" "0232" "0133" "0112" "0211"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "0313" "0111" "0211" "0141" "0112" "022"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "0111" "01132" "0141" "022" "022" "0211"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "0311" "0211" "0142" "022" "0121" "0121"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "022311" "0312" "0312" "0211" "0143" "0211"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "01133" "0211" "0231" "0212" "0111" "01131"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "0233" "0313" "0112" "022" "022" "022"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "0121" "0212" "01133" "0211" "01221" "0112"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "0111" "0212" "022" "022312" "0141" "0111"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "0322" "0233" "0111" "0111" "0313" "022"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "0311" "022" "0312" "022" "0314" "01222"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "0141" "01224" "0321" "01221" "0121" "0312"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "022312" "0121" "01222" "0211" "0121" "01131"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "0112" "0231" "0212" "01131" "0143" "0231"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "0111" "0211" "0314" "0212" "0212" "022"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "01221" "0212" "022313" "01223" "01223" "0112"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "0142" "0313" "022" "0133" "0211" "0231"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "01133" "0312" "0214" "0212" "0311" "022"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "022" "022312" "0211" "0143" "022" "022"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "0111" "0211" "022" "0311" "0231" "0211"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "01222" "022" "0212" "01133" "0121" "0212"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "0321" "01222" "01222" "0211" "0121" "022"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "0212" "0211" "0211" "0311" "0142" "0112"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "01222" "0211" "0123" "022" "0112" "022"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "022312" "0112" "0211" "022" "022" "022"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "022" "0211" "022" "0213" "0134" "022"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "01312" "0322" "022" "0211" "01132" "0311"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "022" "0211" "01222" "0322" "0232" "01221"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "0211" "022" "0211" "0112" "022" "0121"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "0211" "0212" "0233" "01222" "0313" "01133"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "0134" "0211" "022" "0212" "0211" "022311"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "0311" "022" "0142" "0311" "0134" "0111"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "0211" "022313" "022" "0121" "0311" "0314"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "022" "0312" "022" "0143" "01222" "0212"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "0112" "0111" "0211" "0141" "022" "022"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "0314" "0121" "0143" "0211" "0211" "0321"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "0111" "022" "0312" "0142" "0141" "0231"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "0212" "0314" "022" "0211" "01311" "0212"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "0232" "0312" "0323" "01312" "01132" "0142"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "0111" "0141" "01132" "0141" "0211" "0211"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "0212" "0111" "0322" "0212" "0211" "0211"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "0121" "0313" "033" "0311" "01224" "0212"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "022" "022" "0132" "0233" "0111" "0211"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "0311" "022" "022" "01225" "0112" "0121"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "0211" "022" "0231" "022" "01133" "022311"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "0314" "0211" "0311" "0322" "0233"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "0212" "01225" "01224" "0311" "0233" "0111"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "022" "022" "022" "0212" "0321" "0212"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "0212" "0322" "0112" "022" "01221" "0132"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "0211" "022" "022" "0212" "0232" "022"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0132" "0211" "0212" "01313" "0311" "022"
#> TCGA.74.6578.01
#> "0143"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4112))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "0312" "021" "033" "022" "033" "01222"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "022" "021" "0142" "0133" "0143" "022"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "01132" "0231" "01131" "0313" "0231" "0312"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "01311" "022311" "0121" "0232" "0231" "021"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "0312" "021" "0111" "0313" "021" "022311"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "0132" "0322" "0112" "0313" "033" "022"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "022" "0121" "0231" "022" "0312" "0312"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "0313" "0111" "022" "0121" "0311" "01132"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "01221" "01132" "033" "021" "0121" "0312"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0143" "0111" "021" "021" "021" "022"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "0111" "021" "0121" "021" "0123" "0132"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "01224" "0231" "0111" "0142" "0311" "021"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "021" "0143" "0313" "022" "01221" "0314"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "0314" "01132" "0321" "022" "033" "0231"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "022" "022311" "0312" "021" "021" "0233"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "0322" "022" "021" "0311" "0321" "0232"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "0314" "022" "022" "0111" "01132" "0141"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "0141" "0111" "0231" "021" "0143" "0111"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "0121" "022" "0323" "021" "021" "021"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "0322" "0121" "0311" "0232" "021" "0121"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "0133" "022" "01131" "022" "0312" "0112"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "0112" "021" "0141" "022" "021" "022"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "021" "0233" "022" "01132" "0311" "021"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "021" "01311" "021" "0322" "022" "0313"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "0133" "0123" "0322" "0323" "022" "0142"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "0141" "01221" "021" "021" "0312" "0132"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "0143" "021" "021" "0312" "0121" "021"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "021" "022" "0133" "0111" "022" "022"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "0231" "01312" "022" "0133" "021" "0314"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "0111" "01131" "0322" "021" "0313" "0141"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "021" "0121" "01225" "021" "022" "021"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "021" "0233" "022" "021" "022" "021"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "022" "022311" "0121" "022" "0112" "021"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "022" "0112" "0143" "0111" "0112" "021"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "0231" "022" "021" "0111" "0112" "0134"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "01131" "021" "022312" "022" "0111" "0123"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "0314" "022" "022311" "0123" "021" "021"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "021" "0132" "0232" "0311" "0121" "0321"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "0112" "0133" "021" "022" "0321" "021"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "022" "01224" "0313" "01311" "022" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "0141" "0231" "022" "0313" "0112" "022"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "021" "022" "022" "022311" "01313" "0311"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "0312" "0121" "01225" "0321" "0313" "021"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "0142" "021" "033" "0233" "022312" "01311"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "0111" "021" "021" "021" "0313" "021"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "0111" "022" "022" "0111" "022312" "022"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "01222" "021" "01132" "0231" "021" "0121"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "021" "021" "01221" "021" "022" "022"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "0313" "021" "021" "0321" "0111" "0142"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "021" "0121" "0314" "0313" "021" "021"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "0141" "0313" "021" "021" "0311" "0111"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "022" "0232" "021" "0121" "0141" "0312"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "021" "0134" "0121" "0311" "0111" "0133"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "0121" "021" "0321" "0232" "022" "0133"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "01311" "01221" "022" "021" "0132" "0133"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "021" "0322" "01222" "022311" "01311" "022"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "021" "01312" "021" "021" "0133" "0121"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "022" "0313" "022" "0311" "021" "022"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "0121" "0111" "022312" "021" "01313" "021"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "021" "021" "0134" "0231" "0134" "022311"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "0121" "0121" "022" "021" "022" "01225"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "0112" "0111" "0111" "0312" "022" "0143"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "0142" "0233" "021" "021" "021" "021"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "0111" "0143" "0232" "0133" "0112" "021"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "0313" "0111" "021" "0141" "0112" "022"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "0111" "01132" "0141" "022" "022" "021"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "0311" "021" "0142" "022" "0121" "0121"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "022311" "0312" "0312" "021" "0143" "021"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "01133" "021" "0231" "021" "0111" "01131"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "0233" "0313" "0112" "022" "022" "022"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "0121" "021" "01133" "021" "01221" "0112"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "0111" "021" "022" "022312" "0141" "0111"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "0322" "0233" "0111" "0111" "0313" "022"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "0311" "022" "0312" "022" "0314" "01222"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "0141" "01224" "0321" "01221" "0121" "0312"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "022312" "0121" "01222" "021" "0121" "01131"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "0112" "0231" "021" "01131" "0143" "0231"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "0111" "021" "0314" "021" "021" "022"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "01221" "021" "022313" "01223" "01223" "0112"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "0142" "0313" "022" "0133" "021" "0231"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "01133" "0312" "021" "021" "0311" "022"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "022" "022312" "021" "0143" "022" "022"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "0111" "021" "022" "0311" "0231" "021"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "01222" "022" "021" "01133" "0121" "021"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "0321" "01222" "01222" "021" "0121" "022"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "021" "021" "021" "0311" "0142" "0112"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "01222" "021" "0123" "022" "0112" "022"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "022312" "0112" "021" "022" "022" "022"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "022" "021" "022" "021" "0134" "022"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "01312" "0322" "022" "021" "01132" "0311"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "022" "021" "01222" "0322" "0232" "01221"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "021" "022" "021" "0112" "022" "0121"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "021" "021" "0233" "01222" "0313" "01133"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "0134" "021" "022" "021" "021" "022311"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "0311" "022" "0142" "0311" "0134" "0111"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "021" "022313" "022" "0121" "0311" "0314"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "022" "0312" "022" "0143" "01222" "021"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "0112" "0111" "021" "0141" "022" "022"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "0314" "0121" "0143" "021" "021" "0321"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "0111" "022" "0312" "0142" "0141" "0231"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "021" "0314" "022" "021" "01311" "021"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "0232" "0312" "0323" "01312" "01132" "0142"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "0111" "0141" "01132" "0141" "021" "021"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "021" "0111" "0322" "021" "021" "021"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "0121" "0313" "033" "0311" "01224" "021"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "022" "022" "0132" "0233" "0111" "021"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "0311" "022" "022" "01225" "0112" "0121"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "021" "022" "0231" "022" "01133" "022311"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "0314" "021" "0311" "0322" "0233"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "021" "01225" "01224" "0311" "0233" "0111"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "022" "022" "022" "021" "0321" "021"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "021" "0322" "0112" "022" "01221" "0132"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "021" "022" "022" "021" "0232" "022"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0132" "021" "021" "01313" "0311" "022"
#> TCGA.74.6578.01
#> "0143"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4199))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "0312" "021" "033" "022" "033" "01222"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "022" "021" "0142" "0133" "0143" "022"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "01132" "0231" "01131" "0313" "0231" "0312"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "01311" "022" "0121" "0232" "0231" "021"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "0312" "021" "0111" "0313" "021" "022"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "0132" "0322" "0112" "0313" "033" "022"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "022" "0121" "0231" "022" "0312" "0312"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "0313" "0111" "022" "0121" "0311" "01132"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "01221" "01132" "033" "021" "0121" "0312"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0143" "0111" "021" "021" "021" "022"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "0111" "021" "0121" "021" "0123" "0132"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "01224" "0231" "0111" "0142" "0311" "021"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "021" "0143" "0313" "022" "01221" "0314"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "0314" "01132" "0321" "022" "033" "0231"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "022" "022" "0312" "021" "021" "0233"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "0322" "022" "021" "0311" "0321" "0232"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "0314" "022" "022" "0111" "01132" "0141"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "0141" "0111" "0231" "021" "0143" "0111"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "0121" "022" "0323" "021" "021" "021"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "0322" "0121" "0311" "0232" "021" "0121"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "0133" "022" "01131" "022" "0312" "0112"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "0112" "021" "0141" "022" "021" "022"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "021" "0233" "022" "01132" "0311" "021"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "021" "01311" "021" "0322" "022" "0313"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "0133" "0123" "0322" "0323" "022" "0142"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "0141" "01221" "021" "021" "0312" "0132"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "0143" "021" "021" "0312" "0121" "021"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "021" "022" "0133" "0111" "022" "022"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "0231" "01312" "022" "0133" "021" "0314"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "0111" "01131" "0322" "021" "0313" "0141"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "021" "0121" "01225" "021" "022" "021"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "021" "0233" "022" "021" "022" "021"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "022" "022" "0121" "022" "0112" "021"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "022" "0112" "0143" "0111" "0112" "021"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "0231" "022" "021" "0111" "0112" "0134"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "01131" "021" "022" "022" "0111" "0123"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "0314" "022" "022" "0123" "021" "021"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "021" "0132" "0232" "0311" "0121" "0321"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "0112" "0133" "021" "022" "0321" "021"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "022" "01224" "0313" "01311" "022" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "0141" "0231" "022" "0313" "0112" "022"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "021" "022" "022" "022" "01313" "0311"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "0312" "0121" "01225" "0321" "0313" "021"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "0142" "021" "033" "0233" "022" "01311"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "0111" "021" "021" "021" "0313" "021"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "0111" "022" "022" "0111" "022" "022"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "01222" "021" "01132" "0231" "021" "0121"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "021" "021" "01221" "021" "022" "022"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "0313" "021" "021" "0321" "0111" "0142"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "021" "0121" "0314" "0313" "021" "021"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "0141" "0313" "021" "021" "0311" "0111"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "022" "0232" "021" "0121" "0141" "0312"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "021" "0134" "0121" "0311" "0111" "0133"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "0121" "021" "0321" "0232" "022" "0133"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "01311" "01221" "022" "021" "0132" "0133"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "021" "0322" "01222" "022" "01311" "022"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "021" "01312" "021" "021" "0133" "0121"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "022" "0313" "022" "0311" "021" "022"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "0121" "0111" "022" "021" "01313" "021"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "021" "021" "0134" "0231" "0134" "022"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "0121" "0121" "022" "021" "022" "01225"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "0112" "0111" "0111" "0312" "022" "0143"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "0142" "0233" "021" "021" "021" "021"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "0111" "0143" "0232" "0133" "0112" "021"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "0313" "0111" "021" "0141" "0112" "022"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "0111" "01132" "0141" "022" "022" "021"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "0311" "021" "0142" "022" "0121" "0121"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "022" "0312" "0312" "021" "0143" "021"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "01133" "021" "0231" "021" "0111" "01131"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "0233" "0313" "0112" "022" "022" "022"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "0121" "021" "01133" "021" "01221" "0112"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "0111" "021" "022" "022" "0141" "0111"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "0322" "0233" "0111" "0111" "0313" "022"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "0311" "022" "0312" "022" "0314" "01222"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "0141" "01224" "0321" "01221" "0121" "0312"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "022" "0121" "01222" "021" "0121" "01131"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "0112" "0231" "021" "01131" "0143" "0231"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "0111" "021" "0314" "021" "021" "022"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "01221" "021" "022" "01223" "01223" "0112"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "0142" "0313" "022" "0133" "021" "0231"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "01133" "0312" "021" "021" "0311" "022"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "022" "022" "021" "0143" "022" "022"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "0111" "021" "022" "0311" "0231" "021"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "01222" "022" "021" "01133" "0121" "021"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "0321" "01222" "01222" "021" "0121" "022"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "021" "021" "021" "0311" "0142" "0112"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "01222" "021" "0123" "022" "0112" "022"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "022" "0112" "021" "022" "022" "022"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "022" "021" "022" "021" "0134" "022"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "01312" "0322" "022" "021" "01132" "0311"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "022" "021" "01222" "0322" "0232" "01221"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "021" "022" "021" "0112" "022" "0121"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "021" "021" "0233" "01222" "0313" "01133"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "0134" "021" "022" "021" "021" "022"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "0311" "022" "0142" "0311" "0134" "0111"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "021" "022" "022" "0121" "0311" "0314"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "022" "0312" "022" "0143" "01222" "021"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "0112" "0111" "021" "0141" "022" "022"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "0314" "0121" "0143" "021" "021" "0321"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "0111" "022" "0312" "0142" "0141" "0231"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "021" "0314" "022" "021" "01311" "021"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "0232" "0312" "0323" "01312" "01132" "0142"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "0111" "0141" "01132" "0141" "021" "021"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "021" "0111" "0322" "021" "021" "021"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "0121" "0313" "033" "0311" "01224" "021"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "022" "022" "0132" "0233" "0111" "021"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "0311" "022" "022" "01225" "0112" "0121"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "021" "022" "0231" "022" "01133" "022"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "0314" "021" "0311" "0322" "0233"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "021" "01225" "01224" "0311" "0233" "0111"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "022" "022" "022" "021" "0321" "021"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "021" "0322" "0112" "022" "01221" "0132"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "021" "022" "022" "021" "0232" "022"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0132" "021" "021" "01313" "0311" "022"
#> TCGA.74.6578.01
#> "0143"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4915))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "0312" "021" "033" "022" "033" "01222"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "022" "021" "0142" "0133" "0143" "022"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "0113" "0231" "0113" "0313" "0231" "0312"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "01311" "022" "0121" "0232" "0231" "021"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "0312" "021" "0111" "0313" "021" "022"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "0132" "0322" "0112" "0313" "033" "022"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "022" "0121" "0231" "022" "0312" "0312"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "0313" "0111" "022" "0121" "0311" "0113"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "01221" "0113" "033" "021" "0121" "0312"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0143" "0111" "021" "021" "021" "022"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "0111" "021" "0121" "021" "0123" "0132"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "01224" "0231" "0111" "0142" "0311" "021"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "021" "0143" "0313" "022" "01221" "0314"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "0314" "0113" "0321" "022" "033" "0231"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "022" "022" "0312" "021" "021" "0233"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "0322" "022" "021" "0311" "0321" "0232"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "0314" "022" "022" "0111" "0113" "0141"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "0141" "0111" "0231" "021" "0143" "0111"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "0121" "022" "0323" "021" "021" "021"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "0322" "0121" "0311" "0232" "021" "0121"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "0133" "022" "0113" "022" "0312" "0112"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "0112" "021" "0141" "022" "021" "022"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "021" "0233" "022" "0113" "0311" "021"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "021" "01311" "021" "0322" "022" "0313"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "0133" "0123" "0322" "0323" "022" "0142"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "0141" "01221" "021" "021" "0312" "0132"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "0143" "021" "021" "0312" "0121" "021"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "021" "022" "0133" "0111" "022" "022"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "0231" "01312" "022" "0133" "021" "0314"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "0111" "0113" "0322" "021" "0313" "0141"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "021" "0121" "01225" "021" "022" "021"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "021" "0233" "022" "021" "022" "021"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "022" "022" "0121" "022" "0112" "021"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "022" "0112" "0143" "0111" "0112" "021"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "0231" "022" "021" "0111" "0112" "0134"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "0113" "021" "022" "022" "0111" "0123"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "0314" "022" "022" "0123" "021" "021"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "021" "0132" "0232" "0311" "0121" "0321"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "0112" "0133" "021" "022" "0321" "021"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "022" "01224" "0313" "01311" "022" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "0141" "0231" "022" "0313" "0112" "022"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "021" "022" "022" "022" "01313" "0311"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "0312" "0121" "01225" "0321" "0313" "021"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "0142" "021" "033" "0233" "022" "01311"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "0111" "021" "021" "021" "0313" "021"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "0111" "022" "022" "0111" "022" "022"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "01222" "021" "0113" "0231" "021" "0121"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "021" "021" "01221" "021" "022" "022"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "0313" "021" "021" "0321" "0111" "0142"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "021" "0121" "0314" "0313" "021" "021"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "0141" "0313" "021" "021" "0311" "0111"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "022" "0232" "021" "0121" "0141" "0312"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "021" "0134" "0121" "0311" "0111" "0133"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "0121" "021" "0321" "0232" "022" "0133"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "01311" "01221" "022" "021" "0132" "0133"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "021" "0322" "01222" "022" "01311" "022"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "021" "01312" "021" "021" "0133" "0121"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "022" "0313" "022" "0311" "021" "022"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "0121" "0111" "022" "021" "01313" "021"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "021" "021" "0134" "0231" "0134" "022"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "0121" "0121" "022" "021" "022" "01225"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "0112" "0111" "0111" "0312" "022" "0143"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "0142" "0233" "021" "021" "021" "021"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "0111" "0143" "0232" "0133" "0112" "021"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "0313" "0111" "021" "0141" "0112" "022"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "0111" "0113" "0141" "022" "022" "021"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "0311" "021" "0142" "022" "0121" "0121"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "022" "0312" "0312" "021" "0143" "021"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "0113" "021" "0231" "021" "0111" "0113"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "0233" "0313" "0112" "022" "022" "022"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "0121" "021" "0113" "021" "01221" "0112"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "0111" "021" "022" "022" "0141" "0111"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "0322" "0233" "0111" "0111" "0313" "022"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "0311" "022" "0312" "022" "0314" "01222"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "0141" "01224" "0321" "01221" "0121" "0312"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "022" "0121" "01222" "021" "0121" "0113"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "0112" "0231" "021" "0113" "0143" "0231"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "0111" "021" "0314" "021" "021" "022"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "01221" "021" "022" "01223" "01223" "0112"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "0142" "0313" "022" "0133" "021" "0231"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "0113" "0312" "021" "021" "0311" "022"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "022" "022" "021" "0143" "022" "022"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "0111" "021" "022" "0311" "0231" "021"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "01222" "022" "021" "0113" "0121" "021"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "0321" "01222" "01222" "021" "0121" "022"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "021" "021" "021" "0311" "0142" "0112"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "01222" "021" "0123" "022" "0112" "022"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "022" "0112" "021" "022" "022" "022"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "022" "021" "022" "021" "0134" "022"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "01312" "0322" "022" "021" "0113" "0311"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "022" "021" "01222" "0322" "0232" "01221"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "021" "022" "021" "0112" "022" "0121"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "021" "021" "0233" "01222" "0313" "0113"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "0134" "021" "022" "021" "021" "022"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "0311" "022" "0142" "0311" "0134" "0111"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "021" "022" "022" "0121" "0311" "0314"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "022" "0312" "022" "0143" "01222" "021"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "0112" "0111" "021" "0141" "022" "022"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "0314" "0121" "0143" "021" "021" "0321"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "0111" "022" "0312" "0142" "0141" "0231"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "021" "0314" "022" "021" "01311" "021"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "0232" "0312" "0323" "01312" "0113" "0142"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "0111" "0141" "0113" "0141" "021" "021"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "021" "0111" "0322" "021" "021" "021"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "0121" "0313" "033" "0311" "01224" "021"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "022" "022" "0132" "0233" "0111" "021"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "0311" "022" "022" "01225" "0112" "0121"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "021" "022" "0231" "022" "0113" "022"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "0314" "021" "0311" "0322" "0233"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "021" "01225" "01224" "0311" "0233" "0111"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "022" "022" "022" "021" "0321" "021"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "021" "0322" "0112" "022" "01221" "0132"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "021" "022" "022" "021" "0232" "022"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0132" "021" "021" "01313" "0311" "022"
#> TCGA.74.6578.01
#> "0143"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5006))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "0312" "021" "033" "022" "033" "01222"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "022" "021" "0142" "0133" "0143" "022"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "0113" "0231" "0113" "0313" "0231" "0312"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "0131" "022" "0121" "0232" "0231" "021"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "0312" "021" "0111" "0313" "021" "022"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "0132" "0322" "0112" "0313" "033" "022"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "022" "0121" "0231" "022" "0312" "0312"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "0313" "0111" "022" "0121" "0311" "0113"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "01221" "0113" "033" "021" "0121" "0312"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0143" "0111" "021" "021" "021" "022"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "0111" "021" "0121" "021" "0123" "0132"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "01224" "0231" "0111" "0142" "0311" "021"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "021" "0143" "0313" "022" "01221" "0314"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "0314" "0113" "0321" "022" "033" "0231"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "022" "022" "0312" "021" "021" "0233"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "0322" "022" "021" "0311" "0321" "0232"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "0314" "022" "022" "0111" "0113" "0141"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "0141" "0111" "0231" "021" "0143" "0111"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "0121" "022" "0323" "021" "021" "021"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "0322" "0121" "0311" "0232" "021" "0121"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "0133" "022" "0113" "022" "0312" "0112"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "0112" "021" "0141" "022" "021" "022"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "021" "0233" "022" "0113" "0311" "021"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "021" "0131" "021" "0322" "022" "0313"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "0133" "0123" "0322" "0323" "022" "0142"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "0141" "01221" "021" "021" "0312" "0132"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "0143" "021" "021" "0312" "0121" "021"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "021" "022" "0133" "0111" "022" "022"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "0231" "0131" "022" "0133" "021" "0314"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "0111" "0113" "0322" "021" "0313" "0141"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "021" "0121" "01225" "021" "022" "021"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "021" "0233" "022" "021" "022" "021"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "022" "022" "0121" "022" "0112" "021"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "022" "0112" "0143" "0111" "0112" "021"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "0231" "022" "021" "0111" "0112" "0134"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "0113" "021" "022" "022" "0111" "0123"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "0314" "022" "022" "0123" "021" "021"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "021" "0132" "0232" "0311" "0121" "0321"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "0112" "0133" "021" "022" "0321" "021"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "022" "01224" "0313" "0131" "022" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "0141" "0231" "022" "0313" "0112" "022"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "021" "022" "022" "022" "0131" "0311"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "0312" "0121" "01225" "0321" "0313" "021"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "0142" "021" "033" "0233" "022" "0131"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "0111" "021" "021" "021" "0313" "021"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "0111" "022" "022" "0111" "022" "022"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "01222" "021" "0113" "0231" "021" "0121"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "021" "021" "01221" "021" "022" "022"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "0313" "021" "021" "0321" "0111" "0142"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "021" "0121" "0314" "0313" "021" "021"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "0141" "0313" "021" "021" "0311" "0111"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "022" "0232" "021" "0121" "0141" "0312"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "021" "0134" "0121" "0311" "0111" "0133"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "0121" "021" "0321" "0232" "022" "0133"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "0131" "01221" "022" "021" "0132" "0133"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "021" "0322" "01222" "022" "0131" "022"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "021" "0131" "021" "021" "0133" "0121"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "022" "0313" "022" "0311" "021" "022"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "0121" "0111" "022" "021" "0131" "021"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "021" "021" "0134" "0231" "0134" "022"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "0121" "0121" "022" "021" "022" "01225"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "0112" "0111" "0111" "0312" "022" "0143"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "0142" "0233" "021" "021" "021" "021"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "0111" "0143" "0232" "0133" "0112" "021"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "0313" "0111" "021" "0141" "0112" "022"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "0111" "0113" "0141" "022" "022" "021"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "0311" "021" "0142" "022" "0121" "0121"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "022" "0312" "0312" "021" "0143" "021"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "0113" "021" "0231" "021" "0111" "0113"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "0233" "0313" "0112" "022" "022" "022"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "0121" "021" "0113" "021" "01221" "0112"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "0111" "021" "022" "022" "0141" "0111"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "0322" "0233" "0111" "0111" "0313" "022"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "0311" "022" "0312" "022" "0314" "01222"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "0141" "01224" "0321" "01221" "0121" "0312"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "022" "0121" "01222" "021" "0121" "0113"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "0112" "0231" "021" "0113" "0143" "0231"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "0111" "021" "0314" "021" "021" "022"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "01221" "021" "022" "01223" "01223" "0112"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "0142" "0313" "022" "0133" "021" "0231"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "0113" "0312" "021" "021" "0311" "022"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "022" "022" "021" "0143" "022" "022"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "0111" "021" "022" "0311" "0231" "021"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "01222" "022" "021" "0113" "0121" "021"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "0321" "01222" "01222" "021" "0121" "022"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "021" "021" "021" "0311" "0142" "0112"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "01222" "021" "0123" "022" "0112" "022"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "022" "0112" "021" "022" "022" "022"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "022" "021" "022" "021" "0134" "022"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "0131" "0322" "022" "021" "0113" "0311"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "022" "021" "01222" "0322" "0232" "01221"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "021" "022" "021" "0112" "022" "0121"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "021" "021" "0233" "01222" "0313" "0113"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "0134" "021" "022" "021" "021" "022"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "0311" "022" "0142" "0311" "0134" "0111"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "021" "022" "022" "0121" "0311" "0314"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "022" "0312" "022" "0143" "01222" "021"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "0112" "0111" "021" "0141" "022" "022"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "0314" "0121" "0143" "021" "021" "0321"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "0111" "022" "0312" "0142" "0141" "0231"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "021" "0314" "022" "021" "0131" "021"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "0232" "0312" "0323" "0131" "0113" "0142"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "0111" "0141" "0113" "0141" "021" "021"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "021" "0111" "0322" "021" "021" "021"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "0121" "0313" "033" "0311" "01224" "021"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "022" "022" "0132" "0233" "0111" "021"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "0311" "022" "022" "01225" "0112" "0121"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "021" "022" "0231" "022" "0113" "022"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "0314" "021" "0311" "0322" "0233"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "021" "01225" "01224" "0311" "0233" "0111"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "022" "022" "022" "021" "0321" "021"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "021" "0322" "0112" "022" "01221" "0132"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "021" "022" "022" "021" "0232" "022"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0132" "021" "021" "0131" "0311" "022"
#> TCGA.74.6578.01
#> "0143"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5899))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "031" "021" "033" "022" "033" "01222"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "022" "021" "0142" "0133" "0143" "022"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "0113" "0231" "0113" "031" "0231" "031"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "0131" "022" "0121" "0232" "0231" "021"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "031" "021" "0111" "031" "021" "022"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "0132" "0322" "0112" "031" "033" "022"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "022" "0121" "0231" "022" "031" "031"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "031" "0111" "022" "0121" "031" "0113"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "01221" "0113" "033" "021" "0121" "031"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0143" "0111" "021" "021" "021" "022"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "0111" "021" "0121" "021" "0123" "0132"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "01224" "0231" "0111" "0142" "031" "021"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "021" "0143" "031" "022" "01221" "031"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "031" "0113" "0321" "022" "033" "0231"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "022" "022" "031" "021" "021" "0233"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "0322" "022" "021" "031" "0321" "0232"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "031" "022" "022" "0111" "0113" "0141"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "0141" "0111" "0231" "021" "0143" "0111"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "0121" "022" "0323" "021" "021" "021"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "0322" "0121" "031" "0232" "021" "0121"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "0133" "022" "0113" "022" "031" "0112"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "0112" "021" "0141" "022" "021" "022"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "021" "0233" "022" "0113" "031" "021"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "021" "0131" "021" "0322" "022" "031"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "0133" "0123" "0322" "0323" "022" "0142"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "0141" "01221" "021" "021" "031" "0132"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "0143" "021" "021" "031" "0121" "021"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "021" "022" "0133" "0111" "022" "022"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "0231" "0131" "022" "0133" "021" "031"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "0111" "0113" "0322" "021" "031" "0141"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "021" "0121" "01225" "021" "022" "021"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "021" "0233" "022" "021" "022" "021"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "022" "022" "0121" "022" "0112" "021"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "022" "0112" "0143" "0111" "0112" "021"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "0231" "022" "021" "0111" "0112" "0134"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "0113" "021" "022" "022" "0111" "0123"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "031" "022" "022" "0123" "021" "021"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "021" "0132" "0232" "031" "0121" "0321"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "0112" "0133" "021" "022" "0321" "021"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "022" "01224" "031" "0131" "022" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "0141" "0231" "022" "031" "0112" "022"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "021" "022" "022" "022" "0131" "031"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "031" "0121" "01225" "0321" "031" "021"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "0142" "021" "033" "0233" "022" "0131"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "0111" "021" "021" "021" "031" "021"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "0111" "022" "022" "0111" "022" "022"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "01222" "021" "0113" "0231" "021" "0121"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "021" "021" "01221" "021" "022" "022"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "031" "021" "021" "0321" "0111" "0142"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "021" "0121" "031" "031" "021" "021"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "0141" "031" "021" "021" "031" "0111"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "022" "0232" "021" "0121" "0141" "031"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "021" "0134" "0121" "031" "0111" "0133"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "0121" "021" "0321" "0232" "022" "0133"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "0131" "01221" "022" "021" "0132" "0133"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "021" "0322" "01222" "022" "0131" "022"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "021" "0131" "021" "021" "0133" "0121"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "022" "031" "022" "031" "021" "022"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "0121" "0111" "022" "021" "0131" "021"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "021" "021" "0134" "0231" "0134" "022"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "0121" "0121" "022" "021" "022" "01225"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "0112" "0111" "0111" "031" "022" "0143"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "0142" "0233" "021" "021" "021" "021"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "0111" "0143" "0232" "0133" "0112" "021"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "031" "0111" "021" "0141" "0112" "022"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "0111" "0113" "0141" "022" "022" "021"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "031" "021" "0142" "022" "0121" "0121"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "022" "031" "031" "021" "0143" "021"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "0113" "021" "0231" "021" "0111" "0113"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "0233" "031" "0112" "022" "022" "022"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "0121" "021" "0113" "021" "01221" "0112"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "0111" "021" "022" "022" "0141" "0111"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "0322" "0233" "0111" "0111" "031" "022"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "031" "022" "031" "022" "031" "01222"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "0141" "01224" "0321" "01221" "0121" "031"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "022" "0121" "01222" "021" "0121" "0113"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "0112" "0231" "021" "0113" "0143" "0231"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "0111" "021" "031" "021" "021" "022"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "01221" "021" "022" "01223" "01223" "0112"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "0142" "031" "022" "0133" "021" "0231"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "0113" "031" "021" "021" "031" "022"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "022" "022" "021" "0143" "022" "022"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "0111" "021" "022" "031" "0231" "021"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "01222" "022" "021" "0113" "0121" "021"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "0321" "01222" "01222" "021" "0121" "022"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "021" "021" "021" "031" "0142" "0112"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "01222" "021" "0123" "022" "0112" "022"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "022" "0112" "021" "022" "022" "022"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "022" "021" "022" "021" "0134" "022"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "0131" "0322" "022" "021" "0113" "031"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "022" "021" "01222" "0322" "0232" "01221"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "021" "022" "021" "0112" "022" "0121"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "021" "021" "0233" "01222" "031" "0113"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "0134" "021" "022" "021" "021" "022"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "031" "022" "0142" "031" "0134" "0111"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "021" "022" "022" "0121" "031" "031"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "022" "031" "022" "0143" "01222" "021"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "0112" "0111" "021" "0141" "022" "022"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "031" "0121" "0143" "021" "021" "0321"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "0111" "022" "031" "0142" "0141" "0231"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "021" "031" "022" "021" "0131" "021"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "0232" "031" "0323" "0131" "0113" "0142"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "0111" "0141" "0113" "0141" "021" "021"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "021" "0111" "0322" "021" "021" "021"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "0121" "031" "033" "031" "01224" "021"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "022" "022" "0132" "0233" "0111" "021"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "031" "022" "022" "01225" "0112" "0121"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "021" "022" "0231" "022" "0113" "022"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "031" "021" "031" "0322" "0233"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "021" "01225" "01224" "031" "0233" "0111"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "022" "022" "022" "021" "0321" "021"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "021" "0322" "0112" "022" "01221" "0132"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "021" "022" "022" "021" "0232" "022"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0132" "021" "021" "0131" "031" "022"
#> TCGA.74.6578.01
#> "0143"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6182))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "031" "021" "033" "022" "033" "012"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "022" "021" "0142" "0133" "0143" "022"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "0113" "0231" "0113" "031" "0231" "031"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "0131" "022" "012" "0232" "0231" "021"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "031" "021" "0111" "031" "021" "022"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "0132" "0322" "0112" "031" "033" "022"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "022" "012" "0231" "022" "031" "031"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "031" "0111" "022" "012" "031" "0113"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "012" "0113" "033" "021" "012" "031"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0143" "0111" "021" "021" "021" "022"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "0111" "021" "012" "021" "012" "0132"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "012" "0231" "0111" "0142" "031" "021"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "021" "0143" "031" "022" "012" "031"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "031" "0113" "0321" "022" "033" "0231"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "022" "022" "031" "021" "021" "0233"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "0322" "022" "021" "031" "0321" "0232"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "031" "022" "022" "0111" "0113" "0141"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "0141" "0111" "0231" "021" "0143" "0111"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "012" "022" "0323" "021" "021" "021"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "0322" "012" "031" "0232" "021" "012"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "0133" "022" "0113" "022" "031" "0112"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "0112" "021" "0141" "022" "021" "022"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "021" "0233" "022" "0113" "031" "021"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "021" "0131" "021" "0322" "022" "031"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "0133" "012" "0322" "0323" "022" "0142"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "0141" "012" "021" "021" "031" "0132"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "0143" "021" "021" "031" "012" "021"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "021" "022" "0133" "0111" "022" "022"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "0231" "0131" "022" "0133" "021" "031"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "0111" "0113" "0322" "021" "031" "0141"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "021" "012" "012" "021" "022" "021"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "021" "0233" "022" "021" "022" "021"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "022" "022" "012" "022" "0112" "021"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "022" "0112" "0143" "0111" "0112" "021"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "0231" "022" "021" "0111" "0112" "0134"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "0113" "021" "022" "022" "0111" "012"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "031" "022" "022" "012" "021" "021"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "021" "0132" "0232" "031" "012" "0321"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "0112" "0133" "021" "022" "0321" "021"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "022" "012" "031" "0131" "022" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "0141" "0231" "022" "031" "0112" "022"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "021" "022" "022" "022" "0131" "031"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "031" "012" "012" "0321" "031" "021"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "0142" "021" "033" "0233" "022" "0131"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "0111" "021" "021" "021" "031" "021"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "0111" "022" "022" "0111" "022" "022"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "012" "021" "0113" "0231" "021" "012"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "021" "021" "012" "021" "022" "022"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "031" "021" "021" "0321" "0111" "0142"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "021" "012" "031" "031" "021" "021"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "0141" "031" "021" "021" "031" "0111"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "022" "0232" "021" "012" "0141" "031"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "021" "0134" "012" "031" "0111" "0133"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "012" "021" "0321" "0232" "022" "0133"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "0131" "012" "022" "021" "0132" "0133"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "021" "0322" "012" "022" "0131" "022"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "021" "0131" "021" "021" "0133" "012"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "022" "031" "022" "031" "021" "022"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "012" "0111" "022" "021" "0131" "021"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "021" "021" "0134" "0231" "0134" "022"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "012" "012" "022" "021" "022" "012"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "0112" "0111" "0111" "031" "022" "0143"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "0142" "0233" "021" "021" "021" "021"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "0111" "0143" "0232" "0133" "0112" "021"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "031" "0111" "021" "0141" "0112" "022"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "0111" "0113" "0141" "022" "022" "021"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "031" "021" "0142" "022" "012" "012"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "022" "031" "031" "021" "0143" "021"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "0113" "021" "0231" "021" "0111" "0113"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "0233" "031" "0112" "022" "022" "022"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "012" "021" "0113" "021" "012" "0112"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "0111" "021" "022" "022" "0141" "0111"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "0322" "0233" "0111" "0111" "031" "022"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "031" "022" "031" "022" "031" "012"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "0141" "012" "0321" "012" "012" "031"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "022" "012" "012" "021" "012" "0113"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "0112" "0231" "021" "0113" "0143" "0231"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "0111" "021" "031" "021" "021" "022"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "012" "021" "022" "012" "012" "0112"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "0142" "031" "022" "0133" "021" "0231"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "0113" "031" "021" "021" "031" "022"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "022" "022" "021" "0143" "022" "022"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "0111" "021" "022" "031" "0231" "021"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "012" "022" "021" "0113" "012" "021"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "0321" "012" "012" "021" "012" "022"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "021" "021" "021" "031" "0142" "0112"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "012" "021" "012" "022" "0112" "022"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "022" "0112" "021" "022" "022" "022"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "022" "021" "022" "021" "0134" "022"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "0131" "0322" "022" "021" "0113" "031"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "022" "021" "012" "0322" "0232" "012"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "021" "022" "021" "0112" "022" "012"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "021" "021" "0233" "012" "031" "0113"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "0134" "021" "022" "021" "021" "022"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "031" "022" "0142" "031" "0134" "0111"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "021" "022" "022" "012" "031" "031"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "022" "031" "022" "0143" "012" "021"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "0112" "0111" "021" "0141" "022" "022"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "031" "012" "0143" "021" "021" "0321"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "0111" "022" "031" "0142" "0141" "0231"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "021" "031" "022" "021" "0131" "021"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "0232" "031" "0323" "0131" "0113" "0142"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "0111" "0141" "0113" "0141" "021" "021"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "021" "0111" "0322" "021" "021" "021"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "012" "031" "033" "031" "012" "021"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "022" "022" "0132" "0233" "0111" "021"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "031" "022" "022" "012" "0112" "012"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "021" "022" "0231" "022" "0113" "022"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "031" "021" "031" "0322" "0233"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "021" "012" "012" "031" "0233" "0111"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "022" "022" "022" "021" "0321" "021"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "021" "0322" "0112" "022" "012" "0132"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "021" "022" "022" "021" "0232" "022"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0132" "021" "021" "0131" "031" "022"
#> TCGA.74.6578.01
#> "0143"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7856))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "031" "021" "033" "022" "033" "012"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "022" "021" "0142" "0133" "0143" "022"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "0113" "0231" "0113" "031" "0231" "031"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "0131" "022" "012" "0232" "0231" "021"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "031" "021" "0111" "031" "021" "022"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "0132" "0322" "0112" "031" "033" "022"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "022" "012" "0231" "022" "031" "031"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "031" "0111" "022" "012" "031" "0113"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "012" "0113" "033" "021" "012" "031"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0143" "0111" "021" "021" "021" "022"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "0111" "021" "012" "021" "012" "0132"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "012" "0231" "0111" "0142" "031" "021"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "021" "0143" "031" "022" "012" "031"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "031" "0113" "0321" "022" "033" "0231"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "022" "022" "031" "021" "021" "0233"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "0322" "022" "021" "031" "0321" "0232"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "031" "022" "022" "0111" "0113" "0141"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "0141" "0111" "0231" "021" "0143" "0111"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "012" "022" "0323" "021" "021" "021"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "0322" "012" "031" "0232" "021" "012"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "0133" "022" "0113" "022" "031" "0112"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "0112" "021" "0141" "022" "021" "022"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "021" "0233" "022" "0113" "031" "021"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "021" "0131" "021" "0322" "022" "031"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "0133" "012" "0322" "0323" "022" "0142"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "0141" "012" "021" "021" "031" "0132"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "0143" "021" "021" "031" "012" "021"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "021" "022" "0133" "0111" "022" "022"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "0231" "0131" "022" "0133" "021" "031"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "0111" "0113" "0322" "021" "031" "0141"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "021" "012" "012" "021" "022" "021"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "021" "0233" "022" "021" "022" "021"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "022" "022" "012" "022" "0112" "021"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "022" "0112" "0143" "0111" "0112" "021"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "0231" "022" "021" "0111" "0112" "0134"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "0113" "021" "022" "022" "0111" "012"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "031" "022" "022" "012" "021" "021"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "021" "0132" "0232" "031" "012" "0321"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "0112" "0133" "021" "022" "0321" "021"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "022" "012" "031" "0131" "022" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "0141" "0231" "022" "031" "0112" "022"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "021" "022" "022" "022" "0131" "031"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "031" "012" "012" "0321" "031" "021"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "0142" "021" "033" "0233" "022" "0131"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "0111" "021" "021" "021" "031" "021"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "0111" "022" "022" "0111" "022" "022"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "012" "021" "0113" "0231" "021" "012"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "021" "021" "012" "021" "022" "022"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "031" "021" "021" "0321" "0111" "0142"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "021" "012" "031" "031" "021" "021"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "0141" "031" "021" "021" "031" "0111"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "022" "0232" "021" "012" "0141" "031"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "021" "0134" "012" "031" "0111" "0133"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "012" "021" "0321" "0232" "022" "0133"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "0131" "012" "022" "021" "0132" "0133"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "021" "0322" "012" "022" "0131" "022"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "021" "0131" "021" "021" "0133" "012"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "022" "031" "022" "031" "021" "022"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "012" "0111" "022" "021" "0131" "021"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "021" "021" "0134" "0231" "0134" "022"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "012" "012" "022" "021" "022" "012"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "0112" "0111" "0111" "031" "022" "0143"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "0142" "0233" "021" "021" "021" "021"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "0111" "0143" "0232" "0133" "0112" "021"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "031" "0111" "021" "0141" "0112" "022"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "0111" "0113" "0141" "022" "022" "021"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "031" "021" "0142" "022" "012" "012"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "022" "031" "031" "021" "0143" "021"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "0113" "021" "0231" "021" "0111" "0113"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "0233" "031" "0112" "022" "022" "022"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "012" "021" "0113" "021" "012" "0112"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "0111" "021" "022" "022" "0141" "0111"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "0322" "0233" "0111" "0111" "031" "022"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "031" "022" "031" "022" "031" "012"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "0141" "012" "0321" "012" "012" "031"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "022" "012" "012" "021" "012" "0113"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "0112" "0231" "021" "0113" "0143" "0231"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "0111" "021" "031" "021" "021" "022"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "012" "021" "022" "012" "012" "0112"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "0142" "031" "022" "0133" "021" "0231"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "0113" "031" "021" "021" "031" "022"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "022" "022" "021" "0143" "022" "022"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "0111" "021" "022" "031" "0231" "021"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "012" "022" "021" "0113" "012" "021"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "0321" "012" "012" "021" "012" "022"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "021" "021" "021" "031" "0142" "0112"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "012" "021" "012" "022" "0112" "022"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "022" "0112" "021" "022" "022" "022"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "022" "021" "022" "021" "0134" "022"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "0131" "0322" "022" "021" "0113" "031"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "022" "021" "012" "0322" "0232" "012"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "021" "022" "021" "0112" "022" "012"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "021" "021" "0233" "012" "031" "0113"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "0134" "021" "022" "021" "021" "022"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "031" "022" "0142" "031" "0134" "0111"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "021" "022" "022" "012" "031" "031"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "022" "031" "022" "0143" "012" "021"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "0112" "0111" "021" "0141" "022" "022"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "031" "012" "0143" "021" "021" "0321"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "0111" "022" "031" "0142" "0141" "0231"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "021" "031" "022" "021" "0131" "021"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "0232" "031" "0323" "0131" "0113" "0142"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "0111" "0141" "0113" "0141" "021" "021"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "021" "0111" "0322" "021" "021" "021"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "012" "031" "033" "031" "012" "021"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "022" "022" "0132" "0233" "0111" "021"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "031" "022" "022" "012" "0112" "012"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "021" "022" "0231" "022" "0113" "022"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "031" "021" "031" "0322" "0233"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "021" "012" "012" "031" "0233" "0111"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "022" "022" "022" "021" "0321" "021"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "021" "0322" "0112" "022" "012" "0132"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "021" "022" "022" "021" "0232" "022"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0132" "021" "021" "0131" "031" "022"
#> TCGA.74.6578.01
#> "0143"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7999))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "031" "02" "033" "02" "033" "012"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "02" "02" "0142" "0133" "0143" "02"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "0113" "02" "0113" "031" "02" "031"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "0131" "02" "012" "02" "02" "02"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "031" "02" "0111" "031" "02" "02"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "0132" "0322" "0112" "031" "033" "02"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "02" "012" "02" "02" "031" "031"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "031" "0111" "02" "012" "031" "0113"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "012" "0113" "033" "02" "012" "031"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0143" "0111" "02" "02" "02" "02"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "0111" "02" "012" "02" "012" "0132"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "012" "02" "0111" "0142" "031" "02"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "02" "0143" "031" "02" "012" "031"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "031" "0113" "0321" "02" "033" "02"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "02" "02" "031" "02" "02" "02"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "0322" "02" "02" "031" "0321" "02"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "031" "02" "02" "0111" "0113" "0141"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "0141" "0111" "02" "02" "0143" "0111"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "012" "02" "0323" "02" "02" "02"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "0322" "012" "031" "02" "02" "012"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "0133" "02" "0113" "02" "031" "0112"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "0112" "02" "0141" "02" "02" "02"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "02" "02" "02" "0113" "031" "02"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "02" "0131" "02" "0322" "02" "031"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "0133" "012" "0322" "0323" "02" "0142"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "0141" "012" "02" "02" "031" "0132"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "0143" "02" "02" "031" "012" "02"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "02" "02" "0133" "0111" "02" "02"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "02" "0131" "02" "0133" "02" "031"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "0111" "0113" "0322" "02" "031" "0141"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "02" "012" "012" "02" "02" "02"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "02" "02" "012" "02" "0112" "02"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "02" "0112" "0143" "0111" "0112" "02"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "02" "02" "02" "0111" "0112" "0134"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "0113" "02" "02" "02" "0111" "012"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "031" "02" "02" "012" "02" "02"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "02" "0132" "02" "031" "012" "0321"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "0112" "0133" "02" "02" "0321" "02"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "02" "012" "031" "0131" "02" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "0141" "02" "02" "031" "0112" "02"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "02" "02" "02" "02" "0131" "031"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "031" "012" "012" "0321" "031" "02"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "0142" "02" "033" "02" "02" "0131"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "0111" "02" "02" "02" "031" "02"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "0111" "02" "02" "0111" "02" "02"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "012" "02" "0113" "02" "02" "012"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "02" "02" "012" "02" "02" "02"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "031" "02" "02" "0321" "0111" "0142"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "02" "012" "031" "031" "02" "02"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "0141" "031" "02" "02" "031" "0111"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "02" "02" "02" "012" "0141" "031"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "02" "0134" "012" "031" "0111" "0133"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "012" "02" "0321" "02" "02" "0133"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "0131" "012" "02" "02" "0132" "0133"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "02" "0322" "012" "02" "0131" "02"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "02" "0131" "02" "02" "0133" "012"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "02" "031" "02" "031" "02" "02"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "012" "0111" "02" "02" "0131" "02"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "02" "02" "0134" "02" "0134" "02"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "012" "012" "02" "02" "02" "012"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "0112" "0111" "0111" "031" "02" "0143"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "0142" "02" "02" "02" "02" "02"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "0111" "0143" "02" "0133" "0112" "02"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "031" "0111" "02" "0141" "0112" "02"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "0111" "0113" "0141" "02" "02" "02"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "031" "02" "0142" "02" "012" "012"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "02" "031" "031" "02" "0143" "02"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "0113" "02" "02" "02" "0111" "0113"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "02" "031" "0112" "02" "02" "02"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "012" "02" "0113" "02" "012" "0112"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "0111" "02" "02" "02" "0141" "0111"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "0322" "02" "0111" "0111" "031" "02"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "031" "02" "031" "02" "031" "012"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "0141" "012" "0321" "012" "012" "031"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "02" "012" "012" "02" "012" "0113"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "0112" "02" "02" "0113" "0143" "02"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "0111" "02" "031" "02" "02" "02"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "012" "02" "02" "012" "012" "0112"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "0142" "031" "02" "0133" "02" "02"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "0113" "031" "02" "02" "031" "02"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "02" "02" "02" "0143" "02" "02"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "0111" "02" "02" "031" "02" "02"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "012" "02" "02" "0113" "012" "02"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "0321" "012" "012" "02" "012" "02"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "02" "02" "02" "031" "0142" "0112"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "012" "02" "012" "02" "0112" "02"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "02" "0112" "02" "02" "02" "02"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "02" "02" "02" "02" "0134" "02"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "0131" "0322" "02" "02" "0113" "031"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "02" "02" "012" "0322" "02" "012"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "02" "02" "02" "0112" "02" "012"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "02" "02" "02" "012" "031" "0113"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "0134" "02" "02" "02" "02" "02"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "031" "02" "0142" "031" "0134" "0111"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "02" "02" "02" "012" "031" "031"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "02" "031" "02" "0143" "012" "02"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "0112" "0111" "02" "0141" "02" "02"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "031" "012" "0143" "02" "02" "0321"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "0111" "02" "031" "0142" "0141" "02"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "02" "031" "02" "02" "0131" "02"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "02" "031" "0323" "0131" "0113" "0142"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "0111" "0141" "0113" "0141" "02" "02"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "02" "0111" "0322" "02" "02" "02"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "012" "031" "033" "031" "012" "02"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "02" "02" "0132" "02" "0111" "02"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "031" "02" "02" "012" "0112" "012"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "02" "02" "02" "02" "0113" "02"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "031" "02" "031" "0322" "02"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "02" "012" "012" "031" "02" "0111"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "02" "02" "02" "02" "0321" "02"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "02" "0322" "0112" "02" "012" "0132"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0132" "02" "02" "0131" "031" "02"
#> TCGA.74.6578.01
#> "0143"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8024))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "031" "02" "033" "02" "033" "012"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "02" "02" "0142" "0133" "0143" "02"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "0113" "02" "0113" "031" "02" "031"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "0131" "02" "012" "02" "02" "02"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "031" "02" "0111" "031" "02" "02"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "0132" "032" "0112" "031" "033" "02"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "02" "012" "02" "02" "031" "031"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "031" "0111" "02" "012" "031" "0113"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "012" "0113" "033" "02" "012" "031"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0143" "0111" "02" "02" "02" "02"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "0111" "02" "012" "02" "012" "0132"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "012" "02" "0111" "0142" "031" "02"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "02" "0143" "031" "02" "012" "031"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "031" "0113" "032" "02" "033" "02"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "02" "02" "031" "02" "02" "02"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "032" "02" "02" "031" "032" "02"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "031" "02" "02" "0111" "0113" "0141"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "0141" "0111" "02" "02" "0143" "0111"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "012" "02" "032" "02" "02" "02"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "032" "012" "031" "02" "02" "012"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "0133" "02" "0113" "02" "031" "0112"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "0112" "02" "0141" "02" "02" "02"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "02" "02" "02" "0113" "031" "02"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "02" "0131" "02" "032" "02" "031"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "0133" "012" "032" "032" "02" "0142"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "0141" "012" "02" "02" "031" "0132"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "0143" "02" "02" "031" "012" "02"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "02" "02" "0133" "0111" "02" "02"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "02" "0131" "02" "0133" "02" "031"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "0111" "0113" "032" "02" "031" "0141"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "02" "012" "012" "02" "02" "02"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "02" "02" "012" "02" "0112" "02"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "02" "0112" "0143" "0111" "0112" "02"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "02" "02" "02" "0111" "0112" "0134"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "0113" "02" "02" "02" "0111" "012"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "031" "02" "02" "012" "02" "02"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "02" "0132" "02" "031" "012" "032"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "0112" "0133" "02" "02" "032" "02"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "02" "012" "031" "0131" "02" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "0141" "02" "02" "031" "0112" "02"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "02" "02" "02" "02" "0131" "031"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "031" "012" "012" "032" "031" "02"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "0142" "02" "033" "02" "02" "0131"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "0111" "02" "02" "02" "031" "02"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "0111" "02" "02" "0111" "02" "02"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "012" "02" "0113" "02" "02" "012"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "02" "02" "012" "02" "02" "02"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "031" "02" "02" "032" "0111" "0142"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "02" "012" "031" "031" "02" "02"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "0141" "031" "02" "02" "031" "0111"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "02" "02" "02" "012" "0141" "031"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "02" "0134" "012" "031" "0111" "0133"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "012" "02" "032" "02" "02" "0133"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "0131" "012" "02" "02" "0132" "0133"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "02" "032" "012" "02" "0131" "02"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "02" "0131" "02" "02" "0133" "012"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "02" "031" "02" "031" "02" "02"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "012" "0111" "02" "02" "0131" "02"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "02" "02" "0134" "02" "0134" "02"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "012" "012" "02" "02" "02" "012"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "0112" "0111" "0111" "031" "02" "0143"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "0142" "02" "02" "02" "02" "02"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "0111" "0143" "02" "0133" "0112" "02"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "031" "0111" "02" "0141" "0112" "02"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "0111" "0113" "0141" "02" "02" "02"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "031" "02" "0142" "02" "012" "012"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "02" "031" "031" "02" "0143" "02"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "0113" "02" "02" "02" "0111" "0113"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "02" "031" "0112" "02" "02" "02"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "012" "02" "0113" "02" "012" "0112"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "0111" "02" "02" "02" "0141" "0111"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "032" "02" "0111" "0111" "031" "02"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "031" "02" "031" "02" "031" "012"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "0141" "012" "032" "012" "012" "031"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "02" "012" "012" "02" "012" "0113"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "0112" "02" "02" "0113" "0143" "02"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "0111" "02" "031" "02" "02" "02"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "012" "02" "02" "012" "012" "0112"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "0142" "031" "02" "0133" "02" "02"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "0113" "031" "02" "02" "031" "02"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "02" "02" "02" "0143" "02" "02"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "0111" "02" "02" "031" "02" "02"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "012" "02" "02" "0113" "012" "02"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "032" "012" "012" "02" "012" "02"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "02" "02" "02" "031" "0142" "0112"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "012" "02" "012" "02" "0112" "02"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "02" "0112" "02" "02" "02" "02"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "02" "02" "02" "02" "0134" "02"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "0131" "032" "02" "02" "0113" "031"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "02" "02" "012" "032" "02" "012"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "02" "02" "02" "0112" "02" "012"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "02" "02" "02" "012" "031" "0113"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "0134" "02" "02" "02" "02" "02"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "031" "02" "0142" "031" "0134" "0111"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "02" "02" "02" "012" "031" "031"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "02" "031" "02" "0143" "012" "02"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "0112" "0111" "02" "0141" "02" "02"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "031" "012" "0143" "02" "02" "032"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "0111" "02" "031" "0142" "0141" "02"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "02" "031" "02" "02" "0131" "02"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "02" "031" "032" "0131" "0113" "0142"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "0111" "0141" "0113" "0141" "02" "02"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "02" "0111" "032" "02" "02" "02"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "012" "031" "033" "031" "012" "02"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "02" "02" "0132" "02" "0111" "02"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "031" "02" "02" "012" "0112" "012"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "02" "02" "02" "02" "0113" "02"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "031" "02" "031" "032" "02"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "02" "012" "012" "031" "02" "0111"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "02" "02" "02" "02" "032" "02"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "02" "032" "0112" "02" "012" "0132"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0132" "02" "02" "0131" "031" "02"
#> TCGA.74.6578.01
#> "0143"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 9621))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "031" "02" "033" "02" "033" "012"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "02" "02" "0142" "0133" "0143" "02"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "011" "02" "011" "031" "02" "031"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "0131" "02" "012" "02" "02" "02"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "031" "02" "011" "031" "02" "02"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "0132" "032" "011" "031" "033" "02"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "02" "012" "02" "02" "031" "031"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "031" "011" "02" "012" "031" "011"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "012" "011" "033" "02" "012" "031"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0143" "011" "02" "02" "02" "02"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "011" "02" "012" "02" "012" "0132"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "012" "02" "011" "0142" "031" "02"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "02" "0143" "031" "02" "012" "031"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "031" "011" "032" "02" "033" "02"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "02" "02" "031" "02" "02" "02"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "032" "02" "02" "031" "032" "02"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "031" "02" "02" "011" "011" "0141"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "0141" "011" "02" "02" "0143" "011"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "012" "02" "032" "02" "02" "02"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "032" "012" "031" "02" "02" "012"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "0133" "02" "011" "02" "031" "011"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "011" "02" "0141" "02" "02" "02"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "02" "02" "02" "011" "031" "02"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "02" "0131" "02" "032" "02" "031"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "0133" "012" "032" "032" "02" "0142"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "0141" "012" "02" "02" "031" "0132"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "0143" "02" "02" "031" "012" "02"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "02" "02" "0133" "011" "02" "02"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "02" "0131" "02" "0133" "02" "031"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "011" "011" "032" "02" "031" "0141"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "02" "012" "012" "02" "02" "02"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "02" "02" "012" "02" "011" "02"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "02" "011" "0143" "011" "011" "02"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "02" "02" "02" "011" "011" "0134"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "011" "02" "02" "02" "011" "012"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "031" "02" "02" "012" "02" "02"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "02" "0132" "02" "031" "012" "032"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "011" "0133" "02" "02" "032" "02"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "02" "012" "031" "0131" "02" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "0141" "02" "02" "031" "011" "02"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "02" "02" "02" "02" "0131" "031"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "031" "012" "012" "032" "031" "02"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "0142" "02" "033" "02" "02" "0131"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "011" "02" "02" "02" "031" "02"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "011" "02" "02" "011" "02" "02"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "012" "02" "011" "02" "02" "012"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "02" "02" "012" "02" "02" "02"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "031" "02" "02" "032" "011" "0142"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "02" "012" "031" "031" "02" "02"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "0141" "031" "02" "02" "031" "011"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "02" "02" "02" "012" "0141" "031"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "02" "0134" "012" "031" "011" "0133"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "012" "02" "032" "02" "02" "0133"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "0131" "012" "02" "02" "0132" "0133"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "02" "032" "012" "02" "0131" "02"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "02" "0131" "02" "02" "0133" "012"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "02" "031" "02" "031" "02" "02"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "012" "011" "02" "02" "0131" "02"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "02" "02" "0134" "02" "0134" "02"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "012" "012" "02" "02" "02" "012"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "011" "011" "011" "031" "02" "0143"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "0142" "02" "02" "02" "02" "02"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "011" "0143" "02" "0133" "011" "02"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "031" "011" "02" "0141" "011" "02"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "011" "011" "0141" "02" "02" "02"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "031" "02" "0142" "02" "012" "012"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "02" "031" "031" "02" "0143" "02"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "011" "02" "02" "02" "011" "011"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "02" "031" "011" "02" "02" "02"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "012" "02" "011" "02" "012" "011"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "011" "02" "02" "02" "0141" "011"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "032" "02" "011" "011" "031" "02"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "031" "02" "031" "02" "031" "012"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "0141" "012" "032" "012" "012" "031"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "02" "012" "012" "02" "012" "011"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "011" "02" "02" "011" "0143" "02"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "011" "02" "031" "02" "02" "02"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "012" "02" "02" "012" "012" "011"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "0142" "031" "02" "0133" "02" "02"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "011" "031" "02" "02" "031" "02"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "02" "02" "02" "0143" "02" "02"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "011" "02" "02" "031" "02" "02"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "012" "02" "02" "011" "012" "02"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "032" "012" "012" "02" "012" "02"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "02" "02" "02" "031" "0142" "011"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "012" "02" "012" "02" "011" "02"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "02" "011" "02" "02" "02" "02"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "02" "02" "02" "02" "0134" "02"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "0131" "032" "02" "02" "011" "031"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "02" "02" "012" "032" "02" "012"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "02" "02" "02" "011" "02" "012"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "02" "02" "02" "012" "031" "011"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "0134" "02" "02" "02" "02" "02"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "031" "02" "0142" "031" "0134" "011"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "02" "02" "02" "012" "031" "031"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "02" "031" "02" "0143" "012" "02"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "011" "011" "02" "0141" "02" "02"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "031" "012" "0143" "02" "02" "032"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "011" "02" "031" "0142" "0141" "02"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "02" "031" "02" "02" "0131" "02"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "02" "031" "032" "0131" "011" "0142"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "011" "0141" "011" "0141" "02" "02"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "02" "011" "032" "02" "02" "02"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "012" "031" "033" "031" "012" "02"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "02" "02" "0132" "02" "011" "02"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "031" "02" "02" "012" "011" "012"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "02" "02" "02" "02" "011" "02"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "031" "02" "031" "032" "02"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "02" "012" "012" "031" "02" "011"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "02" "02" "02" "02" "032" "02"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "02" "032" "011" "02" "012" "0132"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0132" "02" "02" "0131" "031" "02"
#> TCGA.74.6578.01
#> "0143"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 9856))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "031" "02" "033" "02" "033" "012"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "02" "02" "014" "0133" "014" "02"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "011" "02" "011" "031" "02" "031"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "0131" "02" "012" "02" "02" "02"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "031" "02" "011" "031" "02" "02"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "0132" "032" "011" "031" "033" "02"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "02" "012" "02" "02" "031" "031"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "031" "011" "02" "012" "031" "011"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "012" "011" "033" "02" "012" "031"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "014" "011" "02" "02" "02" "02"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "011" "02" "012" "02" "012" "0132"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "012" "02" "011" "014" "031" "02"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "02" "014" "031" "02" "012" "031"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "031" "011" "032" "02" "033" "02"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "02" "02" "031" "02" "02" "02"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "032" "02" "02" "031" "032" "02"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "031" "02" "02" "011" "011" "014"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "014" "011" "02" "02" "014" "011"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "012" "02" "032" "02" "02" "02"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "032" "012" "031" "02" "02" "012"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "0133" "02" "011" "02" "031" "011"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "011" "02" "014" "02" "02" "02"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "02" "02" "02" "011" "031" "02"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "02" "0131" "02" "032" "02" "031"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "0133" "012" "032" "032" "02" "014"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "014" "012" "02" "02" "031" "0132"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "014" "02" "02" "031" "012" "02"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "02" "02" "0133" "011" "02" "02"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "02" "0131" "02" "0133" "02" "031"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "011" "011" "032" "02" "031" "014"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "02" "012" "012" "02" "02" "02"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "02" "02" "012" "02" "011" "02"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "02" "011" "014" "011" "011" "02"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "02" "02" "02" "011" "011" "0134"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "011" "02" "02" "02" "011" "012"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "031" "02" "02" "012" "02" "02"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "02" "0132" "02" "031" "012" "032"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "011" "0133" "02" "02" "032" "02"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "02" "012" "031" "0131" "02" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "014" "02" "02" "031" "011" "02"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "02" "02" "02" "02" "0131" "031"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "031" "012" "012" "032" "031" "02"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "014" "02" "033" "02" "02" "0131"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "011" "02" "02" "02" "031" "02"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "011" "02" "02" "011" "02" "02"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "012" "02" "011" "02" "02" "012"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "02" "02" "012" "02" "02" "02"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "031" "02" "02" "032" "011" "014"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "02" "012" "031" "031" "02" "02"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "014" "031" "02" "02" "031" "011"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "02" "02" "02" "012" "014" "031"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "02" "0134" "012" "031" "011" "0133"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "012" "02" "032" "02" "02" "0133"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "0131" "012" "02" "02" "0132" "0133"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "02" "032" "012" "02" "0131" "02"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "02" "0131" "02" "02" "0133" "012"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "02" "031" "02" "031" "02" "02"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "012" "011" "02" "02" "0131" "02"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "02" "02" "0134" "02" "0134" "02"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "012" "012" "02" "02" "02" "012"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "011" "011" "011" "031" "02" "014"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "014" "02" "02" "02" "02" "02"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "011" "014" "02" "0133" "011" "02"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "031" "011" "02" "014" "011" "02"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "011" "011" "014" "02" "02" "02"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "031" "02" "014" "02" "012" "012"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "02" "031" "031" "02" "014" "02"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "011" "02" "02" "02" "011" "011"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "02" "031" "011" "02" "02" "02"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "012" "02" "011" "02" "012" "011"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "011" "02" "02" "02" "014" "011"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "032" "02" "011" "011" "031" "02"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "031" "02" "031" "02" "031" "012"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "014" "012" "032" "012" "012" "031"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "02" "012" "012" "02" "012" "011"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "011" "02" "02" "011" "014" "02"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "011" "02" "031" "02" "02" "02"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "012" "02" "02" "012" "012" "011"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "014" "031" "02" "0133" "02" "02"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "011" "031" "02" "02" "031" "02"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "02" "02" "02" "014" "02" "02"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "011" "02" "02" "031" "02" "02"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "012" "02" "02" "011" "012" "02"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "032" "012" "012" "02" "012" "02"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "02" "02" "02" "031" "014" "011"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "012" "02" "012" "02" "011" "02"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "02" "011" "02" "02" "02" "02"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "02" "02" "02" "02" "0134" "02"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "0131" "032" "02" "02" "011" "031"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "02" "02" "012" "032" "02" "012"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "02" "02" "02" "011" "02" "012"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "02" "02" "02" "012" "031" "011"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "0134" "02" "02" "02" "02" "02"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "031" "02" "014" "031" "0134" "011"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "02" "02" "02" "012" "031" "031"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "02" "031" "02" "014" "012" "02"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "011" "011" "02" "014" "02" "02"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "031" "012" "014" "02" "02" "032"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "011" "02" "031" "014" "014" "02"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "02" "031" "02" "02" "0131" "02"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "02" "031" "032" "0131" "011" "014"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "011" "014" "011" "014" "02" "02"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "02" "011" "032" "02" "02" "02"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "012" "031" "033" "031" "012" "02"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "02" "02" "0132" "02" "011" "02"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "031" "02" "02" "012" "011" "012"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "02" "02" "02" "02" "011" "02"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "031" "02" "031" "032" "02"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "02" "012" "012" "031" "02" "011"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "02" "02" "02" "02" "032" "02"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "02" "032" "011" "02" "012" "0132"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0132" "02" "02" "0131" "031" "02"
#> TCGA.74.6578.01
#> "014"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 15681))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "031" "02" "033" "02" "033" "012"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "02" "02" "014" "013" "014" "02"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "011" "02" "011" "031" "02" "031"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "013" "02" "012" "02" "02" "02"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "031" "02" "011" "031" "02" "02"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "013" "032" "011" "031" "033" "02"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "02" "012" "02" "02" "031" "031"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "031" "011" "02" "012" "031" "011"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "012" "011" "033" "02" "012" "031"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "014" "011" "02" "02" "02" "02"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "011" "02" "012" "02" "012" "013"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "012" "02" "011" "014" "031" "02"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "02" "014" "031" "02" "012" "031"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "031" "011" "032" "02" "033" "02"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "02" "02" "031" "02" "02" "02"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "032" "02" "02" "031" "032" "02"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "031" "02" "02" "011" "011" "014"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "014" "011" "02" "02" "014" "011"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "012" "02" "032" "02" "02" "02"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "032" "012" "031" "02" "02" "012"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "013" "02" "011" "02" "031" "011"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "011" "02" "014" "02" "02" "02"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "02" "02" "02" "011" "031" "02"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "02" "013" "02" "032" "02" "031"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "013" "012" "032" "032" "02" "014"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "014" "012" "02" "02" "031" "013"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "014" "02" "02" "031" "012" "02"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "02" "02" "013" "011" "02" "02"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "02" "013" "02" "013" "02" "031"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "011" "011" "032" "02" "031" "014"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "02" "012" "012" "02" "02" "02"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "02" "02" "012" "02" "011" "02"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "02" "011" "014" "011" "011" "02"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "02" "02" "02" "011" "011" "013"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "011" "02" "02" "02" "011" "012"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "031" "02" "02" "012" "02" "02"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "02" "013" "02" "031" "012" "032"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "011" "013" "02" "02" "032" "02"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "02" "012" "031" "013" "02" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "014" "02" "02" "031" "011" "02"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "02" "02" "02" "02" "013" "031"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "031" "012" "012" "032" "031" "02"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "014" "02" "033" "02" "02" "013"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "011" "02" "02" "02" "031" "02"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "011" "02" "02" "011" "02" "02"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "012" "02" "011" "02" "02" "012"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "02" "02" "012" "02" "02" "02"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "031" "02" "02" "032" "011" "014"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "02" "012" "031" "031" "02" "02"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "014" "031" "02" "02" "031" "011"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "02" "02" "02" "012" "014" "031"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "02" "013" "012" "031" "011" "013"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "012" "02" "032" "02" "02" "013"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "013" "012" "02" "02" "013" "013"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "02" "032" "012" "02" "013" "02"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "02" "013" "02" "02" "013" "012"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "02" "031" "02" "031" "02" "02"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "012" "011" "02" "02" "013" "02"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "02" "02" "013" "02" "013" "02"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "012" "012" "02" "02" "02" "012"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "011" "011" "011" "031" "02" "014"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "014" "02" "02" "02" "02" "02"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "011" "014" "02" "013" "011" "02"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "031" "011" "02" "014" "011" "02"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "011" "011" "014" "02" "02" "02"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "031" "02" "014" "02" "012" "012"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "02" "031" "031" "02" "014" "02"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "011" "02" "02" "02" "011" "011"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "02" "031" "011" "02" "02" "02"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "012" "02" "011" "02" "012" "011"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "011" "02" "02" "02" "014" "011"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "032" "02" "011" "011" "031" "02"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "031" "02" "031" "02" "031" "012"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "014" "012" "032" "012" "012" "031"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "02" "012" "012" "02" "012" "011"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "011" "02" "02" "011" "014" "02"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "011" "02" "031" "02" "02" "02"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "012" "02" "02" "012" "012" "011"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "014" "031" "02" "013" "02" "02"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "011" "031" "02" "02" "031" "02"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "02" "02" "02" "014" "02" "02"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "011" "02" "02" "031" "02" "02"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "012" "02" "02" "011" "012" "02"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "032" "012" "012" "02" "012" "02"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "02" "02" "02" "031" "014" "011"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "012" "02" "012" "02" "011" "02"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "02" "011" "02" "02" "02" "02"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "02" "02" "02" "02" "013" "02"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "013" "032" "02" "02" "011" "031"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "02" "02" "012" "032" "02" "012"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "02" "02" "02" "011" "02" "012"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "02" "02" "02" "012" "031" "011"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "013" "02" "02" "02" "02" "02"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "031" "02" "014" "031" "013" "011"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "02" "02" "02" "012" "031" "031"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "02" "031" "02" "014" "012" "02"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "011" "011" "02" "014" "02" "02"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "031" "012" "014" "02" "02" "032"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "011" "02" "031" "014" "014" "02"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "02" "031" "02" "02" "013" "02"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "02" "031" "032" "013" "011" "014"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "011" "014" "011" "014" "02" "02"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "02" "011" "032" "02" "02" "02"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "012" "031" "033" "031" "012" "02"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "02" "02" "013" "02" "011" "02"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "031" "02" "02" "012" "011" "012"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "02" "02" "02" "02" "011" "02"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "031" "02" "031" "032" "02"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "02" "012" "012" "031" "02" "011"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "02" "02" "02" "02" "032" "02"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "02" "032" "011" "02" "012" "013"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "013" "02" "02" "013" "031" "02"
#> TCGA.74.6578.01
#> "014"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 18000))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "031" "02" "033" "02" "033" "012"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "02" "02" "014" "013" "014" "02"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "011" "02" "011" "031" "02" "031"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "013" "02" "012" "02" "02" "02"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "031" "02" "011" "031" "02" "02"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "013" "032" "011" "031" "033" "02"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "02" "012" "02" "02" "031" "031"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "031" "011" "02" "012" "031" "011"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "012" "011" "033" "02" "012" "031"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "014" "011" "02" "02" "02" "02"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "011" "02" "012" "02" "012" "013"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "012" "02" "011" "014" "031" "02"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "02" "014" "031" "02" "012" "031"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "031" "011" "032" "02" "033" "02"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "02" "02" "031" "02" "02" "02"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "032" "02" "02" "031" "032" "02"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "031" "02" "02" "011" "011" "014"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "014" "011" "02" "02" "014" "011"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "012" "02" "032" "02" "02" "02"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "032" "012" "031" "02" "02" "012"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "013" "02" "011" "02" "031" "011"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "011" "02" "014" "02" "02" "02"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "02" "02" "02" "011" "031" "02"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "02" "013" "02" "032" "02" "031"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "013" "012" "032" "032" "02" "014"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "014" "012" "02" "02" "031" "013"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "014" "02" "02" "031" "012" "02"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "02" "02" "013" "011" "02" "02"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "02" "013" "02" "013" "02" "031"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "011" "011" "032" "02" "031" "014"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "02" "012" "012" "02" "02" "02"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "02" "02" "012" "02" "011" "02"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "02" "011" "014" "011" "011" "02"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "02" "02" "02" "011" "011" "013"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "011" "02" "02" "02" "011" "012"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "031" "02" "02" "012" "02" "02"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "02" "013" "02" "031" "012" "032"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "011" "013" "02" "02" "032" "02"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "02" "012" "031" "013" "02" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "014" "02" "02" "031" "011" "02"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "02" "02" "02" "02" "013" "031"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "031" "012" "012" "032" "031" "02"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "014" "02" "033" "02" "02" "013"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "011" "02" "02" "02" "031" "02"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "011" "02" "02" "011" "02" "02"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "012" "02" "011" "02" "02" "012"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "02" "02" "012" "02" "02" "02"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "031" "02" "02" "032" "011" "014"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "02" "012" "031" "031" "02" "02"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "014" "031" "02" "02" "031" "011"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "02" "02" "02" "012" "014" "031"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "02" "013" "012" "031" "011" "013"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "012" "02" "032" "02" "02" "013"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "013" "012" "02" "02" "013" "013"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "02" "032" "012" "02" "013" "02"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "02" "013" "02" "02" "013" "012"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "02" "031" "02" "031" "02" "02"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "012" "011" "02" "02" "013" "02"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "02" "02" "013" "02" "013" "02"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "012" "012" "02" "02" "02" "012"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "011" "011" "011" "031" "02" "014"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "014" "02" "02" "02" "02" "02"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "011" "014" "02" "013" "011" "02"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "031" "011" "02" "014" "011" "02"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "011" "011" "014" "02" "02" "02"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "031" "02" "014" "02" "012" "012"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "02" "031" "031" "02" "014" "02"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "011" "02" "02" "02" "011" "011"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "02" "031" "011" "02" "02" "02"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "012" "02" "011" "02" "012" "011"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "011" "02" "02" "02" "014" "011"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "032" "02" "011" "011" "031" "02"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "031" "02" "031" "02" "031" "012"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "014" "012" "032" "012" "012" "031"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "02" "012" "012" "02" "012" "011"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "011" "02" "02" "011" "014" "02"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "011" "02" "031" "02" "02" "02"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "012" "02" "02" "012" "012" "011"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "014" "031" "02" "013" "02" "02"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "011" "031" "02" "02" "031" "02"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "02" "02" "02" "014" "02" "02"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "011" "02" "02" "031" "02" "02"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "012" "02" "02" "011" "012" "02"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "032" "012" "012" "02" "012" "02"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "02" "02" "02" "031" "014" "011"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "012" "02" "012" "02" "011" "02"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "02" "011" "02" "02" "02" "02"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "02" "02" "02" "02" "013" "02"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "013" "032" "02" "02" "011" "031"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "02" "02" "012" "032" "02" "012"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "02" "02" "02" "011" "02" "012"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "02" "02" "02" "012" "031" "011"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "013" "02" "02" "02" "02" "02"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "031" "02" "014" "031" "013" "011"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "02" "02" "02" "012" "031" "031"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "02" "031" "02" "014" "012" "02"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "011" "011" "02" "014" "02" "02"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "031" "012" "014" "02" "02" "032"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "011" "02" "031" "014" "014" "02"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "02" "031" "02" "02" "013" "02"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "02" "031" "032" "013" "011" "014"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "011" "014" "011" "014" "02" "02"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "02" "011" "032" "02" "02" "02"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "012" "031" "033" "031" "012" "02"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "02" "02" "013" "02" "011" "02"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "031" "02" "02" "012" "011" "012"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "02" "02" "02" "02" "011" "02"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "031" "02" "031" "032" "02"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "02" "012" "012" "031" "02" "011"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "02" "02" "02" "02" "032" "02"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "02" "032" "011" "02" "012" "013"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "013" "02" "02" "013" "031" "02"
#> TCGA.74.6578.01
#> "014"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 18964))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "031" "02" "033" "02" "033" "01"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "02" "02" "01" "01" "01" "02"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "01" "02" "01" "031" "02" "031"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "01" "02" "01" "02" "02" "02"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "031" "02" "01" "031" "02" "02"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "01" "032" "01" "031" "033" "02"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "02" "01" "02" "02" "031" "031"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "031" "01" "02" "01" "031" "01"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "01" "01" "033" "02" "01" "031"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "01" "02" "01" "02" "01" "01"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "01" "02" "01" "01" "031" "02"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "02" "01" "031" "02" "01" "031"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "031" "01" "032" "02" "033" "02"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "02" "02" "031" "02" "02" "02"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "032" "02" "02" "031" "032" "02"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "031" "02" "02" "01" "01" "01"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "01" "01" "02" "02" "01" "01"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "01" "02" "032" "02" "02" "02"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "032" "01" "031" "02" "02" "01"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "01" "02" "01" "02" "031" "01"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "01" "02" "01" "02" "02" "02"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "02" "02" "02" "01" "031" "02"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "02" "01" "02" "032" "02" "031"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "01" "01" "032" "032" "02" "01"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "01" "01" "02" "02" "031" "01"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "01" "02" "02" "031" "01" "02"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "02" "02" "01" "01" "02" "02"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "02" "01" "02" "01" "02" "031"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "01" "01" "032" "02" "031" "01"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "02" "01" "01" "02" "02" "02"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "02" "02" "01" "02" "01" "02"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "02" "01" "01" "01" "01" "02"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "02" "02" "02" "01" "01" "01"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "01" "02" "02" "02" "01" "01"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "031" "02" "02" "01" "02" "02"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "02" "01" "02" "031" "01" "032"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "01" "01" "02" "02" "032" "02"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "02" "01" "031" "01" "02" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "01" "02" "02" "031" "01" "02"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "02" "02" "02" "02" "01" "031"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "031" "01" "01" "032" "031" "02"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "01" "02" "033" "02" "02" "01"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "01" "02" "02" "02" "031" "02"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "01" "02" "02" "01" "02" "02"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "01" "02" "01" "02" "02" "01"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "02" "02" "01" "02" "02" "02"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "031" "02" "02" "032" "01" "01"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "02" "01" "031" "031" "02" "02"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "01" "031" "02" "02" "031" "01"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "02" "02" "02" "01" "01" "031"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "02" "01" "01" "031" "01" "01"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "01" "02" "032" "02" "02" "01"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "01" "01" "02" "02" "01" "01"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "02" "032" "01" "02" "01" "02"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "02" "01" "02" "02" "01" "01"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "02" "031" "02" "031" "02" "02"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "01" "01" "02" "02" "01" "02"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "02" "02" "01" "02" "01" "02"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "01" "01" "02" "02" "02" "01"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "01" "01" "01" "031" "02" "01"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "01" "02" "02" "02" "02" "02"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "01" "01" "02" "01" "01" "02"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "031" "01" "02" "01" "01" "02"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "01" "01" "01" "02" "02" "02"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "031" "02" "01" "02" "01" "01"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "02" "031" "031" "02" "01" "02"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "01" "02" "02" "02" "01" "01"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "02" "031" "01" "02" "02" "02"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "01" "02" "01" "02" "01" "01"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "01" "02" "02" "02" "01" "01"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "032" "02" "01" "01" "031" "02"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "031" "02" "031" "02" "031" "01"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "01" "01" "032" "01" "01" "031"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "02" "01" "01" "02" "01" "01"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "01" "02" "02" "01" "01" "02"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "01" "02" "031" "02" "02" "02"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "01" "02" "02" "01" "01" "01"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "01" "031" "02" "01" "02" "02"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "01" "031" "02" "02" "031" "02"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "02" "02" "02" "01" "02" "02"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "01" "02" "02" "031" "02" "02"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "01" "02" "02" "01" "01" "02"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "032" "01" "01" "02" "01" "02"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "02" "02" "02" "031" "01" "01"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "01" "02" "01" "02" "01" "02"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "02" "01" "02" "02" "02" "02"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "02" "02" "02" "02" "01" "02"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "01" "032" "02" "02" "01" "031"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "02" "02" "01" "032" "02" "01"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "02" "02" "02" "01" "02" "01"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "02" "02" "02" "01" "031" "01"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "01" "02" "02" "02" "02" "02"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "031" "02" "01" "031" "01" "01"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "02" "02" "02" "01" "031" "031"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "02" "031" "02" "01" "01" "02"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "01" "01" "02" "01" "02" "02"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "031" "01" "01" "02" "02" "032"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "01" "02" "031" "01" "01" "02"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "02" "031" "02" "02" "01" "02"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "02" "031" "032" "01" "01" "01"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "01" "01" "01" "01" "02" "02"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "02" "01" "032" "02" "02" "02"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "01" "031" "033" "031" "01" "02"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "02" "02" "01" "02" "01" "02"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "031" "02" "02" "01" "01" "01"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "02" "02" "02" "02" "01" "02"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "031" "02" "031" "032" "02"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "02" "01" "01" "031" "02" "01"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "02" "02" "02" "02" "032" "02"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "02" "032" "01" "02" "01" "01"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "01" "02" "02" "01" "031" "02"
#> TCGA.74.6578.01
#> "01"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 20318))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "031" "02" "033" "02" "033" "01"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "02" "02" "01" "01" "01" "02"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "01" "02" "01" "031" "02" "031"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "01" "02" "01" "02" "02" "02"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "031" "02" "01" "031" "02" "02"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "01" "032" "01" "031" "033" "02"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "02" "01" "02" "02" "031" "031"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "031" "01" "02" "01" "031" "01"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "01" "01" "033" "02" "01" "031"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "01" "02" "01" "02" "01" "01"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "01" "02" "01" "01" "031" "02"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "02" "01" "031" "02" "01" "031"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "031" "01" "032" "02" "033" "02"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "02" "02" "031" "02" "02" "02"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "032" "02" "02" "031" "032" "02"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "031" "02" "02" "01" "01" "01"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "01" "01" "02" "02" "01" "01"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "01" "02" "032" "02" "02" "02"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "032" "01" "031" "02" "02" "01"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "01" "02" "01" "02" "031" "01"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "01" "02" "01" "02" "02" "02"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "02" "02" "02" "01" "031" "02"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "02" "01" "02" "032" "02" "031"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "01" "01" "032" "032" "02" "01"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "01" "01" "02" "02" "031" "01"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "01" "02" "02" "031" "01" "02"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "02" "02" "01" "01" "02" "02"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "02" "01" "02" "01" "02" "031"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "01" "01" "032" "02" "031" "01"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "02" "01" "01" "02" "02" "02"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "02" "02" "01" "02" "01" "02"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "02" "01" "01" "01" "01" "02"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "02" "02" "02" "01" "01" "01"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "01" "02" "02" "02" "01" "01"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "031" "02" "02" "01" "02" "02"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "02" "01" "02" "031" "01" "032"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "01" "01" "02" "02" "032" "02"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "02" "01" "031" "01" "02" "033"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "01" "02" "02" "031" "01" "02"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "02" "02" "02" "02" "01" "031"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "031" "01" "01" "032" "031" "02"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "01" "02" "033" "02" "02" "01"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "01" "02" "02" "02" "031" "02"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "01" "02" "02" "01" "02" "02"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "01" "02" "01" "02" "02" "01"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "02" "02" "01" "02" "02" "02"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "031" "02" "02" "032" "01" "01"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "02" "01" "031" "031" "02" "02"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "01" "031" "02" "02" "031" "01"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "02" "02" "02" "01" "01" "031"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "02" "01" "01" "031" "01" "01"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "01" "02" "032" "02" "02" "01"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "01" "01" "02" "02" "01" "01"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "02" "032" "01" "02" "01" "02"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "02" "01" "02" "02" "01" "01"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "02" "031" "02" "031" "02" "02"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "01" "01" "02" "02" "01" "02"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "02" "02" "01" "02" "01" "02"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "01" "01" "02" "02" "02" "01"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "01" "01" "01" "031" "02" "01"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "01" "02" "02" "02" "02" "02"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "01" "01" "02" "01" "01" "02"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "031" "01" "02" "01" "01" "02"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "01" "01" "01" "02" "02" "02"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "031" "02" "01" "02" "01" "01"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "02" "031" "031" "02" "01" "02"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "01" "02" "02" "02" "01" "01"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "02" "031" "01" "02" "02" "02"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "01" "02" "01" "02" "01" "01"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "01" "02" "02" "02" "01" "01"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "032" "02" "01" "01" "031" "02"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "031" "02" "031" "02" "031" "01"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "01" "01" "032" "01" "01" "031"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "02" "01" "01" "02" "01" "01"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "01" "02" "02" "01" "01" "02"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "01" "02" "031" "02" "02" "02"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "01" "02" "02" "01" "01" "01"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "01" "031" "02" "01" "02" "02"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "01" "031" "02" "02" "031" "02"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "02" "02" "02" "01" "02" "02"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "01" "02" "02" "031" "02" "02"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "01" "02" "02" "01" "01" "02"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "032" "01" "01" "02" "01" "02"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "02" "02" "02" "031" "01" "01"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "01" "02" "01" "02" "01" "02"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "02" "01" "02" "02" "02" "02"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "02" "02" "02" "02" "01" "02"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "01" "032" "02" "02" "01" "031"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "02" "02" "01" "032" "02" "01"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "02" "02" "02" "01" "02" "01"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "02" "02" "02" "01" "031" "01"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "01" "02" "02" "02" "02" "02"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "031" "02" "01" "031" "01" "01"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "02" "02" "02" "01" "031" "031"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "02" "031" "02" "01" "01" "02"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "01" "01" "02" "01" "02" "02"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "031" "01" "01" "02" "02" "032"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "01" "02" "031" "01" "01" "02"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "02" "031" "02" "02" "01" "02"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "02" "031" "032" "01" "01" "01"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "01" "01" "01" "01" "02" "02"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "02" "01" "032" "02" "02" "02"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "01" "031" "033" "031" "01" "02"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "02" "02" "01" "02" "01" "02"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "031" "02" "02" "01" "01" "01"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "02" "02" "02" "02" "01" "02"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "033" "031" "02" "031" "032" "02"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "02" "01" "01" "031" "02" "01"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "02" "02" "02" "02" "032" "02"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "02" "032" "01" "02" "01" "01"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "01" "02" "02" "01" "031" "02"
#> TCGA.74.6578.01
#> "01"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 21160))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "03" "02" "03" "02" "03" "01"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "02" "02" "01" "01" "01" "02"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "01" "02" "01" "03" "02" "03"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "01" "02" "01" "02" "02" "02"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "03" "02" "01" "03" "02" "02"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "01" "03" "01" "03" "03" "02"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "02" "01" "02" "02" "03" "03"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "03" "01" "02" "01" "03" "01"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "01" "01" "03" "02" "01" "03"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "01" "02" "01" "02" "01" "01"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "01" "02" "01" "01" "03" "02"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "02" "01" "03" "02" "01" "03"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "03" "01" "03" "02" "03" "02"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "02" "02" "03" "02" "02" "02"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "03" "02" "02" "03" "03" "02"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "03" "02" "02" "01" "01" "01"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "01" "01" "02" "02" "01" "01"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "01" "02" "03" "02" "02" "02"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "03" "01" "03" "02" "02" "01"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "01" "02" "01" "02" "03" "01"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "01" "02" "01" "02" "02" "02"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "02" "02" "02" "01" "03" "02"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "02" "01" "02" "03" "02" "03"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "01" "01" "03" "03" "02" "01"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "01" "01" "02" "02" "03" "01"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "01" "02" "02" "03" "01" "02"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "02" "02" "01" "01" "02" "02"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "02" "01" "02" "01" "02" "03"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "01" "01" "03" "02" "03" "01"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "02" "01" "01" "02" "02" "02"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "02" "02" "01" "02" "01" "02"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "02" "01" "01" "01" "01" "02"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "02" "02" "02" "01" "01" "01"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "01" "02" "02" "02" "01" "01"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "03" "02" "02" "01" "02" "02"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "02" "01" "02" "03" "01" "03"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "01" "01" "02" "02" "03" "02"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "02" "01" "03" "01" "02" "03"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "01" "02" "02" "03" "01" "02"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "02" "02" "02" "02" "01" "03"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "03" "01" "01" "03" "03" "02"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "01" "02" "03" "02" "02" "01"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "01" "02" "02" "02" "03" "02"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "01" "02" "02" "01" "02" "02"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "01" "02" "01" "02" "02" "01"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "02" "02" "01" "02" "02" "02"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "03" "02" "02" "03" "01" "01"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "02" "01" "03" "03" "02" "02"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "01" "03" "02" "02" "03" "01"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "02" "02" "02" "01" "01" "03"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "02" "01" "01" "03" "01" "01"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "01" "02" "03" "02" "02" "01"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "01" "01" "02" "02" "01" "01"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "02" "03" "01" "02" "01" "02"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "02" "01" "02" "02" "01" "01"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "02" "03" "02" "03" "02" "02"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "01" "01" "02" "02" "01" "02"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "02" "02" "01" "02" "01" "02"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "01" "01" "02" "02" "02" "01"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "01" "01" "01" "03" "02" "01"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "01" "02" "02" "02" "02" "02"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "01" "01" "02" "01" "01" "02"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "03" "01" "02" "01" "01" "02"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "01" "01" "01" "02" "02" "02"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "03" "02" "01" "02" "01" "01"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "02" "03" "03" "02" "01" "02"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "01" "02" "02" "02" "01" "01"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "02" "03" "01" "02" "02" "02"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "01" "02" "01" "02" "01" "01"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "01" "02" "02" "02" "01" "01"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "03" "02" "01" "01" "03" "02"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "03" "02" "03" "02" "03" "01"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "01" "01" "03" "01" "01" "03"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "02" "01" "01" "02" "01" "01"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "01" "02" "02" "01" "01" "02"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "01" "02" "03" "02" "02" "02"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "01" "02" "02" "01" "01" "01"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "01" "03" "02" "01" "02" "02"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "01" "03" "02" "02" "03" "02"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "02" "02" "02" "01" "02" "02"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "01" "02" "02" "03" "02" "02"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "01" "02" "02" "01" "01" "02"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "03" "01" "01" "02" "01" "02"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "02" "02" "02" "03" "01" "01"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "01" "02" "01" "02" "01" "02"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "02" "01" "02" "02" "02" "02"
#> TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01 TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01
#> "02" "02" "02" "02" "01" "02"
#> TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01 TCGA.S9.A6U9.01 TCGA.74.6573.01 TCGA.CS.6290.01
#> "01" "03" "02" "02" "01" "03"
#> TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.06.5858.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01 TCGA.HT.7860.01
#> "02" "02" "01" "03" "02" "01"
#> TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.14.0740.01 TCGA.S9.A7J3.01 TCGA.81.5911.01
#> "02" "02" "02" "01" "02" "01"
#> TCGA.06.6701.01 TCGA.P5.A5F2.01 TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01
#> "02" "02" "02" "01" "03" "01"
#> TCGA.06.6390.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01 TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01
#> "01" "02" "02" "02" "02" "02"
#> TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.06.A5U0.01 TCGA.TM.A84L.01 TCGA.DU.8161.01 TCGA.19.5959.01
#> "03" "02" "01" "03" "01" "01"
#> TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01 TCGA.TM.A7C4.01
#> "02" "02" "02" "01" "03" "03"
#> TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.06.5413.01 TCGA.19.5947.01 TCGA.HT.8108.01
#> "02" "03" "02" "01" "01" "02"
#> TCGA.E1.A7YD.01 TCGA.19.5960.01 TCGA.DU.7304.01 TCGA.14.1034.02 TCGA.S9.A7IY.01 TCGA.FG.7641.01
#> "01" "01" "02" "01" "02" "02"
#> TCGA.P5.A736.01 TCGA.14.0736.02 TCGA.19.5952.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01 TCGA.HT.7470.01
#> "03" "01" "01" "02" "02" "03"
#> TCGA.28.5208.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.76.6280.01 TCGA.FG.A4MY.01
#> "01" "02" "03" "01" "01" "02"
#> TCGA.TM.A7CF.01 TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01
#> "02" "03" "02" "02" "01" "02"
#> TCGA.DU.7010.01 TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.28.2510.01 TCGA.DU.A7TD.01 TCGA.14.0736.01
#> "02" "03" "03" "01" "01" "01"
#> TCGA.DU.6405.01 TCGA.06.0152.02 TCGA.06.0152.01 TCGA.76.4927.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "01" "01" "01" "01" "02" "02"
#> TCGA.DU.6401.01 TCGA.26.5132.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01
#> "02" "01" "03" "02" "02" "02"
#> TCGA.HT.A74H.01 TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01
#> "01" "03" "03" "03" "01" "02"
#> TCGA.DB.A64L.01 TCGA.VV.A829.01 TCGA.19.A6J4.01 TCGA.HT.A61B.01 TCGA.12.5299.01 TCGA.DH.A66B.01
#> "02" "02" "01" "02" "01" "02"
#> TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01 TCGA.HT.A4DS.01 TCGA.12.5301.01 TCGA.RR.A6KB.01
#> "03" "02" "02" "01" "01" "01"
#> TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01 TCGA.DB.A64P.01
#> "02" "02" "02" "02" "01" "02"
#> TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01 TCGA.06.6389.01
#> "03" "03" "02" "03" "03" "02"
#> TCGA.HW.A5KL.01 TCGA.06.5416.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.26.5139.01
#> "02" "01" "01" "03" "02" "01"
#> TCGA.QH.A6CZ.01 TCGA.DH.A669.02 TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01
#> "02" "02" "02" "02" "03" "02"
#> TCGA.TQ.A7RJ.01 TCGA.WY.A858.01 TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.41.6646.01 TCGA.14.0781.01
#> "02" "03" "01" "02" "01" "01"
#> TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01 TCGA.TM.A84I.01 TCGA.CS.5394.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01 TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "01" "02" "02" "01" "03" "02"
#> TCGA.74.6578.01
#> "01"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 39547))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "03" "02" "03" "02" "03" "01"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.74.6577.01 TCGA.06.AABW.11 TCGA.06.0125.02 TCGA.HT.A74L.01
#> "02" "02" "01" "01" "01" "02"
#> TCGA.26.A7UX.01 TCGA.DU.A5TS.01 TCGA.06.6388.01 TCGA.DB.A4XA.01 TCGA.06.A7TL.01 TCGA.HT.A4DV.01
#> "01" "02" "01" "03" "02" "03"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.28.5213.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01
#> "01" "02" "01" "02" "02" "02"
#> TCGA.HT.8113.01 TCGA.DH.A66G.01 TCGA.76.4932.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01
#> "03" "02" "01" "03" "02" "02"
#> TCGA.06.5412.01 TCGA.HT.7689.01 TCGA.06.6694.01 TCGA.HT.8109.01 TCGA.E1.A7YE.01 TCGA.S9.A7R1.01
#> "01" "03" "01" "03" "03" "02"
#> TCGA.FG.A710.01 TCGA.19.1389.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01 TCGA.QH.A6CU.01
#> "02" "01" "02" "02" "03" "03"
#> TCGA.HW.7486.01 TCGA.12.5295.01 TCGA.FG.7634.01 TCGA.19.5953.01 TCGA.DU.8163.01 TCGA.28.5220.01
#> "03" "01" "02" "01" "03" "01"
#> TCGA.4W.AA9T.01 TCGA.OX.A56R.01 TCGA.DU.6407.02 TCGA.DU.6407.01 TCGA.S9.A7IX.01 TCGA.HT.8010.01
#> "01" "01" "03" "02" "01" "03"
#> TCGA.06.0171.01 TCGA.06.0125.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.06.6700.01 TCGA.DU.7299.01 TCGA.28.5218.01 TCGA.06.0171.02
#> "01" "02" "01" "02" "01" "01"
#> TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.06.5856.01 TCGA.26.5136.01 TCGA.DU.7011.01 TCGA.TM.A84Q.01
#> "01" "02" "01" "01" "03" "02"
#> TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.76.6663.01 TCGA.DB.5270.01
#> "02" "01" "03" "02" "01" "03"
#> TCGA.S9.A6WQ.01 TCGA.76.4926.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.26.5133.01 TCGA.E1.A7YU.01
#> "03" "01" "03" "02" "03" "02"
#> TCGA.W9.A837.01 TCGA.TM.A7C5.01 TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01
#> "02" "02" "03" "02" "02" "02"
#> TCGA.HT.7601.01 TCGA.P5.A5ET.01 TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.26.1442.01 TCGA.19.A6J5.01
#> "03" "02" "02" "03" "03" "02"
#> TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.06.0211.02 TCGA.28.5207.01 TCGA.14.1402.01
#> "03" "02" "02" "01" "01" "01"
#> TCGA.06.0211.01 TCGA.14.1402.02 TCGA.HT.7873.01 TCGA.CS.4938.01 TCGA.19.4065.02 TCGA.RR.A6KC.01
#> "01" "01" "02" "02" "01" "01"
#> TCGA.19.4065.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "01" "02" "03" "02" "02" "02"
#> TCGA.HT.8563.01 TCGA.CS.4941.01 TCGA.RY.A843.01 TCGA.S9.A7IS.01 TCGA.TQ.A8XE.02 TCGA.S9.A6U0.01
#> "03" "01" "03" "02" "02" "01"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.06.5408.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.76.6285.01
#> "01" "02" "01" "02" "03" "01"
#> TCGA.DU.6403.01 TCGA.HW.7493.01 TCGA.19.5950.01 TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01
#> "01" "02" "01" "02" "02" "02"
#> TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01 TCGA.14.1395.01 TCGA.DH.A7UT.01 TCGA.DU.7015.01
#> "02" "02" "02" "01" "03" "02"
#> TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01 TCGA.FG.A60K.01 TCGA.HT.7856.01
#> "02" "01" "02" "03" "02" "03"
#> TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01 TCGA.S9.A6TY.01 TCGA.CS.5395.01
#> "01" "01" "03" "03" "02" "01"
#> TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01 TCGA.TM.A84O.01 TCGA.06.5410.01
#> "01" "01" "02" "02" "03" "01"
#> TCGA.19.5958.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.28.5211.01 TCGA.DU.5855.01
#> "01" "02" "02" "03" "01" "02"
#> TCGA.HT.7884.01 TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01
#> "02" "02" "01" "01" "02" "02"
#> TCGA.WH.A86K.01 TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01
#> "02" "01" "02" "01" "02" "03"
#> TCGA.06.6695.01 TCGA.06.5418.01 TCGA.HT.A618.01 TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.06.5415.01
#> "01" "01" "03" "02" "03" "01"
#> TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.06.A6S1.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01 TCGA.S9.A7IZ.01
#> "02" "01" "01" "02" "02" "02"
#> TCGA.DU.A6S7.01 TCGA.06.0221.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.26.5135.01 TCGA.P5.A5F4.01
#> "02" "02" "01" "02" "01" "02"
#> TCGA.QH.A65V.01 TCGA.28.5219.01 TCGA.4W.AA9S.01 TCGA.19.A60I.01 TCGA.76.4934.01 TCGA.FG.8191.01
#> "02" "01" "01" "01" "01" "02"
#> TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.32.5222.01 TCGA.76.6191.01 TCGA.06.1806.01
#> "02" "02" "02" "01" "01" "01"
#> TCGA.06.6693.01 TCGA.CS.6666.01 TCGA.DU.7298.01 TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01
#> "01" "02" "02" "02" "01" "01"
#> TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01 TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01
#> "03" "02" "02" "01" "02" "02"
#> TCGA.DH.A66D.01 TCGA.06.6697.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01 TCGA.DU.A76K.01 TCGA.TQ.A7RR.01
#> "02" "01" "02" "03" "01" "03"
#> TCGA.28.5215.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.15.1444.01 TCGA.P5.A735.01
#> "01" "01" "02" "02" "03" "02"
#> TCGA.DU.7294.01 TCGA.E1.A7YQ.01 TCGA.HT.7881.01 TCGA.QH.A6CS.01 TCGA.HT.7695.01 TCGA.P5.A5EU.01
#> "02" "01" "03" "01" "02" "03"
#> TCGA.76.6283.01 TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.76.4929.01 TCGA.S9.A6U5.01
#> "01" "02" "02" "03" "01" "02"
#> TCGA.HT.7609.01 TCGA.DB.5274.01 TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01
#> "02" "02" "02" "02" "01" "03"
#> TCGA.DU.A6S2.01 TCGA.19.1389.02 TCGA.26.6174.01 TCGA.S9.A7R7.01 TCGA.TM.A84R.01 TCGA.DB.A75M.01
#> "03" "01" "01" "03" "03" "02"
#> TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.06.0221.02 TCGA.HT.7477.01 TCGA.HT.8012.01 TCGA.32.1980.01
#> "01" "02" "03" "02" "02" "01"
#> TCGA.76.6661.01 TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01
#> "01" "02" "02" "02" "03" "02"
#> TCGA.28.5209.01 TCGA.S9.A7QZ.01 TCGA.QH.A6X4.01 TCGA.19.5951.01 TCGA.P5.A77W.01 TCGA.DU.7302.01
#> "01" "02" "02" "01" "02" "02"
#> TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.06.A6S0.01 TCGA.E1.5307.01 TCGA.S9.A7QW.01 TCGA.DU.6402.01
#> "01" "02" "01" "02" "02" "01"
#> TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01 TCGA.HW.7495.01 TCGA.QH.A65R.01
#> "02" "02" "01" "02" "02" "02"
#> TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01 TCGA.HT.8104.01 TCGA.FG.A70Z.01
#> "03" "02" "02" "03" "01" "01"
#> TCGA.DU.A7TC.01 TCGA.14.0862.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01 TCGA.E1.5303.01
#> "02" "01" "03" "03" "02" "02"
#> TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01 TCGA.FG.A4MU.01
#> "01" "03" "02" "02" "03" "01"
#> TCGA.HT.7875.01 TCGA.06.5417.01 TCGA.HT.7473.01 TCGA.19.5955.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01
#> "02" "02" "02" "01" "01" "03"
#> TCGA.DU.7008.01 TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.74.6581.01 TCGA.FG.8189.01
#> "02" "01" "01" "03" "01" "01"
#> TCGA.76.6662.01 TCGA.DB.A75O.01 TCGA.HT.7688.01 TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01
#> "01" "02" "03" "02" "02" "01"
#> TCGA.P5.A5EY.01 TCGA.RR.A6KA.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01 TCGA.DU.5872.02 TCGA.74.6573.11
#> "01" "01" "02" "02" "01" "01"
#> TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01 TCGA.DU.5874.01
#> "02" "03" "01" "02" "01" "02"
#> TCGA.S9.A6WE.01 TCGA.06.0650.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "02" "01" "02" "02" "01" "01"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "02" "03" "02" "03" "02" "02"
#> TCGA.76.6193.01 TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01
#> "01" "01" "02" "02" "01" "02"
#> TCGA.DB.A4XF.01 TCGA.HT.A74O.01 TCGA.06.6698.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01
#> "02" "02" "01" "02" "01" "02"
#> TCGA.14.1043.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01 TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.06.6391.01
#> "01" "01" "02" "02" "02" "01"
#> TCGA.76.4935.01 TCGA.E1.A7YJ.01 TCGA.06.5414.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.06.A7TK.01
#> "01" "01" "01" "03" "02" "01"
#> TCGA.06.5411.01 TCGA.S9.A6TS.01 TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01
#> "01" "02" "02" "02" "02" "02"
#> TCGA.76.6656.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01 TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01
#> "01" "01" "02" "01" "01" "02"
#> TCGA.DU.5849.01 TCGA.76.4925.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01 TCGA.4W.AA9R.01 TCGA.HT.7468.01
#> "03" "01" "02" "01" "01" "02"
#> TCGA.FG.6692.01 TCGA.81.5910.01 TCGA.28.5214.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01
#> "01" "01" "01" "02" "02" "02"
#> TCGA.HW.7489.01 TCGA.R8.A6YH.01 TCGA.74.6584.01 TCGA.DU.7018.01 TCGA.06.0190.01 TCGA.06.0190.02
#> "03" "02" "01" "02" "01" "01"
#> TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01 TCGA.76.6664.01 TCGA.HT.7690.01
#> "02" "03" "03" "02" "01" "02"
#> TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01 TCGA.HT.A5RA.01
#> "01" "02" "02" "02" "01" "01"
#> TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.26.5134.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "02" "03" "01" "02" "02" "02"
#> TCGA.28.2501.01 TCGA.HT.8013.01 TCGA.76.6286.01 TCGA.HW.7490.01 TCGA.14.1450.01 TCGA.76.6660.01
#> "01" "02" "01" "02" "01" "01"
#> TCGA.28.5204.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01 TCGA.06.1804.01
#> "01" "02" "02" "02" "01" "01"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.76.4931.01 TCGA.DB.A64V.01 TCGA.RY.A840.01
#> "03" "02" "01" "01" "03" "02"
#> TCGA.E1.5302.01 TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01
#> "03" "02" "03" "02" "03" "01"
#> TCGA.28.6450.01 TCGA.DU.5847.01 TCGA.E1.A7YK.01 TCGA.76.4928.01 TCGA.26.6173.01 TCGA.HT.7874.01
#> "01" "01" "03" "01" "01" "03"
#> TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01 TCGA.76.6282.01 TCGA.19.5954.01
#> "02" "01" "01" "02" "01" "01"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.32.1979.01 TCGA.DU.6408.01
#> "01" "02" "02" "01" "01" "02"
#> TCGA.87.5896.01 TCGA.DB.A4XB.01 TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01
#> "01" "02" "03" "02" "02" "02"
#> TCGA.P5.A72U.01 TCGA.QH.A870.01 TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.19.0957.01
#> "01" "02" "02" "01" "01" "01"
#> TCGA.19.0957.02 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01 TCGA.DU.A7TA.01 TCGA.HW.8319.01
#> "01" "03" "02" "01" "02" "02"
#> TCGA.06.5859.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01 TCGA.DU.6400.01
#> "01" "03" "02" "02" "03" "02"
#> TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.76.6657.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "02" "02" "02" "01" "02" "02"
#> TCGA.06.6699.01 TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01
#> "01" "02" "02" "03" "02" "02"
#> TCGA.E1.A7YN.01 TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.41.5651.01 TCGA.76.6192.01 TCGA.QH.A6XA.01
#> "01" "02" "02" "01" "01" "02"
#> TCGA.HT.8111.01 TCGA.74.6575.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01 TCGA.VM.A8CD.01 TCGA.RY.A83Y.01
#> "03" "01" "01" "02" "01" "02"
#> TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01 TCGA.06.0210.01 TCGA.06.0210.02
#> "02" "02" "02" "03" "01" "01"
#> TCGA.06.A5U1.01 TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.19.5956.01 TCGA.DB.A64W.01
#> "01" "02" "01" "02" "01" "02"
#> TCGA.R8.A6MO.01 TCGA.28.5216.01 TCGA.DU.A7T8.01 TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01
#> "02" "01" "02" "02" "02" "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 = 3442),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3442),
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 = 3477),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3477),
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 = 3513),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3513),
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 = 3544),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3544),
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 = 3605),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3605),
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 = 3621),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3621),
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 = 3669),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3669),
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 = 3702),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3702),
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 = 3736),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3736),
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 = 3806),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3806),
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 = 3846),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3846),
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 = 3958),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3958),
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 = 4112),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4112),
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 = 4199),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4199),
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 = 4915),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4915),
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 = 5006),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5006),
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 = 5899),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5899),
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 = 6182),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 6182),
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 = 7856),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 7856),
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 = 7999),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 7999),
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 = 8024),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 8024),
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 = 9621),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 9621),
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 = 9856),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 9856),
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 = 15681),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 15681),
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 = 18000),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 18000),
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 = 18964),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 18964),
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 = 20318),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 20318),
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 = 21160),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 21160),
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 = 39547),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 39547),
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 = 3442))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3477))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3513))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3544))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3605))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3621))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3669))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3702))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3736))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3806))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3846))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3958))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4112))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4199))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4915))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5006))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5899))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 6182))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 7856))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 7999))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 8024))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 9621))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 9856))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 15681))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 18000))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 18964))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 20318))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 21160))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 39547))
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 .
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 375962 rows and 500 columns, randomly sampled from 685 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 '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 1.000 1.000 0.4687 0.532 0.532
#> 3 3 1.000 0.986 0.994 0.3134 0.848 0.715
#> 4 4 0.770 0.660 0.835 0.1135 0.877 0.697
#> 5 5 0.822 0.696 0.859 0.0882 0.917 0.750
#> 6 6 0.783 0.705 0.829 0.0324 0.943 0.796
#> 7 7 0.758 0.609 0.734 0.0289 0.914 0.655
#> 8 8 0.748 0.688 0.780 0.0266 0.932 0.666
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.
get_classes(res, k = 2)
#> class p
#> TCGA.E1.5319.01 2 0.000
#> TCGA.HT.7693.01 2 0.000
#> TCGA.CS.6665.01 2 0.000
#> TCGA.S9.A7J2.01 2 0.000
#> TCGA.FG.A6J3.01 2 0.000
#> TCGA.FG.6688.01 1 0.000
#> TCGA.S9.A6TX.01 2 0.000
#> TCGA.VM.A8C8.01 2 0.000
#> TCGA.74.6577.01 1 0.000
#> TCGA.06.AABW.11 1 0.000
#> TCGA.06.0125.02 1 0.000
#> TCGA.HT.A74L.01 2 0.000
#> TCGA.26.A7UX.01 1 0.000
#> TCGA.DU.A5TS.01 2 0.000
#> TCGA.06.6388.01 1 0.000
#> TCGA.DB.A4XA.01 2 0.000
#> TCGA.06.A7TL.01 2 0.000
#> TCGA.HT.A4DV.01 2 0.000
#> TCGA.TQ.A7RP.01 1 0.000
#> TCGA.E1.5311.01 2 0.000
#> TCGA.28.5213.01 1 0.000
#> TCGA.E1.A7YI.01 2 0.000
#> TCGA.E1.5305.01 2 0.000
#> TCGA.F6.A8O4.01 2 0.000
#> TCGA.HT.8113.01 2 0.000
#> TCGA.DH.A66G.01 2 0.000
#> TCGA.76.4932.01 1 0.000
#> TCGA.HT.7620.01 2 0.000
#> TCGA.P5.A731.01 2 0.000
#> TCGA.HT.7480.01 2 0.000
#> TCGA.06.5412.01 1 0.000
#> TCGA.HT.7689.01 2 0.000
#> TCGA.06.6694.01 1 0.000
#> TCGA.HT.8109.01 2 0.000
#> TCGA.E1.A7YE.01 2 0.000
#> TCGA.S9.A7R1.01 2 0.000
#> TCGA.FG.A710.01 2 0.000
#> TCGA.19.1389.01 1 0.000
#> TCGA.S9.A7J0.01 2 0.000
#> TCGA.DU.A6S6.01 2 0.000
#> TCGA.HT.7877.01 2 0.000
#> TCGA.QH.A6CU.01 2 0.000
#> TCGA.HW.7486.01 2 0.000
#> TCGA.12.5295.01 1 0.000
#> TCGA.FG.7634.01 2 0.000
#> TCGA.19.5953.01 1 0.000
#> TCGA.DU.8163.01 2 0.000
#> TCGA.28.5220.01 1 0.000
#> TCGA.4W.AA9T.01 1 0.000
#> TCGA.OX.A56R.01 1 0.000
#> TCGA.DU.6407.02 2 0.000
#> TCGA.DU.6407.01 2 0.000
#> TCGA.S9.A7IX.01 1 0.000
#> TCGA.HT.8010.01 2 0.000
#> TCGA.06.0171.01 1 0.000
#> TCGA.06.0125.01 1 0.000
#> TCGA.P5.A5F1.01 2 0.000
#> TCGA.VM.A8CF.01 2 0.000
#> TCGA.DU.6542.01 2 0.000
#> TCGA.FG.7638.01 2 0.000
#> TCGA.VW.A8FI.01 1 0.000
#> TCGA.DH.5143.01 2 0.000
#> TCGA.06.6700.01 1 0.000
#> TCGA.DU.7299.01 2 0.000
#> TCGA.28.5218.01 1 0.000
#> TCGA.06.0171.02 1 0.000
#> TCGA.DU.8165.01 1 0.000
#> TCGA.CS.5393.01 2 0.000
#> TCGA.06.5856.01 1 0.000
#> TCGA.26.5136.01 1 0.000
#> TCGA.DU.7011.01 2 0.000
#> TCGA.TM.A84Q.01 2 0.000
#> TCGA.DB.5281.01 2 0.000
#> TCGA.DU.A76L.01 1 0.000
#> TCGA.HT.7605.01 2 0.000
#> TCGA.FG.A6J1.01 2 0.000
#> TCGA.76.6663.01 1 0.000
#> TCGA.DB.5270.01 2 0.000
#> TCGA.S9.A6WQ.01 2 0.000
#> TCGA.76.4926.01 1 0.000
#> TCGA.HT.8106.01 2 0.000
#> TCGA.HT.7608.01 2 0.000
#> TCGA.26.5133.01 2 0.000
#> TCGA.E1.A7YU.01 2 0.000
#> TCGA.W9.A837.01 2 0.000
#> TCGA.TM.A7C5.01 2 0.000
#> TCGA.S9.A7QY.01 2 0.000
#> TCGA.QH.A6CW.01 2 0.000
#> TCGA.S9.A6WO.01 2 0.000
#> TCGA.IK.7675.01 2 0.000
#> TCGA.HT.7601.01 2 0.000
#> TCGA.P5.A5ET.01 2 0.000
#> TCGA.HT.7472.01 2 0.000
#> TCGA.HT.7880.01 2 0.000
#> TCGA.26.1442.01 2 0.000
#> TCGA.19.A6J5.01 2 0.000
#> TCGA.E1.A7Z3.01 2 0.000
#> TCGA.P5.A77X.01 2 0.000
#> TCGA.FG.A6IZ.01 2 0.000
#> TCGA.06.0211.02 1 0.000
#> TCGA.28.5207.01 1 0.000
#> TCGA.14.1402.01 1 0.000
#> TCGA.06.0211.01 1 0.000
#> TCGA.14.1402.02 1 0.000
#> TCGA.HT.7873.01 2 0.000
#> TCGA.CS.4938.01 2 0.000
#> TCGA.19.4065.02 1 0.000
#> TCGA.RR.A6KC.01 1 0.000
#> TCGA.19.4065.01 1 0.000
#> TCGA.KT.A74X.01 2 0.000
#> TCGA.P5.A5EX.01 2 0.000
#> TCGA.VM.A8CH.01 2 0.000
#> TCGA.HT.7476.01 2 0.000
#> TCGA.DB.A75L.01 2 0.000
#> TCGA.HT.8563.01 2 0.000
#> TCGA.CS.4941.01 1 0.000
#> TCGA.RY.A843.01 2 0.000
#> TCGA.S9.A7IS.01 2 0.000
#> TCGA.TQ.A8XE.02 2 0.000
#> TCGA.S9.A6U0.01 1 0.000
#> TCGA.FG.7643.01 1 0.000
#> TCGA.E1.A7YO.01 2 0.000
#> TCGA.06.5408.01 1 0.000
#> TCGA.TQ.A7RG.01 2 0.000
#> TCGA.QH.A6X5.01 2 0.000
#> TCGA.76.6285.01 1 0.000
#> TCGA.DU.6403.01 1 0.000
#> TCGA.HW.7493.01 2 0.000
#> TCGA.19.5950.01 1 0.000
#> TCGA.RY.A847.01 2 0.000
#> TCGA.DU.8166.01 2 0.000
#> TCGA.VM.A8CA.01 2 0.000
#> TCGA.HT.7855.01 2 0.000
#> TCGA.S9.A89Z.01 2 0.000
#> TCGA.DB.A4XG.01 2 0.000
#> TCGA.14.1395.01 1 0.000
#> TCGA.DH.A7UT.01 2 0.000
#> TCGA.DU.7015.01 2 0.000
#> TCGA.HT.A616.01 2 0.000
#> TCGA.FG.8181.01 1 0.000
#> TCGA.HT.7611.01 2 0.000
#> TCGA.HT.8018.01 2 0.000
#> TCGA.FG.A60K.01 2 0.000
#> TCGA.HT.7856.01 2 0.000
#> TCGA.FG.5963.01 1 0.000
#> TCGA.FG.5963.02 1 0.000
#> TCGA.DU.5851.01 2 0.000
#> TCGA.DU.A7T6.01 2 0.000
#> TCGA.S9.A6TY.01 2 0.000
#> TCGA.CS.5395.01 1 0.000
#> TCGA.DU.7292.01 1 0.000
#> TCGA.HT.A5RC.01 1 0.000
#> TCGA.WY.A85C.01 2 0.000
#> TCGA.DB.A4XC.01 2 0.000
#> TCGA.TM.A84O.01 2 0.000
#> TCGA.06.5410.01 1 0.000
#> TCGA.19.5958.01 1 0.000
#> TCGA.P5.A72W.01 2 0.000
#> TCGA.S9.A6TU.01 2 0.000
#> TCGA.HT.A61A.01 2 0.000
#> TCGA.28.5211.01 1 0.000
#> TCGA.DU.5855.01 2 0.000
#> TCGA.HT.7884.01 2 0.000
#> TCGA.TQ.A7RQ.01 2 0.000
#> TCGA.TM.A84C.01 1 0.000
#> TCGA.FG.A4MW.01 1 0.000
#> TCGA.IK.8125.01 2 0.000
#> TCGA.HT.A74K.01 2 0.000
#> TCGA.WH.A86K.01 2 0.000
#> TCGA.DB.A75P.01 1 0.000
#> TCGA.QH.A6X8.01 2 0.000
#> TCGA.S9.A89V.01 1 0.000
#> TCGA.WY.A85E.01 2 0.000
#> TCGA.HT.A5R5.01 2 0.000
#> TCGA.06.6695.01 1 0.000
#> TCGA.06.5418.01 1 0.000
#> TCGA.HT.A618.01 2 0.000
#> TCGA.FG.6691.01 2 0.000
#> TCGA.HT.7467.01 2 0.000
#> TCGA.06.5415.01 1 0.000
#> TCGA.S9.A7R3.01 2 0.000
#> TCGA.QH.A6CX.01 1 0.000
#> TCGA.06.A6S1.01 1 0.000
#> TCGA.FG.A4MX.01 2 0.000
#> TCGA.HT.7681.01 2 0.000
#> TCGA.S9.A7IZ.01 2 0.000
#> TCGA.DU.A6S7.01 2 0.000
#> TCGA.06.0221.01 2 0.000
#> TCGA.P5.A72Z.01 2 0.000
#> TCGA.HT.8114.01 2 0.000
#> TCGA.DU.8168.01 2 0.000
#> TCGA.HW.8321.01 2 0.000
#> TCGA.TQ.A7RN.01 2 0.000
#> TCGA.DH.5141.01 2 0.000
#> TCGA.CS.6186.01 1 0.000
#> TCGA.EZ.7264.01 2 0.000
#> TCGA.26.5135.01 1 0.000
#> TCGA.P5.A5F4.01 2 0.000
#> TCGA.QH.A65V.01 2 0.000
#> TCGA.28.5219.01 1 0.000
#> TCGA.4W.AA9S.01 1 0.000
#> TCGA.19.A60I.01 1 0.000
#> TCGA.76.4934.01 1 0.000
#> TCGA.FG.8191.01 2 0.000
#> TCGA.DH.5142.01 2 0.000
#> TCGA.DU.A6S8.01 2 0.000
#> TCGA.E1.A7YW.01 2 0.000
#> TCGA.32.5222.01 1 0.000
#> TCGA.76.6191.01 1 0.000
#> TCGA.06.1806.01 1 0.000
#> TCGA.06.6693.01 1 0.000
#> TCGA.CS.6666.01 2 0.000
#> TCGA.DU.7298.01 2 0.000
#> TCGA.DB.A64R.01 2 0.000
#> TCGA.DU.6406.01 1 0.000
#> TCGA.S9.A6UA.01 1 0.000
#> TCGA.FG.A60L.01 2 0.000
#> TCGA.CS.5390.01 2 0.000
#> TCGA.S9.A6WP.01 2 0.000
#> TCGA.DU.A7TB.01 1 0.000
#> TCGA.DB.5280.01 2 0.000
#> TCGA.TM.A84T.01 2 0.000
#> TCGA.DH.A66D.01 2 0.000
#> TCGA.06.6697.01 1 0.000
#> TCGA.RY.A83Z.01 2 0.000
#> TCGA.DB.5278.01 2 0.000
#> TCGA.DU.A76K.01 1 0.000
#> TCGA.TQ.A7RR.01 2 0.000
#> TCGA.28.5215.01 1 0.000
#> TCGA.DU.8162.01 1 0.000
#> TCGA.TQ.A7RH.01 2 0.000
#> TCGA.E1.A7YS.01 2 0.000
#> TCGA.15.1444.01 2 0.000
#> TCGA.P5.A735.01 2 0.000
#> TCGA.DU.7294.01 2 0.000
#> TCGA.E1.A7YQ.01 1 0.000
#> TCGA.HT.7881.01 2 0.000
#> TCGA.QH.A6CS.01 1 0.000
#> TCGA.HT.7695.01 2 0.000
#> TCGA.P5.A5EU.01 2 0.000
#> TCGA.76.6283.01 1 0.000
#> TCGA.DB.A64X.01 2 0.000
#> TCGA.FG.7637.01 2 0.000
#> TCGA.VM.A8CE.01 2 0.000
#> TCGA.76.4929.01 1 0.000
#> TCGA.S9.A6U5.01 2 0.000
#> TCGA.HT.7609.01 2 0.000
#> TCGA.DB.5274.01 2 0.000
#> TCGA.HW.7487.01 2 0.000
#> TCGA.HW.7491.01 2 0.000
#> TCGA.HT.7691.01 1 0.000
#> TCGA.CS.4944.01 2 0.000
#> TCGA.DU.A6S2.01 2 0.000
#> TCGA.19.1389.02 1 0.000
#> TCGA.26.6174.01 1 0.000
#> TCGA.S9.A7R7.01 2 0.000
#> TCGA.TM.A84R.01 2 0.000
#> TCGA.DB.A75M.01 2 0.000
#> TCGA.DU.6392.01 1 0.000
#> TCGA.HW.A5KM.01 2 0.000
#> TCGA.06.0221.02 2 0.000
#> TCGA.HT.7477.01 2 0.000
#> TCGA.HT.8012.01 2 0.000
#> TCGA.32.1980.01 1 0.000
#> TCGA.76.6661.01 1 0.000
#> TCGA.DU.8167.01 2 0.000
#> TCGA.S9.A6U1.01 2 0.000
#> TCGA.FG.5965.01 2 0.000
#> TCGA.FG.8187.01 2 0.000
#> TCGA.HT.A614.01 2 0.000
#> TCGA.28.5209.01 1 0.000
#> TCGA.S9.A7QZ.01 2 0.000
#> TCGA.QH.A6X4.01 2 0.000
#> TCGA.19.5951.01 1 0.000
#> TCGA.P5.A77W.01 2 0.000
#> TCGA.DU.7302.01 2 0.000
#> TCGA.DU.7012.01 1 0.000
#> TCGA.DU.6399.01 2 0.000
#> TCGA.06.A6S0.01 1 0.000
#> TCGA.E1.5307.01 2 0.000
#> TCGA.S9.A7QW.01 2 0.000
#> TCGA.DU.6402.01 1 0.000
#> TCGA.HT.7604.01 2 0.000
#> TCGA.P5.A733.01 2 0.000
#> TCGA.FG.A87Q.01 1 0.000
#> TCGA.HT.7684.01 2 0.000
#> TCGA.HW.7495.01 2 0.000
#> TCGA.QH.A65R.01 2 0.000
#> TCGA.DU.A7TG.01 2 0.000
#> TCGA.DH.A7UV.01 2 0.000
#> TCGA.HT.7879.01 2 0.000
#> TCGA.TM.A84F.01 2 0.000
#> TCGA.HT.8104.01 1 0.000
#> TCGA.FG.A70Z.01 1 0.000
#> TCGA.DU.A7TC.01 2 0.000
#> TCGA.14.0862.01 1 0.000
#> TCGA.HT.7610.01 2 0.000
#> TCGA.S9.A6TW.01 2 0.000
#> TCGA.FG.A60J.01 2 0.000
#> TCGA.E1.5303.01 2 0.000
#> TCGA.QH.A6XC.01 1 0.000
#> TCGA.HT.7481.01 2 0.000
#> TCGA.FN.7833.01 2 0.000
#> TCGA.E1.A7Z4.01 2 0.000
#> TCGA.DU.A5TR.01 2 0.000
#> TCGA.FG.A4MU.01 1 0.000
#> TCGA.HT.7875.01 2 0.000
#> TCGA.06.5417.01 2 0.000
#> TCGA.HT.7473.01 2 0.000
#> TCGA.19.5955.01 1 0.000
#> TCGA.TM.A7C3.01 1 0.000
#> TCGA.S9.A7IQ.01 2 0.000
#> TCGA.DU.7008.01 2 0.000
#> TCGA.DB.A64O.01 1 0.000
#> TCGA.DU.A5TT.01 1 0.000
#> TCGA.S9.A6WG.01 2 0.000
#> TCGA.74.6581.01 1 0.000
#> TCGA.FG.8189.01 1 0.000
#> TCGA.76.6662.01 1 0.000
#> TCGA.DB.A75O.01 2 0.000
#> TCGA.HT.7688.01 2 0.000
#> TCGA.DU.7304.02 2 0.000
#> TCGA.DU.6394.01 2 0.000
#> TCGA.HT.8019.01 1 0.000
#> TCGA.P5.A5EY.01 1 0.000
#> TCGA.RR.A6KA.01 1 0.000
#> TCGA.S9.A6WD.01 2 0.000
#> TCGA.DU.5872.01 2 0.000
#> TCGA.DU.5872.02 1 0.000
#> TCGA.74.6573.11 1 0.000
#> TCGA.FG.8185.01 2 0.000
#> TCGA.HT.7902.01 2 0.000
#> TCGA.CS.5397.01 1 0.000
#> TCGA.TQ.A7RU.01 2 0.000
#> TCGA.HW.A5KK.01 1 0.000
#> TCGA.DU.5874.01 2 0.000
#> TCGA.S9.A6WE.01 2 0.000
#> TCGA.06.0650.01 1 0.000
#> TCGA.FG.6690.01 2 0.000
#> TCGA.HW.8320.01 2 0.000
#> TCGA.CS.6669.01 1 0.000
#> TCGA.S9.A7R2.01 1 0.000
#> TCGA.R8.A6MK.01 2 0.000
#> TCGA.QH.A6CY.01 2 0.000
#> TCGA.S9.A7J1.01 2 0.000
#> TCGA.P5.A72X.01 2 0.000
#> TCGA.E1.5322.01 2 0.000
#> TCGA.P5.A5F0.01 2 0.000
#> TCGA.76.6193.01 1 0.000
#> TCGA.S9.A6WM.01 1 0.000
#> TCGA.R8.A73M.01 2 0.000
#> TCGA.CS.4942.01 2 0.000
#> TCGA.HT.7680.01 1 0.000
#> TCGA.DB.A4X9.01 2 0.000
#> TCGA.DB.A4XF.01 2 0.000
#> TCGA.HT.A74O.01 2 0.000
#> TCGA.06.6698.01 1 0.000
#> TCGA.FG.8188.01 2 0.000
#> TCGA.P5.A5F6.01 1 0.000
#> TCGA.DU.A6S3.01 2 0.000
#> TCGA.14.1043.01 1 0.000
#> TCGA.HT.8110.01 1 0.000
#> TCGA.DB.A4XH.01 2 0.000
#> TCGA.HT.7485.01 2 0.000
#> TCGA.VW.A7QS.01 2 0.000
#> TCGA.06.6391.01 1 0.000
#> TCGA.76.4935.01 1 0.000
#> TCGA.E1.A7YJ.01 1 0.000
#> TCGA.06.5414.01 1 0.000
#> TCGA.S9.A6WI.01 2 0.000
#> TCGA.DU.8164.01 2 0.000
#> TCGA.06.A7TK.01 1 0.000
#> TCGA.06.5411.01 1 0.000
#> TCGA.S9.A6TS.01 2 0.000
#> TCGA.DB.A64S.01 2 0.000
#> TCGA.VV.A86M.01 2 0.000
#> TCGA.TQ.A8XE.01 2 0.000
#> TCGA.CS.6667.01 2 0.000
#> TCGA.76.6656.01 1 0.000
#> TCGA.E1.A7YL.01 1 0.000
#> TCGA.E1.A7YV.01 2 0.000
#> TCGA.HT.8558.01 1 0.000
#> TCGA.HT.A61C.01 1 0.000
#> TCGA.TQ.A7RW.01 2 0.000
#> TCGA.DU.5849.01 2 0.000
#> TCGA.76.4925.01 1 0.000
#> TCGA.DU.A7TI.01 2 0.000
#> TCGA.QH.A6CV.01 1 0.000
#> TCGA.4W.AA9R.01 1 0.000
#> TCGA.HT.7468.01 2 0.000
#> TCGA.FG.6692.01 1 0.000
#> TCGA.81.5910.01 1 0.000
#> TCGA.28.5214.01 1 0.000
#> TCGA.TQ.A7RI.01 2 0.000
#> TCGA.DB.5279.01 2 0.000
#> TCGA.S9.A6U8.01 2 0.000
#> TCGA.HW.7489.01 2 0.000
#> TCGA.R8.A6YH.01 2 0.000
#> TCGA.74.6584.01 1 0.000
#> TCGA.DU.7018.01 2 0.000
#> TCGA.06.0190.01 1 0.000
#> TCGA.06.0190.02 1 0.000
#> TCGA.HT.7677.01 2 0.000
#> TCGA.FG.A713.01 2 0.000
#> TCGA.DU.7300.01 2 0.000
#> TCGA.TM.A7CA.01 2 0.000
#> TCGA.76.6664.01 1 0.000
#> TCGA.HT.7690.01 2 0.000
#> TCGA.DU.7013.01 1 0.000
#> TCGA.FG.6689.01 2 0.000
#> TCGA.DU.7007.01 2 0.000
#> TCGA.TQ.A7RF.01 2 0.000
#> TCGA.KT.A7W1.01 1 0.000
#> TCGA.HT.A5RA.01 1 0.000
#> TCGA.DB.5277.01 2 0.000
#> TCGA.HT.7694.01 2 0.000
#> TCGA.26.5134.01 1 0.000
#> TCGA.TM.A84M.01 2 0.000
#> TCGA.F6.A8O3.01 2 0.000
#> TCGA.QH.A86X.01 2 0.000
#> TCGA.28.2501.01 1 0.000
#> TCGA.HT.8013.01 2 0.000
#> TCGA.76.6286.01 1 0.000
#> TCGA.HW.7490.01 2 0.000
#> TCGA.14.1450.01 1 0.000
#> TCGA.76.6660.01 1 0.000
#> TCGA.28.5204.01 1 0.000
#> TCGA.QH.A65S.01 2 0.000
#> TCGA.DU.A76R.01 2 0.000
#> TCGA.DH.5144.01 2 0.000
#> TCGA.CS.6188.01 1 0.000
#> TCGA.06.1804.01 1 0.000
#> TCGA.P5.A780.01 2 0.000
#> TCGA.HT.7606.01 2 0.000
#> TCGA.DU.A7TJ.01 1 0.000
#> TCGA.76.4931.01 1 0.000
#> TCGA.DB.A64V.01 2 0.000
#> TCGA.RY.A840.01 2 0.000
#> TCGA.E1.5302.01 2 0.000
#> TCGA.HW.A5KJ.01 2 0.000
#> TCGA.HT.A615.01 2 0.000
#> TCGA.HT.8105.01 2 0.000
#> TCGA.DU.7309.01 2 0.000
#> TCGA.DU.A5TY.01 1 0.000
#> TCGA.28.6450.01 1 0.000
#> TCGA.DU.5847.01 1 0.000
#> TCGA.E1.A7YK.01 2 0.000
#> TCGA.76.4928.01 1 0.000
#> TCGA.26.6173.01 1 0.000
#> TCGA.HT.7874.01 2 0.000
#> TCGA.HT.7471.01 2 0.000
#> TCGA.HT.7882.01 1 0.000
#> TCGA.DU.5854.01 1 0.000
#> TCGA.DU.6395.01 2 0.000
#> TCGA.76.6282.01 1 0.000
#> TCGA.19.5954.01 1 0.000
#> TCGA.HT.8011.01 1 0.000
#> TCGA.S9.A6TV.01 2 0.000
#> TCGA.P5.A5EW.01 2 0.000
#> TCGA.DU.5852.01 1 0.000
#> TCGA.32.1979.01 1 0.000
#> TCGA.DU.6408.01 2 0.000
#> TCGA.87.5896.01 1 0.000
#> TCGA.DB.A4XB.01 2 0.000
#> TCGA.E1.A7YY.01 1 1.000
#> TCGA.FG.A4MT.01 2 0.000
#> TCGA.FG.A4MT.02 2 0.000
#> TCGA.HT.A619.01 2 0.000
#> TCGA.P5.A72U.01 1 0.000
#> TCGA.QH.A870.01 2 0.000
#> TCGA.HT.A5R9.01 2 0.000
#> TCGA.DU.6404.02 1 0.000
#> TCGA.DU.6404.01 1 0.000
#> TCGA.19.0957.01 1 0.000
#> TCGA.19.0957.02 1 0.000
#> TCGA.FG.5964.01 2 0.000
#> TCGA.CS.5396.01 2 0.000
#> TCGA.HT.8107.01 1 0.000
#> TCGA.DU.A7TA.01 2 0.000
#> TCGA.HW.8319.01 2 0.000
#> TCGA.06.5859.01 1 0.000
#> TCGA.DH.A7UR.01 2 0.000
#> TCGA.TM.A84H.01 2 0.000
#> TCGA.S9.A6TZ.01 2 0.000
#> TCGA.HT.7479.01 2 0.000
#> TCGA.DU.6400.01 2 0.000
#> TCGA.S9.A6WL.01 2 0.000
#> TCGA.DB.A75K.01 2 0.000
#> TCGA.DB.A4XD.01 2 0.000
#> TCGA.76.6657.01 1 0.000
#> TCGA.DB.A64Q.01 2 0.000
#> TCGA.P5.A737.01 2 0.000
#> TCGA.06.6699.01 1 0.000
#> TCGA.DB.5275.01 2 0.000
#> TCGA.S9.A6WH.01 2 0.000
#> TCGA.HT.7602.01 2 0.000
#> TCGA.DU.A5TU.01 2 0.000
#> TCGA.HT.A5RB.01 2 0.000
#> TCGA.E1.A7YN.01 1 0.000
#> TCGA.HT.7616.01 2 0.000
#> TCGA.S9.A7R8.01 2 0.000
#> TCGA.41.5651.01 1 0.000
#> TCGA.76.6192.01 1 0.000
#> TCGA.QH.A6XA.01 2 0.000
#> TCGA.HT.8111.01 2 0.000
#> TCGA.74.6575.01 1 0.000
#> TCGA.E1.A7Z2.01 1 0.000
#> TCGA.DU.A5TP.01 2 0.000
#> TCGA.VM.A8CD.01 1 0.000
#> TCGA.RY.A83Y.01 2 0.000
#> TCGA.HT.7482.01 2 0.000
#> TCGA.TQ.A7RK.02 2 0.000
#> TCGA.TQ.A7RK.01 2 0.000
#> TCGA.HT.7858.01 2 0.000
#> TCGA.06.0210.01 1 0.000
#> TCGA.06.0210.02 1 0.000
#> TCGA.06.A5U1.01 1 0.000
#> TCGA.HT.7475.01 2 0.000
#> TCGA.HT.8564.01 1 0.000
#> TCGA.DB.A64U.01 2 0.000
#> TCGA.19.5956.01 1 0.000
#> TCGA.DB.A64W.01 2 0.000
#> TCGA.R8.A6MO.01 2 0.000
#> TCGA.28.5216.01 1 0.000
#> TCGA.DU.A7T8.01 2 0.000
#> TCGA.HW.8322.01 2 0.000
#> TCGA.DU.5870.02 2 0.000
#> TCGA.CS.6668.01 2 0.000
#> TCGA.DU.5870.01 2 0.000
#> TCGA.FG.7636.01 2 0.000
#> TCGA.HT.7692.01 2 0.000
#> TCGA.WY.A859.01 2 0.000
#> TCGA.HT.7854.01 1 0.000
#> TCGA.R8.A6ML.01 2 0.000
#> TCGA.VM.A8C9.01 1 0.000
#> TCGA.HT.7686.01 2 0.000
#> TCGA.DU.6410.01 2 0.000
#> TCGA.S9.A6U9.01 2 0.000
#> TCGA.74.6573.01 1 0.000
#> TCGA.CS.6290.01 2 0.000
#> TCGA.TQ.A7RO.01 2 0.000
#> TCGA.DU.7019.01 2 0.000
#> TCGA.06.5858.01 1 0.000
#> TCGA.FG.A711.01 2 0.000
#> TCGA.TQ.A7RM.01 2 0.000
#> TCGA.HT.7860.01 1 0.000
#> TCGA.S9.A7R4.01 2 0.000
#> TCGA.E1.5318.01 2 0.000
#> TCGA.HT.7676.01 2 0.000
#> TCGA.14.0740.01 1 0.000
#> TCGA.S9.A7J3.01 2 0.000
#> TCGA.81.5911.01 1 0.000
#> TCGA.06.6701.01 2 0.000
#> TCGA.P5.A5F2.01 2 0.000
#> TCGA.E1.5304.01 2 0.000
#> TCGA.DU.7006.01 1 0.000
#> TCGA.TM.A84S.01 2 0.000
#> TCGA.HT.7469.01 1 0.253
#> TCGA.06.6390.01 1 0.000
#> TCGA.WY.A85B.01 2 0.000
#> TCGA.TQ.A7RS.01 2 0.000
#> TCGA.S9.A7QX.01 2 0.000
#> TCGA.CS.4943.01 2 0.000
#> TCGA.QH.A65Z.01 2 0.000
#> TCGA.DB.5276.01 2 0.000
#> TCGA.P5.A730.01 2 0.000
#> TCGA.06.A5U0.01 1 0.000
#> TCGA.TM.A84L.01 2 0.000
#> TCGA.DU.8161.01 1 0.000
#> TCGA.19.5959.01 1 0.000
#> TCGA.WY.A85D.01 2 0.000
#> TCGA.RY.A83X.01 2 0.000
#> TCGA.S9.A6UB.01 2 0.000
#> TCGA.E1.A7YM.01 1 0.000
#> TCGA.DB.5273.01 2 0.000
#> TCGA.TM.A7C4.01 2 0.000
#> TCGA.DH.A66F.01 2 0.000
#> TCGA.HT.7607.01 2 0.000
#> TCGA.DU.6393.01 2 0.000
#> TCGA.06.5413.01 1 0.000
#> TCGA.19.5947.01 1 0.000
#> TCGA.HT.8108.01 2 0.000
#> TCGA.E1.A7YD.01 1 0.000
#> TCGA.19.5960.01 1 0.000
#> TCGA.DU.7304.01 2 0.000
#> TCGA.14.1034.02 1 0.000
#> TCGA.S9.A7IY.01 2 0.000
#> TCGA.FG.7641.01 2 0.000
#> TCGA.P5.A736.01 2 0.000
#> TCGA.14.0736.02 1 0.000
#> TCGA.19.5952.01 1 0.000
#> TCGA.P5.A5EV.01 2 0.000
#> TCGA.DU.7301.01 2 0.000
#> TCGA.HT.7470.01 2 0.000
#> TCGA.28.5208.01 1 0.000
#> TCGA.DU.7009.01 2 0.000
#> TCGA.P5.A781.01 2 0.000
#> TCGA.DH.5140.01 1 0.000
#> TCGA.76.6280.01 1 0.000
#> TCGA.FG.A4MY.01 2 0.000
#> TCGA.TM.A7CF.01 2 0.000
#> TCGA.TM.A7CF.02 2 0.000
#> TCGA.FG.8186.01 2 0.000
#> TCGA.S9.A6U6.01 2 0.000
#> TCGA.HT.8015.01 1 0.000
#> TCGA.RY.A845.01 2 0.000
#> TCGA.DU.7010.01 2 0.000
#> TCGA.S9.A6U2.01 2 0.000
#> TCGA.S9.A6WN.01 2 0.000
#> TCGA.28.2510.01 1 0.000
#> TCGA.DU.A7TD.01 1 0.000
#> TCGA.14.0736.01 1 0.000
#> TCGA.DU.6405.01 1 0.000
#> TCGA.06.0152.02 1 0.000
#> TCGA.06.0152.01 1 0.000
#> TCGA.76.4927.01 1 0.000
#> TCGA.FG.8182.01 2 0.000
#> TCGA.QH.A6X3.01 2 0.000
#> TCGA.DU.6401.01 2 0.000
#> TCGA.26.5132.01 1 0.000
#> TCGA.DU.6396.01 2 0.000
#> TCGA.E1.A7YH.01 2 0.000
#> TCGA.DU.7306.01 2 0.000
#> TCGA.HT.A74J.01 2 0.000
#> TCGA.HT.A74H.01 1 0.000
#> TCGA.DH.A7US.01 2 0.000
#> TCGA.FG.A87N.01 2 0.000
#> TCGA.HT.7478.01 2 0.000
#> TCGA.DU.7290.01 1 0.000
#> TCGA.DB.A4XE.01 2 0.000
#> TCGA.DB.A64L.01 2 0.000
#> TCGA.VV.A829.01 2 0.000
#> TCGA.19.A6J4.01 1 0.000
#> TCGA.HT.A61B.01 2 0.000
#> TCGA.12.5299.01 1 0.000
#> TCGA.DH.A66B.01 2 0.000
#> TCGA.HT.7603.01 2 0.000
#> TCGA.DU.6397.02 2 0.000
#> TCGA.DU.6397.01 2 0.000
#> TCGA.HT.A4DS.01 1 0.000
#> TCGA.12.5301.01 1 0.000
#> TCGA.RR.A6KB.01 1 0.000
#> TCGA.DU.5853.01 2 0.000
#> TCGA.CS.6670.01 2 0.000
#> TCGA.DU.7014.01 2 0.000
#> TCGA.QH.A65X.01 2 0.000
#> TCGA.TM.A84B.01 1 0.000
#> TCGA.DB.A64P.01 2 0.000
#> TCGA.FG.5965.02 2 0.000
#> TCGA.FG.A70Y.01 2 0.000
#> TCGA.TQ.A7RV.01 2 0.000
#> TCGA.TQ.A7RV.02 2 0.000
#> TCGA.HT.A5R7.01 2 0.000
#> TCGA.06.6389.01 2 0.000
#> TCGA.HW.A5KL.01 2 0.000
#> TCGA.06.5416.01 1 0.000
#> TCGA.DU.8158.01 1 0.000
#> TCGA.HT.7474.01 2 0.000
#> TCGA.DH.A7UU.01 2 0.000
#> TCGA.26.5139.01 1 0.000
#> TCGA.QH.A6CZ.01 2 0.000
#> TCGA.DH.A669.02 2 0.000
#> TCGA.DH.A669.01 2 0.000
#> TCGA.QH.A6X9.01 2 0.000
#> TCGA.P5.A5EZ.01 2 0.000
#> TCGA.DU.5871.01 2 0.000
#> TCGA.TQ.A7RJ.01 2 0.000
#> TCGA.WY.A858.01 2 0.000
#> TCGA.TM.A84J.01 1 1.000
#> TCGA.VM.A8CB.01 2 0.000
#> TCGA.41.6646.01 1 0.000
#> TCGA.14.0781.01 1 0.000
#> TCGA.HT.7483.01 2 0.000
#> TCGA.HT.7687.01 2 0.000
#> TCGA.TM.A84G.01 2 0.000
#> TCGA.E1.A7Z6.01 2 0.000
#> TCGA.TM.A84I.01 2 0.000
#> TCGA.CS.5394.01 2 0.000
#> TCGA.HT.A617.01 1 0.000
#> TCGA.DU.A76O.01 2 0.000
#> TCGA.DU.A5TW.01 2 0.000
#> TCGA.HT.7857.01 1 0.000
#> TCGA.WY.A85A.01 2 0.000
#> TCGA.FG.5962.01 2 0.000
#> TCGA.74.6578.01 1 0.000
get_classes(res, k = 3)
#> class p
#> TCGA.E1.5319.01 3 0.751
#> TCGA.HT.7693.01 2 0.000
#> TCGA.CS.6665.01 3 0.000
#> TCGA.S9.A7J2.01 2 0.000
#> TCGA.FG.A6J3.01 3 0.000
#> TCGA.FG.6688.01 1 0.000
#> TCGA.S9.A6TX.01 2 0.000
#> TCGA.VM.A8C8.01 2 0.000
#> TCGA.74.6577.01 1 0.000
#> TCGA.06.AABW.11 1 0.000
#> TCGA.06.0125.02 1 0.000
#> TCGA.HT.A74L.01 2 0.000
#> TCGA.26.A7UX.01 1 0.000
#> TCGA.DU.A5TS.01 2 0.000
#> TCGA.06.6388.01 1 0.000
#> TCGA.DB.A4XA.01 3 0.000
#> TCGA.06.A7TL.01 2 0.000
#> TCGA.HT.A4DV.01 3 0.000
#> TCGA.TQ.A7RP.01 1 0.000
#> TCGA.E1.5311.01 2 0.000
#> TCGA.28.5213.01 1 0.000
#> TCGA.E1.A7YI.01 2 1.000
#> TCGA.E1.5305.01 2 0.000
#> TCGA.F6.A8O4.01 2 0.000
#> TCGA.HT.8113.01 3 0.000
#> TCGA.DH.A66G.01 2 0.000
#> TCGA.76.4932.01 1 0.000
#> TCGA.HT.7620.01 3 0.000
#> TCGA.P5.A731.01 2 0.000
#> TCGA.HT.7480.01 2 0.000
#> TCGA.06.5412.01 1 0.000
#> TCGA.HT.7689.01 3 0.000
#> TCGA.06.6694.01 1 0.000
#> TCGA.HT.8109.01 3 0.000
#> TCGA.E1.A7YE.01 3 0.000
#> TCGA.S9.A7R1.01 2 0.000
#> TCGA.FG.A710.01 2 0.000
#> TCGA.19.1389.01 1 0.000
#> TCGA.S9.A7J0.01 2 0.000
#> TCGA.DU.A6S6.01 2 0.000
#> TCGA.HT.7877.01 3 0.000
#> TCGA.QH.A6CU.01 3 0.000
#> TCGA.HW.7486.01 3 0.000
#> TCGA.12.5295.01 1 0.000
#> TCGA.FG.7634.01 2 0.000
#> TCGA.19.5953.01 1 0.000
#> TCGA.DU.8163.01 3 0.000
#> TCGA.28.5220.01 1 0.000
#> TCGA.4W.AA9T.01 1 0.000
#> TCGA.OX.A56R.01 1 0.000
#> TCGA.DU.6407.02 3 0.000
#> TCGA.DU.6407.01 2 0.000
#> TCGA.S9.A7IX.01 1 0.000
#> TCGA.HT.8010.01 3 0.000
#> TCGA.06.0171.01 1 0.000
#> TCGA.06.0125.01 1 0.000
#> TCGA.P5.A5F1.01 2 0.000
#> TCGA.VM.A8CF.01 2 0.000
#> TCGA.DU.6542.01 2 0.000
#> TCGA.FG.7638.01 2 0.000
#> TCGA.VW.A8FI.01 1 0.000
#> TCGA.DH.5143.01 2 0.000
#> TCGA.06.6700.01 1 0.000
#> TCGA.DU.7299.01 2 0.000
#> TCGA.28.5218.01 1 0.000
#> TCGA.06.0171.02 1 0.000
#> TCGA.DU.8165.01 1 0.000
#> TCGA.CS.5393.01 2 0.000
#> TCGA.06.5856.01 1 0.000
#> TCGA.26.5136.01 1 0.000
#> TCGA.DU.7011.01 3 0.000
#> TCGA.TM.A84Q.01 2 0.000
#> TCGA.DB.5281.01 2 0.000
#> TCGA.DU.A76L.01 1 0.000
#> TCGA.HT.7605.01 3 0.000
#> TCGA.FG.A6J1.01 2 0.000
#> TCGA.76.6663.01 1 0.000
#> TCGA.DB.5270.01 3 0.000
#> TCGA.S9.A6WQ.01 3 0.000
#> TCGA.76.4926.01 1 0.000
#> TCGA.HT.8106.01 3 0.000
#> TCGA.HT.7608.01 2 0.000
#> TCGA.26.5133.01 3 0.000
#> TCGA.E1.A7YU.01 2 0.000
#> TCGA.W9.A837.01 2 0.000
#> TCGA.TM.A7C5.01 2 0.000
#> TCGA.S9.A7QY.01 3 0.249
#> TCGA.QH.A6CW.01 2 0.000
#> TCGA.S9.A6WO.01 2 0.000
#> TCGA.IK.7675.01 2 0.000
#> TCGA.HT.7601.01 3 0.000
#> TCGA.P5.A5ET.01 2 0.000
#> TCGA.HT.7472.01 2 0.000
#> TCGA.HT.7880.01 3 0.000
#> TCGA.26.1442.01 3 1.000
#> TCGA.19.A6J5.01 2 0.000
#> TCGA.E1.A7Z3.01 3 0.000
#> TCGA.P5.A77X.01 2 0.000
#> TCGA.FG.A6IZ.01 2 0.000
#> TCGA.06.0211.02 1 0.000
#> TCGA.28.5207.01 1 0.000
#> TCGA.14.1402.01 1 0.000
#> TCGA.06.0211.01 1 0.000
#> TCGA.14.1402.02 1 0.000
#> TCGA.HT.7873.01 2 0.000
#> TCGA.CS.4938.01 2 0.000
#> TCGA.19.4065.02 1 0.000
#> TCGA.RR.A6KC.01 1 0.000
#> TCGA.19.4065.01 1 0.000
#> TCGA.KT.A74X.01 2 0.000
#> TCGA.P5.A5EX.01 3 0.000
#> TCGA.VM.A8CH.01 2 0.000
#> TCGA.HT.7476.01 2 1.000
#> TCGA.DB.A75L.01 2 0.000
#> TCGA.HT.8563.01 3 0.000
#> TCGA.CS.4941.01 1 0.000
#> TCGA.RY.A843.01 3 0.000
#> TCGA.S9.A7IS.01 2 1.000
#> TCGA.TQ.A8XE.02 2 0.000
#> TCGA.S9.A6U0.01 1 0.000
#> TCGA.FG.7643.01 1 0.000
#> TCGA.E1.A7YO.01 2 0.000
#> TCGA.06.5408.01 1 0.000
#> TCGA.TQ.A7RG.01 2 0.000
#> TCGA.QH.A6X5.01 3 0.000
#> TCGA.76.6285.01 1 0.000
#> TCGA.DU.6403.01 1 0.000
#> TCGA.HW.7493.01 2 0.000
#> TCGA.19.5950.01 1 0.000
#> TCGA.RY.A847.01 2 0.000
#> TCGA.DU.8166.01 2 0.000
#> TCGA.VM.A8CA.01 2 0.000
#> TCGA.HT.7855.01 2 0.000
#> TCGA.S9.A89Z.01 2 0.000
#> TCGA.DB.A4XG.01 2 0.000
#> TCGA.14.1395.01 1 0.000
#> TCGA.DH.A7UT.01 3 0.000
#> TCGA.DU.7015.01 2 0.000
#> TCGA.HT.A616.01 2 0.000
#> TCGA.FG.8181.01 1 0.000
#> TCGA.HT.7611.01 2 0.000
#> TCGA.HT.8018.01 3 0.000
#> TCGA.FG.A60K.01 2 0.000
#> TCGA.HT.7856.01 3 0.000
#> TCGA.FG.5963.01 1 0.000
#> TCGA.FG.5963.02 1 0.000
#> TCGA.DU.5851.01 3 0.000
#> TCGA.DU.A7T6.01 3 0.000
#> TCGA.S9.A6TY.01 2 0.000
#> TCGA.CS.5395.01 1 0.000
#> TCGA.DU.7292.01 1 0.000
#> TCGA.HT.A5RC.01 1 0.000
#> TCGA.WY.A85C.01 2 0.000
#> TCGA.DB.A4XC.01 2 0.000
#> TCGA.TM.A84O.01 3 0.000
#> TCGA.06.5410.01 1 0.000
#> TCGA.19.5958.01 1 0.000
#> TCGA.P5.A72W.01 2 0.000
#> TCGA.S9.A6TU.01 2 0.000
#> TCGA.HT.A61A.01 3 0.000
#> TCGA.28.5211.01 1 0.000
#> TCGA.DU.5855.01 2 0.000
#> TCGA.HT.7884.01 2 0.000
#> TCGA.TQ.A7RQ.01 2 0.000
#> TCGA.TM.A84C.01 1 0.000
#> TCGA.FG.A4MW.01 1 0.000
#> TCGA.IK.8125.01 2 0.000
#> TCGA.HT.A74K.01 2 0.000
#> TCGA.WH.A86K.01 2 0.000
#> TCGA.DB.A75P.01 1 0.000
#> TCGA.QH.A6X8.01 2 0.000
#> TCGA.S9.A89V.01 1 0.000
#> TCGA.WY.A85E.01 2 0.000
#> TCGA.HT.A5R5.01 3 0.000
#> TCGA.06.6695.01 1 0.000
#> TCGA.06.5418.01 1 0.000
#> TCGA.HT.A618.01 3 0.000
#> TCGA.FG.6691.01 2 1.000
#> TCGA.HT.7467.01 3 0.000
#> TCGA.06.5415.01 1 0.000
#> TCGA.S9.A7R3.01 2 0.000
#> TCGA.QH.A6CX.01 1 0.000
#> TCGA.06.A6S1.01 1 0.000
#> TCGA.FG.A4MX.01 2 0.000
#> TCGA.HT.7681.01 2 0.000
#> TCGA.S9.A7IZ.01 2 0.000
#> TCGA.DU.A6S7.01 2 0.000
#> TCGA.06.0221.01 2 0.000
#> TCGA.P5.A72Z.01 2 0.000
#> TCGA.HT.8114.01 2 0.000
#> TCGA.DU.8168.01 2 0.000
#> TCGA.HW.8321.01 2 0.000
#> TCGA.TQ.A7RN.01 2 0.000
#> TCGA.DH.5141.01 2 0.000
#> TCGA.CS.6186.01 1 0.000
#> TCGA.EZ.7264.01 2 0.000
#> TCGA.26.5135.01 1 0.000
#> TCGA.P5.A5F4.01 2 0.000
#> TCGA.QH.A65V.01 2 0.000
#> TCGA.28.5219.01 1 0.000
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#> TCGA.QH.A6CZ.01 2 0.000
#> TCGA.DH.A669.02 2 0.000
#> TCGA.DH.A669.01 2 0.000
#> TCGA.QH.A6X9.01 2 0.000
#> TCGA.P5.A5EZ.01 3 0.000
#> TCGA.DU.5871.01 2 0.000
#> TCGA.TQ.A7RJ.01 2 0.000
#> TCGA.WY.A858.01 3 0.000
#> TCGA.TM.A84J.01 1 1.000
#> TCGA.VM.A8CB.01 2 0.000
#> TCGA.41.6646.01 1 0.000
#> TCGA.14.0781.01 1 0.000
#> TCGA.HT.7483.01 2 0.000
#> TCGA.HT.7687.01 2 0.000
#> TCGA.TM.A84G.01 2 0.000
#> TCGA.E1.A7Z6.01 2 0.000
#> TCGA.TM.A84I.01 2 0.000
#> TCGA.CS.5394.01 2 0.000
#> TCGA.HT.A617.01 1 0.000
#> TCGA.DU.A76O.01 2 0.000
#> TCGA.DU.A5TW.01 2 0.000
#> TCGA.HT.7857.01 1 0.000
#> TCGA.WY.A85A.01 3 0.000
#> TCGA.FG.5962.01 2 0.000
#> TCGA.74.6578.01 1 0.000
get_classes(res, k = 4)
#> class p
#> TCGA.E1.5319.01 2 0.000
#> TCGA.HT.7693.01 2 0.000
#> TCGA.CS.6665.01 3 0.000
#> TCGA.S9.A7J2.01 2 0.000
#> TCGA.FG.A6J3.01 3 0.000
#> TCGA.FG.6688.01 1 0.000
#> TCGA.S9.A6TX.01 2 0.000
#> TCGA.VM.A8C8.01 2 0.000
#> TCGA.74.6577.01 1 0.000
#> TCGA.06.AABW.11 1 0.000
#> TCGA.06.0125.02 1 0.000
#> TCGA.HT.A74L.01 2 0.000
#> TCGA.26.A7UX.01 1 0.000
#> TCGA.DU.A5TS.01 2 0.000
#> TCGA.06.6388.01 1 0.000
#> TCGA.DB.A4XA.01 3 0.502
#> TCGA.06.A7TL.01 2 0.000
#> TCGA.HT.A4DV.01 3 0.000
#> TCGA.TQ.A7RP.01 1 0.000
#> TCGA.E1.5311.01 2 0.000
#> TCGA.28.5213.01 1 0.000
#> TCGA.E1.A7YI.01 3 0.000
#> TCGA.E1.5305.01 2 0.000
#> TCGA.F6.A8O4.01 2 0.000
#> TCGA.HT.8113.01 3 0.000
#> TCGA.DH.A66G.01 2 0.000
#> TCGA.76.4932.01 1 0.000
#> TCGA.HT.7620.01 3 0.000
#> TCGA.P5.A731.01 2 0.000
#> TCGA.HT.7480.01 2 0.000
#> TCGA.06.5412.01 1 0.000
#> TCGA.HT.7689.01 3 0.249
#> TCGA.06.6694.01 1 0.000
#> TCGA.HT.8109.01 3 0.000
#> TCGA.E1.A7YE.01 3 0.000
#> TCGA.S9.A7R1.01 2 0.000
#> TCGA.FG.A710.01 2 0.000
#> TCGA.19.1389.01 1 0.000
#> TCGA.S9.A7J0.01 2 0.000
#> TCGA.DU.A6S6.01 2 0.000
#> TCGA.HT.7877.01 3 0.000
#> TCGA.QH.A6CU.01 3 0.000
#> TCGA.HW.7486.01 3 0.000
#> TCGA.12.5295.01 1 0.000
#> TCGA.FG.7634.01 2 0.000
#> TCGA.19.5953.01 1 0.000
#> TCGA.DU.8163.01 2 1.000
#> TCGA.28.5220.01 1 0.000
#> TCGA.4W.AA9T.01 1 0.000
#> TCGA.OX.A56R.01 1 0.000
#> TCGA.DU.6407.02 3 0.000
#> TCGA.DU.6407.01 2 0.000
#> TCGA.S9.A7IX.01 1 0.000
#> TCGA.HT.8010.01 3 0.000
#> TCGA.06.0171.01 1 0.000
#> TCGA.06.0125.01 1 0.000
#> TCGA.P5.A5F1.01 2 0.000
#> TCGA.VM.A8CF.01 2 0.000
#> TCGA.DU.6542.01 2 0.000
#> TCGA.FG.7638.01 2 0.000
#> TCGA.VW.A8FI.01 1 0.000
#> TCGA.DH.5143.01 2 0.000
#> TCGA.06.6700.01 1 0.000
#> TCGA.DU.7299.01 2 0.000
#> TCGA.28.5218.01 1 0.000
#> TCGA.06.0171.02 1 0.000
#> TCGA.DU.8165.01 1 0.000
#> TCGA.CS.5393.01 2 0.000
#> TCGA.06.5856.01 1 0.000
#> TCGA.26.5136.01 1 0.000
#> TCGA.DU.7011.01 3 0.000
#> TCGA.TM.A84Q.01 2 0.000
#> TCGA.DB.5281.01 2 0.000
#> TCGA.DU.A76L.01 1 0.000
#> TCGA.HT.7605.01 3 0.000
#> TCGA.FG.A6J1.01 2 0.000
#> TCGA.76.6663.01 1 0.000
#> TCGA.DB.5270.01 3 0.000
#> TCGA.S9.A6WQ.01 3 0.000
#> TCGA.76.4926.01 1 0.000
#> TCGA.HT.8106.01 3 0.000
#> TCGA.HT.7608.01 2 0.000
#> TCGA.26.5133.01 3 0.000
#> TCGA.E1.A7YU.01 2 0.000
#> TCGA.W9.A837.01 2 0.000
#> TCGA.TM.A7C5.01 2 0.000
#> TCGA.S9.A7QY.01 3 1.000
#> TCGA.QH.A6CW.01 2 0.000
#> TCGA.S9.A6WO.01 2 0.000
#> TCGA.IK.7675.01 2 0.000
#> TCGA.HT.7601.01 3 0.000
#> TCGA.P5.A5ET.01 2 0.000
#> TCGA.HT.7472.01 2 0.000
#> TCGA.HT.7880.01 3 0.000
#> TCGA.26.1442.01 2 0.000
#> TCGA.19.A6J5.01 2 0.000
#> TCGA.E1.A7Z3.01 3 0.000
#> TCGA.P5.A77X.01 2 0.000
#> TCGA.FG.A6IZ.01 2 0.000
#> TCGA.06.0211.02 1 0.000
#> TCGA.28.5207.01 1 0.000
#> TCGA.14.1402.01 1 0.000
#> TCGA.06.0211.01 1 0.000
#> TCGA.14.1402.02 1 0.000
#> TCGA.HT.7873.01 2 0.000
#> TCGA.CS.4938.01 2 0.000
#> TCGA.19.4065.02 1 0.000
#> TCGA.RR.A6KC.01 1 0.000
#> TCGA.19.4065.01 1 0.000
#> TCGA.KT.A74X.01 2 0.000
#> TCGA.P5.A5EX.01 3 0.000
#> TCGA.VM.A8CH.01 2 0.000
#> TCGA.HT.7476.01 2 0.000
#> TCGA.DB.A75L.01 2 0.000
#> TCGA.HT.8563.01 3 0.000
#> TCGA.CS.4941.01 1 0.000
#> TCGA.RY.A843.01 3 0.000
#> TCGA.S9.A7IS.01 3 0.000
#> TCGA.TQ.A8XE.02 2 0.000
#> TCGA.S9.A6U0.01 1 0.000
#> TCGA.FG.7643.01 1 0.000
#> TCGA.E1.A7YO.01 2 0.000
#> TCGA.06.5408.01 1 0.000
#> TCGA.TQ.A7RG.01 2 0.000
#> TCGA.QH.A6X5.01 3 0.000
#> TCGA.76.6285.01 1 0.000
#> TCGA.DU.6403.01 1 0.000
#> TCGA.HW.7493.01 2 0.000
#> TCGA.19.5950.01 1 0.000
#> TCGA.RY.A847.01 2 0.000
#> TCGA.DU.8166.01 2 0.000
#> TCGA.VM.A8CA.01 2 0.000
#> TCGA.HT.7855.01 2 0.000
#> TCGA.S9.A89Z.01 2 0.000
#> TCGA.DB.A4XG.01 2 0.000
#> TCGA.14.1395.01 1 0.000
#> TCGA.DH.A7UT.01 3 0.000
#> TCGA.DU.7015.01 2 0.000
#> TCGA.HT.A616.01 2 0.000
#> TCGA.FG.8181.01 1 0.000
#> TCGA.HT.7611.01 2 0.000
#> TCGA.HT.8018.01 3 0.000
#> TCGA.FG.A60K.01 2 0.000
#> TCGA.HT.7856.01 3 0.000
#> TCGA.FG.5963.01 1 0.000
#> TCGA.FG.5963.02 1 0.253
#> TCGA.DU.5851.01 3 0.000
#> TCGA.DU.A7T6.01 3 0.000
#> TCGA.S9.A6TY.01 2 0.000
#> TCGA.CS.5395.01 1 0.000
#> TCGA.DU.7292.01 1 0.000
#> TCGA.HT.A5RC.01 1 0.000
#> TCGA.WY.A85C.01 2 0.000
#> TCGA.DB.A4XC.01 2 0.000
#> TCGA.TM.A84O.01 3 0.000
#> TCGA.06.5410.01 1 0.000
#> TCGA.19.5958.01 1 0.000
#> TCGA.P5.A72W.01 2 0.000
#> TCGA.S9.A6TU.01 2 0.000
#> TCGA.HT.A61A.01 3 0.000
#> TCGA.28.5211.01 1 0.000
#> TCGA.DU.5855.01 2 0.000
#> TCGA.HT.7884.01 2 0.000
#> TCGA.TQ.A7RQ.01 2 0.000
#> TCGA.TM.A84C.01 1 0.000
#> TCGA.FG.A4MW.01 1 0.000
#> TCGA.IK.8125.01 2 0.000
#> TCGA.HT.A74K.01 2 0.000
#> TCGA.WH.A86K.01 2 0.000
#> TCGA.DB.A75P.01 1 0.000
#> TCGA.QH.A6X8.01 2 0.000
#> TCGA.S9.A89V.01 1 0.000
#> TCGA.WY.A85E.01 2 0.000
#> TCGA.HT.A5R5.01 3 0.000
#> TCGA.06.6695.01 1 0.000
#> TCGA.06.5418.01 1 0.000
#> TCGA.HT.A618.01 3 0.000
#> TCGA.FG.6691.01 2 0.000
#> TCGA.HT.7467.01 3 0.000
#> TCGA.06.5415.01 1 0.000
#> TCGA.S9.A7R3.01 2 0.000
#> TCGA.QH.A6CX.01 1 0.000
#> TCGA.06.A6S1.01 1 0.000
#> TCGA.FG.A4MX.01 2 0.000
#> TCGA.HT.7681.01 2 0.000
#> TCGA.S9.A7IZ.01 2 0.000
#> TCGA.DU.A6S7.01 2 0.000
#> TCGA.06.0221.01 2 0.000
#> TCGA.P5.A72Z.01 2 0.000
#> TCGA.HT.8114.01 2 0.000
#> TCGA.DU.8168.01 2 0.000
#> TCGA.HW.8321.01 2 0.000
#> TCGA.TQ.A7RN.01 2 0.000
#> TCGA.DH.5141.01 2 0.000
#> TCGA.CS.6186.01 1 0.000
#> TCGA.EZ.7264.01 2 0.000
#> TCGA.26.5135.01 1 0.000
#> TCGA.P5.A5F4.01 2 0.000
#> TCGA.QH.A65V.01 2 0.000
#> TCGA.28.5219.01 1 0.000
#> TCGA.4W.AA9S.01 1 0.000
#> TCGA.19.A60I.01 1 0.000
#> TCGA.76.4934.01 1 0.000
#> TCGA.FG.8191.01 2 0.000
#> TCGA.DH.5142.01 2 0.000
#> TCGA.DU.A6S8.01 2 0.000
#> TCGA.E1.A7YW.01 2 0.000
#> TCGA.32.5222.01 1 0.000
#> TCGA.76.6191.01 1 0.000
#> TCGA.06.1806.01 1 0.000
#> TCGA.06.6693.01 1 0.000
#> TCGA.CS.6666.01 2 0.000
#> TCGA.DU.7298.01 2 0.000
#> TCGA.DB.A64R.01 2 0.000
#> TCGA.DU.6406.01 1 0.000
#> TCGA.S9.A6UA.01 1 0.000
#> TCGA.FG.A60L.01 3 0.000
#> TCGA.CS.5390.01 2 0.000
#> TCGA.S9.A6WP.01 2 0.000
#> TCGA.DU.A7TB.01 1 0.000
#> TCGA.DB.5280.01 2 0.000
#> TCGA.TM.A84T.01 2 0.000
#> TCGA.DH.A66D.01 2 0.000
#> TCGA.06.6697.01 1 0.000
#> TCGA.RY.A83Z.01 2 0.000
#> TCGA.DB.5278.01 3 0.751
#> TCGA.DU.A76K.01 1 0.000
#> TCGA.TQ.A7RR.01 3 0.000
#> TCGA.28.5215.01 1 0.000
#> TCGA.DU.8162.01 1 0.000
#> TCGA.TQ.A7RH.01 2 0.000
#> TCGA.E1.A7YS.01 2 0.000
#> TCGA.15.1444.01 3 0.000
#> TCGA.P5.A735.01 2 0.000
#> TCGA.DU.7294.01 2 0.000
#> TCGA.E1.A7YQ.01 1 0.000
#> TCGA.HT.7881.01 3 0.000
#> TCGA.QH.A6CS.01 1 0.000
#> TCGA.HT.7695.01 2 0.000
#> TCGA.P5.A5EU.01 3 0.000
#> TCGA.76.6283.01 1 0.000
#> TCGA.DB.A64X.01 2 0.000
#> TCGA.FG.7637.01 2 0.000
#> TCGA.VM.A8CE.01 3 0.000
#> TCGA.76.4929.01 1 0.000
#> TCGA.S9.A6U5.01 2 0.000
#> TCGA.HT.7609.01 2 0.000
#> TCGA.DB.5274.01 2 0.000
#> TCGA.HW.7487.01 2 0.000
#> TCGA.HW.7491.01 2 0.000
#> TCGA.HT.7691.01 1 0.000
#> TCGA.CS.4944.01 2 1.000
#> TCGA.DU.A6S2.01 3 0.000
#> TCGA.19.1389.02 1 0.000
#> TCGA.26.6174.01 1 0.000
#> TCGA.S9.A7R7.01 3 0.000
#> TCGA.TM.A84R.01 3 0.000
#> TCGA.DB.A75M.01 2 0.000
#> TCGA.DU.6392.01 1 0.000
#> TCGA.HW.A5KM.01 2 0.000
#> TCGA.06.0221.02 3 0.000
#> TCGA.HT.7477.01 2 0.000
#> TCGA.HT.8012.01 2 0.000
#> TCGA.32.1980.01 1 0.000
#> TCGA.76.6661.01 1 0.000
#> TCGA.DU.8167.01 2 0.000
#> TCGA.S9.A6U1.01 2 0.000
#> TCGA.FG.5965.01 2 0.000
#> TCGA.FG.8187.01 3 0.000
#> TCGA.HT.A614.01 2 0.000
#> TCGA.28.5209.01 1 0.000
#> TCGA.S9.A7QZ.01 2 0.000
#> TCGA.QH.A6X4.01 2 0.000
#> TCGA.19.5951.01 1 0.000
#> TCGA.P5.A77W.01 2 0.000
#> TCGA.DU.7302.01 2 0.000
#> TCGA.DU.7012.01 1 0.000
#> TCGA.DU.6399.01 2 0.000
#> TCGA.06.A6S0.01 1 0.000
#> TCGA.E1.5307.01 2 0.000
#> TCGA.S9.A7QW.01 2 0.000
#> TCGA.DU.6402.01 1 0.000
#> TCGA.HT.7604.01 2 0.000
#> TCGA.P5.A733.01 2 0.000
#> TCGA.FG.A87Q.01 1 0.000
#> TCGA.HT.7684.01 2 0.000
#> TCGA.HW.7495.01 2 0.000
#> TCGA.QH.A65R.01 2 0.000
#> TCGA.DU.A7TG.01 3 0.000
#> TCGA.DH.A7UV.01 2 0.000
#> TCGA.HT.7879.01 2 0.000
#> TCGA.TM.A84F.01 3 0.000
#> TCGA.HT.8104.01 1 0.000
#> TCGA.FG.A70Z.01 1 0.000
#> TCGA.DU.A7TC.01 2 0.000
#> TCGA.14.0862.01 1 0.000
#> TCGA.HT.7610.01 3 1.000
#> TCGA.S9.A6TW.01 3 0.000
#> TCGA.FG.A60J.01 2 0.000
#> TCGA.E1.5303.01 2 0.000
#> TCGA.QH.A6XC.01 1 0.000
#> TCGA.HT.7481.01 3 0.000
#> TCGA.FN.7833.01 2 0.000
#> TCGA.E1.A7Z4.01 2 0.000
#> TCGA.DU.A5TR.01 3 0.000
#> TCGA.FG.A4MU.01 1 0.000
#> TCGA.HT.7875.01 2 0.000
#> TCGA.06.5417.01 2 0.000
#> TCGA.HT.7473.01 2 0.000
#> TCGA.19.5955.01 1 0.000
#> TCGA.TM.A7C3.01 1 0.000
#> TCGA.S9.A7IQ.01 3 0.000
#> TCGA.DU.7008.01 2 0.000
#> TCGA.DB.A64O.01 1 0.000
#> TCGA.DU.A5TT.01 1 0.000
#> TCGA.S9.A6WG.01 3 0.000
#> TCGA.74.6581.01 1 0.000
#> TCGA.FG.8189.01 1 1.000
#> TCGA.76.6662.01 1 0.000
#> TCGA.DB.A75O.01 2 0.000
#> TCGA.HT.7688.01 2 0.000
#> TCGA.DU.7304.02 2 0.000
#> TCGA.DU.6394.01 2 0.000
#> TCGA.HT.8019.01 1 0.000
#> TCGA.P5.A5EY.01 1 0.000
#> TCGA.RR.A6KA.01 1 0.000
#> TCGA.S9.A6WD.01 2 0.000
#> TCGA.DU.5872.01 2 0.000
#> TCGA.DU.5872.02 1 0.000
#> TCGA.74.6573.11 1 0.000
#> TCGA.FG.8185.01 2 0.000
#> TCGA.HT.7902.01 3 0.000
#> TCGA.CS.5397.01 1 0.000
#> TCGA.TQ.A7RU.01 2 0.000
#> TCGA.HW.A5KK.01 1 0.000
#> TCGA.DU.5874.01 2 0.000
#> TCGA.S9.A6WE.01 2 0.000
#> TCGA.06.0650.01 1 0.000
#> TCGA.FG.6690.01 2 0.000
#> TCGA.HW.8320.01 2 0.000
#> TCGA.CS.6669.01 1 0.000
#> TCGA.S9.A7R2.01 1 0.000
#> TCGA.R8.A6MK.01 2 0.000
#> TCGA.QH.A6CY.01 3 0.000
#> TCGA.S9.A7J1.01 2 0.000
#> TCGA.P5.A72X.01 3 1.000
#> TCGA.E1.5322.01 2 0.000
#> TCGA.P5.A5F0.01 2 0.000
#> TCGA.76.6193.01 1 0.000
#> TCGA.S9.A6WM.01 1 0.000
#> TCGA.R8.A73M.01 2 0.000
#> TCGA.CS.4942.01 2 0.000
#> TCGA.HT.7680.01 1 0.000
#> TCGA.DB.A4X9.01 2 0.000
#> TCGA.DB.A4XF.01 2 0.000
#> TCGA.HT.A74O.01 2 0.000
#> TCGA.06.6698.01 1 0.000
#> TCGA.FG.8188.01 2 0.000
#> TCGA.P5.A5F6.01 1 0.000
#> TCGA.DU.A6S3.01 2 0.000
#> TCGA.14.1043.01 1 0.000
#> TCGA.HT.8110.01 1 0.000
#> TCGA.DB.A4XH.01 2 0.000
#> TCGA.HT.7485.01 2 0.000
#> TCGA.VW.A7QS.01 2 0.000
#> TCGA.06.6391.01 1 0.000
#> TCGA.76.4935.01 1 0.000
#> TCGA.E1.A7YJ.01 1 0.000
#> TCGA.06.5414.01 1 0.000
#> TCGA.S9.A6WI.01 3 0.000
#> TCGA.DU.8164.01 2 0.000
#> TCGA.06.A7TK.01 1 0.000
#> TCGA.06.5411.01 1 0.000
#> TCGA.S9.A6TS.01 2 0.000
#> TCGA.DB.A64S.01 2 0.000
#> TCGA.VV.A86M.01 2 0.000
#> TCGA.TQ.A8XE.01 2 0.000
#> TCGA.CS.6667.01 2 0.000
#> TCGA.76.6656.01 1 0.000
#> TCGA.E1.A7YL.01 1 0.000
#> TCGA.E1.A7YV.01 2 0.751
#> TCGA.HT.8558.01 1 0.000
#> TCGA.HT.A61C.01 1 0.000
#> TCGA.TQ.A7RW.01 2 0.000
#> TCGA.DU.5849.01 3 0.000
#> TCGA.76.4925.01 1 0.000
#> TCGA.DU.A7TI.01 2 0.000
#> TCGA.QH.A6CV.01 1 0.000
#> TCGA.4W.AA9R.01 1 0.000
#> TCGA.HT.7468.01 2 0.000
#> TCGA.FG.6692.01 1 0.000
#> TCGA.81.5910.01 1 0.000
#> TCGA.28.5214.01 1 0.000
#> TCGA.TQ.A7RI.01 2 0.000
#> TCGA.DB.5279.01 2 0.000
#> TCGA.S9.A6U8.01 2 0.000
#> TCGA.HW.7489.01 3 0.000
#> TCGA.R8.A6YH.01 2 0.000
#> TCGA.74.6584.01 1 0.000
#> TCGA.DU.7018.01 2 0.000
#> TCGA.06.0190.01 1 0.000
#> TCGA.06.0190.02 1 0.000
#> TCGA.HT.7677.01 2 0.000
#> TCGA.FG.A713.01 3 0.000
#> TCGA.DU.7300.01 3 0.000
#> TCGA.TM.A7CA.01 2 0.000
#> TCGA.76.6664.01 1 0.000
#> TCGA.HT.7690.01 2 0.000
#> TCGA.DU.7013.01 1 0.000
#> TCGA.FG.6689.01 2 0.000
#> TCGA.DU.7007.01 2 0.000
#> TCGA.TQ.A7RF.01 2 0.000
#> TCGA.KT.A7W1.01 1 0.000
#> TCGA.HT.A5RA.01 1 0.000
#> TCGA.DB.5277.01 2 0.000
#> TCGA.HT.7694.01 3 0.000
#> TCGA.26.5134.01 1 0.000
#> TCGA.TM.A84M.01 2 0.000
#> TCGA.F6.A8O3.01 2 0.000
#> TCGA.QH.A86X.01 2 0.000
#> TCGA.28.2501.01 1 0.000
#> TCGA.HT.8013.01 2 0.000
#> TCGA.76.6286.01 1 0.000
#> TCGA.HW.7490.01 2 0.000
#> TCGA.14.1450.01 1 0.000
#> TCGA.76.6660.01 1 0.000
#> TCGA.28.5204.01 1 0.000
#> TCGA.QH.A65S.01 2 0.000
#> TCGA.DU.A76R.01 2 0.000
#> TCGA.DH.5144.01 2 0.000
#> TCGA.CS.6188.01 1 0.000
#> TCGA.06.1804.01 1 0.000
#> TCGA.P5.A780.01 2 0.000
#> TCGA.HT.7606.01 2 0.000
#> TCGA.DU.A7TJ.01 1 0.000
#> TCGA.76.4931.01 1 0.000
#> TCGA.DB.A64V.01 3 0.000
#> TCGA.RY.A840.01 2 0.000
#> TCGA.E1.5302.01 3 0.751
#> TCGA.HW.A5KJ.01 2 0.000
#> TCGA.HT.A615.01 3 1.000
#> TCGA.HT.8105.01 2 0.000
#> TCGA.DU.7309.01 2 1.000
#> TCGA.DU.A5TY.01 1 0.000
#> TCGA.28.6450.01 1 0.000
#> TCGA.DU.5847.01 1 0.000
#> TCGA.E1.A7YK.01 3 0.000
#> TCGA.76.4928.01 1 0.000
#> TCGA.26.6173.01 1 0.000
#> TCGA.HT.7874.01 3 0.000
#> TCGA.HT.7471.01 2 0.000
#> TCGA.HT.7882.01 1 0.000
#> TCGA.DU.5854.01 1 0.000
#> TCGA.DU.6395.01 2 0.000
#> TCGA.76.6282.01 1 0.000
#> TCGA.19.5954.01 1 0.000
#> TCGA.HT.8011.01 1 0.000
#> TCGA.S9.A6TV.01 2 0.000
#> TCGA.P5.A5EW.01 2 0.000
#> TCGA.DU.5852.01 1 0.000
#> TCGA.32.1979.01 1 0.000
#> TCGA.DU.6408.01 2 0.000
#> TCGA.87.5896.01 1 0.000
#> TCGA.DB.A4XB.01 2 0.000
#> TCGA.E1.A7YY.01 3 0.000
#> TCGA.FG.A4MT.01 2 0.000
#> TCGA.FG.A4MT.02 2 0.000
#> TCGA.HT.A619.01 2 0.000
#> TCGA.P5.A72U.01 1 0.000
#> TCGA.QH.A870.01 2 0.000
#> TCGA.HT.A5R9.01 2 0.000
#> TCGA.DU.6404.02 1 0.000
#> TCGA.DU.6404.01 1 0.000
#> TCGA.19.0957.01 1 0.000
#> TCGA.19.0957.02 1 0.000
#> TCGA.FG.5964.01 3 0.000
#> TCGA.CS.5396.01 2 0.000
#> TCGA.HT.8107.01 1 0.000
#> TCGA.DU.A7TA.01 2 0.000
#> TCGA.HW.8319.01 2 0.000
#> TCGA.06.5859.01 1 0.000
#> TCGA.DH.A7UR.01 3 0.000
#> TCGA.TM.A84H.01 2 0.000
#> TCGA.S9.A6TZ.01 2 0.000
#> TCGA.HT.7479.01 3 0.000
#> TCGA.DU.6400.01 2 0.000
#> TCGA.S9.A6WL.01 2 0.000
#> TCGA.DB.A75K.01 2 0.000
#> TCGA.DB.A4XD.01 2 0.000
#> TCGA.76.6657.01 1 0.000
#> TCGA.DB.A64Q.01 2 0.000
#> TCGA.P5.A737.01 2 0.000
#> TCGA.06.6699.01 1 0.000
#> TCGA.DB.5275.01 2 0.000
#> TCGA.S9.A6WH.01 2 0.000
#> TCGA.HT.7602.01 3 0.000
#> TCGA.DU.A5TU.01 2 0.000
#> TCGA.HT.A5RB.01 2 0.000
#> TCGA.E1.A7YN.01 1 0.000
#> TCGA.HT.7616.01 2 0.000
#> TCGA.S9.A7R8.01 2 0.000
#> TCGA.41.5651.01 1 0.000
#> TCGA.76.6192.01 1 0.000
#> TCGA.QH.A6XA.01 2 0.000
#> TCGA.HT.8111.01 3 0.000
#> TCGA.74.6575.01 1 0.000
#> TCGA.E1.A7Z2.01 1 0.000
#> TCGA.DU.A5TP.01 2 0.000
#> TCGA.VM.A8CD.01 1 0.000
#> TCGA.RY.A83Y.01 2 0.000
#> TCGA.HT.7482.01 2 0.000
#> TCGA.TQ.A7RK.02 2 0.000
#> TCGA.TQ.A7RK.01 2 0.000
#> TCGA.HT.7858.01 3 1.000
#> TCGA.06.0210.01 1 0.000
#> TCGA.06.0210.02 1 0.000
#> TCGA.06.A5U1.01 1 0.000
#> TCGA.HT.7475.01 2 0.000
#> TCGA.HT.8564.01 1 0.000
#> TCGA.DB.A64U.01 2 0.000
#> TCGA.19.5956.01 1 0.000
#> TCGA.DB.A64W.01 2 0.000
#> TCGA.R8.A6MO.01 2 0.000
#> TCGA.28.5216.01 1 0.000
#> TCGA.DU.A7T8.01 2 0.000
#> TCGA.HW.8322.01 2 0.000
#> TCGA.DU.5870.02 2 0.000
#> TCGA.CS.6668.01 2 0.000
#> TCGA.DU.5870.01 2 0.000
#> TCGA.FG.7636.01 2 0.000
#> TCGA.HT.7692.01 2 0.000
#> TCGA.WY.A859.01 2 0.000
#> TCGA.HT.7854.01 1 0.000
#> TCGA.R8.A6ML.01 2 0.000
#> TCGA.VM.A8C9.01 1 0.000
#> TCGA.HT.7686.01 3 0.000
#> TCGA.DU.6410.01 2 0.000
#> TCGA.S9.A6U9.01 2 0.000
#> TCGA.74.6573.01 1 0.000
#> TCGA.CS.6290.01 3 0.000
#> TCGA.TQ.A7RO.01 2 0.000
#> TCGA.DU.7019.01 2 0.000
#> TCGA.06.5858.01 1 0.000
#> TCGA.FG.A711.01 3 0.249
#> TCGA.TQ.A7RM.01 2 0.000
#> TCGA.HT.7860.01 1 0.000
#> TCGA.S9.A7R4.01 2 0.000
#> TCGA.E1.5318.01 2 0.000
#> TCGA.HT.7676.01 2 0.000
#> TCGA.14.0740.01 1 0.000
#> TCGA.S9.A7J3.01 2 0.000
#> TCGA.81.5911.01 1 0.000
#> TCGA.06.6701.01 2 0.000
#> TCGA.P5.A5F2.01 2 0.000
#> TCGA.E1.5304.01 2 0.000
#> TCGA.DU.7006.01 1 0.000
#> TCGA.TM.A84S.01 3 0.000
#> TCGA.HT.7469.01 1 1.000
#> TCGA.06.6390.01 1 0.000
#> TCGA.WY.A85B.01 2 0.000
#> TCGA.TQ.A7RS.01 2 0.000
#> TCGA.S9.A7QX.01 2 0.000
#> TCGA.CS.4943.01 2 0.000
#> TCGA.QH.A65Z.01 2 0.000
#> TCGA.DB.5276.01 3 0.000
#> TCGA.P5.A730.01 2 0.000
#> TCGA.06.A5U0.01 1 0.000
#> TCGA.TM.A84L.01 3 0.000
#> TCGA.DU.8161.01 1 0.000
#> TCGA.19.5959.01 1 0.000
#> TCGA.WY.A85D.01 2 0.000
#> TCGA.RY.A83X.01 2 0.000
#> TCGA.S9.A6UB.01 2 0.000
#> TCGA.E1.A7YM.01 1 0.000
#> TCGA.DB.5273.01 2 0.000
#> TCGA.TM.A7C4.01 3 0.000
#> TCGA.DH.A66F.01 2 0.000
#> TCGA.HT.7607.01 3 0.000
#> TCGA.DU.6393.01 2 0.000
#> TCGA.06.5413.01 1 0.000
#> TCGA.19.5947.01 1 0.000
#> TCGA.HT.8108.01 2 0.000
#> TCGA.E1.A7YD.01 1 0.000
#> TCGA.19.5960.01 1 0.000
#> TCGA.DU.7304.01 2 0.000
#> TCGA.14.1034.02 1 0.000
#> TCGA.S9.A7IY.01 2 0.000
#> TCGA.FG.7641.01 2 0.000
#> TCGA.P5.A736.01 3 0.000
#> TCGA.14.0736.02 1 0.000
#> TCGA.19.5952.01 1 0.000
#> TCGA.P5.A5EV.01 2 0.000
#> TCGA.DU.7301.01 2 0.000
#> TCGA.HT.7470.01 3 0.000
#> TCGA.28.5208.01 1 0.000
#> TCGA.DU.7009.01 2 0.000
#> TCGA.P5.A781.01 3 1.000
#> TCGA.DH.5140.01 1 0.000
#> TCGA.76.6280.01 1 0.000
#> TCGA.FG.A4MY.01 2 0.000
#> TCGA.TM.A7CF.01 2 0.000
#> TCGA.TM.A7CF.02 3 0.000
#> TCGA.FG.8186.01 2 0.000
#> TCGA.S9.A6U6.01 2 0.000
#> TCGA.HT.8015.01 1 0.000
#> TCGA.RY.A845.01 2 0.000
#> TCGA.DU.7010.01 2 1.000
#> TCGA.S9.A6U2.01 3 1.000
#> TCGA.S9.A6WN.01 3 0.000
#> TCGA.28.2510.01 1 0.000
#> TCGA.DU.A7TD.01 1 0.000
#> TCGA.14.0736.01 1 0.000
#> TCGA.DU.6405.01 1 0.000
#> TCGA.06.0152.02 1 0.000
#> TCGA.06.0152.01 1 0.000
#> TCGA.76.4927.01 1 0.000
#> TCGA.FG.8182.01 2 0.000
#> TCGA.QH.A6X3.01 2 0.000
#> TCGA.DU.6401.01 2 0.000
#> TCGA.26.5132.01 1 0.000
#> TCGA.DU.6396.01 2 0.000
#> TCGA.E1.A7YH.01 2 0.000
#> TCGA.DU.7306.01 2 0.000
#> TCGA.HT.A74J.01 2 0.000
#> TCGA.HT.A74H.01 1 0.000
#> TCGA.DH.A7US.01 3 1.000
#> TCGA.FG.A87N.01 3 0.000
#> TCGA.HT.7478.01 3 0.000
#> TCGA.DU.7290.01 1 0.000
#> TCGA.DB.A4XE.01 2 0.000
#> TCGA.DB.A64L.01 2 0.000
#> TCGA.VV.A829.01 2 0.000
#> TCGA.19.A6J4.01 1 0.000
#> TCGA.HT.A61B.01 2 0.000
#> TCGA.12.5299.01 1 0.000
#> TCGA.DH.A66B.01 2 0.000
#> TCGA.HT.7603.01 3 0.000
#> TCGA.DU.6397.02 2 0.000
#> TCGA.DU.6397.01 2 0.000
#> TCGA.HT.A4DS.01 1 0.000
#> TCGA.12.5301.01 1 0.000
#> TCGA.RR.A6KB.01 1 0.000
#> TCGA.DU.5853.01 2 0.000
#> TCGA.CS.6670.01 2 0.000
#> TCGA.DU.7014.01 2 0.000
#> TCGA.QH.A65X.01 2 0.000
#> TCGA.TM.A84B.01 1 0.000
#> TCGA.DB.A64P.01 2 0.000
#> TCGA.FG.5965.02 3 0.000
#> TCGA.FG.A70Y.01 3 1.000
#> TCGA.TQ.A7RV.01 2 0.000
#> TCGA.TQ.A7RV.02 3 0.000
#> TCGA.HT.A5R7.01 3 0.000
#> TCGA.06.6389.01 2 0.000
#> TCGA.HW.A5KL.01 2 0.000
#> TCGA.06.5416.01 1 0.000
#> TCGA.DU.8158.01 1 0.000
#> TCGA.HT.7474.01 3 0.000
#> TCGA.DH.A7UU.01 2 0.000
#> TCGA.26.5139.01 1 0.000
#> TCGA.QH.A6CZ.01 2 0.000
#> TCGA.DH.A669.02 2 0.000
#> TCGA.DH.A669.01 2 0.000
#> TCGA.QH.A6X9.01 2 0.000
#> TCGA.P5.A5EZ.01 3 0.000
#> TCGA.DU.5871.01 2 0.000
#> TCGA.TQ.A7RJ.01 2 0.000
#> TCGA.WY.A858.01 3 0.000
#> TCGA.TM.A84J.01 1 1.000
#> TCGA.VM.A8CB.01 2 0.000
#> TCGA.41.6646.01 1 0.000
#> TCGA.14.0781.01 1 0.000
#> TCGA.HT.7483.01 2 0.000
#> TCGA.HT.7687.01 2 0.000
#> TCGA.TM.A84G.01 2 0.000
#> TCGA.E1.A7Z6.01 2 0.000
#> TCGA.TM.A84I.01 2 0.000
#> TCGA.CS.5394.01 2 0.000
#> TCGA.HT.A617.01 1 0.000
#> TCGA.DU.A76O.01 2 0.000
#> TCGA.DU.A5TW.01 2 0.000
#> TCGA.HT.7857.01 1 0.000
#> TCGA.WY.A85A.01 3 1.000
#> TCGA.FG.5962.01 2 0.000
#> TCGA.74.6578.01 1 0.000
get_classes(res, k = 5)
#> class p
#> TCGA.E1.5319.01 3 0.000
#> TCGA.HT.7693.01 2 0.000
#> TCGA.CS.6665.01 3 0.000
#> TCGA.S9.A7J2.01 2 0.000
#> TCGA.FG.A6J3.01 3 0.000
#> TCGA.FG.6688.01 5 0.751
#> TCGA.S9.A6TX.01 3 0.000
#> TCGA.VM.A8C8.01 3 0.000
#> TCGA.74.6577.01 1 0.000
#> TCGA.06.AABW.11 5 0.000
#> TCGA.06.0125.02 1 0.502
#> TCGA.HT.A74L.01 2 0.000
#> TCGA.26.A7UX.01 1 0.000
#> TCGA.DU.A5TS.01 3 0.000
#> TCGA.06.6388.01 1 0.000
#> TCGA.DB.A4XA.01 3 0.000
#> TCGA.06.A7TL.01 3 0.000
#> TCGA.HT.A4DV.01 4 0.000
#> TCGA.TQ.A7RP.01 5 1.000
#> TCGA.E1.5311.01 2 0.000
#> TCGA.28.5213.01 1 0.000
#> TCGA.E1.A7YI.01 3 0.000
#> TCGA.E1.5305.01 2 0.000
#> TCGA.F6.A8O4.01 3 0.000
#> TCGA.HT.8113.01 4 0.000
#> TCGA.DH.A66G.01 3 0.000
#> TCGA.76.4932.01 1 0.000
#> TCGA.HT.7620.01 4 0.000
#> TCGA.P5.A731.01 3 0.000
#> TCGA.HT.7480.01 2 0.000
#> TCGA.06.5412.01 1 0.000
#> TCGA.HT.7689.01 3 0.000
#> TCGA.06.6694.01 1 1.000
#> TCGA.HT.8109.01 3 0.000
#> TCGA.E1.A7YE.01 3 0.000
#> TCGA.S9.A7R1.01 2 0.000
#> TCGA.FG.A710.01 3 0.000
#> TCGA.19.1389.01 1 0.000
#> TCGA.S9.A7J0.01 2 0.000
#> TCGA.DU.A6S6.01 2 0.000
#> TCGA.HT.7877.01 3 0.000
#> TCGA.QH.A6CU.01 3 0.000
#> TCGA.HW.7486.01 4 0.000
#> TCGA.12.5295.01 1 0.000
#> TCGA.FG.7634.01 3 0.000
#> TCGA.19.5953.01 1 1.000
#> TCGA.DU.8163.01 3 0.000
#> TCGA.28.5220.01 1 0.000
#> TCGA.4W.AA9T.01 1 0.000
#> TCGA.OX.A56R.01 1 0.000
#> TCGA.DU.6407.02 3 0.000
#> TCGA.DU.6407.01 2 0.000
#> TCGA.S9.A7IX.01 1 1.000
#> TCGA.HT.8010.01 4 0.000
#> TCGA.06.0171.01 1 0.000
#> TCGA.06.0125.01 1 0.000
#> TCGA.P5.A5F1.01 2 1.000
#> TCGA.VM.A8CF.01 3 0.000
#> TCGA.DU.6542.01 2 0.000
#> TCGA.FG.7638.01 3 0.000
#> TCGA.VW.A8FI.01 1 0.747
#> TCGA.DH.5143.01 2 0.000
#> TCGA.06.6700.01 5 0.000
#> TCGA.DU.7299.01 2 0.000
#> TCGA.28.5218.01 1 0.000
#> TCGA.06.0171.02 1 1.000
#> TCGA.DU.8165.01 1 0.000
#> TCGA.CS.5393.01 3 0.000
#> TCGA.06.5856.01 1 1.000
#> TCGA.26.5136.01 1 0.000
#> TCGA.DU.7011.01 3 0.000
#> TCGA.TM.A84Q.01 3 0.000
#> TCGA.DB.5281.01 2 0.000
#> TCGA.DU.A76L.01 1 1.000
#> TCGA.HT.7605.01 3 0.000
#> TCGA.FG.A6J1.01 2 0.000
#> TCGA.76.6663.01 1 1.000
#> TCGA.DB.5270.01 4 0.000
#> TCGA.S9.A6WQ.01 3 0.000
#> TCGA.76.4926.01 1 0.000
#> TCGA.HT.8106.01 4 0.000
#> TCGA.HT.7608.01 3 0.000
#> TCGA.26.5133.01 4 0.000
#> TCGA.E1.A7YU.01 3 0.000
#> TCGA.W9.A837.01 3 0.000
#> TCGA.TM.A7C5.01 2 0.000
#> TCGA.S9.A7QY.01 3 0.000
#> TCGA.QH.A6CW.01 2 0.000
#> TCGA.S9.A6WO.01 2 0.000
#> TCGA.IK.7675.01 2 0.000
#> TCGA.HT.7601.01 4 0.249
#> TCGA.P5.A5ET.01 2 0.000
#> TCGA.HT.7472.01 3 0.000
#> TCGA.HT.7880.01 4 0.000
#> TCGA.26.1442.01 3 0.000
#> TCGA.19.A6J5.01 2 0.000
#> TCGA.E1.A7Z3.01 4 0.000
#> TCGA.P5.A77X.01 3 0.000
#> TCGA.FG.A6IZ.01 2 0.000
#> TCGA.06.0211.02 1 0.000
#> TCGA.28.5207.01 1 1.000
#> TCGA.14.1402.01 1 0.751
#> TCGA.06.0211.01 1 0.000
#> TCGA.14.1402.02 1 1.000
#> TCGA.HT.7873.01 2 0.000
#> TCGA.CS.4938.01 2 0.000
#> TCGA.19.4065.02 1 0.253
#> TCGA.RR.A6KC.01 1 0.000
#> TCGA.19.4065.01 5 1.000
#> TCGA.KT.A74X.01 2 0.000
#> TCGA.P5.A5EX.01 4 0.000
#> TCGA.VM.A8CH.01 2 0.000
#> TCGA.HT.7476.01 3 0.000
#> TCGA.DB.A75L.01 2 0.000
#> TCGA.HT.8563.01 4 0.000
#> TCGA.CS.4941.01 1 0.000
#> TCGA.RY.A843.01 3 0.000
#> TCGA.S9.A7IS.01 3 0.000
#> TCGA.TQ.A8XE.02 3 0.000
#> TCGA.S9.A6U0.01 1 0.000
#> TCGA.FG.7643.01 5 0.000
#> TCGA.E1.A7YO.01 2 0.000
#> TCGA.06.5408.01 1 0.000
#> TCGA.TQ.A7RG.01 2 0.000
#> TCGA.QH.A6X5.01 3 0.000
#> TCGA.76.6285.01 1 0.249
#> TCGA.DU.6403.01 1 0.000
#> TCGA.HW.7493.01 3 0.000
#> TCGA.19.5950.01 1 0.000
#> TCGA.RY.A847.01 3 0.000
#> TCGA.DU.8166.01 2 0.000
#> TCGA.VM.A8CA.01 3 0.000
#> TCGA.HT.7855.01 2 0.000
#> TCGA.S9.A89Z.01 3 0.000
#> TCGA.DB.A4XG.01 2 0.000
#> TCGA.14.1395.01 1 0.502
#> TCGA.DH.A7UT.01 3 0.000
#> TCGA.DU.7015.01 2 0.000
#> TCGA.HT.A616.01 3 0.000
#> TCGA.FG.8181.01 5 0.000
#> TCGA.HT.7611.01 2 0.000
#> TCGA.HT.8018.01 4 0.000
#> TCGA.FG.A60K.01 2 0.000
#> TCGA.HT.7856.01 4 0.000
#> TCGA.FG.5963.01 5 0.000
#> TCGA.FG.5963.02 5 0.000
#> TCGA.DU.5851.01 4 0.000
#> TCGA.DU.A7T6.01 4 0.502
#> TCGA.S9.A6TY.01 2 0.000
#> TCGA.CS.5395.01 1 0.000
#> TCGA.DU.7292.01 5 0.000
#> TCGA.HT.A5RC.01 1 0.751
#> TCGA.WY.A85C.01 2 0.000
#> TCGA.DB.A4XC.01 3 0.000
#> TCGA.TM.A84O.01 3 0.000
#> TCGA.06.5410.01 1 0.000
#> TCGA.19.5958.01 1 0.000
#> TCGA.P5.A72W.01 2 0.000
#> TCGA.S9.A6TU.01 2 0.249
#> TCGA.HT.A61A.01 4 0.000
#> TCGA.28.5211.01 1 0.000
#> TCGA.DU.5855.01 3 0.000
#> TCGA.HT.7884.01 2 0.000
#> TCGA.TQ.A7RQ.01 2 0.000
#> TCGA.TM.A84C.01 5 0.000
#> TCGA.FG.A4MW.01 1 1.000
#> TCGA.IK.8125.01 3 0.000
#> TCGA.HT.A74K.01 3 0.000
#> TCGA.WH.A86K.01 2 0.000
#> TCGA.DB.A75P.01 5 1.000
#> TCGA.QH.A6X8.01 3 0.000
#> TCGA.S9.A89V.01 1 1.000
#> TCGA.WY.A85E.01 3 0.000
#> TCGA.HT.A5R5.01 4 1.000
#> TCGA.06.6695.01 1 0.747
#> TCGA.06.5418.01 1 0.000
#> TCGA.HT.A618.01 4 1.000
#> TCGA.FG.6691.01 3 0.000
#> TCGA.HT.7467.01 4 0.000
#> TCGA.06.5415.01 1 0.000
#> TCGA.S9.A7R3.01 2 0.000
#> TCGA.QH.A6CX.01 5 1.000
#> TCGA.06.A6S1.01 1 0.000
#> TCGA.FG.A4MX.01 2 0.000
#> TCGA.HT.7681.01 3 0.000
#> TCGA.S9.A7IZ.01 3 0.000
#> TCGA.DU.A6S7.01 2 0.000
#> TCGA.06.0221.01 3 0.000
#> TCGA.P5.A72Z.01 2 0.000
#> TCGA.HT.8114.01 3 0.000
#> TCGA.DU.8168.01 2 0.000
#> TCGA.HW.8321.01 3 0.000
#> TCGA.TQ.A7RN.01 2 0.000
#> TCGA.DH.5141.01 3 0.000
#> TCGA.CS.6186.01 1 1.000
#> TCGA.EZ.7264.01 2 0.000
#> TCGA.26.5135.01 5 1.000
#> TCGA.P5.A5F4.01 3 0.000
#> TCGA.QH.A65V.01 3 0.000
#> TCGA.28.5219.01 1 1.000
#> TCGA.4W.AA9S.01 1 0.000
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#> TCGA.DH.A669.02 2 0.000
#> TCGA.DH.A669.01 2 0.000
#> TCGA.QH.A6X9.01 3 0.000
#> TCGA.P5.A5EZ.01 3 0.000
#> TCGA.DU.5871.01 2 0.000
#> TCGA.TQ.A7RJ.01 3 0.000
#> TCGA.WY.A858.01 3 0.000
#> TCGA.TM.A84J.01 4 0.751
#> TCGA.VM.A8CB.01 2 0.000
#> TCGA.41.6646.01 1 0.000
#> TCGA.14.0781.01 1 0.000
#> TCGA.HT.7483.01 3 1.000
#> TCGA.HT.7687.01 2 0.000
#> TCGA.TM.A84G.01 2 0.000
#> TCGA.E1.A7Z6.01 2 0.249
#> TCGA.TM.A84I.01 2 0.000
#> TCGA.CS.5394.01 2 0.000
#> TCGA.HT.A617.01 1 1.000
#> TCGA.DU.A76O.01 3 0.000
#> TCGA.DU.A5TW.01 2 0.000
#> TCGA.HT.7857.01 5 0.000
#> TCGA.WY.A85A.01 3 0.000
#> TCGA.FG.5962.01 2 0.000
#> TCGA.74.6578.01 1 0.000
get_classes(res, k = 6)
#> class p
#> TCGA.E1.5319.01 3 0.000
#> TCGA.HT.7693.01 2 0.000
#> TCGA.CS.6665.01 3 0.000
#> TCGA.S9.A7J2.01 2 0.000
#> TCGA.FG.A6J3.01 3 0.000
#> TCGA.FG.6688.01 5 0.000
#> TCGA.S9.A6TX.01 3 0.000
#> TCGA.VM.A8C8.01 3 0.000
#> TCGA.74.6577.01 1 0.000
#> TCGA.06.AABW.11 5 0.000
#> TCGA.06.0125.02 1 1.000
#> TCGA.HT.A74L.01 2 0.000
#> TCGA.26.A7UX.01 1 0.000
#> TCGA.DU.A5TS.01 3 0.000
#> TCGA.06.6388.01 1 0.000
#> TCGA.DB.A4XA.01 3 0.000
#> TCGA.06.A7TL.01 3 0.000
#> TCGA.HT.A4DV.01 4 0.000
#> TCGA.TQ.A7RP.01 5 1.000
#> TCGA.E1.5311.01 2 0.000
#> TCGA.28.5213.01 1 0.000
#> TCGA.E1.A7YI.01 3 0.000
#> TCGA.E1.5305.01 2 0.000
#> TCGA.F6.A8O4.01 3 0.000
#> TCGA.HT.8113.01 4 0.000
#> TCGA.DH.A66G.01 3 0.000
#> TCGA.76.4932.01 1 0.249
#> TCGA.HT.7620.01 4 0.000
#> TCGA.P5.A731.01 3 0.000
#> TCGA.HT.7480.01 2 0.000
#> TCGA.06.5412.01 1 1.000
#> TCGA.HT.7689.01 3 0.000
#> TCGA.06.6694.01 1 1.000
#> TCGA.HT.8109.01 3 0.000
#> TCGA.E1.A7YE.01 3 0.000
#> TCGA.S9.A7R1.01 2 0.000
#> TCGA.FG.A710.01 3 0.000
#> TCGA.19.1389.01 1 0.000
#> TCGA.S9.A7J0.01 2 0.000
#> TCGA.DU.A6S6.01 2 0.000
#> TCGA.HT.7877.01 3 0.000
#> TCGA.QH.A6CU.01 3 0.000
#> TCGA.HW.7486.01 4 0.000
#> TCGA.12.5295.01 1 0.751
#> TCGA.FG.7634.01 3 0.000
#> TCGA.19.5953.01 5 1.000
#> TCGA.DU.8163.01 3 0.000
#> TCGA.28.5220.01 1 0.000
#> TCGA.4W.AA9T.01 1 0.000
#> TCGA.OX.A56R.01 1 0.000
#> TCGA.DU.6407.02 3 0.000
#> TCGA.DU.6407.01 2 0.000
#> TCGA.S9.A7IX.01 1 1.000
#> TCGA.HT.8010.01 4 0.000
#> TCGA.06.0171.01 1 0.498
#> TCGA.06.0125.01 1 0.000
#> TCGA.P5.A5F1.01 3 0.000
#> TCGA.VM.A8CF.01 3 0.000
#> TCGA.DU.6542.01 2 0.000
#> TCGA.FG.7638.01 3 0.000
#> TCGA.VW.A8FI.01 1 0.751
#> TCGA.DH.5143.01 2 1.000
#> TCGA.06.6700.01 5 0.000
#> TCGA.DU.7299.01 2 0.000
#> TCGA.28.5218.01 5 1.000
#> TCGA.06.0171.02 1 1.000
#> TCGA.DU.8165.01 1 0.000
#> TCGA.CS.5393.01 3 0.000
#> TCGA.06.5856.01 1 0.751
#> TCGA.26.5136.01 1 0.000
#> TCGA.DU.7011.01 3 0.000
#> TCGA.TM.A84Q.01 3 0.000
#> TCGA.DB.5281.01 2 0.000
#> TCGA.DU.A76L.01 1 1.000
#> TCGA.HT.7605.01 3 0.000
#> TCGA.FG.A6J1.01 2 0.000
#> TCGA.76.6663.01 1 1.000
#> TCGA.DB.5270.01 4 0.000
#> TCGA.S9.A6WQ.01 3 0.000
#> TCGA.76.4926.01 1 0.000
#> TCGA.HT.8106.01 4 0.000
#> TCGA.HT.7608.01 3 0.000
#> TCGA.26.5133.01 4 0.249
#> TCGA.E1.A7YU.01 3 0.000
#> TCGA.W9.A837.01 3 0.000
#> TCGA.TM.A7C5.01 2 0.000
#> TCGA.S9.A7QY.01 3 0.000
#> TCGA.QH.A6CW.01 2 0.000
#> TCGA.S9.A6WO.01 2 0.000
#> TCGA.IK.7675.01 2 0.000
#> TCGA.HT.7601.01 3 0.000
#> TCGA.P5.A5ET.01 2 0.000
#> TCGA.HT.7472.01 3 0.000
#> TCGA.HT.7880.01 4 0.000
#> TCGA.26.1442.01 3 0.000
#> TCGA.19.A6J5.01 2 0.000
#> TCGA.E1.A7Z3.01 4 1.000
#> TCGA.P5.A77X.01 3 0.000
#> TCGA.FG.A6IZ.01 2 0.000
#> TCGA.06.0211.02 1 0.000
#> TCGA.28.5207.01 1 0.000
#> TCGA.14.1402.01 1 1.000
#> TCGA.06.0211.01 1 0.000
#> TCGA.14.1402.02 1 1.000
#> TCGA.HT.7873.01 2 0.000
#> TCGA.CS.4938.01 2 0.000
#> TCGA.19.4065.02 1 1.000
#> TCGA.RR.A6KC.01 1 0.000
#> TCGA.19.4065.01 5 0.000
#> TCGA.KT.A74X.01 2 0.000
#> TCGA.P5.A5EX.01 4 1.000
#> TCGA.VM.A8CH.01 2 0.000
#> TCGA.HT.7476.01 3 0.000
#> TCGA.DB.A75L.01 2 0.000
#> TCGA.HT.8563.01 4 0.000
#> TCGA.CS.4941.01 1 0.000
#> TCGA.RY.A843.01 3 0.000
#> TCGA.S9.A7IS.01 3 0.000
#> TCGA.TQ.A8XE.02 3 0.000
#> TCGA.S9.A6U0.01 1 0.000
#> TCGA.FG.7643.01 5 0.000
#> TCGA.E1.A7YO.01 2 0.000
#> TCGA.06.5408.01 1 0.000
#> TCGA.TQ.A7RG.01 3 0.000
#> TCGA.QH.A6X5.01 3 0.000
#> TCGA.76.6285.01 1 0.751
#> TCGA.DU.6403.01 1 0.000
#> TCGA.HW.7493.01 3 0.000
#> TCGA.19.5950.01 1 0.000
#> TCGA.RY.A847.01 3 0.000
#> TCGA.DU.8166.01 2 0.000
#> TCGA.VM.A8CA.01 3 0.000
#> TCGA.HT.7855.01 2 0.000
#> TCGA.S9.A89Z.01 3 0.000
#> TCGA.DB.A4XG.01 2 0.000
#> TCGA.14.1395.01 1 1.000
#> TCGA.DH.A7UT.01 3 0.000
#> TCGA.DU.7015.01 2 0.000
#> TCGA.HT.A616.01 3 0.000
#> TCGA.FG.8181.01 5 0.000
#> TCGA.HT.7611.01 2 0.000
#> TCGA.HT.8018.01 4 0.000
#> TCGA.FG.A60K.01 2 0.000
#> TCGA.HT.7856.01 4 0.000
#> TCGA.FG.5963.01 5 0.000
#> TCGA.FG.5963.02 5 0.000
#> TCGA.DU.5851.01 4 0.000
#> TCGA.DU.A7T6.01 3 0.000
#> TCGA.S9.A6TY.01 2 0.000
#> TCGA.CS.5395.01 1 0.000
#> TCGA.DU.7292.01 5 0.000
#> TCGA.HT.A5RC.01 1 1.000
#> TCGA.WY.A85C.01 2 0.000
#> TCGA.DB.A4XC.01 3 0.000
#> TCGA.TM.A84O.01 3 0.000
#> TCGA.06.5410.01 1 0.751
#> TCGA.19.5958.01 1 0.000
#> TCGA.P5.A72W.01 2 0.000
#> TCGA.S9.A6TU.01 3 1.000
#> TCGA.HT.A61A.01 4 0.000
#> TCGA.28.5211.01 1 0.000
#> TCGA.DU.5855.01 3 0.000
#> TCGA.HT.7884.01 2 0.000
#> TCGA.TQ.A7RQ.01 2 0.000
#> TCGA.TM.A84C.01 5 0.000
#> TCGA.FG.A4MW.01 5 1.000
#> TCGA.IK.8125.01 3 0.000
#> TCGA.HT.A74K.01 3 0.000
#> TCGA.WH.A86K.01 2 0.000
#> TCGA.DB.A75P.01 5 1.000
#> TCGA.QH.A6X8.01 3 0.000
#> TCGA.S9.A89V.01 1 1.000
#> TCGA.WY.A85E.01 3 0.000
#> TCGA.HT.A5R5.01 3 1.000
#> TCGA.06.6695.01 1 1.000
#> TCGA.06.5418.01 1 0.000
#> TCGA.HT.A618.01 3 0.000
#> TCGA.FG.6691.01 3 0.000
#> TCGA.HT.7467.01 4 0.000
#> TCGA.06.5415.01 1 0.249
#> TCGA.S9.A7R3.01 2 0.000
#> TCGA.QH.A6CX.01 5 1.000
#> TCGA.06.A6S1.01 1 1.000
#> TCGA.FG.A4MX.01 2 0.000
#> TCGA.HT.7681.01 3 0.000
#> TCGA.S9.A7IZ.01 3 0.000
#> TCGA.DU.A6S7.01 2 0.000
#> TCGA.06.0221.01 3 0.000
#> TCGA.P5.A72Z.01 2 0.000
#> TCGA.HT.8114.01 3 0.000
#> TCGA.DU.8168.01 2 0.000
#> TCGA.HW.8321.01 3 0.000
#> TCGA.TQ.A7RN.01 2 0.000
#> TCGA.DH.5141.01 3 0.000
#> TCGA.CS.6186.01 1 1.000
#> TCGA.EZ.7264.01 2 0.000
#> TCGA.26.5135.01 5 1.000
#> TCGA.P5.A5F4.01 3 0.000
#> TCGA.QH.A65V.01 3 0.000
#> TCGA.28.5219.01 1 1.000
#> TCGA.4W.AA9S.01 1 0.000
#> TCGA.19.A60I.01 1 0.000
#> TCGA.76.4934.01 1 1.000
#> TCGA.FG.8191.01 3 0.000
#> TCGA.DH.5142.01 2 0.000
#> TCGA.DU.A6S8.01 2 0.000
#> TCGA.E1.A7YW.01 2 0.000
#> TCGA.32.5222.01 1 0.000
#> TCGA.76.6191.01 1 1.000
#> TCGA.06.1806.01 1 1.000
#> TCGA.06.6693.01 1 0.000
#> TCGA.CS.6666.01 2 0.000
#> TCGA.DU.7298.01 3 0.000
#> TCGA.DB.A64R.01 2 0.000
#> TCGA.DU.6406.01 1 0.000
#> TCGA.S9.A6UA.01 5 0.000
#> TCGA.FG.A60L.01 3 0.000
#> TCGA.CS.5390.01 2 0.000
#> TCGA.S9.A6WP.01 2 0.000
#> TCGA.DU.A7TB.01 1 1.000
#> TCGA.DB.5280.01 2 0.000
#> TCGA.TM.A84T.01 2 0.000
#> TCGA.DH.A66D.01 2 0.000
#> TCGA.06.6697.01 1 0.000
#> TCGA.RY.A83Z.01 3 1.000
#> TCGA.DB.5278.01 3 0.000
#> TCGA.DU.A76K.01 1 1.000
#> TCGA.TQ.A7RR.01 3 0.000
#> TCGA.28.5215.01 1 0.000
#> TCGA.DU.8162.01 5 0.000
#> TCGA.TQ.A7RH.01 3 0.000
#> TCGA.E1.A7YS.01 2 0.000
#> TCGA.15.1444.01 4 0.000
#> TCGA.P5.A735.01 2 0.000
#> TCGA.DU.7294.01 2 0.000
#> TCGA.E1.A7YQ.01 5 0.000
#> TCGA.HT.7881.01 4 0.000
#> TCGA.QH.A6CS.01 5 1.000
#> TCGA.HT.7695.01 3 0.000
#> TCGA.P5.A5EU.01 3 0.000
#> TCGA.76.6283.01 5 0.000
#> TCGA.DB.A64X.01 2 0.000
#> TCGA.FG.7637.01 2 0.000
#> TCGA.VM.A8CE.01 3 0.000
#> TCGA.76.4929.01 1 1.000
#> TCGA.S9.A6U5.01 3 0.000
#> TCGA.HT.7609.01 2 0.000
#> TCGA.DB.5274.01 2 1.000
#> TCGA.HW.7487.01 3 0.000
#> TCGA.HW.7491.01 2 0.000
#> TCGA.HT.7691.01 5 0.249
#> TCGA.CS.4944.01 3 0.000
#> TCGA.DU.A6S2.01 3 0.000
#> TCGA.19.1389.02 1 0.000
#> TCGA.26.6174.01 5 0.000
#> TCGA.S9.A7R7.01 3 0.000
#> TCGA.TM.A84R.01 4 0.000
#> TCGA.DB.A75M.01 2 0.000
#> TCGA.DU.6392.01 5 0.000
#> TCGA.HW.A5KM.01 3 0.000
#> TCGA.06.0221.02 3 0.000
#> TCGA.HT.7477.01 3 0.000
#> TCGA.HT.8012.01 2 0.000
#> TCGA.32.1980.01 5 0.000
#> TCGA.76.6661.01 1 0.000
#> TCGA.DU.8167.01 2 0.000
#> TCGA.S9.A6U1.01 3 0.000
#> TCGA.FG.5965.01 3 0.000
#> TCGA.FG.8187.01 3 0.000
#> TCGA.HT.A614.01 3 0.000
#> TCGA.28.5209.01 1 0.000
#> TCGA.S9.A7QZ.01 2 0.000
#> TCGA.QH.A6X4.01 2 0.000
#> TCGA.19.5951.01 1 0.751
#> TCGA.P5.A77W.01 3 0.000
#> TCGA.DU.7302.01 2 0.000
#> TCGA.DU.7012.01 1 1.000
#> TCGA.DU.6399.01 2 0.000
#> TCGA.06.A6S0.01 1 0.000
#> TCGA.E1.5307.01 2 0.000
#> TCGA.S9.A7QW.01 2 0.000
#> TCGA.DU.6402.01 1 0.000
#> TCGA.HT.7604.01 2 0.000
#> TCGA.P5.A733.01 3 0.000
#> TCGA.FG.A87Q.01 1 1.000
#> TCGA.HT.7684.01 3 0.000
#> TCGA.HW.7495.01 3 0.000
#> TCGA.QH.A65R.01 2 0.000
#> TCGA.DU.A7TG.01 4 0.000
#> TCGA.DH.A7UV.01 2 0.000
#> TCGA.HT.7879.01 2 0.000
#> TCGA.TM.A84F.01 4 0.000
#> TCGA.HT.8104.01 1 0.000
#> TCGA.FG.A70Z.01 1 0.751
#> TCGA.DU.A7TC.01 2 0.000
#> TCGA.14.0862.01 5 0.502
#> TCGA.HT.7610.01 3 0.000
#> TCGA.S9.A6TW.01 3 0.000
#> TCGA.FG.A60J.01 2 0.000
#> TCGA.E1.5303.01 3 0.000
#> TCGA.QH.A6XC.01 1 0.498
#> TCGA.HT.7481.01 4 0.000
#> TCGA.FN.7833.01 2 0.000
#> TCGA.E1.A7Z4.01 2 0.000
#> TCGA.DU.A5TR.01 3 0.000
#> TCGA.FG.A4MU.01 1 0.000
#> TCGA.HT.7875.01 2 0.000
#> TCGA.06.5417.01 2 0.000
#> TCGA.HT.7473.01 3 0.000
#> TCGA.19.5955.01 1 0.000
#> TCGA.TM.A7C3.01 1 0.000
#> TCGA.S9.A7IQ.01 4 0.000
#> TCGA.DU.7008.01 2 0.000
#> TCGA.DB.A64O.01 1 1.000
#> TCGA.DU.A5TT.01 1 1.000
#> TCGA.S9.A6WG.01 4 0.000
#> TCGA.74.6581.01 1 0.000
#> TCGA.FG.8189.01 5 0.000
#> TCGA.76.6662.01 1 1.000
#> TCGA.DB.A75O.01 3 0.000
#> TCGA.HT.7688.01 3 0.000
#> TCGA.DU.7304.02 2 0.000
#> TCGA.DU.6394.01 2 0.000
#> TCGA.HT.8019.01 5 0.000
#> TCGA.P5.A5EY.01 5 0.000
#> TCGA.RR.A6KA.01 5 0.000
#> TCGA.S9.A6WD.01 3 0.000
#> TCGA.DU.5872.01 3 0.000
#> TCGA.DU.5872.02 5 0.000
#> TCGA.74.6573.11 5 0.000
#> TCGA.FG.8185.01 2 0.000
#> TCGA.HT.7902.01 4 0.000
#> TCGA.CS.5397.01 1 1.000
#> TCGA.TQ.A7RU.01 2 0.000
#> TCGA.HW.A5KK.01 5 1.000
#> TCGA.DU.5874.01 2 0.000
#> TCGA.S9.A6WE.01 2 0.000
#> TCGA.06.0650.01 1 1.000
#> TCGA.FG.6690.01 2 0.000
#> TCGA.HW.8320.01 2 0.000
#> TCGA.CS.6669.01 5 0.000
#> TCGA.S9.A7R2.01 1 1.000
#> TCGA.R8.A6MK.01 3 0.000
#> TCGA.QH.A6CY.01 3 0.000
#> TCGA.S9.A7J1.01 3 0.000
#> TCGA.P5.A72X.01 3 0.000
#> TCGA.E1.5322.01 2 0.000
#> TCGA.P5.A5F0.01 3 0.000
#> TCGA.76.6193.01 1 1.000
#> TCGA.S9.A6WM.01 1 0.000
#> TCGA.R8.A73M.01 2 0.000
#> TCGA.CS.4942.01 3 0.000
#> TCGA.HT.7680.01 1 1.000
#> TCGA.DB.A4X9.01 2 0.000
#> TCGA.DB.A4XF.01 2 0.000
#> TCGA.HT.A74O.01 2 0.000
#> TCGA.06.6698.01 1 0.000
#> TCGA.FG.8188.01 2 1.000
#> TCGA.P5.A5F6.01 5 0.000
#> TCGA.DU.A6S3.01 3 0.000
#> TCGA.14.1043.01 5 0.000
#> TCGA.HT.8110.01 1 0.000
#> TCGA.DB.A4XH.01 2 0.000
#> TCGA.HT.7485.01 2 1.000
#> TCGA.VW.A7QS.01 2 0.000
#> TCGA.06.6391.01 5 0.000
#> TCGA.76.4935.01 5 1.000
#> TCGA.E1.A7YJ.01 5 1.000
#> TCGA.06.5414.01 1 0.000
#> TCGA.S9.A6WI.01 4 0.000
#> TCGA.DU.8164.01 2 0.000
#> TCGA.06.A7TK.01 5 0.000
#> TCGA.06.5411.01 5 0.000
#> TCGA.S9.A6TS.01 3 0.000
#> TCGA.DB.A64S.01 3 0.000
#> TCGA.VV.A86M.01 2 0.000
#> TCGA.TQ.A8XE.01 3 0.000
#> TCGA.CS.6667.01 2 0.000
#> TCGA.76.6656.01 1 0.249
#> TCGA.E1.A7YL.01 1 1.000
#> TCGA.E1.A7YV.01 3 0.000
#> TCGA.HT.8558.01 5 0.000
#> TCGA.HT.A61C.01 1 1.000
#> TCGA.TQ.A7RW.01 3 0.000
#> TCGA.DU.5849.01 3 0.000
#> TCGA.76.4925.01 1 0.000
#> TCGA.DU.A7TI.01 3 0.000
#> TCGA.QH.A6CV.01 1 0.000
#> TCGA.4W.AA9R.01 1 0.000
#> TCGA.HT.7468.01 2 0.000
#> TCGA.FG.6692.01 1 0.000
#> TCGA.81.5910.01 1 0.000
#> TCGA.28.5214.01 1 1.000
#> TCGA.TQ.A7RI.01 3 0.000
#> TCGA.DB.5279.01 2 0.000
#> TCGA.S9.A6U8.01 3 0.000
#> TCGA.HW.7489.01 3 0.000
#> TCGA.R8.A6YH.01 2 0.000
#> TCGA.74.6584.01 5 0.000
#> TCGA.DU.7018.01 2 0.000
#> TCGA.06.0190.01 1 0.000
#> TCGA.06.0190.02 1 0.000
#> TCGA.HT.7677.01 2 0.000
#> TCGA.FG.A713.01 4 0.000
#> TCGA.DU.7300.01 3 0.000
#> TCGA.TM.A7CA.01 3 0.000
#> TCGA.76.6664.01 1 0.000
#> TCGA.HT.7690.01 2 0.000
#> TCGA.DU.7013.01 1 1.000
#> TCGA.FG.6689.01 3 0.000
#> TCGA.DU.7007.01 2 1.000
#> TCGA.TQ.A7RF.01 2 0.000
#> TCGA.KT.A7W1.01 1 0.000
#> TCGA.HT.A5RA.01 1 0.000
#> TCGA.DB.5277.01 2 0.000
#> TCGA.HT.7694.01 4 0.000
#> TCGA.26.5134.01 1 1.000
#> TCGA.TM.A84M.01 2 0.000
#> TCGA.F6.A8O3.01 2 0.000
#> TCGA.QH.A86X.01 2 1.000
#> TCGA.28.2501.01 5 1.000
#> TCGA.HT.8013.01 2 0.000
#> TCGA.76.6286.01 1 1.000
#> TCGA.HW.7490.01 2 0.000
#> TCGA.14.1450.01 1 0.000
#> TCGA.76.6660.01 1 1.000
#> TCGA.28.5204.01 1 0.000
#> TCGA.QH.A65S.01 3 0.000
#> TCGA.DU.A76R.01 3 0.000
#> TCGA.DH.5144.01 2 0.000
#> TCGA.CS.6188.01 1 0.000
#> TCGA.06.1804.01 1 0.000
#> TCGA.P5.A780.01 3 0.000
#> TCGA.HT.7606.01 2 0.000
#> TCGA.DU.A7TJ.01 1 0.000
#> TCGA.76.4931.01 1 0.000
#> TCGA.DB.A64V.01 4 0.000
#> TCGA.RY.A840.01 2 0.000
#> TCGA.E1.5302.01 3 0.000
#> TCGA.HW.A5KJ.01 3 0.000
#> TCGA.HT.A615.01 3 0.000
#> TCGA.HT.8105.01 2 0.000
#> TCGA.DU.7309.01 3 0.000
#> TCGA.DU.A5TY.01 1 0.000
#> TCGA.28.6450.01 1 1.000
#> TCGA.DU.5847.01 1 0.249
#> TCGA.E1.A7YK.01 4 0.000
#> TCGA.76.4928.01 1 0.000
#> TCGA.26.6173.01 1 0.000
#> TCGA.HT.7874.01 4 0.000
#> TCGA.HT.7471.01 2 0.000
#> TCGA.HT.7882.01 1 1.000
#> TCGA.DU.5854.01 5 1.000
#> TCGA.DU.6395.01 2 0.000
#> TCGA.76.6282.01 1 0.000
#> TCGA.19.5954.01 1 0.000
#> TCGA.HT.8011.01 5 0.000
#> TCGA.S9.A6TV.01 2 0.000
#> TCGA.P5.A5EW.01 2 0.000
#> TCGA.DU.5852.01 1 0.000
#> TCGA.32.1979.01 1 1.000
#> TCGA.DU.6408.01 3 0.000
#> TCGA.87.5896.01 1 0.498
#> TCGA.DB.A4XB.01 2 0.000
#> TCGA.E1.A7YY.01 4 0.000
#> TCGA.FG.A4MT.01 2 0.000
#> TCGA.FG.A4MT.02 3 0.000
#> TCGA.HT.A619.01 2 0.000
#> TCGA.P5.A72U.01 1 1.000
#> TCGA.QH.A870.01 2 0.000
#> TCGA.HT.A5R9.01 3 0.000
#> TCGA.DU.6404.02 5 0.000
#> TCGA.DU.6404.01 5 0.000
#> TCGA.19.0957.01 5 0.000
#> TCGA.19.0957.02 5 0.000
#> TCGA.FG.5964.01 4 0.000
#> TCGA.CS.5396.01 2 0.000
#> TCGA.HT.8107.01 5 0.000
#> TCGA.DU.A7TA.01 3 0.000
#> TCGA.HW.8319.01 2 0.253
#> TCGA.06.5859.01 5 0.000
#> TCGA.DH.A7UR.01 3 0.000
#> TCGA.TM.A84H.01 2 0.000
#> TCGA.S9.A6TZ.01 2 0.000
#> TCGA.HT.7479.01 3 0.000
#> TCGA.DU.6400.01 2 0.000
#> TCGA.S9.A6WL.01 3 0.000
#> TCGA.DB.A75K.01 2 0.000
#> TCGA.DB.A4XD.01 2 0.000
#> TCGA.76.6657.01 1 0.000
#> TCGA.DB.A64Q.01 3 0.000
#> TCGA.P5.A737.01 2 0.000
#> TCGA.06.6699.01 1 0.000
#> TCGA.DB.5275.01 2 0.000
#> TCGA.S9.A6WH.01 2 0.000
#> TCGA.HT.7602.01 4 0.000
#> TCGA.DU.A5TU.01 3 0.000
#> TCGA.HT.A5RB.01 2 0.000
#> TCGA.E1.A7YN.01 1 1.000
#> TCGA.HT.7616.01 3 0.000
#> TCGA.S9.A7R8.01 2 0.000
#> TCGA.41.5651.01 5 1.000
#> TCGA.76.6192.01 1 0.000
#> TCGA.QH.A6XA.01 3 0.000
#> TCGA.HT.8111.01 3 0.000
#> TCGA.74.6575.01 1 1.000
#> TCGA.E1.A7Z2.01 1 1.000
#> TCGA.DU.A5TP.01 3 0.000
#> TCGA.VM.A8CD.01 1 0.498
#> TCGA.RY.A83Y.01 2 0.000
#> TCGA.HT.7482.01 3 0.000
#> TCGA.TQ.A7RK.02 2 0.000
#> TCGA.TQ.A7RK.01 2 0.000
#> TCGA.HT.7858.01 3 0.000
#> TCGA.06.0210.01 1 1.000
#> TCGA.06.0210.02 5 0.000
#> TCGA.06.A5U1.01 1 0.000
#> TCGA.HT.7475.01 2 0.751
#> TCGA.HT.8564.01 5 0.000
#> TCGA.DB.A64U.01 3 0.000
#> TCGA.19.5956.01 5 0.000
#> TCGA.DB.A64W.01 2 0.000
#> TCGA.R8.A6MO.01 3 0.000
#> TCGA.28.5216.01 1 1.000
#> TCGA.DU.A7T8.01 2 0.000
#> TCGA.HW.8322.01 2 0.000
#> TCGA.DU.5870.02 2 0.000
#> TCGA.CS.6668.01 2 0.000
#> TCGA.DU.5870.01 3 0.000
#> TCGA.FG.7636.01 2 0.000
#> TCGA.HT.7692.01 2 0.000
#> TCGA.WY.A859.01 3 0.000
#> TCGA.HT.7854.01 5 0.000
#> TCGA.R8.A6ML.01 2 0.000
#> TCGA.VM.A8C9.01 1 1.000
#> TCGA.HT.7686.01 3 0.000
#> TCGA.DU.6410.01 2 0.000
#> TCGA.S9.A6U9.01 3 0.000
#> TCGA.74.6573.01 1 0.000
#> TCGA.CS.6290.01 4 1.000
#> TCGA.TQ.A7RO.01 3 0.000
#> TCGA.DU.7019.01 3 0.000
#> TCGA.06.5858.01 1 0.000
#> TCGA.FG.A711.01 3 0.000
#> TCGA.TQ.A7RM.01 2 0.000
#> TCGA.HT.7860.01 1 1.000
#> TCGA.S9.A7R4.01 2 0.000
#> TCGA.E1.5318.01 2 0.000
#> TCGA.HT.7676.01 2 0.000
#> TCGA.14.0740.01 5 0.502
#> TCGA.S9.A7J3.01 3 0.000
#> TCGA.81.5911.01 1 0.000
#> TCGA.06.6701.01 2 0.000
#> TCGA.P5.A5F2.01 3 0.000
#> TCGA.E1.5304.01 2 0.000
#> TCGA.DU.7006.01 5 0.751
#> TCGA.TM.A84S.01 3 0.000
#> TCGA.HT.7469.01 5 0.498
#> TCGA.06.6390.01 1 0.000
#> TCGA.WY.A85B.01 2 0.000
#> TCGA.TQ.A7RS.01 2 0.000
#> TCGA.S9.A7QX.01 2 0.000
#> TCGA.CS.4943.01 2 0.000
#> TCGA.QH.A65Z.01 2 0.000
#> TCGA.DB.5276.01 4 0.000
#> TCGA.P5.A730.01 2 0.000
#> TCGA.06.A5U0.01 5 0.000
#> TCGA.TM.A84L.01 3 0.000
#> TCGA.DU.8161.01 1 1.000
#> TCGA.19.5959.01 1 0.253
#> TCGA.WY.A85D.01 2 0.000
#> TCGA.RY.A83X.01 3 0.000
#> TCGA.S9.A6UB.01 2 0.000
#> TCGA.E1.A7YM.01 1 1.000
#> TCGA.DB.5273.01 3 0.000
#> TCGA.TM.A7C4.01 3 0.000
#> TCGA.DH.A66F.01 2 0.000
#> TCGA.HT.7607.01 4 0.000
#> TCGA.DU.6393.01 2 0.000
#> TCGA.06.5413.01 1 0.000
#> TCGA.19.5947.01 1 0.000
#> TCGA.HT.8108.01 2 0.000
#> TCGA.E1.A7YD.01 1 0.000
#> TCGA.19.5960.01 5 0.000
#> TCGA.DU.7304.01 3 0.000
#> TCGA.14.1034.02 1 0.498
#> TCGA.S9.A7IY.01 3 0.000
#> TCGA.FG.7641.01 3 0.000
#> TCGA.P5.A736.01 3 0.000
#> TCGA.14.0736.02 5 1.000
#> TCGA.19.5952.01 1 0.000
#> TCGA.P5.A5EV.01 2 0.000
#> TCGA.DU.7301.01 2 0.000
#> TCGA.HT.7470.01 3 0.000
#> TCGA.28.5208.01 1 0.000
#> TCGA.DU.7009.01 2 0.000
#> TCGA.P5.A781.01 3 0.000
#> TCGA.DH.5140.01 5 0.000
#> TCGA.76.6280.01 1 0.000
#> TCGA.FG.A4MY.01 3 0.000
#> TCGA.TM.A7CF.01 3 0.000
#> TCGA.TM.A7CF.02 4 0.000
#> TCGA.FG.8186.01 2 1.000
#> TCGA.S9.A6U6.01 3 0.000
#> TCGA.HT.8015.01 5 0.000
#> TCGA.RY.A845.01 3 0.000
#> TCGA.DU.7010.01 3 0.000
#> TCGA.S9.A6U2.01 3 0.000
#> TCGA.S9.A6WN.01 4 0.000
#> TCGA.28.2510.01 5 0.000
#> TCGA.DU.A7TD.01 1 0.000
#> TCGA.14.0736.01 1 0.000
#> TCGA.DU.6405.01 5 0.249
#> TCGA.06.0152.02 1 1.000
#> TCGA.06.0152.01 1 0.000
#> TCGA.76.4927.01 1 0.000
#> TCGA.FG.8182.01 3 0.000
#> TCGA.QH.A6X3.01 2 0.000
#> TCGA.DU.6401.01 2 0.000
#> TCGA.26.5132.01 1 0.000
#> TCGA.DU.6396.01 3 0.000
#> TCGA.E1.A7YH.01 3 0.000
#> TCGA.DU.7306.01 2 0.000
#> TCGA.HT.A74J.01 3 0.000
#> TCGA.HT.A74H.01 5 1.000
#> TCGA.DH.A7US.01 3 0.000
#> TCGA.FG.A87N.01 3 0.000
#> TCGA.HT.7478.01 3 0.000
#> TCGA.DU.7290.01 1 0.000
#> TCGA.DB.A4XE.01 2 0.000
#> TCGA.DB.A64L.01 3 0.000
#> TCGA.VV.A829.01 2 0.000
#> TCGA.19.A6J4.01 1 0.000
#> TCGA.HT.A61B.01 2 0.000
#> TCGA.12.5299.01 1 1.000
#> TCGA.DH.A66B.01 2 0.000
#> TCGA.HT.7603.01 4 0.000
#> TCGA.DU.6397.02 2 0.000
#> TCGA.DU.6397.01 3 0.000
#> TCGA.HT.A4DS.01 1 0.000
#> TCGA.12.5301.01 1 0.747
#> TCGA.RR.A6KB.01 5 0.249
#> TCGA.DU.5853.01 3 0.000
#> TCGA.CS.6670.01 2 0.000
#> TCGA.DU.7014.01 2 0.000
#> TCGA.QH.A65X.01 2 0.000
#> TCGA.TM.A84B.01 1 1.000
#> TCGA.DB.A64P.01 2 0.000
#> TCGA.FG.5965.02 4 0.000
#> TCGA.FG.A70Y.01 3 0.000
#> TCGA.TQ.A7RV.01 3 0.000
#> TCGA.TQ.A7RV.02 4 0.000
#> TCGA.HT.A5R7.01 4 0.000
#> TCGA.06.6389.01 3 0.000
#> TCGA.HW.A5KL.01 2 0.000
#> TCGA.06.5416.01 1 0.000
#> TCGA.DU.8158.01 5 1.000
#> TCGA.HT.7474.01 3 0.000
#> TCGA.DH.A7UU.01 2 0.000
#> TCGA.26.5139.01 1 0.000
#> TCGA.QH.A6CZ.01 2 0.000
#> TCGA.DH.A669.02 2 0.000
#> TCGA.DH.A669.01 2 0.000
#> TCGA.QH.A6X9.01 3 0.000
#> TCGA.P5.A5EZ.01 3 0.000
#> TCGA.DU.5871.01 3 0.502
#> TCGA.TQ.A7RJ.01 3 0.000
#> TCGA.WY.A858.01 3 0.000
#> TCGA.TM.A84J.01 5 0.498
#> TCGA.VM.A8CB.01 2 0.000
#> TCGA.41.6646.01 1 0.000
#> TCGA.14.0781.01 1 0.000
#> TCGA.HT.7483.01 3 0.000
#> TCGA.HT.7687.01 2 0.000
#> TCGA.TM.A84G.01 2 0.000
#> TCGA.E1.A7Z6.01 3 0.000
#> TCGA.TM.A84I.01 2 0.751
#> TCGA.CS.5394.01 2 0.000
#> TCGA.HT.A617.01 1 1.000
#> TCGA.DU.A76O.01 3 0.000
#> TCGA.DU.A5TW.01 2 0.000
#> TCGA.HT.7857.01 5 0.000
#> TCGA.WY.A85A.01 3 0.000
#> TCGA.FG.5962.01 2 0.000
#> TCGA.74.6578.01 1 0.000
get_classes(res, k = 7)
#> class p
#> TCGA.E1.5319.01 3 0.000
#> TCGA.HT.7693.01 6 0.000
#> TCGA.CS.6665.01 3 0.000
#> TCGA.S9.A7J2.01 6 0.000
#> TCGA.FG.A6J3.01 3 0.000
#> TCGA.FG.6688.01 5 0.000
#> TCGA.S9.A6TX.01 2 0.000
#> TCGA.VM.A8C8.01 3 0.000
#> TCGA.74.6577.01 1 0.000
#> TCGA.06.AABW.11 5 0.000
#> TCGA.06.0125.02 1 1.000
#> TCGA.HT.A74L.01 6 0.000
#> TCGA.26.A7UX.01 1 0.000
#> TCGA.DU.A5TS.01 3 0.000
#> TCGA.06.6388.01 1 0.000
#> TCGA.DB.A4XA.01 3 0.000
#> TCGA.06.A7TL.01 3 0.000
#> TCGA.HT.A4DV.01 4 0.000
#> TCGA.TQ.A7RP.01 5 0.000
#> TCGA.E1.5311.01 2 0.000
#> TCGA.28.5213.01 1 0.000
#> TCGA.E1.A7YI.01 3 0.000
#> TCGA.E1.5305.01 6 0.000
#> TCGA.F6.A8O4.01 3 0.000
#> TCGA.HT.8113.01 4 0.000
#> TCGA.DH.A66G.01 3 0.000
#> TCGA.76.4932.01 1 0.751
#> TCGA.HT.7620.01 4 0.000
#> TCGA.P5.A731.01 2 0.000
#> TCGA.HT.7480.01 2 0.000
#> TCGA.06.5412.01 1 1.000
#> TCGA.HT.7689.01 3 0.000
#> TCGA.06.6694.01 5 1.000
#> TCGA.HT.8109.01 3 0.000
#> TCGA.E1.A7YE.01 3 0.000
#> TCGA.S9.A7R1.01 2 0.000
#> TCGA.FG.A710.01 3 0.000
#> TCGA.19.1389.01 1 0.253
#> TCGA.S9.A7J0.01 6 0.000
#> TCGA.DU.A6S6.01 2 0.000
#> TCGA.HT.7877.01 3 0.000
#> TCGA.QH.A6CU.01 3 0.000
#> TCGA.HW.7486.01 4 0.000
#> TCGA.12.5295.01 1 0.502
#> TCGA.FG.7634.01 3 0.000
#> TCGA.19.5953.01 5 0.000
#> TCGA.DU.8163.01 3 0.000
#> TCGA.28.5220.01 1 0.000
#> TCGA.4W.AA9T.01 1 0.751
#> TCGA.OX.A56R.01 1 0.000
#> TCGA.DU.6407.02 3 0.000
#> TCGA.DU.6407.01 6 0.000
#> TCGA.S9.A7IX.01 1 1.000
#> TCGA.HT.8010.01 4 0.000
#> TCGA.06.0171.01 1 0.751
#> TCGA.06.0125.01 1 0.000
#> TCGA.P5.A5F1.01 2 0.000
#> TCGA.VM.A8CF.01 3 0.000
#> TCGA.DU.6542.01 6 1.000
#> TCGA.FG.7638.01 2 0.000
#> TCGA.VW.A8FI.01 1 1.000
#> TCGA.DH.5143.01 2 0.000
#> TCGA.06.6700.01 5 0.000
#> TCGA.DU.7299.01 2 0.000
#> TCGA.28.5218.01 5 0.000
#> TCGA.06.0171.02 5 1.000
#> TCGA.DU.8165.01 1 0.000
#> TCGA.CS.5393.01 3 0.000
#> TCGA.06.5856.01 1 1.000
#> TCGA.26.5136.01 1 0.000
#> TCGA.DU.7011.01 3 0.000
#> TCGA.TM.A84Q.01 2 0.000
#> TCGA.DB.5281.01 6 0.000
#> TCGA.DU.A76L.01 1 1.000
#> TCGA.HT.7605.01 3 0.000
#> TCGA.FG.A6J1.01 2 0.000
#> TCGA.76.6663.01 1 1.000
#> TCGA.DB.5270.01 4 0.000
#> TCGA.S9.A6WQ.01 3 0.000
#> TCGA.76.4926.01 1 0.000
#> TCGA.HT.8106.01 4 0.000
#> TCGA.HT.7608.01 3 0.000
#> TCGA.26.5133.01 4 0.000
#> TCGA.E1.A7YU.01 3 0.000
#> TCGA.W9.A837.01 3 0.000
#> TCGA.TM.A7C5.01 6 0.000
#> TCGA.S9.A7QY.01 3 0.000
#> TCGA.QH.A6CW.01 2 0.000
#> TCGA.S9.A6WO.01 2 0.000
#> TCGA.IK.7675.01 6 0.000
#> TCGA.HT.7601.01 3 0.000
#> TCGA.P5.A5ET.01 2 0.000
#> TCGA.HT.7472.01 2 0.000
#> TCGA.HT.7880.01 4 0.000
#> TCGA.26.1442.01 3 0.000
#> TCGA.19.A6J5.01 2 0.000
#> TCGA.E1.A7Z3.01 4 1.000
#> TCGA.P5.A77X.01 2 0.000
#> TCGA.FG.A6IZ.01 6 0.000
#> TCGA.06.0211.02 1 0.000
#> TCGA.28.5207.01 1 1.000
#> TCGA.14.1402.01 1 1.000
#> TCGA.06.0211.01 1 0.000
#> TCGA.14.1402.02 1 1.000
#> TCGA.HT.7873.01 2 0.000
#> TCGA.CS.4938.01 6 0.249
#> TCGA.19.4065.02 1 1.000
#> TCGA.RR.A6KC.01 1 0.253
#> TCGA.19.4065.01 5 0.000
#> TCGA.KT.A74X.01 2 0.000
#> TCGA.P5.A5EX.01 4 1.000
#> TCGA.VM.A8CH.01 2 0.000
#> TCGA.HT.7476.01 3 0.000
#> TCGA.DB.A75L.01 2 0.000
#> TCGA.HT.8563.01 4 0.000
#> TCGA.CS.4941.01 1 0.000
#> TCGA.RY.A843.01 3 0.000
#> TCGA.S9.A7IS.01 3 0.000
#> TCGA.TQ.A8XE.02 2 0.000
#> TCGA.S9.A6U0.01 1 0.751
#> TCGA.FG.7643.01 5 0.000
#> TCGA.E1.A7YO.01 2 0.000
#> TCGA.06.5408.01 1 0.000
#> TCGA.TQ.A7RG.01 2 0.000
#> TCGA.QH.A6X5.01 3 0.000
#> TCGA.76.6285.01 1 0.751
#> TCGA.DU.6403.01 1 0.000
#> TCGA.HW.7493.01 3 0.000
#> TCGA.19.5950.01 1 0.000
#> TCGA.RY.A847.01 3 0.000
#> TCGA.DU.8166.01 6 0.498
#> TCGA.VM.A8CA.01 3 0.000
#> TCGA.HT.7855.01 6 0.000
#> TCGA.S9.A89Z.01 3 0.000
#> TCGA.DB.A4XG.01 6 0.000
#> TCGA.14.1395.01 1 1.000
#> TCGA.DH.A7UT.01 3 0.000
#> TCGA.DU.7015.01 2 0.000
#> TCGA.HT.A616.01 3 0.000
#> TCGA.FG.8181.01 5 0.000
#> TCGA.HT.7611.01 6 0.000
#> TCGA.HT.8018.01 4 0.000
#> TCGA.FG.A60K.01 2 0.000
#> TCGA.HT.7856.01 4 0.000
#> TCGA.FG.5963.01 5 0.000
#> TCGA.FG.5963.02 5 0.000
#> TCGA.DU.5851.01 4 0.000
#> TCGA.DU.A7T6.01 3 0.000
#> TCGA.S9.A6TY.01 2 0.000
#> TCGA.CS.5395.01 1 0.000
#> TCGA.DU.7292.01 5 0.000
#> TCGA.HT.A5RC.01 1 1.000
#> TCGA.WY.A85C.01 2 0.000
#> TCGA.DB.A4XC.01 3 0.000
#> TCGA.TM.A84O.01 3 0.000
#> TCGA.06.5410.01 1 1.000
#> TCGA.19.5958.01 1 0.000
#> TCGA.P5.A72W.01 6 0.000
#> TCGA.S9.A6TU.01 2 0.000
#> TCGA.HT.A61A.01 4 0.000
#> TCGA.28.5211.01 1 0.502
#> TCGA.DU.5855.01 3 0.000
#> TCGA.HT.7884.01 2 0.000
#> TCGA.TQ.A7RQ.01 6 0.000
#> TCGA.TM.A84C.01 5 0.000
#> TCGA.FG.A4MW.01 5 1.000
#> TCGA.IK.8125.01 2 0.000
#> TCGA.HT.A74K.01 3 0.000
#> TCGA.WH.A86K.01 2 0.000
#> TCGA.DB.A75P.01 5 0.000
#> TCGA.QH.A6X8.01 2 0.000
#> TCGA.S9.A89V.01 5 1.000
#> TCGA.WY.A85E.01 2 0.000
#> TCGA.HT.A5R5.01 3 0.747
#> TCGA.06.6695.01 1 1.000
#> TCGA.06.5418.01 1 0.253
#> TCGA.HT.A618.01 3 0.000
#> TCGA.FG.6691.01 3 0.000
#> TCGA.HT.7467.01 4 0.000
#> TCGA.06.5415.01 1 1.000
#> TCGA.S9.A7R3.01 6 0.000
#> TCGA.QH.A6CX.01 5 0.000
#> TCGA.06.A6S1.01 1 1.000
#> TCGA.FG.A4MX.01 6 0.000
#> TCGA.HT.7681.01 3 0.000
#> TCGA.S9.A7IZ.01 3 0.000
#> TCGA.DU.A6S7.01 6 0.000
#> TCGA.06.0221.01 3 0.000
#> TCGA.P5.A72Z.01 6 0.000
#> TCGA.HT.8114.01 2 0.000
#> TCGA.DU.8168.01 6 0.000
#> TCGA.HW.8321.01 3 0.000
#> TCGA.TQ.A7RN.01 2 0.000
#> TCGA.DH.5141.01 3 0.000
#> TCGA.CS.6186.01 1 1.000
#> TCGA.EZ.7264.01 6 0.000
#> TCGA.26.5135.01 1 1.000
#> TCGA.P5.A5F4.01 3 0.000
#> TCGA.QH.A65V.01 3 0.000
#> TCGA.28.5219.01 1 1.000
#> TCGA.4W.AA9S.01 1 0.000
#> TCGA.19.A60I.01 1 0.000
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#> TCGA.DH.A669.01 6 0.000
#> TCGA.QH.A6X9.01 2 0.000
#> TCGA.P5.A5EZ.01 3 0.000
#> TCGA.DU.5871.01 2 0.000
#> TCGA.TQ.A7RJ.01 3 0.000
#> TCGA.WY.A858.01 3 0.000
#> TCGA.TM.A84J.01 4 0.498
#> TCGA.VM.A8CB.01 6 0.000
#> TCGA.41.6646.01 1 1.000
#> TCGA.14.0781.01 1 1.000
#> TCGA.HT.7483.01 2 0.000
#> TCGA.HT.7687.01 2 0.000
#> TCGA.TM.A84G.01 6 0.000
#> TCGA.E1.A7Z6.01 2 0.000
#> TCGA.TM.A84I.01 2 0.000
#> TCGA.CS.5394.01 6 0.000
#> TCGA.HT.A617.01 5 1.000
#> TCGA.DU.A76O.01 2 0.000
#> TCGA.DU.A5TW.01 6 0.000
#> TCGA.HT.7857.01 5 0.000
#> TCGA.WY.A85A.01 3 0.000
#> TCGA.FG.5962.01 2 0.000
#> TCGA.74.6578.01 1 0.000
get_classes(res, k = 8)
#> class p
#> TCGA.E1.5319.01 3 0.000
#> TCGA.HT.7693.01 6 0.000
#> TCGA.CS.6665.01 3 1.000
#> TCGA.S9.A7J2.01 6 0.000
#> TCGA.FG.A6J3.01 5 0.000
#> TCGA.FG.6688.01 4 0.000
#> TCGA.S9.A6TX.01 2 0.000
#> TCGA.VM.A8C8.01 3 0.000
#> TCGA.74.6577.01 1 0.253
#> TCGA.06.AABW.11 4 0.000
#> TCGA.06.0125.02 1 1.000
#> TCGA.HT.A74L.01 6 0.000
#> TCGA.26.A7UX.01 1 0.000
#> TCGA.DU.A5TS.01 3 0.000
#> TCGA.06.6388.01 1 0.253
#> TCGA.DB.A4XA.01 3 0.000
#> TCGA.06.A7TL.01 3 0.000
#> TCGA.HT.A4DV.01 7 0.000
#> TCGA.TQ.A7RP.01 4 0.000
#> TCGA.E1.5311.01 2 0.000
#> TCGA.28.5213.01 1 0.000
#> TCGA.E1.A7YI.01 5 0.000
#> TCGA.E1.5305.01 6 0.000
#> TCGA.F6.A8O4.01 3 0.000
#> TCGA.HT.8113.01 7 0.000
#> TCGA.DH.A66G.01 3 0.000
#> TCGA.76.4932.01 1 0.751
#> TCGA.HT.7620.01 7 0.000
#> TCGA.P5.A731.01 2 0.000
#> TCGA.HT.7480.01 2 0.000
#> TCGA.06.5412.01 1 1.000
#> TCGA.HT.7689.01 3 0.000
#> TCGA.06.6694.01 4 0.000
#> TCGA.HT.8109.01 3 0.000
#> TCGA.E1.A7YE.01 5 0.000
#> TCGA.S9.A7R1.01 2 0.000
#> TCGA.FG.A710.01 3 0.000
#> TCGA.19.1389.01 1 0.253
#> TCGA.S9.A7J0.01 6 0.000
#> TCGA.DU.A6S6.01 2 0.000
#> TCGA.HT.7877.01 3 0.000
#> TCGA.QH.A6CU.01 3 0.000
#> TCGA.HW.7486.01 3 0.000
#> TCGA.12.5295.01 1 1.000
#> TCGA.FG.7634.01 3 0.000
#> TCGA.19.5953.01 4 0.000
#> TCGA.DU.8163.01 3 0.000
#> TCGA.28.5220.01 1 0.000
#> TCGA.4W.AA9T.01 1 0.751
#> TCGA.OX.A56R.01 1 0.000
#> TCGA.DU.6407.02 5 1.000
#> TCGA.DU.6407.01 6 0.000
#> TCGA.S9.A7IX.01 1 1.000
#> TCGA.HT.8010.01 7 0.000
#> TCGA.06.0171.01 1 1.000
#> TCGA.06.0125.01 1 0.000
#> TCGA.P5.A5F1.01 2 0.000
#> TCGA.VM.A8CF.01 3 0.000
#> TCGA.DU.6542.01 6 1.000
#> TCGA.FG.7638.01 2 0.000
#> TCGA.VW.A8FI.01 1 1.000
#> TCGA.DH.5143.01 2 0.000
#> TCGA.06.6700.01 4 0.000
#> TCGA.DU.7299.01 2 0.000
#> TCGA.28.5218.01 4 0.000
#> TCGA.06.0171.02 4 1.000
#> TCGA.DU.8165.01 1 0.000
#> TCGA.CS.5393.01 3 0.000
#> TCGA.06.5856.01 1 1.000
#> TCGA.26.5136.01 1 0.000
#> TCGA.DU.7011.01 3 0.000
#> TCGA.TM.A84Q.01 2 0.000
#> TCGA.DB.5281.01 6 0.000
#> TCGA.DU.A76L.01 1 1.000
#> TCGA.HT.7605.01 3 0.000
#> TCGA.FG.A6J1.01 2 0.000
#> TCGA.76.6663.01 1 1.000
#> TCGA.DB.5270.01 7 1.000
#> TCGA.S9.A6WQ.01 3 0.000
#> TCGA.76.4926.01 1 0.000
#> TCGA.HT.8106.01 7 0.000
#> TCGA.HT.7608.01 3 0.000
#> TCGA.26.5133.01 5 0.000
#> TCGA.E1.A7YU.01 3 0.000
#> TCGA.W9.A837.01 3 0.000
#> TCGA.TM.A7C5.01 6 0.000
#> TCGA.S9.A7QY.01 3 0.000
#> TCGA.QH.A6CW.01 2 0.000
#> TCGA.S9.A6WO.01 2 0.000
#> TCGA.IK.7675.01 6 0.000
#> TCGA.HT.7601.01 3 0.000
#> TCGA.P5.A5ET.01 2 0.000
#> TCGA.HT.7472.01 2 0.000
#> TCGA.HT.7880.01 7 0.000
#> TCGA.26.1442.01 3 0.000
#> TCGA.19.A6J5.01 6 0.502
#> TCGA.E1.A7Z3.01 3 0.000
#> TCGA.P5.A77X.01 2 0.000
#> TCGA.FG.A6IZ.01 6 0.000
#> TCGA.06.0211.02 1 0.751
#> TCGA.28.5207.01 1 0.751
#> TCGA.14.1402.01 1 1.000
#> TCGA.06.0211.01 1 0.253
#> TCGA.14.1402.02 4 1.000
#> TCGA.HT.7873.01 2 0.000
#> TCGA.CS.4938.01 6 0.502
#> TCGA.19.4065.02 1 1.000
#> TCGA.RR.A6KC.01 1 0.502
#> TCGA.19.4065.01 4 0.000
#> TCGA.KT.A74X.01 2 0.000
#> TCGA.P5.A5EX.01 3 0.000
#> TCGA.VM.A8CH.01 2 0.000
#> TCGA.HT.7476.01 3 0.000
#> TCGA.DB.A75L.01 2 0.000
#> TCGA.HT.8563.01 7 0.000
#> TCGA.CS.4941.01 1 0.000
#> TCGA.RY.A843.01 3 0.000
#> TCGA.S9.A7IS.01 5 0.000
#> TCGA.TQ.A8XE.02 2 0.000
#> TCGA.S9.A6U0.01 1 0.751
#> TCGA.FG.7643.01 4 0.000
#> TCGA.E1.A7YO.01 2 0.000
#> TCGA.06.5408.01 1 0.000
#> TCGA.TQ.A7RG.01 2 0.000
#> TCGA.QH.A6X5.01 3 0.000
#> TCGA.76.6285.01 1 1.000
#> TCGA.DU.6403.01 1 0.000
#> TCGA.HW.7493.01 3 0.000
#> TCGA.19.5950.01 1 0.000
#> TCGA.RY.A847.01 3 0.000
#> TCGA.DU.8166.01 6 1.000
#> TCGA.VM.A8CA.01 3 0.000
#> TCGA.HT.7855.01 6 0.000
#> TCGA.S9.A89Z.01 3 0.000
#> TCGA.DB.A4XG.01 6 0.000
#> TCGA.14.1395.01 4 0.000
#> TCGA.DH.A7UT.01 3 0.000
#> TCGA.DU.7015.01 2 0.000
#> TCGA.HT.A616.01 3 0.000
#> TCGA.FG.8181.01 4 0.000
#> TCGA.HT.7611.01 6 0.000
#> TCGA.HT.8018.01 7 0.000
#> TCGA.FG.A60K.01 2 0.000
#> TCGA.HT.7856.01 7 0.000
#> TCGA.FG.5963.01 4 0.000
#> TCGA.FG.5963.02 4 0.000
#> TCGA.DU.5851.01 7 0.000
#> TCGA.DU.A7T6.01 3 0.751
#> TCGA.S9.A6TY.01 2 0.000
#> TCGA.CS.5395.01 1 1.000
#> TCGA.DU.7292.01 4 0.000
#> TCGA.HT.A5RC.01 4 1.000
#> TCGA.WY.A85C.01 2 0.000
#> TCGA.DB.A4XC.01 3 0.000
#> TCGA.TM.A84O.01 3 0.000
#> TCGA.06.5410.01 1 1.000
#> TCGA.19.5958.01 1 0.000
#> TCGA.P5.A72W.01 6 0.000
#> TCGA.S9.A6TU.01 2 0.000
#> TCGA.HT.A61A.01 7 0.000
#> TCGA.28.5211.01 1 1.000
#> TCGA.DU.5855.01 3 0.000
#> TCGA.HT.7884.01 2 0.000
#> TCGA.TQ.A7RQ.01 6 0.000
#> TCGA.TM.A84C.01 4 0.000
#> TCGA.FG.A4MW.01 4 0.253
#> TCGA.IK.8125.01 2 0.000
#> TCGA.HT.A74K.01 3 0.000
#> TCGA.WH.A86K.01 2 0.000
#> TCGA.DB.A75P.01 4 0.000
#> TCGA.QH.A6X8.01 2 0.000
#> TCGA.S9.A89V.01 4 1.000
#> TCGA.WY.A85E.01 2 0.000
#> TCGA.HT.A5R5.01 3 0.000
#> TCGA.06.6695.01 1 1.000
#> TCGA.06.5418.01 1 0.253
#> TCGA.HT.A618.01 3 0.000
#> TCGA.FG.6691.01 3 0.000
#> TCGA.HT.7467.01 7 0.000
#> TCGA.06.5415.01 1 1.000
#> TCGA.S9.A7R3.01 6 0.000
#> TCGA.QH.A6CX.01 4 0.000
#> TCGA.06.A6S1.01 1 1.000
#> TCGA.FG.A4MX.01 6 0.000
#> TCGA.HT.7681.01 3 0.000
#> TCGA.S9.A7IZ.01 3 0.000
#> TCGA.DU.A6S7.01 6 0.000
#> TCGA.06.0221.01 3 0.000
#> TCGA.P5.A72Z.01 6 0.000
#> TCGA.HT.8114.01 2 0.000
#> TCGA.DU.8168.01 6 0.000
#> TCGA.HW.8321.01 3 0.000
#> TCGA.TQ.A7RN.01 2 0.000
#> TCGA.DH.5141.01 3 0.000
#> TCGA.CS.6186.01 1 1.000
#> TCGA.EZ.7264.01 6 0.000
#> TCGA.26.5135.01 4 0.249
#> TCGA.P5.A5F4.01 3 0.000
#> TCGA.QH.A65V.01 3 0.000
#> TCGA.28.5219.01 1 1.000
#> TCGA.4W.AA9S.01 1 0.000
#> TCGA.19.A60I.01 1 0.000
#> TCGA.76.4934.01 4 0.249
#> TCGA.FG.8191.01 3 0.000
#> TCGA.DH.5142.01 2 0.000
#> TCGA.DU.A6S8.01 6 1.000
#> TCGA.E1.A7YW.01 2 0.000
#> TCGA.32.5222.01 1 0.249
#> TCGA.76.6191.01 1 1.000
#> TCGA.06.1806.01 1 1.000
#> TCGA.06.6693.01 1 0.751
#> TCGA.CS.6666.01 6 0.000
#> TCGA.DU.7298.01 3 0.000
#> TCGA.DB.A64R.01 6 0.000
#> TCGA.DU.6406.01 1 0.000
#> TCGA.S9.A6UA.01 4 0.000
#> TCGA.FG.A60L.01 3 0.000
#> TCGA.CS.5390.01 6 0.000
#> TCGA.S9.A6WP.01 2 0.000
#> TCGA.DU.A7TB.01 4 1.000
#> TCGA.DB.5280.01 6 0.000
#> TCGA.TM.A84T.01 2 0.000
#> TCGA.DH.A66D.01 2 0.000
#> TCGA.06.6697.01 1 0.751
#> TCGA.RY.A83Z.01 5 0.000
#> TCGA.DB.5278.01 3 0.000
#> TCGA.DU.A76K.01 4 1.000
#> TCGA.TQ.A7RR.01 3 0.000
#> TCGA.28.5215.01 1 0.000
#> TCGA.DU.8162.01 4 0.000
#> TCGA.TQ.A7RH.01 3 0.000
#> TCGA.E1.A7YS.01 6 0.000
#> TCGA.15.1444.01 7 0.000
#> TCGA.P5.A735.01 6 0.502
#> TCGA.DU.7294.01 6 0.000
#> TCGA.E1.A7YQ.01 4 0.000
#> TCGA.HT.7881.01 7 0.000
#> TCGA.QH.A6CS.01 4 0.000
#> TCGA.HT.7695.01 3 0.000
#> TCGA.P5.A5EU.01 5 0.000
#> TCGA.76.6283.01 4 0.000
#> TCGA.DB.A64X.01 6 0.000
#> TCGA.FG.7637.01 6 1.000
#> TCGA.VM.A8CE.01 3 0.000
#> TCGA.76.4929.01 1 1.000
#> TCGA.S9.A6U5.01 3 0.000
#> TCGA.HT.7609.01 2 0.000
#> TCGA.DB.5274.01 2 0.000
#> TCGA.HW.7487.01 3 0.000
#> TCGA.HW.7491.01 6 0.000
#> TCGA.HT.7691.01 4 0.000
#> TCGA.CS.4944.01 3 0.000
#> TCGA.DU.A6S2.01 3 0.000
#> TCGA.19.1389.02 1 0.000
#> TCGA.26.6174.01 4 0.000
#> TCGA.S9.A7R7.01 3 0.000
#> TCGA.TM.A84R.01 7 0.000
#> TCGA.DB.A75M.01 2 0.000
#> TCGA.DU.6392.01 4 0.000
#> TCGA.HW.A5KM.01 2 0.000
#> TCGA.06.0221.02 5 0.000
#> TCGA.HT.7477.01 2 1.000
#> TCGA.HT.8012.01 6 0.000
#> TCGA.32.1980.01 4 0.000
#> TCGA.76.6661.01 1 1.000
#> TCGA.DU.8167.01 2 0.000
#> TCGA.S9.A6U1.01 3 0.000
#> TCGA.FG.5965.01 3 0.000
#> TCGA.FG.8187.01 3 0.000
#> TCGA.HT.A614.01 3 0.249
#> TCGA.28.5209.01 1 0.000
#> TCGA.S9.A7QZ.01 2 0.000
#> TCGA.QH.A6X4.01 2 0.000
#> TCGA.19.5951.01 1 0.751
#> TCGA.P5.A77W.01 2 0.000
#> TCGA.DU.7302.01 2 0.000
#> TCGA.DU.7012.01 1 1.000
#> TCGA.DU.6399.01 2 0.000
#> TCGA.06.A6S0.01 1 0.000
#> TCGA.E1.5307.01 6 0.000
#> TCGA.S9.A7QW.01 6 0.000
#> TCGA.DU.6402.01 1 0.000
#> TCGA.HT.7604.01 6 0.000
#> TCGA.P5.A733.01 3 0.000
#> TCGA.FG.A87Q.01 1 1.000
#> TCGA.HT.7684.01 2 0.000
#> TCGA.HW.7495.01 3 0.000
#> TCGA.QH.A65R.01 2 0.000
#> TCGA.DU.A7TG.01 7 0.000
#> TCGA.DH.A7UV.01 6 0.000
#> TCGA.HT.7879.01 2 0.000
#> TCGA.TM.A84F.01 7 0.000
#> TCGA.HT.8104.01 1 0.253
#> TCGA.FG.A70Z.01 1 1.000
#> TCGA.DU.A7TC.01 2 0.000
#> TCGA.14.0862.01 4 0.000
#> TCGA.HT.7610.01 3 0.000
#> TCGA.S9.A6TW.01 3 0.000
#> TCGA.FG.A60J.01 2 0.000
#> TCGA.E1.5303.01 3 0.000
#> TCGA.QH.A6XC.01 1 1.000
#> TCGA.HT.7481.01 3 0.000
#> TCGA.FN.7833.01 6 0.000
#> TCGA.E1.A7Z4.01 6 0.000
#> TCGA.DU.A5TR.01 3 0.000
#> TCGA.FG.A4MU.01 1 0.000
#> TCGA.HT.7875.01 6 0.000
#> TCGA.06.5417.01 5 1.000
#> TCGA.HT.7473.01 3 0.000
#> TCGA.19.5955.01 1 1.000
#> TCGA.TM.A7C3.01 1 1.000
#> TCGA.S9.A7IQ.01 7 0.000
#> TCGA.DU.7008.01 6 0.000
#> TCGA.DB.A64O.01 1 1.000
#> TCGA.DU.A5TT.01 1 1.000
#> TCGA.S9.A6WG.01 7 1.000
#> TCGA.74.6581.01 1 0.502
#> TCGA.FG.8189.01 7 1.000
#> TCGA.76.6662.01 4 0.502
#> TCGA.DB.A75O.01 3 0.000
#> TCGA.HT.7688.01 3 0.000
#> TCGA.DU.7304.02 6 0.000
#> TCGA.DU.6394.01 6 0.000
#> TCGA.HT.8019.01 4 0.000
#> TCGA.P5.A5EY.01 4 0.000
#> TCGA.RR.A6KA.01 4 0.000
#> TCGA.S9.A6WD.01 3 0.000
#> TCGA.DU.5872.01 3 0.000
#> TCGA.DU.5872.02 4 0.000
#> TCGA.74.6573.11 4 0.000
#> TCGA.FG.8185.01 6 0.000
#> TCGA.HT.7902.01 7 0.000
#> TCGA.CS.5397.01 1 1.000
#> TCGA.TQ.A7RU.01 6 0.000
#> TCGA.HW.A5KK.01 4 0.253
#> TCGA.DU.5874.01 6 0.000
#> TCGA.S9.A6WE.01 2 0.000
#> TCGA.06.0650.01 1 1.000
#> TCGA.FG.6690.01 2 0.000
#> TCGA.HW.8320.01 6 0.000
#> TCGA.CS.6669.01 4 0.000
#> TCGA.S9.A7R2.01 1 1.000
#> TCGA.R8.A6MK.01 2 0.000
#> TCGA.QH.A6CY.01 3 0.000
#> TCGA.S9.A7J1.01 3 0.000
#> TCGA.P5.A72X.01 3 0.000
#> TCGA.E1.5322.01 2 1.000
#> TCGA.P5.A5F0.01 3 0.000
#> TCGA.76.6193.01 4 1.000
#> TCGA.S9.A6WM.01 1 0.000
#> TCGA.R8.A73M.01 6 0.000
#> TCGA.CS.4942.01 3 0.000
#> TCGA.HT.7680.01 1 1.000
#> TCGA.DB.A4X9.01 6 0.000
#> TCGA.DB.A4XF.01 6 0.000
#> TCGA.HT.A74O.01 2 0.000
#> TCGA.06.6698.01 1 0.000
#> TCGA.FG.8188.01 2 0.000
#> TCGA.P5.A5F6.01 4 0.000
#> TCGA.DU.A6S3.01 3 0.000
#> TCGA.14.1043.01 4 0.000
#> TCGA.HT.8110.01 1 0.000
#> TCGA.DB.A4XH.01 2 0.000
#> TCGA.HT.7485.01 2 0.000
#> TCGA.VW.A7QS.01 6 0.000
#> TCGA.06.6391.01 4 0.000
#> TCGA.76.4935.01 4 0.000
#> TCGA.E1.A7YJ.01 4 0.751
#> TCGA.06.5414.01 1 0.000
#> TCGA.S9.A6WI.01 7 0.000
#> TCGA.DU.8164.01 6 0.000
#> TCGA.06.A7TK.01 4 0.000
#> TCGA.06.5411.01 4 0.000
#> TCGA.S9.A6TS.01 2 0.000
#> TCGA.DB.A64S.01 3 0.000
#> TCGA.VV.A86M.01 6 0.000
#> TCGA.TQ.A8XE.01 2 0.000
#> TCGA.CS.6667.01 2 0.000
#> TCGA.76.6656.01 1 1.000
#> TCGA.E1.A7YL.01 1 1.000
#> TCGA.E1.A7YV.01 5 0.000
#> TCGA.HT.8558.01 4 0.000
#> TCGA.HT.A61C.01 1 1.000
#> TCGA.TQ.A7RW.01 3 0.000
#> TCGA.DU.5849.01 3 0.000
#> TCGA.76.4925.01 1 0.000
#> TCGA.DU.A7TI.01 3 0.000
#> TCGA.QH.A6CV.01 1 1.000
#> TCGA.4W.AA9R.01 1 1.000
#> TCGA.HT.7468.01 6 0.000
#> TCGA.FG.6692.01 1 0.000
#> TCGA.81.5910.01 1 0.000
#> TCGA.28.5214.01 1 1.000
#> TCGA.TQ.A7RI.01 3 0.000
#> TCGA.DB.5279.01 6 0.000
#> TCGA.S9.A6U8.01 3 0.000
#> TCGA.HW.7489.01 3 0.000
#> TCGA.R8.A6YH.01 6 0.000
#> TCGA.74.6584.01 4 0.000
#> TCGA.DU.7018.01 6 0.000
#> TCGA.06.0190.01 1 0.000
#> TCGA.06.0190.02 1 0.000
#> TCGA.HT.7677.01 6 0.253
#> TCGA.FG.A713.01 7 0.000
#> TCGA.DU.7300.01 3 0.000
#> TCGA.TM.A7CA.01 2 0.000
#> TCGA.76.6664.01 1 0.000
#> TCGA.HT.7690.01 2 0.000
#> TCGA.DU.7013.01 1 1.000
#> TCGA.FG.6689.01 3 0.000
#> TCGA.DU.7007.01 2 0.000
#> TCGA.TQ.A7RF.01 6 0.000
#> TCGA.KT.A7W1.01 1 0.000
#> TCGA.HT.A5RA.01 1 0.000
#> TCGA.DB.5277.01 2 0.000
#> TCGA.HT.7694.01 7 0.000
#> TCGA.26.5134.01 1 1.000
#> TCGA.TM.A84M.01 6 0.000
#> TCGA.F6.A8O3.01 2 0.000
#> TCGA.QH.A86X.01 2 0.000
#> TCGA.28.2501.01 4 0.000
#> TCGA.HT.8013.01 2 0.000
#> TCGA.76.6286.01 4 0.249
#> TCGA.HW.7490.01 2 0.000
#> TCGA.14.1450.01 1 0.000
#> TCGA.76.6660.01 1 1.000
#> TCGA.28.5204.01 1 0.000
#> TCGA.QH.A65S.01 3 0.000
#> TCGA.DU.A76R.01 3 0.000
#> TCGA.DH.5144.01 6 0.000
#> TCGA.CS.6188.01 1 0.751
#> TCGA.06.1804.01 1 0.000
#> TCGA.P5.A780.01 3 0.000
#> TCGA.HT.7606.01 6 0.000
#> TCGA.DU.A7TJ.01 1 0.000
#> TCGA.76.4931.01 1 0.000
#> TCGA.DB.A64V.01 3 0.000
#> TCGA.RY.A840.01 6 0.000
#> TCGA.E1.5302.01 3 0.000
#> TCGA.HW.A5KJ.01 2 0.000
#> TCGA.HT.A615.01 3 0.000
#> TCGA.HT.8105.01 2 0.000
#> TCGA.DU.7309.01 3 0.000
#> TCGA.DU.A5TY.01 1 0.000
#> TCGA.28.6450.01 1 1.000
#> TCGA.DU.5847.01 1 1.000
#> TCGA.E1.A7YK.01 7 0.000
#> TCGA.76.4928.01 1 0.000
#> TCGA.26.6173.01 1 0.000
#> TCGA.HT.7874.01 7 0.000
#> TCGA.HT.7471.01 6 0.000
#> TCGA.HT.7882.01 4 1.000
#> TCGA.DU.5854.01 4 1.000
#> TCGA.DU.6395.01 2 0.000
#> TCGA.76.6282.01 1 0.000
#> TCGA.19.5954.01 1 0.000
#> TCGA.HT.8011.01 4 0.000
#> TCGA.S9.A6TV.01 2 0.000
#> TCGA.P5.A5EW.01 6 0.000
#> TCGA.DU.5852.01 1 0.000
#> TCGA.32.1979.01 1 1.000
#> TCGA.DU.6408.01 2 0.000
#> TCGA.87.5896.01 1 1.000
#> TCGA.DB.A4XB.01 2 0.000
#> TCGA.E1.A7YY.01 7 0.000
#> TCGA.FG.A4MT.01 6 0.000
#> TCGA.FG.A4MT.02 3 0.000
#> TCGA.HT.A619.01 6 0.000
#> TCGA.P5.A72U.01 1 1.000
#> TCGA.QH.A870.01 2 0.000
#> TCGA.HT.A5R9.01 2 0.000
#> TCGA.DU.6404.02 4 0.000
#> TCGA.DU.6404.01 4 0.000
#> TCGA.19.0957.01 4 0.000
#> TCGA.19.0957.02 4 0.000
#> TCGA.FG.5964.01 3 0.000
#> TCGA.CS.5396.01 2 0.000
#> TCGA.HT.8107.01 4 0.000
#> TCGA.DU.A7TA.01 3 0.502
#> TCGA.HW.8319.01 2 0.000
#> TCGA.06.5859.01 4 0.000
#> TCGA.DH.A7UR.01 3 0.000
#> TCGA.TM.A84H.01 2 0.000
#> TCGA.S9.A6TZ.01 2 0.000
#> TCGA.HT.7479.01 3 0.000
#> TCGA.DU.6400.01 6 0.000
#> TCGA.S9.A6WL.01 3 0.000
#> TCGA.DB.A75K.01 2 0.000
#> TCGA.DB.A4XD.01 6 0.000
#> TCGA.76.6657.01 1 1.000
#> TCGA.DB.A64Q.01 2 0.000
#> TCGA.P5.A737.01 6 0.000
#> TCGA.06.6699.01 1 0.000
#> TCGA.DB.5275.01 6 0.000
#> TCGA.S9.A6WH.01 6 0.000
#> TCGA.HT.7602.01 7 0.000
#> TCGA.DU.A5TU.01 2 0.000
#> TCGA.HT.A5RB.01 2 0.000
#> TCGA.E1.A7YN.01 4 0.000
#> TCGA.HT.7616.01 3 0.000
#> TCGA.S9.A7R8.01 6 0.000
#> TCGA.41.5651.01 4 0.000
#> TCGA.76.6192.01 1 0.000
#> TCGA.QH.A6XA.01 2 0.498
#> TCGA.HT.8111.01 3 0.000
#> TCGA.74.6575.01 1 1.000
#> TCGA.E1.A7Z2.01 1 1.000
#> TCGA.DU.A5TP.01 3 0.000
#> TCGA.VM.A8CD.01 1 1.000
#> TCGA.RY.A83Y.01 2 0.000
#> TCGA.HT.7482.01 3 0.000
#> TCGA.TQ.A7RK.02 2 0.000
#> TCGA.TQ.A7RK.01 6 0.000
#> TCGA.HT.7858.01 3 0.000
#> TCGA.06.0210.01 1 1.000
#> TCGA.06.0210.02 4 0.000
#> TCGA.06.A5U1.01 1 0.253
#> TCGA.HT.7475.01 2 0.000
#> TCGA.HT.8564.01 4 0.000
#> TCGA.DB.A64U.01 3 0.000
#> TCGA.19.5956.01 4 0.000
#> TCGA.DB.A64W.01 6 0.000
#> TCGA.R8.A6MO.01 3 0.000
#> TCGA.28.5216.01 1 1.000
#> TCGA.DU.A7T8.01 6 0.000
#> TCGA.HW.8322.01 6 0.000
#> TCGA.DU.5870.02 2 0.000
#> TCGA.CS.6668.01 6 0.000
#> TCGA.DU.5870.01 3 0.000
#> TCGA.FG.7636.01 2 0.000
#> TCGA.HT.7692.01 2 1.000
#> TCGA.WY.A859.01 3 0.000
#> TCGA.HT.7854.01 4 0.000
#> TCGA.R8.A6ML.01 6 0.000
#> TCGA.VM.A8C9.01 1 1.000
#> TCGA.HT.7686.01 3 0.000
#> TCGA.DU.6410.01 6 0.000
#> TCGA.S9.A6U9.01 2 0.000
#> TCGA.74.6573.01 1 1.000
#> TCGA.CS.6290.01 3 0.000
#> TCGA.TQ.A7RO.01 3 0.000
#> TCGA.DU.7019.01 3 0.000
#> TCGA.06.5858.01 1 0.751
#> TCGA.FG.A711.01 3 0.000
#> TCGA.TQ.A7RM.01 6 0.000
#> TCGA.HT.7860.01 1 1.000
#> TCGA.S9.A7R4.01 2 0.000
#> TCGA.E1.5318.01 6 0.000
#> TCGA.HT.7676.01 2 0.000
#> TCGA.14.0740.01 4 0.000
#> TCGA.S9.A7J3.01 3 0.000
#> TCGA.81.5911.01 1 0.000
#> TCGA.06.6701.01 2 0.000
#> TCGA.P5.A5F2.01 3 0.000
#> TCGA.E1.5304.01 5 0.000
#> TCGA.DU.7006.01 4 0.000
#> TCGA.TM.A84S.01 3 0.000
#> TCGA.HT.7469.01 7 0.498
#> TCGA.06.6390.01 1 0.000
#> TCGA.WY.A85B.01 2 0.000
#> TCGA.TQ.A7RS.01 6 0.000
#> TCGA.S9.A7QX.01 6 1.000
#> TCGA.CS.4943.01 6 0.000
#> TCGA.QH.A65Z.01 6 0.000
#> TCGA.DB.5276.01 7 0.000
#> TCGA.P5.A730.01 2 0.000
#> TCGA.06.A5U0.01 4 0.000
#> TCGA.TM.A84L.01 3 0.000
#> TCGA.DU.8161.01 1 1.000
#> TCGA.19.5959.01 1 0.498
#> TCGA.WY.A85D.01 2 0.000
#> TCGA.RY.A83X.01 3 0.000
#> TCGA.S9.A6UB.01 6 0.000
#> TCGA.E1.A7YM.01 4 1.000
#> TCGA.DB.5273.01 3 0.000
#> TCGA.TM.A7C4.01 3 0.000
#> TCGA.DH.A66F.01 6 0.000
#> TCGA.HT.7607.01 7 0.000
#> TCGA.DU.6393.01 6 0.000
#> TCGA.06.5413.01 1 0.000
#> TCGA.19.5947.01 1 0.000
#> TCGA.HT.8108.01 2 0.000
#> TCGA.E1.A7YD.01 1 0.000
#> TCGA.19.5960.01 4 0.000
#> TCGA.DU.7304.01 3 0.000
#> TCGA.14.1034.02 1 1.000
#> TCGA.S9.A7IY.01 3 0.000
#> TCGA.FG.7641.01 3 0.000
#> TCGA.P5.A736.01 3 0.000
#> TCGA.14.0736.02 4 0.000
#> TCGA.19.5952.01 1 0.000
#> TCGA.P5.A5EV.01 2 0.000
#> TCGA.DU.7301.01 6 0.000
#> TCGA.HT.7470.01 3 0.000
#> TCGA.28.5208.01 1 0.000
#> TCGA.DU.7009.01 2 0.000
#> TCGA.P5.A781.01 3 0.000
#> TCGA.DH.5140.01 4 0.000
#> TCGA.76.6280.01 1 0.000
#> TCGA.FG.A4MY.01 3 0.000
#> TCGA.TM.A7CF.01 2 0.000
#> TCGA.TM.A7CF.02 7 0.249
#> TCGA.FG.8186.01 2 0.000
#> TCGA.S9.A6U6.01 3 0.000
#> TCGA.HT.8015.01 4 0.000
#> TCGA.RY.A845.01 3 0.000
#> TCGA.DU.7010.01 5 0.000
#> TCGA.S9.A6U2.01 3 0.000
#> TCGA.S9.A6WN.01 7 0.000
#> TCGA.28.2510.01 4 0.000
#> TCGA.DU.A7TD.01 1 0.000
#> TCGA.14.0736.01 1 0.000
#> TCGA.DU.6405.01 4 0.000
#> TCGA.06.0152.02 1 1.000
#> TCGA.06.0152.01 1 0.000
#> TCGA.76.4927.01 1 0.000
#> TCGA.FG.8182.01 3 0.000
#> TCGA.QH.A6X3.01 2 0.000
#> TCGA.DU.6401.01 2 0.000
#> TCGA.26.5132.01 1 0.000
#> TCGA.DU.6396.01 3 0.000
#> TCGA.E1.A7YH.01 3 0.000
#> TCGA.DU.7306.01 2 0.000
#> TCGA.HT.A74J.01 3 0.000
#> TCGA.HT.A74H.01 4 0.000
#> TCGA.DH.A7US.01 3 0.000
#> TCGA.FG.A87N.01 5 0.000
#> TCGA.HT.7478.01 3 0.000
#> TCGA.DU.7290.01 1 1.000
#> TCGA.DB.A4XE.01 2 0.000
#> TCGA.DB.A64L.01 3 0.000
#> TCGA.VV.A829.01 6 0.000
#> TCGA.19.A6J4.01 1 1.000
#> TCGA.HT.A61B.01 2 0.000
#> TCGA.12.5299.01 1 0.498
#> TCGA.DH.A66B.01 2 0.000
#> TCGA.HT.7603.01 3 0.000
#> TCGA.DU.6397.02 2 0.000
#> TCGA.DU.6397.01 2 0.000
#> TCGA.HT.A4DS.01 1 0.000
#> TCGA.12.5301.01 1 1.000
#> TCGA.RR.A6KB.01 4 0.000
#> TCGA.DU.5853.01 3 0.498
#> TCGA.CS.6670.01 2 0.000
#> TCGA.DU.7014.01 6 0.000
#> TCGA.QH.A65X.01 2 0.000
#> TCGA.TM.A84B.01 1 1.000
#> TCGA.DB.A64P.01 2 0.000
#> TCGA.FG.5965.02 7 0.000
#> TCGA.FG.A70Y.01 3 0.000
#> TCGA.TQ.A7RV.01 2 0.000
#> TCGA.TQ.A7RV.02 7 0.000
#> TCGA.HT.A5R7.01 7 0.000
#> TCGA.06.6389.01 2 0.000
#> TCGA.HW.A5KL.01 6 0.000
#> TCGA.06.5416.01 1 0.000
#> TCGA.DU.8158.01 4 0.000
#> TCGA.HT.7474.01 3 0.000
#> TCGA.DH.A7UU.01 6 0.000
#> TCGA.26.5139.01 1 0.000
#> TCGA.QH.A6CZ.01 6 0.000
#> TCGA.DH.A669.02 6 0.000
#> TCGA.DH.A669.01 6 0.000
#> TCGA.QH.A6X9.01 2 0.000
#> TCGA.P5.A5EZ.01 3 0.000
#> TCGA.DU.5871.01 2 0.000
#> TCGA.TQ.A7RJ.01 3 0.000
#> TCGA.WY.A858.01 3 0.000
#> TCGA.TM.A84J.01 7 0.751
#> TCGA.VM.A8CB.01 6 0.000
#> TCGA.41.6646.01 1 1.000
#> TCGA.14.0781.01 1 1.000
#> TCGA.HT.7483.01 2 0.000
#> TCGA.HT.7687.01 2 0.000
#> TCGA.TM.A84G.01 6 0.000
#> TCGA.E1.A7Z6.01 2 0.000
#> TCGA.TM.A84I.01 5 0.000
#> TCGA.CS.5394.01 6 0.000
#> TCGA.HT.A617.01 4 0.751
#> TCGA.DU.A76O.01 2 0.000
#> TCGA.DU.A5TW.01 6 0.000
#> TCGA.HT.7857.01 4 0.000
#> TCGA.WY.A85A.01 3 0.000
#> TCGA.FG.5962.01 2 0.000
#> TCGA.74.6578.01 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 , Node014 , Node021 , Node022 , Node023 , Node031 , Node032 , Node033-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 243 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 0.993 0.997 0.5018 0.499 0.499
#> 3 3 1.000 0.988 0.995 0.2613 0.787 0.605
#> 4 4 1.000 0.982 0.993 0.1497 0.857 0.636
#> 5 5 0.973 0.937 0.974 0.0753 0.887 0.625
#> 6 6 0.884 0.844 0.930 0.0222 0.987 0.942
#> 7 7 0.839 0.743 0.862 0.0317 0.925 0.670
#> 8 8 0.830 0.705 0.864 0.0162 0.977 0.873
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.FG.6688.01 2 0.000 1.000 0.00 1.00
#> TCGA.74.6577.01 1 0.000 0.994 1.00 0.00
#> TCGA.06.AABW.11 2 0.000 1.000 0.00 1.00
#> TCGA.06.0125.02 1 0.000 0.994 1.00 0.00
#> TCGA.26.A7UX.01 1 0.000 0.994 1.00 0.00
#> TCGA.06.6388.01 1 0.000 0.994 1.00 0.00
#> TCGA.TQ.A7RP.01 2 0.000 1.000 0.00 1.00
#> TCGA.28.5213.01 2 0.000 1.000 0.00 1.00
#> TCGA.76.4932.01 1 0.000 0.994 1.00 0.00
#> TCGA.06.5412.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.6694.01 1 0.000 0.994 1.00 0.00
#> TCGA.19.1389.01 2 0.000 1.000 0.00 1.00
#> TCGA.12.5295.01 1 0.000 0.994 1.00 0.00
#> TCGA.19.5953.01 2 0.000 1.000 0.00 1.00
#> TCGA.28.5220.01 1 0.000 0.994 1.00 0.00
#> TCGA.4W.AA9T.01 2 0.000 1.000 0.00 1.00
#> TCGA.OX.A56R.01 1 0.000 0.994 1.00 0.00
#> TCGA.S9.A7IX.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.0171.01 1 0.000 0.994 1.00 0.00
#> TCGA.06.0125.01 1 0.000 0.994 1.00 0.00
#> TCGA.VW.A8FI.01 1 0.000 0.994 1.00 0.00
#> TCGA.06.6700.01 2 0.000 1.000 0.00 1.00
#> TCGA.28.5218.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.0171.02 2 0.000 1.000 0.00 1.00
#> TCGA.DU.8165.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.5856.01 1 0.000 0.994 1.00 0.00
#> TCGA.26.5136.01 1 0.000 0.994 1.00 0.00
#> TCGA.DU.A76L.01 1 0.000 0.994 1.00 0.00
#> TCGA.76.6663.01 2 0.000 1.000 0.00 1.00
#> TCGA.76.4926.01 1 0.000 0.994 1.00 0.00
#> TCGA.06.0211.02 1 0.000 0.994 1.00 0.00
#> TCGA.28.5207.01 1 0.000 0.994 1.00 0.00
#> TCGA.14.1402.01 1 0.000 0.994 1.00 0.00
#> TCGA.06.0211.01 1 0.000 0.994 1.00 0.00
#> TCGA.14.1402.02 1 0.000 0.994 1.00 0.00
#> TCGA.19.4065.02 1 0.827 0.651 0.74 0.26
#> TCGA.RR.A6KC.01 1 0.000 0.994 1.00 0.00
#> TCGA.19.4065.01 2 0.000 1.000 0.00 1.00
#> TCGA.CS.4941.01 2 0.000 1.000 0.00 1.00
#> TCGA.S9.A6U0.01 2 0.000 1.000 0.00 1.00
#> TCGA.FG.7643.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.5408.01 1 0.000 0.994 1.00 0.00
#> TCGA.76.6285.01 1 0.000 0.994 1.00 0.00
#> TCGA.DU.6403.01 1 0.000 0.994 1.00 0.00
#> TCGA.19.5950.01 1 0.000 0.994 1.00 0.00
#> TCGA.14.1395.01 1 0.000 0.994 1.00 0.00
#> TCGA.FG.8181.01 2 0.000 1.000 0.00 1.00
#> TCGA.FG.5963.01 2 0.000 1.000 0.00 1.00
#> TCGA.FG.5963.02 2 0.000 1.000 0.00 1.00
#> TCGA.CS.5395.01 1 0.000 0.994 1.00 0.00
#> TCGA.DU.7292.01 1 0.000 0.994 1.00 0.00
#> TCGA.HT.A5RC.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.5410.01 2 0.000 1.000 0.00 1.00
#> TCGA.19.5958.01 1 0.000 0.994 1.00 0.00
#> TCGA.28.5211.01 2 0.000 1.000 0.00 1.00
#> TCGA.TM.A84C.01 2 0.000 1.000 0.00 1.00
#> TCGA.FG.A4MW.01 1 0.000 0.994 1.00 0.00
#> TCGA.DB.A75P.01 2 0.000 1.000 0.00 1.00
#> TCGA.S9.A89V.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.6695.01 1 0.000 0.994 1.00 0.00
#> TCGA.06.5418.01 1 0.000 0.994 1.00 0.00
#> TCGA.06.5415.01 1 0.000 0.994 1.00 0.00
#> TCGA.QH.A6CX.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.A6S1.01 2 0.000 1.000 0.00 1.00
#> TCGA.CS.6186.01 2 0.000 1.000 0.00 1.00
#> TCGA.26.5135.01 1 0.000 0.994 1.00 0.00
#> TCGA.28.5219.01 1 0.000 0.994 1.00 0.00
#> TCGA.4W.AA9S.01 1 0.000 0.994 1.00 0.00
#> TCGA.19.A60I.01 1 0.000 0.994 1.00 0.00
#> TCGA.76.4934.01 1 0.000 0.994 1.00 0.00
#> TCGA.32.5222.01 1 0.000 0.994 1.00 0.00
#> TCGA.76.6191.01 1 0.000 0.994 1.00 0.00
#> TCGA.06.1806.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.6693.01 1 0.000 0.994 1.00 0.00
#> TCGA.DU.6406.01 1 0.000 0.994 1.00 0.00
#> TCGA.S9.A6UA.01 2 0.000 1.000 0.00 1.00
#> TCGA.DU.A7TB.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.6697.01 2 0.000 1.000 0.00 1.00
#> TCGA.DU.A76K.01 2 0.000 1.000 0.00 1.00
#> TCGA.28.5215.01 1 0.000 0.994 1.00 0.00
#> TCGA.DU.8162.01 2 0.000 1.000 0.00 1.00
#> TCGA.E1.A7YQ.01 2 0.000 1.000 0.00 1.00
#> TCGA.QH.A6CS.01 2 0.000 1.000 0.00 1.00
#> TCGA.76.6283.01 1 0.000 0.994 1.00 0.00
#> TCGA.76.4929.01 1 0.000 0.994 1.00 0.00
#> TCGA.HT.7691.01 2 0.000 1.000 0.00 1.00
#> TCGA.19.1389.02 2 0.000 1.000 0.00 1.00
#> TCGA.26.6174.01 2 0.000 1.000 0.00 1.00
#> TCGA.DU.6392.01 1 0.000 0.994 1.00 0.00
#> TCGA.32.1980.01 2 0.000 1.000 0.00 1.00
#> TCGA.76.6661.01 1 0.000 0.994 1.00 0.00
#> TCGA.28.5209.01 1 0.000 0.994 1.00 0.00
#> TCGA.19.5951.01 1 0.000 0.994 1.00 0.00
#> TCGA.DU.7012.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.A6S0.01 1 0.000 0.994 1.00 0.00
#> TCGA.DU.6402.01 2 0.000 1.000 0.00 1.00
#> TCGA.FG.A87Q.01 2 0.000 1.000 0.00 1.00
#> TCGA.HT.8104.01 1 0.000 0.994 1.00 0.00
#> TCGA.FG.A70Z.01 1 0.000 0.994 1.00 0.00
#> TCGA.14.0862.01 2 0.000 1.000 0.00 1.00
#> TCGA.QH.A6XC.01 1 0.000 0.994 1.00 0.00
#> TCGA.FG.A4MU.01 1 0.000 0.994 1.00 0.00
#> TCGA.19.5955.01 2 0.000 1.000 0.00 1.00
#> TCGA.TM.A7C3.01 1 0.000 0.994 1.00 0.00
#> TCGA.DB.A64O.01 2 0.000 1.000 0.00 1.00
#> TCGA.DU.A5TT.01 2 0.000 1.000 0.00 1.00
#> TCGA.74.6581.01 1 0.000 0.994 1.00 0.00
#> TCGA.FG.8189.01 2 0.000 1.000 0.00 1.00
#> TCGA.76.6662.01 2 0.000 1.000 0.00 1.00
#> TCGA.HT.8019.01 2 0.000 1.000 0.00 1.00
#> TCGA.P5.A5EY.01 2 0.000 1.000 0.00 1.00
#> TCGA.RR.A6KA.01 2 0.000 1.000 0.00 1.00
#> TCGA.DU.5872.02 2 0.000 1.000 0.00 1.00
#> TCGA.74.6573.11 2 0.000 1.000 0.00 1.00
#> TCGA.CS.5397.01 2 0.000 1.000 0.00 1.00
#> TCGA.HW.A5KK.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.0650.01 2 0.000 1.000 0.00 1.00
#> TCGA.CS.6669.01 2 0.000 1.000 0.00 1.00
#> TCGA.S9.A7R2.01 2 0.000 1.000 0.00 1.00
#> TCGA.76.6193.01 2 0.000 1.000 0.00 1.00
#> TCGA.S9.A6WM.01 1 0.000 0.994 1.00 0.00
#> TCGA.HT.7680.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.6698.01 2 0.000 1.000 0.00 1.00
#> TCGA.P5.A5F6.01 2 0.000 1.000 0.00 1.00
#> TCGA.14.1043.01 2 0.000 1.000 0.00 1.00
#> TCGA.HT.8110.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.6391.01 2 0.000 1.000 0.00 1.00
#> TCGA.76.4935.01 1 0.000 0.994 1.00 0.00
#> TCGA.E1.A7YJ.01 1 0.000 0.994 1.00 0.00
#> TCGA.06.5414.01 1 0.000 0.994 1.00 0.00
#> TCGA.06.A7TK.01 1 0.000 0.994 1.00 0.00
#> TCGA.06.5411.01 1 0.000 0.994 1.00 0.00
#> TCGA.76.6656.01 1 0.000 0.994 1.00 0.00
#> TCGA.E1.A7YL.01 1 0.000 0.994 1.00 0.00
#> TCGA.HT.8558.01 2 0.000 1.000 0.00 1.00
#> TCGA.HT.A61C.01 1 0.000 0.994 1.00 0.00
#> TCGA.76.4925.01 1 0.000 0.994 1.00 0.00
#> TCGA.QH.A6CV.01 1 0.000 0.994 1.00 0.00
#> TCGA.4W.AA9R.01 1 0.000 0.994 1.00 0.00
#> TCGA.FG.6692.01 1 0.000 0.994 1.00 0.00
#> TCGA.81.5910.01 1 0.000 0.994 1.00 0.00
#> TCGA.28.5214.01 1 0.000 0.994 1.00 0.00
#> TCGA.74.6584.01 1 0.000 0.994 1.00 0.00
#> TCGA.06.0190.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.0190.02 2 0.000 1.000 0.00 1.00
#> TCGA.76.6664.01 1 0.000 0.994 1.00 0.00
#> TCGA.DU.7013.01 1 0.000 0.994 1.00 0.00
#> TCGA.KT.A7W1.01 1 0.000 0.994 1.00 0.00
#> TCGA.HT.A5RA.01 1 0.000 0.994 1.00 0.00
#> TCGA.26.5134.01 1 0.000 0.994 1.00 0.00
#> TCGA.28.2501.01 2 0.000 1.000 0.00 1.00
#> TCGA.76.6286.01 1 0.000 0.994 1.00 0.00
#> TCGA.14.1450.01 2 0.000 1.000 0.00 1.00
#> TCGA.76.6660.01 1 0.000 0.994 1.00 0.00
#> TCGA.28.5204.01 1 0.000 0.994 1.00 0.00
#> TCGA.CS.6188.01 1 0.242 0.954 0.96 0.04
#> TCGA.06.1804.01 1 0.000 0.994 1.00 0.00
#> TCGA.DU.A7TJ.01 1 0.000 0.994 1.00 0.00
#> TCGA.76.4931.01 1 0.000 0.994 1.00 0.00
#> TCGA.DU.A5TY.01 2 0.000 1.000 0.00 1.00
#> TCGA.28.6450.01 1 0.971 0.339 0.60 0.40
#> TCGA.DU.5847.01 2 0.000 1.000 0.00 1.00
#> TCGA.76.4928.01 2 0.000 1.000 0.00 1.00
#> TCGA.26.6173.01 2 0.000 1.000 0.00 1.00
#> TCGA.HT.7882.01 2 0.000 1.000 0.00 1.00
#> TCGA.DU.5854.01 2 0.000 1.000 0.00 1.00
#> TCGA.76.6282.01 2 0.000 1.000 0.00 1.00
#> TCGA.19.5954.01 1 0.000 0.994 1.00 0.00
#> TCGA.HT.8011.01 1 0.000 0.994 1.00 0.00
#> TCGA.DU.5852.01 1 0.000 0.994 1.00 0.00
#> TCGA.32.1979.01 1 0.000 0.994 1.00 0.00
#> TCGA.87.5896.01 1 0.000 0.994 1.00 0.00
#> TCGA.P5.A72U.01 2 0.000 1.000 0.00 1.00
#> TCGA.DU.6404.02 2 0.000 1.000 0.00 1.00
#> TCGA.DU.6404.01 2 0.000 1.000 0.00 1.00
#> TCGA.19.0957.01 1 0.000 0.994 1.00 0.00
#> TCGA.19.0957.02 1 0.000 0.994 1.00 0.00
#> TCGA.HT.8107.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.5859.01 1 0.000 0.994 1.00 0.00
#> TCGA.76.6657.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.6699.01 1 0.000 0.994 1.00 0.00
#> TCGA.E1.A7YN.01 2 0.000 1.000 0.00 1.00
#> TCGA.41.5651.01 1 0.000 0.994 1.00 0.00
#> TCGA.76.6192.01 2 0.000 1.000 0.00 1.00
#> TCGA.74.6575.01 2 0.000 1.000 0.00 1.00
#> TCGA.E1.A7Z2.01 2 0.000 1.000 0.00 1.00
#> TCGA.VM.A8CD.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.0210.01 1 0.000 0.994 1.00 0.00
#> TCGA.06.0210.02 1 0.000 0.994 1.00 0.00
#> TCGA.06.A5U1.01 2 0.000 1.000 0.00 1.00
#> TCGA.HT.8564.01 2 0.000 1.000 0.00 1.00
#> TCGA.19.5956.01 1 0.000 0.994 1.00 0.00
#> TCGA.28.5216.01 1 0.000 0.994 1.00 0.00
#> TCGA.HT.7854.01 2 0.000 1.000 0.00 1.00
#> TCGA.VM.A8C9.01 2 0.000 1.000 0.00 1.00
#> TCGA.74.6573.01 1 0.000 0.994 1.00 0.00
#> TCGA.06.5858.01 2 0.000 1.000 0.00 1.00
#> TCGA.HT.7860.01 2 0.000 1.000 0.00 1.00
#> TCGA.14.0740.01 1 0.000 0.994 1.00 0.00
#> TCGA.81.5911.01 2 0.000 1.000 0.00 1.00
#> TCGA.DU.7006.01 2 0.000 1.000 0.00 1.00
#> TCGA.HT.7469.01 1 0.000 0.994 1.00 0.00
#> TCGA.06.6390.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.A5U0.01 1 0.000 0.994 1.00 0.00
#> TCGA.DU.8161.01 2 0.000 1.000 0.00 1.00
#> TCGA.19.5959.01 1 0.000 0.994 1.00 0.00
#> TCGA.E1.A7YM.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.5413.01 1 0.000 0.994 1.00 0.00
#> TCGA.19.5947.01 2 0.000 1.000 0.00 1.00
#> TCGA.E1.A7YD.01 1 0.000 0.994 1.00 0.00
#> TCGA.19.5960.01 1 0.000 0.994 1.00 0.00
#> TCGA.14.1034.02 1 0.000 0.994 1.00 0.00
#> TCGA.14.0736.02 2 0.000 1.000 0.00 1.00
#> TCGA.19.5952.01 1 0.000 0.994 1.00 0.00
#> TCGA.28.5208.01 1 0.000 0.994 1.00 0.00
#> TCGA.DH.5140.01 1 0.000 0.994 1.00 0.00
#> TCGA.76.6280.01 1 0.000 0.994 1.00 0.00
#> TCGA.HT.8015.01 2 0.000 1.000 0.00 1.00
#> TCGA.28.2510.01 2 0.000 1.000 0.00 1.00
#> TCGA.DU.A7TD.01 1 0.000 0.994 1.00 0.00
#> TCGA.14.0736.01 1 0.000 0.994 1.00 0.00
#> TCGA.DU.6405.01 1 0.000 0.994 1.00 0.00
#> TCGA.06.0152.02 1 0.000 0.994 1.00 0.00
#> TCGA.06.0152.01 1 0.000 0.994 1.00 0.00
#> TCGA.76.4927.01 1 0.000 0.994 1.00 0.00
#> TCGA.26.5132.01 1 0.000 0.994 1.00 0.00
#> TCGA.HT.A74H.01 2 0.000 1.000 0.00 1.00
#> TCGA.DU.7290.01 2 0.000 1.000 0.00 1.00
#> TCGA.19.A6J4.01 2 0.000 1.000 0.00 1.00
#> TCGA.12.5299.01 1 0.000 0.994 1.00 0.00
#> TCGA.HT.A4DS.01 2 0.000 1.000 0.00 1.00
#> TCGA.12.5301.01 1 0.000 0.994 1.00 0.00
#> TCGA.RR.A6KB.01 2 0.000 1.000 0.00 1.00
#> TCGA.TM.A84B.01 1 0.000 0.994 1.00 0.00
#> TCGA.06.5416.01 2 0.000 1.000 0.00 1.00
#> TCGA.DU.8158.01 2 0.000 1.000 0.00 1.00
#> TCGA.26.5139.01 1 0.000 0.994 1.00 0.00
#> TCGA.TM.A84J.01 1 0.000 0.994 1.00 0.00
#> TCGA.41.6646.01 2 0.000 1.000 0.00 1.00
#> TCGA.14.0781.01 2 0.000 1.000 0.00 1.00
#> TCGA.HT.A617.01 2 0.000 1.000 0.00 1.00
#> TCGA.HT.7857.01 2 0.000 1.000 0.00 1.00
#> TCGA.74.6578.01 1 0.000 0.994 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.FG.6688.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.74.6577.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.06.AABW.11 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.06.0125.02 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.26.A7UX.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.06.6388.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.TQ.A7RP.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.28.5213.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.76.4932.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.06.5412.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.06.6694.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.19.1389.01 3 0.207 0.935 0.00 0.06 0.94
#> TCGA.12.5295.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.19.5953.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.28.5220.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.4W.AA9T.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.OX.A56R.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.S9.A7IX.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.06.0171.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.06.0125.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.VW.A8FI.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.06.6700.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.28.5218.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.06.0171.02 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.DU.8165.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.06.5856.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.26.5136.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.DU.A76L.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.76.6663.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.76.4926.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.06.0211.02 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.28.5207.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.14.1402.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.06.0211.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.14.1402.02 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.19.4065.02 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.RR.A6KC.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.19.4065.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.CS.4941.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.S9.A6U0.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.FG.7643.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.06.5408.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.76.6285.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.DU.6403.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.19.5950.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.14.1395.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.FG.8181.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.FG.5963.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.FG.5963.02 2 0.502 0.685 0.00 0.76 0.24
#> TCGA.CS.5395.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.DU.7292.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.HT.A5RC.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.06.5410.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.19.5958.01 1 0.334 0.854 0.88 0.12 0.00
#> TCGA.28.5211.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.TM.A84C.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.FG.A4MW.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.DB.A75P.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.S9.A89V.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.06.6695.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.06.5418.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.06.5415.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.QH.A6CX.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.06.A6S1.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.CS.6186.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.26.5135.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.28.5219.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.4W.AA9S.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.19.A60I.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.76.4934.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.32.5222.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.76.6191.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.06.1806.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.06.6693.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.DU.6406.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.S9.A6UA.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.DU.A7TB.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.06.6697.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.DU.A76K.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.28.5215.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.DU.8162.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.E1.A7YQ.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.QH.A6CS.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.76.6283.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.76.4929.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.HT.7691.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.19.1389.02 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.26.6174.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.DU.6392.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.32.1980.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.76.6661.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.28.5209.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.19.5951.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.DU.7012.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.06.A6S0.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.DU.6402.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.FG.A87Q.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.HT.8104.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.FG.A70Z.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.14.0862.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.QH.A6XC.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.FG.A4MU.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.19.5955.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.TM.A7C3.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.DB.A64O.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.DU.A5TT.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.74.6581.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.FG.8189.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.76.6662.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.HT.8019.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.P5.A5EY.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.RR.A6KA.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.DU.5872.02 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.74.6573.11 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.CS.5397.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.HW.A5KK.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.06.0650.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.CS.6669.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.S9.A7R2.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.76.6193.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.S9.A6WM.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.HT.7680.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.06.6698.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.P5.A5F6.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.14.1043.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.HT.8110.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.06.6391.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.76.4935.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.E1.A7YJ.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.06.5414.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.06.A7TK.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.06.5411.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.76.6656.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.E1.A7YL.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.HT.8558.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.HT.A61C.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.76.4925.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.QH.A6CV.01 2 0.207 0.918 0.06 0.94 0.00
#> TCGA.4W.AA9R.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.FG.6692.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.81.5910.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.28.5214.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.74.6584.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.06.0190.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.06.0190.02 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.76.6664.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.DU.7013.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.KT.A7W1.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.HT.A5RA.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.26.5134.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.28.2501.01 3 0.254 0.914 0.00 0.08 0.92
#> TCGA.76.6286.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.14.1450.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.76.6660.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.28.5204.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.CS.6188.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.06.1804.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.DU.A7TJ.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.76.4931.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.DU.A5TY.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.28.6450.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.DU.5847.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.76.4928.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.26.6173.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.HT.7882.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.DU.5854.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.76.6282.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.19.5954.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.HT.8011.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.DU.5852.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.32.1979.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.87.5896.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.P5.A72U.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.DU.6404.02 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.DU.6404.01 2 0.369 0.835 0.00 0.86 0.14
#> TCGA.19.0957.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.19.0957.02 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.HT.8107.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.06.5859.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.76.6657.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.06.6699.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.E1.A7YN.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.41.5651.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.76.6192.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.74.6575.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.E1.A7Z2.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.VM.A8CD.01 3 0.455 0.755 0.00 0.20 0.80
#> TCGA.06.0210.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.06.0210.02 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.06.A5U1.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.HT.8564.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.19.5956.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.28.5216.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.HT.7854.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.VM.A8C9.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.74.6573.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.06.5858.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.HT.7860.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.14.0740.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.81.5911.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.DU.7006.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.HT.7469.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.06.6390.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.06.A5U0.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.DU.8161.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.19.5959.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.E1.A7YM.01 2 0.502 0.685 0.00 0.76 0.24
#> TCGA.06.5413.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.19.5947.01 3 0.296 0.892 0.00 0.10 0.90
#> TCGA.E1.A7YD.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.19.5960.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.14.1034.02 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.14.0736.02 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.19.5952.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.28.5208.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.DH.5140.01 1 0.153 0.953 0.96 0.04 0.00
#> TCGA.76.6280.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.HT.8015.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.28.2510.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.DU.A7TD.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.14.0736.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.DU.6405.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.06.0152.02 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.06.0152.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.76.4927.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.26.5132.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.HT.A74H.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.DU.7290.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.19.A6J4.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.12.5299.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.HT.A4DS.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.12.5301.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.RR.A6KB.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.TM.A84B.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.06.5416.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.DU.8158.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.26.5139.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.TM.A84J.01 1 0.000 0.998 1.00 0.00 0.00
#> TCGA.41.6646.01 2 0.000 0.992 0.00 1.00 0.00
#> TCGA.14.0781.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.HT.A617.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.HT.7857.01 3 0.000 0.990 0.00 0.00 1.00
#> TCGA.74.6578.01 1 0.000 0.998 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.FG.6688.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.74.6577.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.06.AABW.11 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.06.0125.02 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.26.A7UX.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.06.6388.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RP.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.28.5213.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.76.4932.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.06.5412.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.06.6694.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.19.1389.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.12.5295.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.19.5953.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.28.5220.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.4W.AA9T.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.OX.A56R.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.S9.A7IX.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.06.0171.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.06.0125.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.VW.A8FI.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.06.6700.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.28.5218.01 2 0.2647 0.8552 0.00 0.88 0.00 0.12
#> TCGA.06.0171.02 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.DU.8165.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.06.5856.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.26.5136.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.DU.A76L.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.76.6663.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.76.4926.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.06.0211.02 1 0.0707 0.9811 0.98 0.00 0.00 0.02
#> TCGA.28.5207.01 1 0.0707 0.9811 0.98 0.00 0.00 0.02
#> TCGA.14.1402.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.06.0211.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.14.1402.02 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.19.4065.02 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.RR.A6KC.01 1 0.0707 0.9811 0.98 0.00 0.00 0.02
#> TCGA.19.4065.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.CS.4941.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.S9.A6U0.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.FG.7643.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.06.5408.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.76.6285.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.DU.6403.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.19.5950.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.14.1395.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.FG.8181.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.FG.5963.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.FG.5963.02 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.CS.5395.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.DU.7292.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.HT.A5RC.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.06.5410.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.19.5958.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.28.5211.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.TM.A84C.01 3 0.4134 0.6502 0.00 0.26 0.74 0.00
#> TCGA.FG.A4MW.01 1 0.0707 0.9811 0.98 0.00 0.00 0.02
#> TCGA.DB.A75P.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.S9.A89V.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.06.6695.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.06.5418.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.06.5415.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.QH.A6CX.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.06.A6S1.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.CS.6186.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.26.5135.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.28.5219.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.4W.AA9S.01 4 0.0707 0.9706 0.02 0.00 0.00 0.98
#> TCGA.19.A60I.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.76.4934.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.32.5222.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.76.6191.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.06.1806.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.06.6693.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.DU.6406.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.S9.A6UA.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.DU.A7TB.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.06.6697.01 3 0.0707 0.9699 0.00 0.02 0.98 0.00
#> TCGA.DU.A76K.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.28.5215.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.DU.8162.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.E1.A7YQ.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.QH.A6CS.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.76.6283.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.76.4929.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.HT.7691.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.19.1389.02 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.26.6174.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.DU.6392.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.32.1980.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.76.6661.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.28.5209.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.19.5951.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.DU.7012.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.06.A6S0.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.DU.6402.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.FG.A87Q.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.HT.8104.01 1 0.0707 0.9811 0.98 0.00 0.00 0.02
#> TCGA.FG.A70Z.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.14.0862.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.QH.A6XC.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.FG.A4MU.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.19.5955.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.TM.A7C3.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.DB.A64O.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.DU.A5TT.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.74.6581.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.FG.8189.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.76.6662.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.HT.8019.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.P5.A5EY.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.RR.A6KA.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.DU.5872.02 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.74.6573.11 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.CS.5397.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.HW.A5KK.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.06.0650.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.CS.6669.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.S9.A7R2.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.76.6193.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.S9.A6WM.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.HT.7680.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.06.6698.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.P5.A5F6.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.14.1043.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.HT.8110.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.06.6391.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.76.4935.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YJ.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.06.5414.01 1 0.0707 0.9811 0.98 0.00 0.00 0.02
#> TCGA.06.A7TK.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.06.5411.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.76.6656.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YL.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.HT.8558.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.HT.A61C.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.76.4925.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.QH.A6CV.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.4W.AA9R.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.FG.6692.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.81.5910.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.28.5214.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.74.6584.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.06.0190.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.06.0190.02 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.76.6664.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.DU.7013.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.KT.A7W1.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.HT.A5RA.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.26.5134.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.28.2501.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.76.6286.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.14.1450.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.76.6660.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.28.5204.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.CS.6188.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.06.1804.01 1 0.1637 0.9401 0.94 0.00 0.00 0.06
#> TCGA.DU.A7TJ.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.76.4931.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.DU.A5TY.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.28.6450.01 4 0.0707 0.9713 0.00 0.02 0.00 0.98
#> TCGA.DU.5847.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.76.4928.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.26.6173.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.HT.7882.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.DU.5854.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.76.6282.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.19.5954.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.HT.8011.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.DU.5852.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.32.1979.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.87.5896.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.P5.A72U.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.DU.6404.02 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.DU.6404.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.19.0957.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.19.0957.02 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.HT.8107.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.06.5859.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.76.6657.01 4 0.3172 0.7981 0.00 0.16 0.00 0.84
#> TCGA.06.6699.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YN.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.41.5651.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.76.6192.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.74.6575.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.E1.A7Z2.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.VM.A8CD.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.06.0210.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.06.0210.02 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.06.A5U1.01 2 0.4994 0.0826 0.00 0.52 0.00 0.48
#> TCGA.HT.8564.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.19.5956.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.28.5216.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.HT.7854.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.VM.A8C9.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.74.6573.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.06.5858.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.HT.7860.01 2 0.4790 0.3907 0.00 0.62 0.00 0.38
#> TCGA.14.0740.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.81.5911.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.DU.7006.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.HT.7469.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.06.6390.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.06.A5U0.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.DU.8161.01 3 0.1211 0.9481 0.00 0.04 0.96 0.00
#> TCGA.19.5959.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YM.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.06.5413.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.19.5947.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.E1.A7YD.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.19.5960.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.14.1034.02 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.14.0736.02 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.19.5952.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.28.5208.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.DH.5140.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.76.6280.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.HT.8015.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.28.2510.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.DU.A7TD.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.14.0736.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.DU.6405.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.06.0152.02 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.06.0152.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.76.4927.01 4 0.0000 0.9941 0.00 0.00 0.00 1.00
#> TCGA.26.5132.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.HT.A74H.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.DU.7290.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.19.A6J4.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.12.5299.01 1 0.0707 0.9811 0.98 0.00 0.00 0.02
#> TCGA.HT.A4DS.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.12.5301.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.RR.A6KB.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.TM.A84B.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.06.5416.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.DU.8158.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.26.5139.01 1 0.0707 0.9811 0.98 0.00 0.00 0.02
#> TCGA.TM.A84J.01 1 0.0000 0.9974 1.00 0.00 0.00 0.00
#> TCGA.41.6646.01 2 0.0000 0.9863 0.00 1.00 0.00 0.00
#> TCGA.14.0781.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.HT.A617.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.HT.7857.01 3 0.0000 0.9907 0.00 0.00 1.00 0.00
#> TCGA.74.6578.01 4 0.0000 0.9941 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.FG.6688.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.74.6577.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.06.AABW.11 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.06.0125.02 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.26.A7UX.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.6388.01 1 0.1732 0.908 0.92 0.00 0.00 0.08 0.00
#> TCGA.TQ.A7RP.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.28.5213.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.76.4932.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.5412.01 3 0.4060 0.458 0.00 0.36 0.64 0.00 0.00
#> TCGA.06.6694.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.19.1389.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.12.5295.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.19.5953.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.28.5220.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.4W.AA9T.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.OX.A56R.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IX.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.06.0171.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.06.0125.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.VW.A8FI.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.6700.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.28.5218.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.06.0171.02 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.8165.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.06.5856.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.26.5136.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.A76L.01 5 0.0609 0.965 0.00 0.00 0.00 0.02 0.98
#> TCGA.76.6663.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.76.4926.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.0211.02 4 0.2280 0.843 0.12 0.00 0.00 0.88 0.00
#> TCGA.28.5207.01 4 0.4227 0.344 0.42 0.00 0.00 0.58 0.00
#> TCGA.14.1402.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.06.0211.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.14.1402.02 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.19.4065.02 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.RR.A6KC.01 4 0.2020 0.862 0.10 0.00 0.00 0.90 0.00
#> TCGA.19.4065.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.CS.4941.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.S9.A6U0.01 5 0.0609 0.965 0.00 0.02 0.00 0.00 0.98
#> TCGA.FG.7643.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.06.5408.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.6285.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6403.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.19.5950.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.14.1395.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8181.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.FG.5963.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.FG.5963.02 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.CS.5395.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.7292.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.A5RC.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.06.5410.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.19.5958.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.28.5211.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.TM.A84C.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.A4MW.01 4 0.1732 0.880 0.08 0.00 0.00 0.92 0.00
#> TCGA.DB.A75P.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A89V.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.06.6695.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.5418.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.5415.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.QH.A6CX.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.06.A6S1.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.CS.6186.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.26.5135.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.28.5219.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.4W.AA9S.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.19.A60I.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.4934.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.32.5222.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.6191.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.1806.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.06.6693.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6406.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6UA.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.A7TB.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.06.6697.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.A76K.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.28.5215.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.8162.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.E1.A7YQ.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.QH.A6CS.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.76.6283.01 5 0.0609 0.965 0.00 0.00 0.00 0.02 0.98
#> TCGA.76.4929.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7691.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.19.1389.02 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.26.6174.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.6392.01 4 0.2280 0.829 0.00 0.00 0.00 0.88 0.12
#> TCGA.32.1980.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.76.6661.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.28.5209.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.19.5951.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7012.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.06.A6S0.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6402.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.FG.A87Q.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.8104.01 4 0.3274 0.733 0.22 0.00 0.00 0.78 0.00
#> TCGA.FG.A70Z.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.14.0862.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.QH.A6XC.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.FG.A4MU.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.19.5955.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.TM.A7C3.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.DB.A64O.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.A5TT.01 2 0.4287 0.253 0.00 0.54 0.00 0.00 0.46
#> TCGA.74.6581.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8189.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.76.6662.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.8019.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.P5.A5EY.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.RR.A6KA.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.5872.02 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.74.6573.11 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.CS.5397.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.HW.A5KK.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.06.0650.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.CS.6669.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A7R2.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.76.6193.01 2 0.1043 0.888 0.00 0.96 0.00 0.00 0.04
#> TCGA.S9.A6WM.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7680.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.06.6698.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.P5.A5F6.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.14.1043.01 5 0.3109 0.721 0.00 0.20 0.00 0.00 0.80
#> TCGA.HT.8110.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.06.6391.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.76.4935.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YJ.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.5414.01 4 0.2929 0.780 0.18 0.00 0.00 0.82 0.00
#> TCGA.06.A7TK.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.06.5411.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.76.6656.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YL.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.8558.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.A61C.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.4925.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CV.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.4W.AA9R.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.6692.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.81.5910.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.28.5214.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.74.6584.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.06.0190.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.06.0190.02 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.76.6664.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.7013.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.KT.A7W1.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A5RA.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.26.5134.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.28.2501.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.76.6286.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.14.1450.01 2 0.4307 0.125 0.00 0.50 0.00 0.00 0.50
#> TCGA.76.6660.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.28.5204.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6188.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.06.1804.01 4 0.2280 0.844 0.12 0.00 0.00 0.88 0.00
#> TCGA.DU.A7TJ.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.4931.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TY.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.28.6450.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.5847.01 2 0.4262 0.310 0.00 0.56 0.00 0.00 0.44
#> TCGA.76.4928.01 2 0.4287 0.252 0.00 0.54 0.00 0.00 0.46
#> TCGA.26.6173.01 2 0.4182 0.404 0.00 0.60 0.00 0.00 0.40
#> TCGA.HT.7882.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.5854.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.76.6282.01 5 0.0609 0.965 0.00 0.02 0.00 0.00 0.98
#> TCGA.19.5954.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8011.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5852.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.32.1979.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.87.5896.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A72U.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.6404.02 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.6404.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.19.0957.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.19.0957.02 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.8107.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.06.5859.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.6657.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.06.6699.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YN.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.41.5651.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.6192.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.74.6575.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.E1.A7Z2.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.VM.A8CD.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.06.0210.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.06.0210.02 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.A5U1.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.8564.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.19.5956.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.28.5216.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7854.01 3 0.1732 0.907 0.00 0.08 0.92 0.00 0.00
#> TCGA.VM.A8C9.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.74.6573.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.5858.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7860.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.14.0740.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.81.5911.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.7006.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.7469.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.6390.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.06.A5U0.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.8161.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.19.5959.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YM.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.06.5413.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.19.5947.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YD.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.19.5960.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.14.1034.02 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.14.0736.02 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.19.5952.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.28.5208.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.5140.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.76.6280.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.8015.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.28.2510.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.A7TD.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.14.0736.01 5 0.3895 0.528 0.00 0.00 0.00 0.32 0.68
#> TCGA.DU.6405.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.0152.02 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.06.0152.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.4927.01 4 0.0000 0.943 0.00 0.00 0.00 1.00 0.00
#> TCGA.26.5132.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A74H.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7290.01 2 0.4227 0.360 0.00 0.58 0.00 0.00 0.42
#> TCGA.19.A6J4.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.12.5299.01 4 0.4262 0.287 0.44 0.00 0.00 0.56 0.00
#> TCGA.HT.A4DS.01 2 0.3983 0.522 0.00 0.66 0.00 0.00 0.34
#> TCGA.12.5301.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.RR.A6KB.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.TM.A84B.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.5416.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.8158.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.26.5139.01 4 0.2929 0.780 0.18 0.00 0.00 0.82 0.00
#> TCGA.TM.A84J.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.41.6646.01 5 0.0000 0.984 0.00 0.00 0.00 0.00 1.00
#> TCGA.14.0781.01 3 0.0000 0.987 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.A617.01 2 0.2280 0.795 0.00 0.88 0.12 0.00 0.00
#> TCGA.HT.7857.01 2 0.0000 0.917 0.00 1.00 0.00 0.00 0.00
#> TCGA.74.6578.01 4 0.0000 0.943 0.00 0.00 0.00 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.FG.6688.01 2 0.0000 0.8965 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.74.6577.01 4 0.3592 0.7321 0.00 0.00 0.00 0.74 0.02 0.24
#> TCGA.06.AABW.11 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.06.0125.02 4 0.3592 0.7321 0.00 0.00 0.00 0.74 0.02 0.24
#> TCGA.26.A7UX.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.6388.01 1 0.3797 0.3948 0.58 0.00 0.00 0.42 0.00 0.00
#> TCGA.TQ.A7RP.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.28.5213.01 2 0.0547 0.8898 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.76.4932.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5412.01 3 0.3578 0.4612 0.00 0.34 0.66 0.00 0.00 0.00
#> TCGA.06.6694.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.1389.01 2 0.0000 0.8965 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.12.5295.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.5953.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.28.5220.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4W.AA9T.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.OX.A56R.01 1 0.3076 0.7278 0.76 0.00 0.00 0.24 0.00 0.00
#> TCGA.S9.A7IX.01 5 0.0547 0.8927 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.06.0171.01 4 0.2048 0.8250 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.06.0125.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VW.A8FI.01 1 0.2631 0.7884 0.82 0.00 0.00 0.18 0.00 0.00
#> TCGA.06.6700.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.28.5218.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.06.0171.02 3 0.0547 0.9605 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.DU.8165.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.06.5856.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.26.5136.01 4 0.0000 0.8413 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.A76L.01 5 0.2941 0.6882 0.00 0.00 0.00 0.00 0.78 0.22
#> TCGA.76.6663.01 2 0.0937 0.8780 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.76.4926.01 1 0.3198 0.7038 0.74 0.00 0.00 0.26 0.00 0.00
#> TCGA.06.0211.02 4 0.0547 0.8281 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.28.5207.01 4 0.2631 0.5322 0.18 0.00 0.00 0.82 0.00 0.00
#> TCGA.14.1402.01 4 0.0000 0.8413 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.06.0211.01 4 0.0547 0.8434 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.14.1402.02 1 0.1814 0.8537 0.90 0.00 0.00 0.10 0.00 0.00
#> TCGA.19.4065.02 5 0.0547 0.8947 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.RR.A6KC.01 4 0.0547 0.8281 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.19.4065.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CS.4941.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A6U0.01 5 0.2454 0.7464 0.00 0.16 0.00 0.00 0.84 0.00
#> TCGA.FG.7643.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.06.5408.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6285.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6403.01 1 0.3198 0.7038 0.74 0.00 0.00 0.26 0.00 0.00
#> TCGA.19.5950.01 4 0.3592 0.7321 0.00 0.00 0.00 0.74 0.02 0.24
#> TCGA.14.1395.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8181.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.5963.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.5963.02 2 0.1814 0.8470 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.CS.5395.01 4 0.3076 0.7512 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.DU.7292.01 4 0.0000 0.8413 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.A5RC.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.06.5410.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.19.5958.01 4 0.3076 0.7512 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.28.5211.01 2 0.0000 0.8965 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84C.01 2 0.1814 0.8470 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.FG.A4MW.01 4 0.0547 0.8281 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DB.A75P.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A89V.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.06.6695.01 1 0.2793 0.7696 0.80 0.00 0.00 0.20 0.00 0.00
#> TCGA.06.5418.01 1 0.3076 0.7279 0.76 0.00 0.00 0.24 0.00 0.00
#> TCGA.06.5415.01 4 0.0547 0.8431 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.QH.A6CX.01 2 0.0000 0.8965 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.A6S1.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CS.6186.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.26.5135.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5219.01 1 0.3198 0.7038 0.74 0.00 0.00 0.26 0.00 0.00
#> TCGA.4W.AA9S.01 4 0.0000 0.8413 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.19.A60I.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.4934.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.32.5222.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6191.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.1806.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.06.6693.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6406.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6UA.01 2 0.1814 0.8470 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.DU.A7TB.01 2 0.1814 0.8470 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.06.6697.01 2 0.0000 0.8965 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A76K.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.28.5215.01 1 0.2793 0.7699 0.80 0.00 0.00 0.20 0.00 0.00
#> TCGA.DU.8162.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YQ.01 2 0.0547 0.8898 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.QH.A6CS.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.76.6283.01 5 0.3076 0.6601 0.00 0.00 0.00 0.00 0.76 0.24
#> TCGA.76.4929.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7691.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.19.1389.02 2 0.0000 0.8965 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.26.6174.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.6392.01 6 0.2190 0.6923 0.00 0.00 0.00 0.04 0.06 0.90
#> TCGA.32.1980.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.76.6661.01 1 0.2793 0.7699 0.80 0.00 0.00 0.20 0.00 0.00
#> TCGA.28.5209.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.5951.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7012.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.06.A6S0.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6402.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FG.A87Q.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.8104.01 4 0.0547 0.8281 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.FG.A70Z.01 4 0.2048 0.8250 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.14.0862.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.QH.A6XC.01 4 0.0000 0.8413 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FG.A4MU.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.5955.01 2 0.0000 0.8965 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A7C3.01 4 0.2631 0.7952 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.DB.A64O.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.A5TT.01 2 0.3828 0.2291 0.00 0.56 0.00 0.00 0.44 0.00
#> TCGA.74.6581.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8189.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.76.6662.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.8019.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A5EY.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.RR.A6KA.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.5872.02 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.74.6573.11 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CS.5397.01 2 0.0000 0.8965 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HW.A5KK.01 2 0.0000 0.8965 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.0650.01 3 0.0547 0.9605 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.CS.6669.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A7R2.01 2 0.0000 0.8965 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.6193.01 2 0.1267 0.8614 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.S9.A6WM.01 1 0.3076 0.7276 0.76 0.00 0.00 0.24 0.00 0.00
#> TCGA.HT.7680.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.06.6698.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A5F6.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.14.1043.01 5 0.2941 0.6671 0.00 0.22 0.00 0.00 0.78 0.00
#> TCGA.HT.8110.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.06.6391.01 2 0.1814 0.8470 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.76.4935.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YJ.01 1 0.3198 0.7038 0.74 0.00 0.00 0.26 0.00 0.00
#> TCGA.06.5414.01 4 0.0547 0.8281 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.06.A7TK.01 4 0.3592 0.7321 0.00 0.00 0.00 0.74 0.02 0.24
#> TCGA.06.5411.01 4 0.3592 0.7321 0.00 0.00 0.00 0.74 0.02 0.24
#> TCGA.76.6656.01 1 0.3198 0.7038 0.74 0.00 0.00 0.26 0.00 0.00
#> TCGA.E1.A7YL.01 4 0.3592 0.7321 0.00 0.00 0.00 0.74 0.02 0.24
#> TCGA.HT.8558.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.A61C.01 1 0.1267 0.8829 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.76.4925.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CV.01 4 0.3076 0.7512 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.4W.AA9R.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.6692.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.81.5910.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5214.01 4 0.2454 0.8072 0.00 0.00 0.00 0.84 0.00 0.16
#> TCGA.74.6584.01 4 0.2260 0.8182 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.06.0190.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.06.0190.02 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.76.6664.01 4 0.2260 0.8178 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.DU.7013.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KT.A7W1.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A5RA.01 1 0.3198 0.7038 0.74 0.00 0.00 0.26 0.00 0.00
#> TCGA.26.5134.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.2501.01 2 0.0000 0.8965 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.6286.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.14.1450.01 5 0.3869 -0.0614 0.00 0.50 0.00 0.00 0.50 0.00
#> TCGA.76.6660.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5204.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6188.01 5 0.3076 0.6601 0.00 0.00 0.00 0.00 0.76 0.24
#> TCGA.06.1804.01 4 0.0547 0.8281 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DU.A7TJ.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.4931.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TY.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.28.6450.01 5 0.2941 0.6892 0.00 0.00 0.00 0.00 0.78 0.22
#> TCGA.DU.5847.01 2 0.3647 0.4421 0.00 0.64 0.00 0.00 0.36 0.00
#> TCGA.76.4928.01 5 0.3864 0.0133 0.00 0.48 0.00 0.00 0.52 0.00
#> TCGA.26.6173.01 2 0.3851 0.1684 0.00 0.54 0.00 0.00 0.46 0.00
#> TCGA.HT.7882.01 2 0.0000 0.8965 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5854.01 2 0.0937 0.8780 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.76.6282.01 5 0.2454 0.7485 0.00 0.16 0.00 0.00 0.84 0.00
#> TCGA.19.5954.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8011.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5852.01 1 0.3198 0.7038 0.74 0.00 0.00 0.26 0.00 0.00
#> TCGA.32.1979.01 4 0.0547 0.8434 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.87.5896.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A72U.01 2 0.0000 0.8965 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6404.02 5 0.1814 0.8367 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.DU.6404.01 2 0.1814 0.8470 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.19.0957.01 1 0.2631 0.7884 0.82 0.00 0.00 0.18 0.00 0.00
#> TCGA.19.0957.02 4 0.3592 0.7321 0.00 0.00 0.00 0.74 0.02 0.24
#> TCGA.HT.8107.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.06.5859.01 1 0.2048 0.8387 0.88 0.00 0.00 0.12 0.00 0.00
#> TCGA.76.6657.01 5 0.1556 0.8494 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.06.6699.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YN.01 2 0.0547 0.8898 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.41.5651.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6192.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.74.6575.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.E1.A7Z2.01 2 0.0937 0.8780 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.VM.A8CD.01 2 0.0000 0.8965 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.0210.01 4 0.0000 0.8413 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.06.0210.02 1 0.3198 0.7038 0.74 0.00 0.00 0.26 0.00 0.00
#> TCGA.06.A5U1.01 5 0.0547 0.8947 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.HT.8564.01 5 0.1814 0.8367 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.19.5956.01 6 0.4078 0.4660 0.34 0.00 0.00 0.02 0.00 0.64
#> TCGA.28.5216.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7854.01 3 0.2048 0.8319 0.00 0.12 0.88 0.00 0.00 0.00
#> TCGA.VM.A8C9.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.74.6573.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5858.01 2 0.0547 0.8898 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.HT.7860.01 5 0.1267 0.8659 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.14.0740.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.81.5911.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.7006.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7469.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.6390.01 3 0.0937 0.9381 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.06.A5U0.01 6 0.3076 0.5832 0.00 0.00 0.00 0.24 0.00 0.76
#> TCGA.DU.8161.01 2 0.0000 0.8965 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.19.5959.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YM.01 2 0.0000 0.8965 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.5413.01 4 0.0000 0.8413 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.19.5947.01 2 0.0000 0.8965 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YD.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.5960.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.14.1034.02 4 0.2454 0.8072 0.00 0.00 0.00 0.84 0.00 0.16
#> TCGA.14.0736.02 2 0.0000 0.8965 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.19.5952.01 4 0.0000 0.8413 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.28.5208.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.5140.01 6 0.1267 0.6980 0.00 0.00 0.00 0.06 0.00 0.94
#> TCGA.76.6280.01 4 0.3076 0.7512 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.HT.8015.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.28.2510.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.A7TD.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.14.0736.01 5 0.5801 0.0633 0.00 0.00 0.00 0.26 0.50 0.24
#> TCGA.DU.6405.01 1 0.3198 0.7038 0.74 0.00 0.00 0.26 0.00 0.00
#> TCGA.06.0152.02 4 0.0000 0.8413 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.06.0152.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.4927.01 4 0.1814 0.8306 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.26.5132.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A74H.01 2 0.0000 0.8965 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7290.01 2 0.3828 0.2281 0.00 0.56 0.00 0.00 0.44 0.00
#> TCGA.19.A6J4.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.12.5299.01 4 0.1814 0.6999 0.10 0.00 0.00 0.90 0.00 0.00
#> TCGA.HT.A4DS.01 2 0.3499 0.5216 0.00 0.68 0.00 0.00 0.32 0.00
#> TCGA.12.5301.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RR.A6KB.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.TM.A84B.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5416.01 2 0.2350 0.8440 0.00 0.88 0.00 0.00 0.02 0.10
#> TCGA.DU.8158.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.26.5139.01 4 0.0547 0.8281 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.TM.A84J.01 1 0.0000 0.9221 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.41.6646.01 5 0.0000 0.9083 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.14.0781.01 3 0.0000 0.9796 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.A617.01 2 0.2048 0.7702 0.00 0.88 0.12 0.00 0.00 0.00
#> TCGA.HT.7857.01 2 0.1814 0.8470 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.74.6578.01 4 0.0000 0.8413 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.FG.6688.01 2 0.0504 0.7853 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.74.6577.01 7 0.4533 0.7280 0.00 0.00 0.00 0.26 0.04 0.04 0.66
#> TCGA.06.AABW.11 3 0.0000 0.9450 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.0125.02 7 0.4533 0.7280 0.00 0.00 0.00 0.26 0.04 0.04 0.66
#> TCGA.26.A7UX.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.6388.01 4 0.2081 0.6197 0.14 0.00 0.00 0.86 0.00 0.00 0.00
#> TCGA.TQ.A7RP.01 3 0.1006 0.9309 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.28.5213.01 2 0.1671 0.7701 0.00 0.90 0.00 0.00 0.10 0.00 0.00
#> TCGA.76.4932.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5412.01 3 0.4622 0.3716 0.00 0.38 0.56 0.00 0.00 0.02 0.04
#> TCGA.06.6694.01 1 0.0504 0.9513 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.19.1389.01 2 0.1363 0.7770 0.00 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.12.5295.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.5953.01 5 0.1363 0.8764 0.00 0.00 0.00 0.00 0.94 0.02 0.04
#> TCGA.28.5220.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4W.AA9T.01 5 0.0000 0.8836 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.OX.A56R.01 4 0.3139 0.5614 0.30 0.00 0.00 0.70 0.00 0.00 0.00
#> TCGA.S9.A7IX.01 5 0.2864 0.7818 0.00 0.12 0.00 0.00 0.84 0.02 0.02
#> TCGA.06.0171.01 7 0.3562 0.5041 0.00 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.06.0125.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VW.A8FI.01 4 0.3525 0.3476 0.44 0.00 0.00 0.56 0.00 0.00 0.00
#> TCGA.06.6700.01 5 0.1363 0.8764 0.00 0.00 0.00 0.00 0.94 0.02 0.04
#> TCGA.28.5218.01 5 0.2278 0.8373 0.00 0.00 0.00 0.00 0.88 0.04 0.08
#> TCGA.06.0171.02 3 0.2769 0.8549 0.00 0.08 0.86 0.00 0.00 0.02 0.04
#> TCGA.DU.8165.01 5 0.1006 0.8757 0.00 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.06.5856.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.26.5136.01 4 0.0504 0.6009 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.DU.A76L.01 7 0.4214 0.2545 0.00 0.00 0.00 0.00 0.40 0.04 0.56
#> TCGA.76.6663.01 2 0.2081 0.7451 0.00 0.86 0.00 0.00 0.14 0.00 0.00
#> TCGA.76.4926.01 4 0.3139 0.5614 0.30 0.00 0.00 0.70 0.00 0.00 0.00
#> TCGA.06.0211.02 4 0.0000 0.6212 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.28.5207.01 4 0.0863 0.6278 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.14.1402.01 4 0.0000 0.6212 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.06.0211.01 4 0.3358 -0.1649 0.00 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.14.1402.02 1 0.3496 0.1239 0.58 0.00 0.00 0.42 0.00 0.00 0.00
#> TCGA.19.4065.02 5 0.2722 0.7980 0.00 0.00 0.00 0.00 0.84 0.04 0.12
#> TCGA.RR.A6KC.01 4 0.0000 0.6212 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.19.4065.01 5 0.1363 0.8764 0.00 0.00 0.00 0.00 0.94 0.02 0.04
#> TCGA.CS.4941.01 5 0.0863 0.8814 0.00 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.S9.A6U0.01 5 0.1433 0.8435 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.FG.7643.01 3 0.1006 0.9309 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.06.5408.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6285.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6403.01 4 0.2945 0.5835 0.26 0.00 0.00 0.74 0.00 0.00 0.00
#> TCGA.19.5950.01 7 0.3139 0.7379 0.00 0.00 0.00 0.30 0.00 0.00 0.70
#> TCGA.14.1395.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8181.01 3 0.0000 0.9450 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.5963.01 3 0.0000 0.9450 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.5963.02 2 0.3755 0.5851 0.00 0.64 0.00 0.00 0.00 0.34 0.02
#> TCGA.CS.5395.01 7 0.3047 0.7386 0.00 0.00 0.00 0.28 0.00 0.00 0.72
#> TCGA.DU.7292.01 4 0.2081 0.4402 0.00 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.HT.A5RC.01 5 0.2569 0.8109 0.00 0.00 0.00 0.00 0.84 0.02 0.14
#> TCGA.06.5410.01 3 0.0000 0.9450 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.19.5958.01 7 0.3221 0.7267 0.00 0.00 0.00 0.32 0.00 0.00 0.68
#> TCGA.28.5211.01 2 0.1671 0.7702 0.00 0.90 0.00 0.00 0.10 0.00 0.00
#> TCGA.TM.A84C.01 2 0.4127 0.5594 0.00 0.60 0.00 0.00 0.00 0.36 0.04
#> TCGA.FG.A4MW.01 4 0.0000 0.6212 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.A75P.01 3 0.0000 0.9450 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A89V.01 3 0.0504 0.9386 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.06.6695.01 4 0.3496 0.3975 0.42 0.00 0.00 0.58 0.00 0.00 0.00
#> TCGA.06.5418.01 4 0.3221 0.5387 0.32 0.00 0.00 0.68 0.00 0.00 0.00
#> TCGA.06.5415.01 4 0.2945 0.1649 0.00 0.00 0.00 0.74 0.00 0.00 0.26
#> TCGA.QH.A6CX.01 2 0.0504 0.7853 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.06.A6S1.01 5 0.2016 0.8533 0.00 0.00 0.00 0.00 0.90 0.04 0.06
#> TCGA.CS.6186.01 5 0.2864 0.8105 0.00 0.02 0.00 0.00 0.84 0.02 0.12
#> TCGA.26.5135.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5219.01 4 0.3139 0.5614 0.30 0.00 0.00 0.70 0.00 0.00 0.00
#> TCGA.4W.AA9S.01 4 0.0000 0.6212 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.19.A60I.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.4934.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.32.5222.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6191.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.1806.01 3 0.0000 0.9450 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.6693.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6406.01 1 0.1166 0.9044 0.94 0.00 0.00 0.06 0.00 0.00 0.00
#> TCGA.S9.A6UA.01 2 0.3139 0.6270 0.00 0.70 0.00 0.00 0.00 0.30 0.00
#> TCGA.DU.A7TB.01 2 0.3294 0.5897 0.00 0.66 0.00 0.00 0.00 0.34 0.00
#> TCGA.06.6697.01 2 0.1363 0.7770 0.00 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.DU.A76K.01 5 0.1006 0.8757 0.00 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.28.5215.01 4 0.3139 0.5614 0.30 0.00 0.00 0.70 0.00 0.00 0.00
#> TCGA.DU.8162.01 3 0.1006 0.9309 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.E1.A7YQ.01 2 0.2081 0.7494 0.00 0.86 0.00 0.00 0.14 0.00 0.00
#> TCGA.QH.A6CS.01 3 0.0000 0.9450 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.6283.01 5 0.4278 0.0567 0.00 0.00 0.00 0.00 0.50 0.04 0.46
#> TCGA.76.4929.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7691.01 3 0.0000 0.9450 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.19.1389.02 2 0.0000 0.7855 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.26.6174.01 5 0.1006 0.8817 0.00 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.DU.6392.01 6 0.3867 0.7477 0.00 0.00 0.00 0.02 0.00 0.60 0.38
#> TCGA.32.1980.01 3 0.0000 0.9450 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.6661.01 4 0.3525 0.3455 0.44 0.00 0.00 0.56 0.00 0.00 0.00
#> TCGA.28.5209.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.5951.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7012.01 5 0.0504 0.8840 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.06.A6S0.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6402.01 5 0.1006 0.8757 0.00 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.FG.A87Q.01 5 0.0000 0.8836 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.8104.01 4 0.0000 0.6212 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.A70Z.01 4 0.3525 -0.3936 0.00 0.00 0.00 0.56 0.00 0.00 0.44
#> TCGA.14.0862.01 5 0.0504 0.8841 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.QH.A6XC.01 4 0.2422 0.3638 0.00 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.FG.A4MU.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.5955.01 2 0.0863 0.7843 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.TM.A7C3.01 7 0.3358 0.7007 0.00 0.00 0.00 0.36 0.00 0.00 0.64
#> TCGA.DB.A64O.01 3 0.1006 0.9309 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.DU.A5TT.01 2 0.3968 0.2967 0.00 0.54 0.00 0.00 0.44 0.00 0.02
#> TCGA.74.6581.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8189.01 3 0.0000 0.9450 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.6662.01 5 0.0504 0.8840 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.HT.8019.01 3 0.0000 0.9450 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A5EY.01 3 0.0000 0.9450 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RR.A6KA.01 5 0.0504 0.8804 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DU.5872.02 3 0.0000 0.9450 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.74.6573.11 3 0.0000 0.9450 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.5397.01 2 0.0504 0.7853 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.HW.A5KK.01 2 0.1363 0.7770 0.00 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.06.0650.01 3 0.2769 0.8549 0.00 0.08 0.86 0.00 0.00 0.02 0.04
#> TCGA.CS.6669.01 3 0.0000 0.9450 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7R2.01 2 0.0000 0.7855 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6193.01 2 0.2572 0.7030 0.00 0.80 0.00 0.00 0.20 0.00 0.00
#> TCGA.S9.A6WM.01 4 0.3047 0.5749 0.28 0.00 0.00 0.72 0.00 0.00 0.00
#> TCGA.HT.7680.01 3 0.0000 0.9450 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.6698.01 3 0.2213 0.8915 0.00 0.04 0.90 0.00 0.00 0.02 0.04
#> TCGA.P5.A5F6.01 3 0.0000 0.9450 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.14.1043.01 5 0.2259 0.7634 0.00 0.16 0.00 0.00 0.84 0.00 0.00
#> TCGA.HT.8110.01 5 0.1363 0.8764 0.00 0.00 0.00 0.00 0.94 0.02 0.04
#> TCGA.06.6391.01 2 0.3755 0.5823 0.00 0.64 0.00 0.00 0.02 0.34 0.00
#> TCGA.76.4935.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YJ.01 4 0.3139 0.5614 0.30 0.00 0.00 0.70 0.00 0.00 0.00
#> TCGA.06.5414.01 4 0.0000 0.6212 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.06.A7TK.01 7 0.4211 0.7321 0.00 0.00 0.00 0.26 0.02 0.04 0.68
#> TCGA.06.5411.01 7 0.4699 0.7157 0.00 0.00 0.00 0.24 0.06 0.04 0.66
#> TCGA.76.6656.01 4 0.2832 0.5903 0.24 0.00 0.00 0.76 0.00 0.00 0.00
#> TCGA.E1.A7YL.01 7 0.3307 0.7264 0.00 0.00 0.00 0.24 0.02 0.00 0.74
#> TCGA.HT.8558.01 3 0.0000 0.9450 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A61C.01 1 0.2572 0.6949 0.80 0.00 0.00 0.20 0.00 0.00 0.00
#> TCGA.76.4925.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CV.01 7 0.3139 0.7379 0.00 0.00 0.00 0.30 0.00 0.00 0.70
#> TCGA.4W.AA9R.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.6692.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.81.5910.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5214.01 7 0.3546 0.5887 0.00 0.00 0.00 0.46 0.00 0.00 0.54
#> TCGA.74.6584.01 4 0.3558 -0.4935 0.00 0.00 0.00 0.52 0.00 0.00 0.48
#> TCGA.06.0190.01 5 0.0000 0.8836 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.06.0190.02 5 0.1363 0.8764 0.00 0.00 0.00 0.00 0.94 0.02 0.04
#> TCGA.76.6664.01 4 0.3525 -0.3936 0.00 0.00 0.00 0.56 0.00 0.00 0.44
#> TCGA.DU.7013.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KT.A7W1.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A5RA.01 4 0.3047 0.5749 0.28 0.00 0.00 0.72 0.00 0.00 0.00
#> TCGA.26.5134.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.2501.01 2 0.1363 0.7770 0.00 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.76.6286.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.14.1450.01 2 0.4421 0.1722 0.00 0.50 0.00 0.00 0.46 0.02 0.02
#> TCGA.76.6660.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5204.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6188.01 7 0.3517 0.3790 0.00 0.00 0.00 0.00 0.28 0.02 0.70
#> TCGA.06.1804.01 4 0.0000 0.6212 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.A7TJ.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.4931.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TY.01 5 0.1006 0.8757 0.00 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.28.6450.01 7 0.3815 0.2777 0.00 0.00 0.00 0.00 0.36 0.02 0.62
#> TCGA.DU.5847.01 2 0.4317 0.4078 0.00 0.58 0.00 0.00 0.38 0.02 0.02
#> TCGA.76.4928.01 5 0.3496 0.1649 0.00 0.42 0.00 0.00 0.58 0.00 0.00
#> TCGA.26.6173.01 2 0.3525 0.3484 0.00 0.56 0.00 0.00 0.44 0.00 0.00
#> TCGA.HT.7882.01 2 0.0504 0.7853 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DU.5854.01 2 0.2906 0.7043 0.00 0.80 0.00 0.00 0.18 0.00 0.02
#> TCGA.76.6282.01 5 0.2422 0.7225 0.00 0.18 0.00 0.00 0.82 0.00 0.00
#> TCGA.19.5954.01 1 0.0863 0.9292 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.HT.8011.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5852.01 4 0.3139 0.5614 0.30 0.00 0.00 0.70 0.00 0.00 0.00
#> TCGA.32.1979.01 4 0.3294 -0.1001 0.00 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.87.5896.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A72U.01 2 0.1166 0.7812 0.00 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.DU.6404.02 5 0.3294 0.5619 0.00 0.00 0.00 0.00 0.66 0.34 0.00
#> TCGA.DU.6404.01 2 0.3755 0.5851 0.00 0.64 0.00 0.00 0.00 0.34 0.02
#> TCGA.19.0957.01 4 0.3546 0.2921 0.46 0.00 0.00 0.54 0.00 0.00 0.00
#> TCGA.19.0957.02 7 0.4699 0.7157 0.00 0.00 0.00 0.24 0.06 0.04 0.66
#> TCGA.HT.8107.01 3 0.0000 0.9450 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.5859.01 1 0.3546 -0.0379 0.54 0.00 0.00 0.46 0.00 0.00 0.00
#> TCGA.76.6657.01 5 0.3052 0.7512 0.00 0.00 0.00 0.00 0.78 0.02 0.20
#> TCGA.06.6699.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YN.01 2 0.1671 0.7702 0.00 0.90 0.00 0.00 0.10 0.00 0.00
#> TCGA.41.5651.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6192.01 5 0.1363 0.8764 0.00 0.00 0.00 0.00 0.94 0.02 0.04
#> TCGA.74.6575.01 5 0.1006 0.8817 0.00 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.E1.A7Z2.01 2 0.2864 0.7410 0.00 0.84 0.00 0.00 0.12 0.02 0.02
#> TCGA.VM.A8CD.01 2 0.1363 0.7770 0.00 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.06.0210.01 4 0.0000 0.6212 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.06.0210.02 4 0.2945 0.5835 0.26 0.00 0.00 0.74 0.00 0.00 0.00
#> TCGA.06.A5U1.01 5 0.2278 0.8373 0.00 0.00 0.00 0.00 0.88 0.04 0.08
#> TCGA.HT.8564.01 5 0.3294 0.5619 0.00 0.00 0.00 0.00 0.66 0.34 0.00
#> TCGA.19.5956.01 6 0.5639 0.6163 0.20 0.00 0.00 0.04 0.00 0.56 0.20
#> TCGA.28.5216.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7854.01 3 0.3991 0.6615 0.00 0.22 0.72 0.00 0.00 0.02 0.04
#> TCGA.VM.A8C9.01 3 0.0000 0.9450 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.74.6573.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5858.01 2 0.2016 0.7768 0.00 0.90 0.00 0.00 0.06 0.04 0.00
#> TCGA.HT.7860.01 5 0.2745 0.7951 0.00 0.00 0.00 0.00 0.82 0.02 0.16
#> TCGA.14.0740.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.81.5911.01 5 0.1006 0.8757 0.00 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.DU.7006.01 5 0.0000 0.8836 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7469.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.6390.01 3 0.3000 0.8327 0.00 0.10 0.84 0.00 0.00 0.02 0.04
#> TCGA.06.A5U0.01 6 0.4870 0.7066 0.00 0.00 0.00 0.14 0.00 0.58 0.28
#> TCGA.DU.8161.01 2 0.1363 0.7770 0.00 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.19.5959.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YM.01 2 0.1363 0.7770 0.00 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.06.5413.01 4 0.0000 0.6212 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.19.5947.01 2 0.1363 0.7770 0.00 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.E1.A7YD.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.5960.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.14.1034.02 7 0.3496 0.6448 0.00 0.00 0.00 0.42 0.00 0.00 0.58
#> TCGA.14.0736.02 2 0.0000 0.7855 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.5952.01 4 0.0000 0.6212 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.28.5208.01 1 0.0504 0.9513 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.DH.5140.01 6 0.3755 0.7662 0.00 0.00 0.00 0.02 0.00 0.64 0.34
#> TCGA.76.6280.01 7 0.3139 0.7379 0.00 0.00 0.00 0.30 0.00 0.00 0.70
#> TCGA.HT.8015.01 3 0.0000 0.9450 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.28.2510.01 3 0.1006 0.9309 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.DU.A7TD.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.14.0736.01 7 0.4960 0.3967 0.00 0.00 0.00 0.06 0.30 0.04 0.60
#> TCGA.DU.6405.01 4 0.3047 0.5742 0.28 0.00 0.00 0.72 0.00 0.00 0.00
#> TCGA.06.0152.02 4 0.0000 0.6212 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.06.0152.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.4927.01 4 0.3496 -0.3411 0.00 0.00 0.00 0.58 0.00 0.00 0.42
#> TCGA.26.5132.01 1 0.0863 0.9287 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.HT.A74H.01 2 0.0000 0.7855 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7290.01 2 0.4317 0.4078 0.00 0.58 0.00 0.00 0.38 0.02 0.02
#> TCGA.19.A6J4.01 3 0.2213 0.8915 0.00 0.04 0.90 0.00 0.00 0.02 0.04
#> TCGA.12.5299.01 4 0.0504 0.6254 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.HT.A4DS.01 2 0.4269 0.4523 0.00 0.60 0.00 0.00 0.36 0.02 0.02
#> TCGA.12.5301.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RR.A6KB.01 5 0.0000 0.8836 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.TM.A84B.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5416.01 2 0.3221 0.6111 0.00 0.68 0.00 0.00 0.00 0.32 0.00
#> TCGA.DU.8158.01 5 0.0000 0.8836 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.26.5139.01 4 0.0000 0.6212 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.TM.A84J.01 1 0.0000 0.9716 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.41.6646.01 5 0.1006 0.8757 0.00 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.14.0781.01 3 0.2213 0.8915 0.00 0.04 0.90 0.00 0.00 0.02 0.04
#> TCGA.HT.A617.01 2 0.2213 0.7486 0.00 0.90 0.04 0.00 0.00 0.02 0.04
#> TCGA.HT.7857.01 2 0.4003 0.5895 0.00 0.64 0.00 0.00 0.00 0.32 0.04
#> TCGA.74.6578.01 4 0.0000 0.6212 0.00 0.00 0.00 1.00 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.FG.6688.01 2 0.0471 0.5436 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.74.6577.01 7 0.3934 0.7221 0.00 0.00 0.00 0.16 0.14 0.00 0.70 0.00
#> TCGA.06.AABW.11 3 0.0000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.0125.02 7 0.3771 0.7351 0.00 0.00 0.00 0.16 0.12 0.00 0.72 0.00
#> TCGA.26.A7UX.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.6388.01 4 0.1091 0.7684 0.06 0.00 0.00 0.94 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RP.01 3 0.2350 0.8658 0.00 0.00 0.86 0.00 0.00 0.00 0.04 0.10
#> TCGA.28.5213.01 2 0.0941 0.5377 0.00 0.96 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.76.4932.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5412.01 2 0.5429 -0.1175 0.00 0.46 0.36 0.00 0.00 0.00 0.04 0.14
#> TCGA.06.6694.01 1 0.1563 0.8582 0.90 0.00 0.00 0.10 0.00 0.00 0.00 0.00
#> TCGA.19.1389.01 2 0.2404 0.4611 0.00 0.84 0.00 0.00 0.00 0.00 0.02 0.14
#> TCGA.12.5295.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.5953.01 5 0.0000 0.8196 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.28.5220.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4W.AA9T.01 5 0.1275 0.8117 0.00 0.02 0.00 0.00 0.94 0.00 0.00 0.04
#> TCGA.OX.A56R.01 4 0.2114 0.7441 0.16 0.00 0.00 0.84 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IX.01 5 0.5936 0.1554 0.00 0.30 0.00 0.00 0.40 0.02 0.02 0.26
#> TCGA.06.0171.01 7 0.3272 0.5687 0.00 0.00 0.00 0.42 0.00 0.00 0.58 0.00
#> TCGA.06.0125.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VW.A8FI.01 4 0.3015 0.5310 0.32 0.00 0.00 0.68 0.00 0.00 0.00 0.00
#> TCGA.06.6700.01 5 0.0000 0.8196 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.28.5218.01 5 0.0471 0.8114 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.06.0171.02 3 0.3986 0.7610 0.00 0.08 0.74 0.00 0.00 0.00 0.04 0.14
#> TCGA.DU.8165.01 5 0.4530 0.6247 0.00 0.06 0.00 0.00 0.66 0.02 0.02 0.24
#> TCGA.06.5856.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.26.5136.01 4 0.0471 0.7463 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.DU.A76L.01 5 0.3272 0.2290 0.00 0.00 0.00 0.00 0.58 0.00 0.42 0.00
#> TCGA.76.6663.01 2 0.2981 0.4201 0.00 0.76 0.00 0.00 0.00 0.02 0.00 0.22
#> TCGA.76.4926.01 4 0.2114 0.7441 0.16 0.00 0.00 0.84 0.00 0.00 0.00 0.00
#> TCGA.06.0211.02 4 0.0000 0.7618 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.28.5207.01 4 0.0471 0.7655 0.02 0.00 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.14.1402.01 4 0.0000 0.7618 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.0211.01 4 0.3318 -0.3080 0.00 0.00 0.00 0.54 0.00 0.00 0.46 0.00
#> TCGA.14.1402.02 1 0.3299 0.1006 0.56 0.00 0.00 0.44 0.00 0.00 0.00 0.00
#> TCGA.19.4065.02 5 0.0808 0.8034 0.00 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.RR.A6KC.01 4 0.0000 0.7618 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.19.4065.01 5 0.0000 0.8196 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CS.4941.01 5 0.0000 0.8196 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6U0.01 5 0.2856 0.6642 0.00 0.20 0.00 0.00 0.78 0.00 0.00 0.02
#> TCGA.FG.7643.01 3 0.2350 0.8658 0.00 0.00 0.86 0.00 0.00 0.00 0.04 0.10
#> TCGA.06.5408.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6285.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6403.01 4 0.1947 0.7548 0.14 0.00 0.00 0.86 0.00 0.00 0.00 0.00
#> TCGA.19.5950.01 7 0.3002 0.7211 0.00 0.00 0.00 0.12 0.02 0.00 0.82 0.04
#> TCGA.14.1395.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8181.01 3 0.0000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.5963.01 3 0.0000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.5963.02 8 0.4004 0.7608 0.00 0.46 0.00 0.00 0.00 0.04 0.00 0.50
#> TCGA.CS.5395.01 7 0.2224 0.7334 0.00 0.00 0.00 0.12 0.02 0.00 0.86 0.00
#> TCGA.DU.7292.01 4 0.2650 0.4116 0.00 0.00 0.00 0.76 0.00 0.00 0.24 0.00
#> TCGA.HT.A5RC.01 5 0.4190 0.6338 0.00 0.00 0.00 0.00 0.66 0.00 0.14 0.20
#> TCGA.06.5410.01 3 0.0000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.5958.01 7 0.2404 0.7338 0.00 0.00 0.00 0.14 0.00 0.00 0.84 0.02
#> TCGA.28.5211.01 2 0.1341 0.5134 0.00 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.TM.A84C.01 8 0.4004 0.7280 0.00 0.46 0.00 0.00 0.00 0.04 0.00 0.50
#> TCGA.FG.A4MW.01 4 0.0000 0.7618 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A75P.01 3 0.0000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A89V.01 3 0.0471 0.9150 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.06.6695.01 4 0.2534 0.6779 0.22 0.00 0.00 0.78 0.00 0.00 0.00 0.00
#> TCGA.06.5418.01 4 0.2267 0.7253 0.18 0.00 0.00 0.82 0.00 0.00 0.00 0.00
#> TCGA.06.5415.01 4 0.3237 -0.0845 0.00 0.00 0.00 0.60 0.00 0.00 0.40 0.00
#> TCGA.QH.A6CX.01 2 0.0471 0.5436 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.06.A6S1.01 5 0.0808 0.8034 0.00 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.CS.6186.01 5 0.4898 0.5246 0.00 0.00 0.00 0.00 0.56 0.02 0.12 0.30
#> TCGA.26.5135.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5219.01 4 0.1947 0.7548 0.14 0.00 0.00 0.86 0.00 0.00 0.00 0.00
#> TCGA.4W.AA9S.01 4 0.0000 0.7618 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.19.A60I.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.4934.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.32.5222.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6191.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.1806.01 3 0.0000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.6693.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6406.01 1 0.0471 0.9581 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.S9.A6UA.01 2 0.3083 -0.4321 0.00 0.66 0.00 0.00 0.00 0.00 0.00 0.34
#> TCGA.DU.A7TB.01 8 0.3992 0.7566 0.00 0.44 0.00 0.00 0.00 0.04 0.00 0.52
#> TCGA.06.6697.01 2 0.2725 0.4484 0.00 0.82 0.00 0.00 0.00 0.00 0.04 0.14
#> TCGA.DU.A76K.01 5 0.1341 0.8054 0.00 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.28.5215.01 4 0.2267 0.7253 0.18 0.00 0.00 0.82 0.00 0.00 0.00 0.00
#> TCGA.DU.8162.01 3 0.2547 0.8533 0.00 0.00 0.84 0.00 0.00 0.00 0.04 0.12
#> TCGA.E1.A7YQ.01 2 0.1341 0.5134 0.00 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.QH.A6CS.01 3 0.0000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6283.01 5 0.3714 0.2120 0.00 0.00 0.00 0.00 0.54 0.00 0.44 0.02
#> TCGA.76.4929.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7691.01 3 0.0000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.1389.02 2 0.0941 0.5377 0.00 0.96 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.26.6174.01 5 0.0471 0.8160 0.00 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.DU.6392.01 6 0.2025 0.8189 0.00 0.00 0.00 0.00 0.02 0.88 0.10 0.00
#> TCGA.32.1980.01 3 0.0000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6661.01 4 0.2756 0.6236 0.26 0.00 0.00 0.74 0.00 0.00 0.00 0.00
#> TCGA.28.5209.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.5951.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7012.01 5 0.0471 0.8160 0.00 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.06.A6S0.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6402.01 5 0.2981 0.7134 0.00 0.00 0.00 0.00 0.76 0.02 0.00 0.22
#> TCGA.FG.A87Q.01 5 0.0808 0.8155 0.00 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.HT.8104.01 4 0.0000 0.7618 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A70Z.01 7 0.3299 0.5281 0.00 0.00 0.00 0.44 0.00 0.00 0.56 0.00
#> TCGA.14.0862.01 5 0.0000 0.8196 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.QH.A6XC.01 4 0.2938 0.2564 0.00 0.00 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.FG.A4MU.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.5955.01 2 0.0000 0.5452 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A7C3.01 7 0.2856 0.7367 0.00 0.00 0.00 0.20 0.00 0.00 0.78 0.02
#> TCGA.DB.A64O.01 3 0.2350 0.8658 0.00 0.00 0.86 0.00 0.00 0.00 0.04 0.10
#> TCGA.DU.A5TT.01 2 0.5402 0.1929 0.00 0.48 0.00 0.00 0.24 0.02 0.00 0.26
#> TCGA.74.6581.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8189.01 3 0.0000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6662.01 5 0.0000 0.8196 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.8019.01 3 0.0000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A5EY.01 3 0.0000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RR.A6KA.01 5 0.0808 0.8155 0.00 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.DU.5872.02 3 0.0000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.74.6573.11 3 0.0000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.5397.01 2 0.0471 0.5436 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.HW.A5KK.01 2 0.2725 0.4484 0.00 0.82 0.00 0.00 0.00 0.00 0.04 0.14
#> TCGA.06.0650.01 3 0.3494 0.8055 0.00 0.04 0.78 0.00 0.00 0.00 0.04 0.14
#> TCGA.CS.6669.01 3 0.0000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7R2.01 2 0.0471 0.5436 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.76.6193.01 2 0.2534 0.3687 0.00 0.78 0.00 0.00 0.22 0.00 0.00 0.00
#> TCGA.S9.A6WM.01 4 0.2267 0.7253 0.18 0.00 0.00 0.82 0.00 0.00 0.00 0.00
#> TCGA.HT.7680.01 3 0.0000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.6698.01 3 0.3002 0.8398 0.00 0.02 0.82 0.00 0.00 0.00 0.04 0.12
#> TCGA.P5.A5F6.01 3 0.0000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.14.1043.01 5 0.3594 0.5302 0.00 0.28 0.00 0.00 0.68 0.00 0.00 0.04
#> TCGA.HT.8110.01 5 0.0000 0.8196 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.06.6391.01 2 0.4137 -0.7414 0.00 0.50 0.00 0.00 0.02 0.02 0.00 0.46
#> TCGA.76.4935.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YJ.01 4 0.2114 0.7441 0.16 0.00 0.00 0.84 0.00 0.00 0.00 0.00
#> TCGA.06.5414.01 4 0.0000 0.7618 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.A7TK.01 7 0.3385 0.7480 0.00 0.00 0.00 0.16 0.08 0.00 0.76 0.00
#> TCGA.06.5411.01 7 0.3934 0.7221 0.00 0.00 0.00 0.16 0.14 0.00 0.70 0.00
#> TCGA.76.6656.01 4 0.1947 0.7548 0.14 0.00 0.00 0.86 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YL.01 7 0.3227 0.7442 0.00 0.00 0.00 0.14 0.08 0.00 0.78 0.00
#> TCGA.HT.8558.01 3 0.0000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A61C.01 1 0.2756 0.6010 0.74 0.00 0.00 0.26 0.00 0.00 0.00 0.00
#> TCGA.76.4925.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CV.01 7 0.2404 0.7338 0.00 0.00 0.00 0.14 0.00 0.00 0.84 0.02
#> TCGA.4W.AA9R.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.6692.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.81.5910.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5214.01 7 0.2852 0.7074 0.00 0.00 0.00 0.28 0.00 0.00 0.72 0.00
#> TCGA.74.6584.01 7 0.3272 0.5628 0.00 0.00 0.00 0.42 0.00 0.00 0.58 0.00
#> TCGA.06.0190.01 5 0.0808 0.8155 0.00 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.06.0190.02 5 0.0000 0.8196 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.76.6664.01 7 0.3329 0.4296 0.00 0.00 0.00 0.48 0.00 0.00 0.52 0.00
#> TCGA.DU.7013.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KT.A7W1.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A5RA.01 4 0.1947 0.7548 0.14 0.00 0.00 0.86 0.00 0.00 0.00 0.00
#> TCGA.26.5134.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.2501.01 2 0.2404 0.4611 0.00 0.84 0.00 0.00 0.00 0.00 0.02 0.14
#> TCGA.76.6286.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.14.1450.01 2 0.5447 0.2534 0.00 0.54 0.00 0.00 0.16 0.02 0.02 0.26
#> TCGA.76.6660.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5204.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6188.01 7 0.3154 0.5515 0.00 0.00 0.00 0.00 0.16 0.00 0.78 0.06
#> TCGA.06.1804.01 4 0.0000 0.7618 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A7TJ.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.4931.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TY.01 5 0.1947 0.7782 0.00 0.00 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.28.6450.01 7 0.4437 0.3167 0.00 0.00 0.00 0.00 0.22 0.00 0.62 0.16
#> TCGA.DU.5847.01 2 0.5180 0.2853 0.00 0.58 0.00 0.00 0.12 0.02 0.02 0.26
#> TCGA.76.4928.01 2 0.3690 0.1612 0.00 0.56 0.00 0.00 0.42 0.00 0.00 0.02
#> TCGA.26.6173.01 2 0.5088 0.2602 0.00 0.56 0.00 0.00 0.20 0.02 0.00 0.22
#> TCGA.HT.7882.01 2 0.0471 0.5436 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DU.5854.01 2 0.2807 0.4740 0.00 0.84 0.00 0.00 0.10 0.02 0.00 0.04
#> TCGA.76.6282.01 5 0.4415 0.3926 0.00 0.32 0.00 0.00 0.60 0.02 0.00 0.06
#> TCGA.19.5954.01 1 0.1341 0.8853 0.92 0.00 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.HT.8011.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5852.01 4 0.2114 0.7441 0.16 0.00 0.00 0.84 0.00 0.00 0.00 0.00
#> TCGA.32.1979.01 4 0.3237 -0.1073 0.00 0.00 0.00 0.60 0.00 0.00 0.40 0.00
#> TCGA.87.5896.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A72U.01 2 0.0471 0.5416 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.DU.6404.02 5 0.4407 0.1938 0.00 0.04 0.00 0.00 0.48 0.02 0.00 0.46
#> TCGA.DU.6404.01 2 0.3729 -0.7345 0.00 0.52 0.00 0.00 0.00 0.02 0.00 0.46
#> TCGA.19.0957.01 4 0.2756 0.6236 0.26 0.00 0.00 0.74 0.00 0.00 0.00 0.00
#> TCGA.19.0957.02 7 0.3771 0.7351 0.00 0.00 0.00 0.16 0.12 0.00 0.72 0.00
#> TCGA.HT.8107.01 3 0.0000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5859.01 4 0.3193 0.4277 0.38 0.00 0.00 0.62 0.00 0.00 0.00 0.00
#> TCGA.76.6657.01 5 0.4799 0.4611 0.00 0.00 0.00 0.00 0.54 0.00 0.28 0.18
#> TCGA.06.6699.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YN.01 2 0.1341 0.5134 0.00 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.41.5651.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6192.01 5 0.0000 0.8196 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.74.6575.01 5 0.0000 0.8196 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.A7Z2.01 2 0.3941 0.3610 0.00 0.68 0.00 0.00 0.00 0.04 0.02 0.26
#> TCGA.VM.A8CD.01 2 0.2404 0.4700 0.00 0.84 0.00 0.00 0.00 0.00 0.02 0.14
#> TCGA.06.0210.01 4 0.0000 0.7618 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.0210.02 4 0.1765 0.7599 0.12 0.00 0.00 0.88 0.00 0.00 0.00 0.00
#> TCGA.06.A5U1.01 5 0.0808 0.8034 0.00 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.HT.8564.01 5 0.3618 0.3997 0.00 0.00 0.00 0.00 0.60 0.02 0.00 0.38
#> TCGA.19.5956.01 6 0.2725 0.6790 0.14 0.00 0.00 0.04 0.00 0.82 0.00 0.00
#> TCGA.28.5216.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7854.01 3 0.4528 0.6742 0.00 0.14 0.68 0.00 0.00 0.00 0.04 0.14
#> TCGA.VM.A8C9.01 3 0.0000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.74.6573.01 1 0.0471 0.9577 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.06.5858.01 2 0.4672 0.2682 0.00 0.64 0.00 0.00 0.02 0.04 0.04 0.26
#> TCGA.HT.7860.01 5 0.4669 0.5361 0.00 0.00 0.00 0.00 0.58 0.00 0.22 0.20
#> TCGA.14.0740.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.81.5911.01 5 0.3303 0.7174 0.00 0.00 0.00 0.00 0.76 0.02 0.02 0.20
#> TCGA.DU.7006.01 5 0.0808 0.8155 0.00 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.HT.7469.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.6390.01 3 0.3986 0.7619 0.00 0.08 0.74 0.00 0.00 0.00 0.04 0.14
#> TCGA.06.A5U0.01 6 0.2407 0.8195 0.00 0.00 0.00 0.06 0.00 0.86 0.08 0.00
#> TCGA.DU.8161.01 2 0.2725 0.4484 0.00 0.82 0.00 0.00 0.00 0.00 0.04 0.14
#> TCGA.19.5959.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YM.01 2 0.2404 0.4700 0.00 0.84 0.00 0.00 0.00 0.00 0.02 0.14
#> TCGA.06.5413.01 4 0.0000 0.7618 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.19.5947.01 2 0.2725 0.4484 0.00 0.82 0.00 0.00 0.00 0.00 0.04 0.14
#> TCGA.E1.A7YD.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.5960.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.14.1034.02 7 0.3404 0.6893 0.00 0.00 0.00 0.24 0.00 0.00 0.72 0.04
#> TCGA.14.0736.02 2 0.0000 0.5452 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.5952.01 4 0.0000 0.7618 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.28.5208.01 1 0.0471 0.9581 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.DH.5140.01 6 0.0808 0.8222 0.00 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.76.6280.01 7 0.2725 0.7252 0.00 0.00 0.00 0.14 0.00 0.00 0.82 0.04
#> TCGA.HT.8015.01 3 0.0000 0.9218 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.2510.01 3 0.2350 0.8658 0.00 0.00 0.86 0.00 0.00 0.00 0.04 0.10
#> TCGA.DU.A7TD.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.14.0736.01 7 0.3992 0.2447 0.00 0.00 0.00 0.04 0.44 0.00 0.52 0.00
#> TCGA.DU.6405.01 4 0.2114 0.7441 0.16 0.00 0.00 0.84 0.00 0.00 0.00 0.00
#> TCGA.06.0152.02 4 0.0000 0.7618 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.0152.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.4927.01 4 0.3333 -0.4222 0.00 0.00 0.00 0.50 0.00 0.00 0.50 0.00
#> TCGA.26.5132.01 1 0.0471 0.9581 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.HT.A74H.01 2 0.0000 0.5452 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7290.01 2 0.5180 0.2853 0.00 0.58 0.00 0.00 0.12 0.02 0.02 0.26
#> TCGA.19.A6J4.01 3 0.3178 0.8240 0.00 0.02 0.80 0.00 0.00 0.00 0.04 0.14
#> TCGA.12.5299.01 4 0.0000 0.7618 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A4DS.01 2 0.5306 0.2890 0.00 0.58 0.00 0.00 0.10 0.04 0.02 0.26
#> TCGA.12.5301.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RR.A6KB.01 5 0.1275 0.8117 0.00 0.02 0.00 0.00 0.94 0.00 0.00 0.04
#> TCGA.TM.A84B.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5416.01 8 0.4906 0.5546 0.00 0.32 0.00 0.00 0.00 0.04 0.08 0.56
#> TCGA.DU.8158.01 5 0.0000 0.8196 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.26.5139.01 4 0.0000 0.7618 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84J.01 1 0.0000 0.9781 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.41.6646.01 5 0.2114 0.7666 0.00 0.00 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.14.0781.01 3 0.3178 0.8240 0.00 0.02 0.80 0.00 0.00 0.00 0.04 0.14
#> TCGA.HT.A617.01 2 0.3494 0.3773 0.00 0.78 0.04 0.00 0.00 0.00 0.04 0.14
#> TCGA.HT.7857.01 8 0.3318 0.6172 0.00 0.46 0.00 0.00 0.00 0.00 0.00 0.54
#> TCGA.74.6578.01 4 0.1091 0.7101 0.00 0.00 0.00 0.94 0.00 0.00 0.06 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 , Node0112 , Node0113 , Node0121 , Node0122 , Node0123-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0141 , Node0142-leaf , Node0143 , Node0211-leaf , Node0212-leaf , Node0213-leaf , Node0214-leaf , Node0221 , Node0222 , Node0223 , Node0231 , Node0232-leaf , Node0233-leaf , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0323-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 86 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 0.999 1.000 0.4731 0.527 0.527
#> 3 3 1.000 0.964 0.985 0.3725 0.746 0.550
#> 4 4 0.711 0.655 0.824 0.1162 0.917 0.770
#> 5 5 0.768 0.607 0.730 0.0854 0.815 0.450
#> 6 6 0.770 0.771 0.854 0.0459 0.911 0.605
#> 7 7 0.859 0.804 0.877 0.0283 0.970 0.824
#> 8 8 0.880 0.745 0.835 0.0205 0.974 0.836
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.26.A7UX.01 2 0.000 0.999 0.00 1.00
#> TCGA.06.6388.01 2 0.141 0.980 0.02 0.98
#> TCGA.76.4932.01 1 0.000 1.000 1.00 0.00
#> TCGA.06.6694.01 2 0.000 0.999 0.00 1.00
#> TCGA.12.5295.01 1 0.000 1.000 1.00 0.00
#> TCGA.28.5220.01 2 0.000 0.999 0.00 1.00
#> TCGA.OX.A56R.01 1 0.000 1.000 1.00 0.00
#> TCGA.06.0125.01 1 0.000 1.000 1.00 0.00
#> TCGA.VW.A8FI.01 1 0.000 1.000 1.00 0.00
#> TCGA.06.5856.01 1 0.000 1.000 1.00 0.00
#> TCGA.76.4926.01 1 0.000 1.000 1.00 0.00
#> TCGA.06.0211.02 1 0.000 1.000 1.00 0.00
#> TCGA.28.5207.01 2 0.141 0.980 0.02 0.98
#> TCGA.14.1402.02 1 0.000 1.000 1.00 0.00
#> TCGA.RR.A6KC.01 1 0.000 1.000 1.00 0.00
#> TCGA.06.5408.01 1 0.000 1.000 1.00 0.00
#> TCGA.76.6285.01 2 0.000 0.999 0.00 1.00
#> TCGA.DU.6403.01 2 0.000 0.999 0.00 1.00
#> TCGA.14.1395.01 1 0.000 1.000 1.00 0.00
#> TCGA.FG.A4MW.01 1 0.000 1.000 1.00 0.00
#> TCGA.06.6695.01 1 0.000 1.000 1.00 0.00
#> TCGA.06.5418.01 1 0.000 1.000 1.00 0.00
#> TCGA.26.5135.01 2 0.000 0.999 0.00 1.00
#> TCGA.28.5219.01 2 0.000 0.999 0.00 1.00
#> TCGA.19.A60I.01 1 0.000 1.000 1.00 0.00
#> TCGA.76.4934.01 2 0.000 0.999 0.00 1.00
#> TCGA.32.5222.01 1 0.000 1.000 1.00 0.00
#> TCGA.76.6191.01 2 0.000 0.999 0.00 1.00
#> TCGA.06.6693.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.6406.01 1 0.000 1.000 1.00 0.00
#> TCGA.28.5215.01 2 0.000 0.999 0.00 1.00
#> TCGA.76.4929.01 2 0.000 0.999 0.00 1.00
#> TCGA.76.6661.01 1 0.000 1.000 1.00 0.00
#> TCGA.28.5209.01 1 0.000 1.000 1.00 0.00
#> TCGA.19.5951.01 1 0.000 1.000 1.00 0.00
#> TCGA.06.A6S0.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.8104.01 1 0.000 1.000 1.00 0.00
#> TCGA.FG.A4MU.01 1 0.000 1.000 1.00 0.00
#> TCGA.74.6581.01 1 0.000 1.000 1.00 0.00
#> TCGA.S9.A6WM.01 1 0.000 1.000 1.00 0.00
#> TCGA.76.4935.01 2 0.000 0.999 0.00 1.00
#> TCGA.E1.A7YJ.01 1 0.000 1.000 1.00 0.00
#> TCGA.06.5414.01 1 0.000 1.000 1.00 0.00
#> TCGA.76.6656.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.A61C.01 2 0.000 0.999 0.00 1.00
#> TCGA.76.4925.01 1 0.000 1.000 1.00 0.00
#> TCGA.4W.AA9R.01 2 0.000 0.999 0.00 1.00
#> TCGA.FG.6692.01 1 0.000 1.000 1.00 0.00
#> TCGA.81.5910.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.7013.01 1 0.000 1.000 1.00 0.00
#> TCGA.KT.A7W1.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.A5RA.01 1 0.000 1.000 1.00 0.00
#> TCGA.26.5134.01 2 0.000 0.999 0.00 1.00
#> TCGA.76.6286.01 2 0.000 0.999 0.00 1.00
#> TCGA.76.6660.01 2 0.000 0.999 0.00 1.00
#> TCGA.28.5204.01 1 0.000 1.000 1.00 0.00
#> TCGA.06.1804.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.A7TJ.01 1 0.000 1.000 1.00 0.00
#> TCGA.76.4931.01 1 0.000 1.000 1.00 0.00
#> TCGA.19.5954.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.8011.01 2 0.000 0.999 0.00 1.00
#> TCGA.DU.5852.01 2 0.000 0.999 0.00 1.00
#> TCGA.87.5896.01 1 0.000 1.000 1.00 0.00
#> TCGA.19.0957.01 2 0.000 0.999 0.00 1.00
#> TCGA.06.5859.01 1 0.000 1.000 1.00 0.00
#> TCGA.06.6699.01 1 0.000 1.000 1.00 0.00
#> TCGA.41.5651.01 2 0.000 0.999 0.00 1.00
#> TCGA.06.0210.02 2 0.000 0.999 0.00 1.00
#> TCGA.19.5956.01 2 0.000 0.999 0.00 1.00
#> TCGA.28.5216.01 2 0.000 0.999 0.00 1.00
#> TCGA.74.6573.01 1 0.000 1.000 1.00 0.00
#> TCGA.14.0740.01 2 0.000 0.999 0.00 1.00
#> TCGA.HT.7469.01 2 0.000 0.999 0.00 1.00
#> TCGA.19.5959.01 1 0.000 1.000 1.00 0.00
#> TCGA.E1.A7YD.01 2 0.000 0.999 0.00 1.00
#> TCGA.19.5960.01 1 0.000 1.000 1.00 0.00
#> TCGA.28.5208.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.A7TD.01 2 0.000 0.999 0.00 1.00
#> TCGA.DU.6405.01 1 0.000 1.000 1.00 0.00
#> TCGA.06.0152.01 1 0.000 1.000 1.00 0.00
#> TCGA.26.5132.01 1 0.000 1.000 1.00 0.00
#> TCGA.12.5299.01 1 0.000 1.000 1.00 0.00
#> TCGA.12.5301.01 2 0.000 0.999 0.00 1.00
#> TCGA.TM.A84B.01 1 0.000 1.000 1.00 0.00
#> TCGA.26.5139.01 1 0.000 1.000 1.00 0.00
#> TCGA.TM.A84J.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.26.A7UX.01 3 0.0000 0.942 0.00 0.00 1.00
#> TCGA.06.6388.01 3 0.0000 0.942 0.00 0.00 1.00
#> TCGA.76.4932.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.06.6694.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.12.5295.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.28.5220.01 3 0.0892 0.927 0.00 0.02 0.98
#> TCGA.OX.A56R.01 3 0.2066 0.894 0.06 0.00 0.94
#> TCGA.06.0125.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.VW.A8FI.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.06.5856.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.76.4926.01 3 0.0000 0.942 0.00 0.00 1.00
#> TCGA.06.0211.02 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.28.5207.01 3 0.0000 0.942 0.00 0.00 1.00
#> TCGA.14.1402.02 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.RR.A6KC.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.06.5408.01 3 0.0000 0.942 0.00 0.00 1.00
#> TCGA.76.6285.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.DU.6403.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.14.1395.01 3 0.0000 0.942 0.00 0.00 1.00
#> TCGA.FG.A4MW.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.06.6695.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.06.5418.01 3 0.0000 0.942 0.00 0.00 1.00
#> TCGA.26.5135.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.28.5219.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.19.A60I.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.76.4934.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.32.5222.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.76.6191.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.06.6693.01 3 0.4002 0.799 0.16 0.00 0.84
#> TCGA.DU.6406.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.28.5215.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.76.4929.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.76.6661.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.28.5209.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.19.5951.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.06.A6S0.01 3 0.0000 0.942 0.00 0.00 1.00
#> TCGA.HT.8104.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.FG.A4MU.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.74.6581.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.S9.A6WM.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.76.4935.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.E1.A7YJ.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.06.5414.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.76.6656.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.HT.A61C.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.76.4925.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.4W.AA9R.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.FG.6692.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.81.5910.01 3 0.0000 0.942 0.00 0.00 1.00
#> TCGA.DU.7013.01 3 0.4002 0.799 0.16 0.00 0.84
#> TCGA.KT.A7W1.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.HT.A5RA.01 3 0.6045 0.420 0.38 0.00 0.62
#> TCGA.26.5134.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.76.6286.01 3 0.0000 0.942 0.00 0.00 1.00
#> TCGA.76.6660.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.28.5204.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.06.1804.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.DU.A7TJ.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.76.4931.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.19.5954.01 3 0.0000 0.942 0.00 0.00 1.00
#> TCGA.HT.8011.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.DU.5852.01 3 0.0000 0.942 0.00 0.00 1.00
#> TCGA.87.5896.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.19.0957.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.06.5859.01 3 0.0000 0.942 0.00 0.00 1.00
#> TCGA.06.6699.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.41.5651.01 3 0.6192 0.270 0.00 0.42 0.58
#> TCGA.06.0210.02 2 0.2066 0.935 0.00 0.94 0.06
#> TCGA.19.5956.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.28.5216.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.74.6573.01 3 0.0000 0.942 0.00 0.00 1.00
#> TCGA.14.0740.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.HT.7469.01 3 0.0000 0.942 0.00 0.00 1.00
#> TCGA.19.5959.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.E1.A7YD.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.19.5960.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.28.5208.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.DU.A7TD.01 3 0.0000 0.942 0.00 0.00 1.00
#> TCGA.DU.6405.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.06.0152.01 3 0.0000 0.942 0.00 0.00 1.00
#> TCGA.26.5132.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.12.5299.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.12.5301.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.TM.A84B.01 3 0.0000 0.942 0.00 0.00 1.00
#> TCGA.26.5139.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.TM.A84J.01 2 0.0000 0.997 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.26.A7UX.01 3 0.0000 0.558 0.00 0.00 1.00 0.00
#> TCGA.06.6388.01 3 0.1211 0.504 0.00 0.00 0.96 0.04
#> TCGA.76.4932.01 1 0.2345 0.803 0.90 0.00 0.00 0.10
#> TCGA.06.6694.01 2 0.2345 0.832 0.00 0.90 0.00 0.10
#> TCGA.12.5295.01 1 0.1211 0.820 0.96 0.00 0.00 0.04
#> TCGA.28.5220.01 4 0.5606 0.437 0.00 0.02 0.48 0.50
#> TCGA.OX.A56R.01 3 0.4948 0.624 0.00 0.00 0.56 0.44
#> TCGA.06.0125.01 1 0.4277 0.733 0.72 0.00 0.00 0.28
#> TCGA.VW.A8FI.01 1 0.4855 0.631 0.60 0.00 0.00 0.40
#> TCGA.06.5856.01 1 0.4522 0.715 0.68 0.00 0.00 0.32
#> TCGA.76.4926.01 3 0.4406 0.721 0.00 0.00 0.70 0.30
#> TCGA.06.0211.02 1 0.0000 0.828 1.00 0.00 0.00 0.00
#> TCGA.28.5207.01 3 0.0707 0.576 0.00 0.00 0.98 0.02
#> TCGA.14.1402.02 1 0.0000 0.828 1.00 0.00 0.00 0.00
#> TCGA.RR.A6KC.01 1 0.0000 0.828 1.00 0.00 0.00 0.00
#> TCGA.06.5408.01 3 0.3801 0.709 0.00 0.00 0.78 0.22
#> TCGA.76.6285.01 2 0.0000 0.907 0.00 1.00 0.00 0.00
#> TCGA.DU.6403.01 4 0.7474 0.429 0.00 0.22 0.28 0.50
#> TCGA.14.1395.01 3 0.4406 0.721 0.00 0.00 0.70 0.30
#> TCGA.FG.A4MW.01 1 0.4522 0.715 0.68 0.00 0.00 0.32
#> TCGA.06.6695.01 1 0.0000 0.828 1.00 0.00 0.00 0.00
#> TCGA.06.5418.01 3 0.4977 0.604 0.00 0.00 0.54 0.46
#> TCGA.26.5135.01 2 0.0000 0.907 0.00 1.00 0.00 0.00
#> TCGA.28.5219.01 2 0.0000 0.907 0.00 1.00 0.00 0.00
#> TCGA.19.A60I.01 1 0.0000 0.828 1.00 0.00 0.00 0.00
#> TCGA.76.4934.01 2 0.0000 0.907 0.00 1.00 0.00 0.00
#> TCGA.32.5222.01 1 0.4522 0.715 0.68 0.00 0.00 0.32
#> TCGA.76.6191.01 2 0.4907 0.386 0.00 0.58 0.00 0.42
#> TCGA.06.6693.01 4 0.7427 -0.319 0.20 0.00 0.30 0.50
#> TCGA.DU.6406.01 1 0.0000 0.828 1.00 0.00 0.00 0.00
#> TCGA.28.5215.01 2 0.0000 0.907 0.00 1.00 0.00 0.00
#> TCGA.76.4929.01 2 0.4977 0.300 0.00 0.54 0.00 0.46
#> TCGA.76.6661.01 1 0.0000 0.828 1.00 0.00 0.00 0.00
#> TCGA.28.5209.01 1 0.0000 0.828 1.00 0.00 0.00 0.00
#> TCGA.19.5951.01 1 0.5000 0.518 0.50 0.00 0.00 0.50
#> TCGA.06.A6S0.01 4 0.4977 0.330 0.00 0.00 0.46 0.54
#> TCGA.HT.8104.01 1 0.0000 0.828 1.00 0.00 0.00 0.00
#> TCGA.FG.A4MU.01 1 0.4948 0.584 0.56 0.00 0.00 0.44
#> TCGA.74.6581.01 4 0.7344 -0.323 0.38 0.00 0.16 0.46
#> TCGA.S9.A6WM.01 4 0.7544 -0.359 0.20 0.00 0.34 0.46
#> TCGA.76.4935.01 2 0.0000 0.907 0.00 1.00 0.00 0.00
#> TCGA.E1.A7YJ.01 1 0.0000 0.828 1.00 0.00 0.00 0.00
#> TCGA.06.5414.01 1 0.0000 0.828 1.00 0.00 0.00 0.00
#> TCGA.76.6656.01 1 0.0000 0.828 1.00 0.00 0.00 0.00
#> TCGA.HT.A61C.01 2 0.0000 0.907 0.00 1.00 0.00 0.00
#> TCGA.76.4925.01 1 0.0000 0.828 1.00 0.00 0.00 0.00
#> TCGA.4W.AA9R.01 4 0.6323 -0.128 0.00 0.44 0.06 0.50
#> TCGA.FG.6692.01 1 0.4522 0.715 0.68 0.00 0.00 0.32
#> TCGA.81.5910.01 3 0.3801 0.709 0.00 0.00 0.78 0.22
#> TCGA.DU.7013.01 3 0.4994 0.590 0.00 0.00 0.52 0.48
#> TCGA.KT.A7W1.01 1 0.0707 0.824 0.98 0.00 0.00 0.02
#> TCGA.HT.A5RA.01 3 0.6011 0.534 0.04 0.00 0.48 0.48
#> TCGA.26.5134.01 2 0.0000 0.907 0.00 1.00 0.00 0.00
#> TCGA.76.6286.01 4 0.4977 0.437 0.00 0.00 0.46 0.54
#> TCGA.76.6660.01 4 0.7427 0.458 0.00 0.20 0.30 0.50
#> TCGA.28.5204.01 1 0.0000 0.828 1.00 0.00 0.00 0.00
#> TCGA.06.1804.01 1 0.4907 0.623 0.58 0.00 0.00 0.42
#> TCGA.DU.A7TJ.01 1 0.6005 0.494 0.50 0.00 0.04 0.46
#> TCGA.76.4931.01 1 0.6005 0.494 0.50 0.00 0.04 0.46
#> TCGA.19.5954.01 3 0.4406 0.721 0.00 0.00 0.70 0.30
#> TCGA.HT.8011.01 2 0.0000 0.907 0.00 1.00 0.00 0.00
#> TCGA.DU.5852.01 4 0.5000 0.412 0.00 0.00 0.50 0.50
#> TCGA.87.5896.01 1 0.0000 0.828 1.00 0.00 0.00 0.00
#> TCGA.19.0957.01 2 0.4948 0.345 0.00 0.56 0.00 0.44
#> TCGA.06.5859.01 3 0.0000 0.558 0.00 0.00 1.00 0.00
#> TCGA.06.6699.01 1 0.3975 0.752 0.76 0.00 0.00 0.24
#> TCGA.41.5651.01 4 0.6881 0.511 0.00 0.12 0.34 0.54
#> TCGA.06.0210.02 4 0.7261 0.502 0.00 0.16 0.34 0.50
#> TCGA.19.5956.01 2 0.0000 0.907 0.00 1.00 0.00 0.00
#> TCGA.28.5216.01 2 0.0000 0.907 0.00 1.00 0.00 0.00
#> TCGA.74.6573.01 3 0.4624 0.698 0.00 0.00 0.66 0.34
#> TCGA.14.0740.01 2 0.0000 0.907 0.00 1.00 0.00 0.00
#> TCGA.HT.7469.01 3 0.0000 0.558 0.00 0.00 1.00 0.00
#> TCGA.19.5959.01 1 0.4406 0.726 0.70 0.00 0.00 0.30
#> TCGA.E1.A7YD.01 2 0.0000 0.907 0.00 1.00 0.00 0.00
#> TCGA.19.5960.01 1 0.4907 0.608 0.58 0.00 0.00 0.42
#> TCGA.28.5208.01 1 0.0000 0.828 1.00 0.00 0.00 0.00
#> TCGA.DU.A7TD.01 3 0.4624 -0.219 0.00 0.00 0.66 0.34
#> TCGA.DU.6405.01 1 0.0000 0.828 1.00 0.00 0.00 0.00
#> TCGA.06.0152.01 3 0.4406 0.721 0.00 0.00 0.70 0.30
#> TCGA.26.5132.01 1 0.0000 0.828 1.00 0.00 0.00 0.00
#> TCGA.12.5299.01 1 0.0000 0.828 1.00 0.00 0.00 0.00
#> TCGA.12.5301.01 2 0.1637 0.866 0.00 0.94 0.00 0.06
#> TCGA.TM.A84B.01 3 0.3801 0.701 0.00 0.00 0.78 0.22
#> TCGA.26.5139.01 1 0.4134 0.744 0.74 0.00 0.00 0.26
#> TCGA.TM.A84J.01 2 0.0000 0.907 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.26.A7UX.01 4 0.4287 0.2627 0.00 0.00 0.46 0.54 0.00
#> TCGA.06.6388.01 4 0.4227 0.2996 0.00 0.00 0.42 0.58 0.00
#> TCGA.76.4932.01 1 0.3971 0.6461 0.80 0.00 0.10 0.00 0.10
#> TCGA.06.6694.01 2 0.4263 0.6989 0.00 0.76 0.00 0.18 0.06
#> TCGA.12.5295.01 1 0.4060 0.1503 0.64 0.00 0.00 0.00 0.36
#> TCGA.28.5220.01 4 0.0000 0.5850 0.00 0.00 0.00 1.00 0.00
#> TCGA.OX.A56R.01 3 0.1410 0.5824 0.00 0.00 0.94 0.00 0.06
#> TCGA.06.0125.01 5 0.4990 0.6742 0.36 0.00 0.04 0.00 0.60
#> TCGA.VW.A8FI.01 5 0.5895 0.0203 0.10 0.00 0.44 0.00 0.46
#> TCGA.06.5856.01 5 0.4613 0.6819 0.36 0.00 0.02 0.00 0.62
#> TCGA.76.4926.01 3 0.0000 0.5827 0.00 0.00 1.00 0.00 0.00
#> TCGA.06.0211.02 1 0.0000 0.9197 1.00 0.00 0.00 0.00 0.00
#> TCGA.28.5207.01 3 0.4302 -0.2270 0.00 0.00 0.52 0.48 0.00
#> TCGA.14.1402.02 1 0.0000 0.9197 1.00 0.00 0.00 0.00 0.00
#> TCGA.RR.A6KC.01 1 0.0000 0.9197 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.5408.01 3 0.3424 0.2911 0.00 0.00 0.76 0.24 0.00
#> TCGA.76.6285.01 2 0.0000 0.9543 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.6403.01 4 0.4854 0.5656 0.00 0.06 0.00 0.68 0.26
#> TCGA.14.1395.01 3 0.0609 0.5673 0.00 0.00 0.98 0.02 0.00
#> TCGA.FG.A4MW.01 5 0.4613 0.6819 0.36 0.00 0.02 0.00 0.62
#> TCGA.06.6695.01 1 0.0000 0.9197 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.5418.01 3 0.3684 0.4540 0.00 0.00 0.72 0.00 0.28
#> TCGA.26.5135.01 2 0.0609 0.9490 0.00 0.98 0.00 0.00 0.02
#> TCGA.28.5219.01 2 0.0609 0.9490 0.00 0.98 0.00 0.00 0.02
#> TCGA.19.A60I.01 1 0.0000 0.9197 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.4934.01 2 0.0000 0.9543 0.00 1.00 0.00 0.00 0.00
#> TCGA.32.5222.01 5 0.4613 0.6819 0.36 0.00 0.02 0.00 0.62
#> TCGA.76.6191.01 4 0.6732 0.1998 0.00 0.34 0.00 0.40 0.26
#> TCGA.06.6693.01 5 0.4252 0.3334 0.02 0.00 0.28 0.00 0.70
#> TCGA.DU.6406.01 1 0.0000 0.9197 1.00 0.00 0.00 0.00 0.00
#> TCGA.28.5215.01 2 0.0000 0.9543 0.00 1.00 0.00 0.00 0.00
#> TCGA.76.4929.01 4 0.6705 0.2424 0.00 0.32 0.00 0.42 0.26
#> TCGA.76.6661.01 1 0.0000 0.9197 1.00 0.00 0.00 0.00 0.00
#> TCGA.28.5209.01 1 0.0000 0.9197 1.00 0.00 0.00 0.00 0.00
#> TCGA.19.5951.01 5 0.5136 0.4230 0.08 0.00 0.26 0.00 0.66
#> TCGA.06.A6S0.01 5 0.5068 0.2428 0.00 0.00 0.06 0.30 0.64
#> TCGA.HT.8104.01 1 0.0000 0.9197 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A4MU.01 3 0.5646 0.1470 0.08 0.00 0.52 0.00 0.40
#> TCGA.74.6581.01 3 0.5131 0.2176 0.04 0.00 0.54 0.00 0.42
#> TCGA.S9.A6WM.01 3 0.5048 0.2829 0.04 0.00 0.58 0.00 0.38
#> TCGA.76.4935.01 2 0.0609 0.9490 0.00 0.98 0.00 0.00 0.02
#> TCGA.E1.A7YJ.01 1 0.0000 0.9197 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.5414.01 1 0.0000 0.9197 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.6656.01 1 0.0000 0.9197 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A61C.01 2 0.0000 0.9543 0.00 1.00 0.00 0.00 0.00
#> TCGA.76.4925.01 1 0.0000 0.9197 1.00 0.00 0.00 0.00 0.00
#> TCGA.4W.AA9R.01 4 0.6438 0.4028 0.00 0.22 0.00 0.50 0.28
#> TCGA.FG.6692.01 5 0.4990 0.6829 0.36 0.00 0.04 0.00 0.60
#> TCGA.81.5910.01 3 0.3796 0.1889 0.00 0.00 0.70 0.30 0.00
#> TCGA.DU.7013.01 3 0.4182 0.3293 0.00 0.00 0.60 0.00 0.40
#> TCGA.KT.A7W1.01 1 0.1410 0.8542 0.94 0.00 0.00 0.00 0.06
#> TCGA.HT.A5RA.01 3 0.4767 0.2623 0.02 0.00 0.56 0.00 0.42
#> TCGA.26.5134.01 2 0.0000 0.9543 0.00 1.00 0.00 0.00 0.00
#> TCGA.76.6286.01 4 0.0609 0.5855 0.00 0.00 0.00 0.98 0.02
#> TCGA.76.6660.01 4 0.4456 0.5680 0.00 0.02 0.00 0.66 0.32
#> TCGA.28.5204.01 1 0.0000 0.9197 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.1804.01 5 0.5273 0.5732 0.16 0.00 0.16 0.00 0.68
#> TCGA.DU.A7TJ.01 3 0.5131 0.2176 0.04 0.00 0.54 0.00 0.42
#> TCGA.76.4931.01 3 0.5131 0.2176 0.04 0.00 0.54 0.00 0.42
#> TCGA.19.5954.01 3 0.0000 0.5827 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.8011.01 2 0.1648 0.9172 0.00 0.94 0.00 0.04 0.02
#> TCGA.DU.5852.01 4 0.1043 0.5723 0.00 0.00 0.04 0.96 0.00
#> TCGA.87.5896.01 1 0.0000 0.9197 1.00 0.00 0.00 0.00 0.00
#> TCGA.19.0957.01 4 0.6732 0.1998 0.00 0.34 0.00 0.40 0.26
#> TCGA.06.5859.01 4 0.4287 0.2627 0.00 0.00 0.46 0.54 0.00
#> TCGA.06.6699.01 5 0.4726 0.6290 0.40 0.00 0.02 0.00 0.58
#> TCGA.41.5651.01 4 0.3983 0.5616 0.00 0.00 0.00 0.66 0.34
#> TCGA.06.0210.02 4 0.1410 0.5917 0.00 0.00 0.00 0.94 0.06
#> TCGA.19.5956.01 2 0.0000 0.9543 0.00 1.00 0.00 0.00 0.00
#> TCGA.28.5216.01 2 0.0000 0.9543 0.00 1.00 0.00 0.00 0.00
#> TCGA.74.6573.01 3 0.1043 0.5872 0.00 0.00 0.96 0.00 0.04
#> TCGA.14.0740.01 2 0.0000 0.9543 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7469.01 4 0.4287 0.2627 0.00 0.00 0.46 0.54 0.00
#> TCGA.19.5959.01 5 0.4613 0.6819 0.36 0.00 0.02 0.00 0.62
#> TCGA.E1.A7YD.01 2 0.0609 0.9490 0.00 0.98 0.00 0.00 0.02
#> TCGA.19.5960.01 5 0.5895 0.0203 0.10 0.00 0.44 0.00 0.46
#> TCGA.28.5208.01 1 0.0000 0.9197 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A7TD.01 4 0.4060 0.3542 0.00 0.00 0.36 0.64 0.00
#> TCGA.DU.6405.01 1 0.0000 0.9197 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.0152.01 3 0.0000 0.5827 0.00 0.00 1.00 0.00 0.00
#> TCGA.26.5132.01 1 0.0000 0.9197 1.00 0.00 0.00 0.00 0.00
#> TCGA.12.5299.01 1 0.1732 0.8294 0.92 0.00 0.00 0.00 0.08
#> TCGA.12.5301.01 2 0.4637 0.6754 0.00 0.74 0.00 0.16 0.10
#> TCGA.TM.A84B.01 3 0.6054 0.2011 0.00 0.00 0.56 0.28 0.16
#> TCGA.26.5139.01 1 0.6459 -0.4550 0.42 0.00 0.18 0.00 0.40
#> TCGA.TM.A84J.01 2 0.0000 0.9543 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.26.A7UX.01 6 0.2474 0.677 0.00 0.00 0.00 0.04 0.08 0.88
#> TCGA.06.6388.01 6 0.3475 0.637 0.00 0.00 0.00 0.06 0.14 0.80
#> TCGA.76.4932.01 3 0.3309 0.515 0.28 0.00 0.72 0.00 0.00 0.00
#> TCGA.06.6694.01 2 0.4067 0.680 0.00 0.70 0.00 0.26 0.04 0.00
#> TCGA.12.5295.01 5 0.4873 0.694 0.32 0.00 0.08 0.00 0.60 0.00
#> TCGA.28.5220.01 4 0.5618 0.323 0.00 0.00 0.00 0.50 0.16 0.34
#> TCGA.OX.A56R.01 3 0.3460 0.613 0.00 0.00 0.76 0.00 0.02 0.22
#> TCGA.06.0125.01 5 0.5102 0.821 0.14 0.00 0.24 0.00 0.62 0.00
#> TCGA.VW.A8FI.01 3 0.1480 0.820 0.02 0.00 0.94 0.00 0.04 0.00
#> TCGA.06.5856.01 5 0.4890 0.857 0.18 0.00 0.16 0.00 0.66 0.00
#> TCGA.76.4926.01 6 0.3647 0.421 0.00 0.00 0.36 0.00 0.00 0.64
#> TCGA.06.0211.02 1 0.0000 0.965 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5207.01 6 0.0000 0.693 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.14.1402.02 1 0.0000 0.965 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RR.A6KC.01 1 0.0000 0.965 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5408.01 6 0.1556 0.683 0.00 0.00 0.08 0.00 0.00 0.92
#> TCGA.76.6285.01 2 0.0000 0.920 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6403.01 4 0.2474 0.758 0.00 0.04 0.00 0.88 0.08 0.00
#> TCGA.14.1395.01 6 0.3578 0.455 0.00 0.00 0.34 0.00 0.00 0.66
#> TCGA.FG.A4MW.01 5 0.4890 0.857 0.18 0.00 0.16 0.00 0.66 0.00
#> TCGA.06.6695.01 1 0.0000 0.965 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5418.01 3 0.2793 0.669 0.00 0.00 0.80 0.00 0.00 0.20
#> TCGA.26.5135.01 2 0.2094 0.894 0.00 0.90 0.00 0.08 0.02 0.00
#> TCGA.28.5219.01 2 0.2094 0.894 0.00 0.90 0.00 0.08 0.02 0.00
#> TCGA.19.A60I.01 1 0.0000 0.965 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.4934.01 2 0.0000 0.920 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.32.5222.01 5 0.4890 0.857 0.18 0.00 0.16 0.00 0.66 0.00
#> TCGA.76.6191.01 4 0.1556 0.748 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.06.6693.01 5 0.3578 0.687 0.00 0.00 0.34 0.00 0.66 0.00
#> TCGA.DU.6406.01 1 0.0000 0.965 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5215.01 2 0.0000 0.920 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.4929.01 4 0.1556 0.748 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.76.6661.01 1 0.0000 0.965 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5209.01 1 0.0000 0.965 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.5951.01 5 0.4144 0.682 0.02 0.00 0.36 0.00 0.62 0.00
#> TCGA.06.A6S0.01 5 0.2784 0.576 0.00 0.00 0.04 0.04 0.88 0.04
#> TCGA.HT.8104.01 1 0.0000 0.965 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A4MU.01 3 0.1092 0.834 0.02 0.00 0.96 0.00 0.02 0.00
#> TCGA.74.6581.01 3 0.0547 0.845 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.S9.A6WM.01 3 0.1480 0.812 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.76.4935.01 2 0.2094 0.894 0.00 0.90 0.00 0.08 0.02 0.00
#> TCGA.E1.A7YJ.01 1 0.0000 0.965 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5414.01 1 0.0000 0.965 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6656.01 1 0.0000 0.965 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A61C.01 2 0.0000 0.920 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.4925.01 1 0.0000 0.965 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4W.AA9R.01 4 0.2956 0.753 0.00 0.04 0.00 0.84 0.12 0.00
#> TCGA.FG.6692.01 5 0.5039 0.853 0.18 0.00 0.18 0.00 0.64 0.00
#> TCGA.81.5910.01 6 0.0547 0.691 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.DU.7013.01 3 0.0547 0.845 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.KT.A7W1.01 1 0.3499 0.529 0.68 0.00 0.32 0.00 0.00 0.00
#> TCGA.HT.A5RA.01 3 0.0547 0.845 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.26.5134.01 2 0.0000 0.920 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.6286.01 4 0.5791 0.193 0.00 0.00 0.00 0.44 0.18 0.38
#> TCGA.76.6660.01 4 0.2956 0.753 0.00 0.04 0.00 0.84 0.12 0.00
#> TCGA.28.5204.01 1 0.0000 0.965 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.1804.01 5 0.4002 0.716 0.02 0.00 0.32 0.00 0.66 0.00
#> TCGA.DU.A7TJ.01 3 0.0547 0.845 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.76.4931.01 3 0.0547 0.845 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.19.5954.01 6 0.3756 0.329 0.00 0.00 0.40 0.00 0.00 0.60
#> TCGA.HT.8011.01 2 0.3270 0.839 0.00 0.82 0.00 0.12 0.06 0.00
#> TCGA.DU.5852.01 6 0.5354 0.261 0.00 0.00 0.00 0.26 0.16 0.58
#> TCGA.87.5896.01 1 0.0000 0.965 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.0957.01 4 0.1556 0.748 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.06.5859.01 6 0.3351 0.650 0.00 0.00 0.00 0.04 0.16 0.80
#> TCGA.06.6699.01 5 0.5039 0.853 0.18 0.00 0.18 0.00 0.64 0.00
#> TCGA.41.5651.01 4 0.2631 0.726 0.00 0.00 0.00 0.82 0.18 0.00
#> TCGA.06.0210.02 4 0.5259 0.444 0.00 0.00 0.00 0.60 0.16 0.24
#> TCGA.19.5956.01 2 0.0000 0.920 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.28.5216.01 2 0.0000 0.920 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.74.6573.01 3 0.3647 0.359 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.14.0740.01 2 0.0000 0.920 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7469.01 6 0.2474 0.677 0.00 0.00 0.00 0.04 0.08 0.88
#> TCGA.19.5959.01 5 0.4890 0.857 0.18 0.00 0.16 0.00 0.66 0.00
#> TCGA.E1.A7YD.01 2 0.2094 0.894 0.00 0.90 0.00 0.08 0.02 0.00
#> TCGA.19.5960.01 3 0.1480 0.820 0.02 0.00 0.94 0.00 0.04 0.00
#> TCGA.28.5208.01 1 0.0000 0.965 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A7TD.01 6 0.3985 0.599 0.00 0.00 0.00 0.10 0.14 0.76
#> TCGA.DU.6405.01 1 0.0000 0.965 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.0152.01 6 0.4078 0.448 0.00 0.00 0.34 0.00 0.02 0.64
#> TCGA.26.5132.01 1 0.0000 0.965 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.12.5299.01 1 0.2941 0.696 0.78 0.00 0.22 0.00 0.00 0.00
#> TCGA.12.5301.01 2 0.4078 0.576 0.00 0.64 0.00 0.34 0.02 0.00
#> TCGA.TM.A84B.01 6 0.4566 0.628 0.00 0.00 0.14 0.00 0.16 0.70
#> TCGA.26.5139.01 3 0.2350 0.748 0.10 0.00 0.88 0.00 0.02 0.00
#> TCGA.TM.A84J.01 2 0.0000 0.920 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.26.A7UX.01 6 0.3139 0.4686 0.00 0.00 0.00 0.00 0.00 0.70 0.30
#> TCGA.06.6388.01 6 0.0000 0.7531 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.76.4932.01 3 0.2708 0.5898 0.22 0.00 0.78 0.00 0.00 0.00 0.00
#> TCGA.06.6694.01 2 0.4507 0.8064 0.00 0.76 0.00 0.08 0.06 0.06 0.04
#> TCGA.12.5295.01 5 0.2163 0.8967 0.10 0.00 0.02 0.00 0.88 0.00 0.00
#> TCGA.28.5220.01 6 0.1433 0.7450 0.00 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.OX.A56R.01 3 0.3909 -0.0579 0.00 0.00 0.58 0.02 0.00 0.00 0.40
#> TCGA.06.0125.01 5 0.2278 0.9541 0.04 0.00 0.08 0.00 0.88 0.00 0.00
#> TCGA.VW.A8FI.01 3 0.2769 0.8012 0.02 0.00 0.86 0.00 0.04 0.00 0.08
#> TCGA.06.5856.01 5 0.2016 0.9578 0.04 0.00 0.06 0.00 0.90 0.00 0.00
#> TCGA.76.4926.01 7 0.4191 0.7048 0.00 0.00 0.30 0.00 0.00 0.06 0.64
#> TCGA.06.0211.02 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5207.01 7 0.3558 0.1402 0.00 0.00 0.00 0.00 0.00 0.48 0.52
#> TCGA.14.1402.02 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RR.A6KC.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5408.01 7 0.4418 0.5793 0.00 0.00 0.08 0.00 0.00 0.30 0.62
#> TCGA.76.6285.01 2 0.0000 0.9214 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6403.01 4 0.0504 0.9407 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.14.1395.01 7 0.4338 0.7173 0.00 0.00 0.28 0.00 0.00 0.08 0.64
#> TCGA.FG.A4MW.01 5 0.2016 0.9578 0.04 0.00 0.06 0.00 0.90 0.00 0.00
#> TCGA.06.6695.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5418.01 3 0.3459 0.0638 0.00 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.26.5135.01 2 0.2509 0.8908 0.00 0.88 0.00 0.02 0.06 0.00 0.04
#> TCGA.28.5219.01 2 0.2509 0.8908 0.00 0.88 0.00 0.02 0.06 0.00 0.04
#> TCGA.19.A60I.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.4934.01 2 0.0000 0.9214 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.32.5222.01 5 0.2016 0.9578 0.04 0.00 0.06 0.00 0.90 0.00 0.00
#> TCGA.76.6191.01 4 0.1860 0.9328 0.00 0.02 0.00 0.92 0.04 0.00 0.02
#> TCGA.06.6693.01 5 0.1928 0.9293 0.00 0.00 0.08 0.00 0.90 0.00 0.02
#> TCGA.DU.6406.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5215.01 2 0.0000 0.9214 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.4929.01 4 0.1860 0.9328 0.00 0.02 0.00 0.92 0.04 0.00 0.02
#> TCGA.76.6661.01 1 0.1886 0.8378 0.88 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.28.5209.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.5951.01 5 0.1886 0.9218 0.00 0.00 0.12 0.00 0.88 0.00 0.00
#> TCGA.06.A6S0.01 5 0.1886 0.8302 0.00 0.00 0.00 0.00 0.88 0.12 0.00
#> TCGA.HT.8104.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A4MU.01 3 0.0504 0.8288 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.74.6581.01 3 0.1664 0.8249 0.00 0.00 0.92 0.00 0.02 0.00 0.06
#> TCGA.S9.A6WM.01 3 0.0000 0.8208 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.4935.01 2 0.2159 0.8969 0.00 0.90 0.00 0.02 0.06 0.00 0.02
#> TCGA.E1.A7YJ.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5414.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6656.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A61C.01 2 0.0000 0.9214 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.4925.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4W.AA9R.01 4 0.1363 0.9346 0.00 0.02 0.00 0.94 0.00 0.00 0.04
#> TCGA.FG.6692.01 5 0.2278 0.9541 0.04 0.00 0.08 0.00 0.88 0.00 0.00
#> TCGA.81.5910.01 7 0.3755 0.4926 0.00 0.00 0.02 0.00 0.00 0.34 0.64
#> TCGA.DU.7013.01 3 0.1928 0.8186 0.00 0.00 0.90 0.00 0.02 0.00 0.08
#> TCGA.KT.A7W1.01 1 0.3558 0.1283 0.52 0.00 0.48 0.00 0.00 0.00 0.00
#> TCGA.HT.A5RA.01 3 0.1664 0.8183 0.00 0.00 0.92 0.00 0.02 0.00 0.06
#> TCGA.26.5134.01 2 0.0000 0.9214 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6286.01 6 0.3848 0.7026 0.00 0.00 0.00 0.06 0.02 0.76 0.16
#> TCGA.76.6660.01 4 0.1363 0.9346 0.00 0.02 0.00 0.94 0.00 0.00 0.04
#> TCGA.28.5204.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.1804.01 5 0.2159 0.9484 0.02 0.00 0.06 0.00 0.90 0.00 0.02
#> TCGA.DU.A7TJ.01 3 0.0504 0.8288 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.76.4931.01 3 0.0504 0.8288 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.19.5954.01 7 0.4003 0.6890 0.00 0.00 0.32 0.00 0.00 0.04 0.64
#> TCGA.HT.8011.01 2 0.4767 0.7528 0.00 0.72 0.00 0.02 0.06 0.14 0.06
#> TCGA.DU.5852.01 6 0.0504 0.7563 0.00 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.87.5896.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.0957.01 4 0.1860 0.9328 0.00 0.02 0.00 0.92 0.04 0.00 0.02
#> TCGA.06.5859.01 6 0.3307 0.6762 0.00 0.00 0.00 0.00 0.02 0.74 0.24
#> TCGA.06.6699.01 5 0.2278 0.9541 0.04 0.00 0.08 0.00 0.88 0.00 0.00
#> TCGA.41.5651.01 4 0.1718 0.9064 0.00 0.00 0.00 0.92 0.04 0.00 0.04
#> TCGA.06.0210.02 6 0.4295 0.6493 0.00 0.00 0.00 0.14 0.06 0.74 0.06
#> TCGA.19.5956.01 2 0.0000 0.9214 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5216.01 2 0.0000 0.9214 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.74.6573.01 7 0.3815 0.6275 0.00 0.00 0.36 0.00 0.00 0.02 0.62
#> TCGA.14.0740.01 2 0.0000 0.9214 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7469.01 6 0.3047 0.5071 0.00 0.00 0.00 0.00 0.00 0.72 0.28
#> TCGA.19.5959.01 5 0.2016 0.9578 0.04 0.00 0.06 0.00 0.90 0.00 0.00
#> TCGA.E1.A7YD.01 2 0.2509 0.8908 0.00 0.88 0.00 0.02 0.06 0.00 0.04
#> TCGA.19.5960.01 3 0.2769 0.8012 0.02 0.00 0.86 0.00 0.04 0.00 0.08
#> TCGA.28.5208.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A7TD.01 6 0.0504 0.7500 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.DU.6405.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.0152.01 7 0.2745 0.6368 0.00 0.00 0.16 0.00 0.02 0.00 0.82
#> TCGA.26.5132.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.12.5299.01 1 0.3221 0.5415 0.68 0.00 0.32 0.00 0.00 0.00 0.00
#> TCGA.12.5301.01 2 0.4589 0.6809 0.00 0.68 0.00 0.22 0.06 0.00 0.04
#> TCGA.TM.A84B.01 6 0.4710 0.3079 0.00 0.00 0.02 0.00 0.04 0.48 0.46
#> TCGA.26.5139.01 3 0.1363 0.8136 0.04 0.00 0.94 0.00 0.02 0.00 0.00
#> TCGA.TM.A84J.01 2 0.0000 0.9214 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.26.A7UX.01 6 0.4940 0.4071 0.00 0.00 0.02 0.00 0.10 0.48 0.40 0.00
#> TCGA.06.6388.01 6 0.1947 0.6943 0.00 0.00 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.76.4932.01 3 0.2569 0.6571 0.16 0.00 0.82 0.00 0.02 0.00 0.00 0.00
#> TCGA.06.6694.01 2 0.3450 0.4149 0.00 0.76 0.00 0.12 0.00 0.12 0.00 0.00
#> TCGA.12.5295.01 8 0.0808 0.9287 0.04 0.00 0.00 0.00 0.00 0.00 0.00 0.96
#> TCGA.28.5220.01 6 0.2407 0.6867 0.00 0.00 0.00 0.08 0.00 0.86 0.06 0.00
#> TCGA.OX.A56R.01 7 0.4607 0.2887 0.00 0.00 0.42 0.00 0.06 0.02 0.50 0.00
#> TCGA.06.0125.01 8 0.0808 0.9458 0.00 0.00 0.04 0.00 0.00 0.00 0.00 0.96
#> TCGA.VW.A8FI.01 3 0.2856 0.6977 0.00 0.00 0.78 0.00 0.20 0.00 0.00 0.02
#> TCGA.06.5856.01 8 0.0000 0.9616 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.76.4926.01 7 0.1563 0.7619 0.00 0.00 0.10 0.00 0.00 0.00 0.90 0.00
#> TCGA.06.0211.02 1 0.0000 0.9765 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5207.01 7 0.2534 0.4612 0.00 0.00 0.00 0.00 0.00 0.22 0.78 0.00
#> TCGA.14.1402.02 1 0.0000 0.9765 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RR.A6KC.01 1 0.0000 0.9765 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5408.01 7 0.0941 0.7120 0.00 0.00 0.02 0.00 0.00 0.02 0.96 0.00
#> TCGA.76.6285.01 2 0.3083 0.7812 0.00 0.66 0.00 0.34 0.00 0.00 0.00 0.00
#> TCGA.DU.6403.01 4 0.4106 0.7959 0.00 0.04 0.00 0.64 0.30 0.02 0.00 0.00
#> TCGA.14.1395.01 7 0.1563 0.7619 0.00 0.00 0.10 0.00 0.00 0.00 0.90 0.00
#> TCGA.FG.A4MW.01 8 0.0000 0.9616 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.06.6695.01 1 0.0000 0.9765 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5418.01 7 0.4040 0.4471 0.00 0.00 0.38 0.02 0.02 0.00 0.58 0.00
#> TCGA.26.5135.01 2 0.0000 0.6678 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5219.01 2 0.0471 0.6553 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.19.A60I.01 1 0.0000 0.9765 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.4934.01 2 0.3083 0.7812 0.00 0.66 0.00 0.34 0.00 0.00 0.00 0.00
#> TCGA.32.5222.01 8 0.0000 0.9616 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.76.6191.01 4 0.4504 0.7707 0.00 0.24 0.00 0.64 0.10 0.02 0.00 0.00
#> TCGA.06.6693.01 8 0.0000 0.9616 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.6406.01 1 0.0000 0.9765 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5215.01 2 0.3083 0.7812 0.00 0.66 0.00 0.34 0.00 0.00 0.00 0.00
#> TCGA.76.4929.01 4 0.4504 0.7707 0.00 0.24 0.00 0.64 0.10 0.02 0.00 0.00
#> TCGA.76.6661.01 1 0.3015 0.4899 0.68 0.00 0.32 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5209.01 1 0.0000 0.9765 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.5951.01 8 0.0808 0.9458 0.00 0.00 0.04 0.00 0.00 0.00 0.00 0.96
#> TCGA.06.A6S0.01 8 0.2650 0.6955 0.00 0.00 0.00 0.00 0.00 0.24 0.00 0.76
#> TCGA.HT.8104.01 1 0.0000 0.9765 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A4MU.01 3 0.1275 0.7307 0.00 0.00 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.74.6581.01 3 0.3169 0.7020 0.00 0.00 0.78 0.02 0.18 0.00 0.00 0.02
#> TCGA.S9.A6WM.01 3 0.2020 0.7157 0.00 0.00 0.90 0.02 0.02 0.00 0.06 0.00
#> TCGA.76.4935.01 2 0.0471 0.6553 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YJ.01 1 0.0000 0.9765 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5414.01 1 0.0000 0.9765 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6656.01 1 0.0000 0.9765 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A61C.01 2 0.3083 0.7812 0.00 0.66 0.00 0.34 0.00 0.00 0.00 0.00
#> TCGA.76.4925.01 1 0.0000 0.9765 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4W.AA9R.01 4 0.3714 0.7845 0.00 0.02 0.00 0.54 0.44 0.00 0.00 0.00
#> TCGA.FG.6692.01 8 0.0471 0.9570 0.00 0.00 0.02 0.00 0.00 0.00 0.00 0.98
#> TCGA.81.5910.01 7 0.1341 0.6482 0.00 0.00 0.00 0.00 0.00 0.08 0.92 0.00
#> TCGA.DU.7013.01 3 0.3198 0.6611 0.00 0.00 0.72 0.00 0.26 0.00 0.02 0.00
#> TCGA.KT.A7W1.01 3 0.3083 0.4500 0.34 0.00 0.66 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A5RA.01 3 0.3970 0.6724 0.00 0.00 0.72 0.00 0.18 0.00 0.08 0.02
#> TCGA.26.5134.01 2 0.3083 0.7812 0.00 0.66 0.00 0.34 0.00 0.00 0.00 0.00
#> TCGA.76.6286.01 6 0.3615 0.6425 0.00 0.00 0.02 0.04 0.20 0.74 0.00 0.00
#> TCGA.76.6660.01 4 0.3714 0.7845 0.00 0.02 0.00 0.54 0.44 0.00 0.00 0.00
#> TCGA.28.5204.01 1 0.0000 0.9765 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.1804.01 8 0.0000 0.9616 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.A7TJ.01 3 0.1275 0.7307 0.00 0.00 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.76.4931.01 3 0.1557 0.7194 0.00 0.00 0.92 0.02 0.00 0.00 0.06 0.00
#> TCGA.19.5954.01 7 0.2224 0.7593 0.00 0.00 0.12 0.02 0.00 0.00 0.86 0.00
#> TCGA.HT.8011.01 2 0.4672 0.0855 0.00 0.60 0.00 0.00 0.10 0.28 0.02 0.00
#> TCGA.DU.5852.01 6 0.2407 0.6976 0.00 0.00 0.00 0.06 0.00 0.86 0.08 0.00
#> TCGA.87.5896.01 1 0.0000 0.9765 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.0957.01 4 0.4504 0.7707 0.00 0.24 0.00 0.64 0.10 0.02 0.00 0.00
#> TCGA.06.5859.01 6 0.4575 0.6121 0.00 0.00 0.02 0.00 0.22 0.64 0.12 0.00
#> TCGA.06.6699.01 8 0.0471 0.9570 0.00 0.00 0.02 0.00 0.00 0.00 0.00 0.98
#> TCGA.41.5651.01 4 0.4516 0.7563 0.00 0.00 0.00 0.52 0.42 0.02 0.02 0.02
#> TCGA.06.0210.02 6 0.5420 0.3598 0.00 0.26 0.00 0.14 0.06 0.54 0.00 0.00
#> TCGA.19.5956.01 2 0.3083 0.7812 0.00 0.66 0.00 0.34 0.00 0.00 0.00 0.00
#> TCGA.28.5216.01 2 0.3083 0.7812 0.00 0.66 0.00 0.34 0.00 0.00 0.00 0.00
#> TCGA.74.6573.01 7 0.2719 0.7386 0.00 0.00 0.18 0.02 0.00 0.00 0.80 0.00
#> TCGA.14.0740.01 2 0.3083 0.7812 0.00 0.66 0.00 0.34 0.00 0.00 0.00 0.00
#> TCGA.HT.7469.01 6 0.4940 0.4071 0.00 0.00 0.02 0.00 0.10 0.48 0.40 0.00
#> TCGA.19.5959.01 8 0.0000 0.9616 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.E1.A7YD.01 2 0.0000 0.6678 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.5960.01 3 0.3291 0.6638 0.00 0.00 0.70 0.00 0.28 0.00 0.00 0.02
#> TCGA.28.5208.01 1 0.0000 0.9765 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A7TD.01 6 0.2224 0.7013 0.00 0.00 0.00 0.02 0.00 0.86 0.12 0.00
#> TCGA.DU.6405.01 1 0.0808 0.9378 0.96 0.00 0.04 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.0152.01 7 0.4834 0.6100 0.00 0.00 0.08 0.02 0.20 0.04 0.66 0.00
#> TCGA.26.5132.01 1 0.0000 0.9765 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.12.5299.01 3 0.3737 0.0455 0.48 0.00 0.50 0.00 0.02 0.00 0.00 0.00
#> TCGA.12.5301.01 2 0.2650 0.3413 0.00 0.76 0.00 0.24 0.00 0.00 0.00 0.00
#> TCGA.TM.A84B.01 6 0.5200 0.3258 0.00 0.00 0.02 0.00 0.40 0.44 0.14 0.00
#> TCGA.26.5139.01 3 0.2071 0.7263 0.04 0.00 0.90 0.00 0.00 0.00 0.04 0.02
#> TCGA.TM.A84J.01 2 0.3083 0.7812 0.00 0.66 0.00 0.34 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: Node011. Child nodes: Node01111-leaf , Node01112-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01211-leaf , Node01212-leaf , Node01213 , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node01224-leaf , Node01225-leaf , Node01311-leaf , Node01312-leaf , Node01313-leaf , Node01411-leaf , Node01412-leaf , Node01431-leaf , Node01432-leaf , Node02211-leaf , Node02212 , Node02221 , Node02222-leaf , Node02223-leaf , Node02231 , Node02232-leaf , Node02233-leaf , Node02234-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0111"]
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 39 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 0.5106 0.490 0.490
#> 3 3 0.749 0.925 0.886 0.2198 0.868 0.730
#> 4 4 0.698 0.800 0.834 0.0956 1.000 1.000
#> 5 5 0.619 0.768 0.755 0.0660 0.843 0.575
#> 6 6 0.701 0.699 0.797 0.0717 0.974 0.887
#> 7 7 0.727 0.758 0.832 0.0474 0.937 0.706
#> 8 8 0.794 0.602 0.778 0.0207 0.970 0.825
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.76.4932.01 2 0 1 0 1
#> TCGA.12.5295.01 2 0 1 0 1
#> TCGA.06.0125.01 2 0 1 0 1
#> TCGA.VW.A8FI.01 1 0 1 1 0
#> TCGA.06.5856.01 1 0 1 1 0
#> TCGA.06.0211.02 1 0 1 1 0
#> TCGA.14.1402.02 2 0 1 0 1
#> TCGA.RR.A6KC.01 1 0 1 1 0
#> TCGA.FG.A4MW.01 1 0 1 1 0
#> TCGA.06.6695.01 1 0 1 1 0
#> TCGA.19.A60I.01 1 0 1 1 0
#> TCGA.32.5222.01 1 0 1 1 0
#> TCGA.DU.6406.01 2 0 1 0 1
#> TCGA.76.6661.01 1 0 1 1 0
#> TCGA.28.5209.01 2 0 1 0 1
#> TCGA.19.5951.01 2 0 1 0 1
#> TCGA.HT.8104.01 2 0 1 0 1
#> TCGA.FG.A4MU.01 1 0 1 1 0
#> TCGA.74.6581.01 1 0 1 1 0
#> TCGA.S9.A6WM.01 2 0 1 0 1
#> TCGA.E1.A7YJ.01 1 0 1 1 0
#> TCGA.06.5414.01 1 0 1 1 0
#> TCGA.76.6656.01 1 0 1 1 0
#> TCGA.76.4925.01 1 0 1 1 0
#> TCGA.FG.6692.01 1 0 1 1 0
#> TCGA.KT.A7W1.01 2 0 1 0 1
#> TCGA.28.5204.01 1 0 1 1 0
#> TCGA.06.1804.01 2 0 1 0 1
#> TCGA.DU.A7TJ.01 1 0 1 1 0
#> TCGA.76.4931.01 2 0 1 0 1
#> TCGA.87.5896.01 2 0 1 0 1
#> TCGA.06.6699.01 2 0 1 0 1
#> TCGA.19.5959.01 2 0 1 0 1
#> TCGA.19.5960.01 1 0 1 1 0
#> TCGA.28.5208.01 1 0 1 1 0
#> TCGA.DU.6405.01 2 0 1 0 1
#> TCGA.26.5132.01 1 0 1 1 0
#> TCGA.12.5299.01 2 0 1 0 1
#> TCGA.26.5139.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.76.4932.01 2 0.4796 0.874 0.00 0.78 0.22
#> TCGA.12.5295.01 2 0.0892 0.920 0.00 0.98 0.02
#> TCGA.06.0125.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.VW.A8FI.01 3 0.5948 1.000 0.36 0.00 0.64
#> TCGA.06.5856.01 1 0.0000 0.963 1.00 0.00 0.00
#> TCGA.06.0211.02 1 0.0000 0.963 1.00 0.00 0.00
#> TCGA.14.1402.02 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.RR.A6KC.01 3 0.5948 1.000 0.36 0.00 0.64
#> TCGA.FG.A4MW.01 1 0.0000 0.963 1.00 0.00 0.00
#> TCGA.06.6695.01 1 0.0000 0.963 1.00 0.00 0.00
#> TCGA.19.A60I.01 1 0.0000 0.963 1.00 0.00 0.00
#> TCGA.32.5222.01 1 0.0000 0.963 1.00 0.00 0.00
#> TCGA.DU.6406.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.76.6661.01 3 0.5948 1.000 0.36 0.00 0.64
#> TCGA.28.5209.01 2 0.3686 0.835 0.00 0.86 0.14
#> TCGA.19.5951.01 2 0.3340 0.902 0.00 0.88 0.12
#> TCGA.HT.8104.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.FG.A4MU.01 3 0.5948 1.000 0.36 0.00 0.64
#> TCGA.74.6581.01 3 0.5948 1.000 0.36 0.00 0.64
#> TCGA.S9.A6WM.01 2 0.4796 0.874 0.00 0.78 0.22
#> TCGA.E1.A7YJ.01 1 0.0000 0.963 1.00 0.00 0.00
#> TCGA.06.5414.01 1 0.0000 0.963 1.00 0.00 0.00
#> TCGA.76.6656.01 1 0.2537 0.848 0.92 0.00 0.08
#> TCGA.76.4925.01 1 0.0000 0.963 1.00 0.00 0.00
#> TCGA.FG.6692.01 1 0.4796 0.497 0.78 0.00 0.22
#> TCGA.KT.A7W1.01 2 0.4796 0.874 0.00 0.78 0.22
#> TCGA.28.5204.01 3 0.5948 1.000 0.36 0.00 0.64
#> TCGA.06.1804.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.DU.A7TJ.01 3 0.5948 1.000 0.36 0.00 0.64
#> TCGA.76.4931.01 2 0.4796 0.874 0.00 0.78 0.22
#> TCGA.87.5896.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.06.6699.01 2 0.0892 0.920 0.00 0.98 0.02
#> TCGA.19.5959.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.19.5960.01 1 0.0000 0.963 1.00 0.00 0.00
#> TCGA.28.5208.01 1 0.0000 0.963 1.00 0.00 0.00
#> TCGA.DU.6405.01 2 0.0000 0.921 0.00 1.00 0.00
#> TCGA.26.5132.01 1 0.0000 0.963 1.00 0.00 0.00
#> TCGA.12.5299.01 2 0.4796 0.874 0.00 0.78 0.22
#> TCGA.26.5139.01 2 0.4796 0.874 0.00 0.78 0.22
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.76.4932.01 2 0.4907 0.715 0.42 0.58 0.00 0.00
#> TCGA.12.5295.01 2 0.1211 0.827 0.04 0.96 0.00 0.00
#> TCGA.06.0125.01 2 0.0000 0.830 0.00 1.00 0.00 0.00
#> TCGA.VW.A8FI.01 3 0.3610 0.878 0.00 0.00 0.80 0.20
#> TCGA.06.5856.01 4 0.0000 0.899 0.00 0.00 0.00 1.00
#> TCGA.06.0211.02 4 0.2830 0.860 0.06 0.00 0.04 0.90
#> TCGA.14.1402.02 2 0.0000 0.830 0.00 1.00 0.00 0.00
#> TCGA.RR.A6KC.01 3 0.4284 0.870 0.02 0.00 0.78 0.20
#> TCGA.FG.A4MW.01 4 0.2830 0.860 0.06 0.00 0.04 0.90
#> TCGA.06.6695.01 4 0.0000 0.899 0.00 0.00 0.00 1.00
#> TCGA.19.A60I.01 4 0.0000 0.899 0.00 0.00 0.00 1.00
#> TCGA.32.5222.01 4 0.0000 0.899 0.00 0.00 0.00 1.00
#> TCGA.DU.6406.01 2 0.0000 0.830 0.00 1.00 0.00 0.00
#> TCGA.76.6661.01 3 0.7004 0.863 0.22 0.00 0.58 0.20
#> TCGA.28.5209.01 2 0.7427 0.411 0.30 0.50 0.20 0.00
#> TCGA.19.5951.01 2 0.2647 0.810 0.12 0.88 0.00 0.00
#> TCGA.HT.8104.01 2 0.0000 0.830 0.00 1.00 0.00 0.00
#> TCGA.FG.A4MU.01 3 0.7004 0.863 0.22 0.00 0.58 0.20
#> TCGA.74.6581.01 3 0.4755 0.882 0.04 0.00 0.76 0.20
#> TCGA.S9.A6WM.01 2 0.4907 0.715 0.42 0.58 0.00 0.00
#> TCGA.E1.A7YJ.01 4 0.1913 0.883 0.04 0.00 0.02 0.94
#> TCGA.06.5414.01 4 0.0000 0.899 0.00 0.00 0.00 1.00
#> TCGA.76.6656.01 4 0.5986 0.387 0.06 0.00 0.32 0.62
#> TCGA.76.4925.01 4 0.0000 0.899 0.00 0.00 0.00 1.00
#> TCGA.FG.6692.01 4 0.6150 0.244 0.06 0.00 0.36 0.58
#> TCGA.KT.A7W1.01 2 0.4907 0.715 0.42 0.58 0.00 0.00
#> TCGA.28.5204.01 3 0.4755 0.855 0.04 0.00 0.76 0.20
#> TCGA.06.1804.01 2 0.0000 0.830 0.00 1.00 0.00 0.00
#> TCGA.DU.A7TJ.01 3 0.7004 0.863 0.22 0.00 0.58 0.20
#> TCGA.76.4931.01 2 0.4907 0.715 0.42 0.58 0.00 0.00
#> TCGA.87.5896.01 2 0.0000 0.830 0.00 1.00 0.00 0.00
#> TCGA.06.6699.01 2 0.1211 0.827 0.04 0.96 0.00 0.00
#> TCGA.19.5959.01 2 0.0000 0.830 0.00 1.00 0.00 0.00
#> TCGA.19.5960.01 4 0.1913 0.881 0.04 0.00 0.02 0.94
#> TCGA.28.5208.01 4 0.0707 0.895 0.02 0.00 0.00 0.98
#> TCGA.DU.6405.01 2 0.0000 0.830 0.00 1.00 0.00 0.00
#> TCGA.26.5132.01 4 0.0000 0.899 0.00 0.00 0.00 1.00
#> TCGA.12.5299.01 2 0.4907 0.715 0.42 0.58 0.00 0.00
#> TCGA.26.5139.01 2 0.4907 0.715 0.42 0.58 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.76.4932.01 1 0.423 1.000 0.58 0.42 0.00 0.00 0.00
#> TCGA.12.5295.01 2 0.407 0.683 0.06 0.78 0.16 0.00 0.00
#> TCGA.06.0125.01 2 0.000 0.759 0.00 1.00 0.00 0.00 0.00
#> TCGA.VW.A8FI.01 3 0.482 0.614 0.00 0.00 0.72 0.18 0.10
#> TCGA.06.5856.01 4 0.000 0.893 0.00 0.00 0.00 1.00 0.00
#> TCGA.06.0211.02 4 0.426 0.733 0.06 0.00 0.18 0.76 0.00
#> TCGA.14.1402.02 2 0.273 0.739 0.00 0.84 0.16 0.00 0.00
#> TCGA.RR.A6KC.01 3 0.482 0.614 0.00 0.00 0.72 0.18 0.10
#> TCGA.FG.A4MW.01 4 0.426 0.733 0.06 0.00 0.18 0.76 0.00
#> TCGA.06.6695.01 4 0.000 0.893 0.00 0.00 0.00 1.00 0.00
#> TCGA.19.A60I.01 4 0.000 0.893 0.00 0.00 0.00 1.00 0.00
#> TCGA.32.5222.01 4 0.000 0.893 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.6406.01 2 0.000 0.759 0.00 1.00 0.00 0.00 0.00
#> TCGA.76.6661.01 5 0.576 0.981 0.00 0.00 0.20 0.18 0.62
#> TCGA.28.5209.01 2 0.667 0.174 0.24 0.42 0.00 0.00 0.34
#> TCGA.19.5951.01 2 0.311 0.330 0.20 0.80 0.00 0.00 0.00
#> TCGA.HT.8104.01 2 0.122 0.737 0.02 0.96 0.02 0.00 0.00
#> TCGA.FG.A4MU.01 5 0.561 0.963 0.00 0.00 0.18 0.18 0.64
#> TCGA.74.6581.01 3 0.611 0.190 0.00 0.00 0.56 0.18 0.26
#> TCGA.S9.A6WM.01 1 0.423 1.000 0.58 0.42 0.00 0.00 0.00
#> TCGA.E1.A7YJ.01 4 0.407 0.757 0.06 0.00 0.16 0.78 0.00
#> TCGA.06.5414.01 4 0.000 0.893 0.00 0.00 0.00 1.00 0.00
#> TCGA.76.6656.01 3 0.446 0.533 0.02 0.00 0.66 0.32 0.00
#> TCGA.76.4925.01 4 0.000 0.893 0.00 0.00 0.00 1.00 0.00
#> TCGA.FG.6692.01 3 0.604 0.456 0.08 0.00 0.56 0.34 0.02
#> TCGA.KT.A7W1.01 1 0.423 1.000 0.58 0.42 0.00 0.00 0.00
#> TCGA.28.5204.01 3 0.484 0.620 0.02 0.00 0.74 0.18 0.06
#> TCGA.06.1804.01 2 0.000 0.759 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.A7TJ.01 5 0.576 0.981 0.00 0.00 0.20 0.18 0.62
#> TCGA.76.4931.01 1 0.423 1.000 0.58 0.42 0.00 0.00 0.00
#> TCGA.87.5896.01 2 0.273 0.739 0.00 0.84 0.16 0.00 0.00
#> TCGA.06.6699.01 2 0.407 0.683 0.06 0.78 0.16 0.00 0.00
#> TCGA.19.5959.01 2 0.252 0.746 0.00 0.86 0.14 0.00 0.00
#> TCGA.19.5960.01 4 0.370 0.792 0.08 0.00 0.10 0.82 0.00
#> TCGA.28.5208.01 4 0.225 0.858 0.02 0.00 0.04 0.92 0.02
#> TCGA.DU.6405.01 2 0.000 0.759 0.00 1.00 0.00 0.00 0.00
#> TCGA.26.5132.01 4 0.000 0.893 0.00 0.00 0.00 1.00 0.00
#> TCGA.12.5299.01 1 0.423 1.000 0.58 0.42 0.00 0.00 0.00
#> TCGA.26.5139.01 1 0.423 1.000 0.58 0.42 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.76.4932.01 1 0.3076 1.000 0.76 0.24 0.00 0.00 0.00 0.00
#> TCGA.12.5295.01 2 0.1807 0.755 0.06 0.92 0.02 0.00 0.00 0.00
#> TCGA.06.0125.01 2 0.3156 0.798 0.02 0.80 0.00 0.00 0.00 0.18
#> TCGA.VW.A8FI.01 3 0.6613 0.363 0.00 0.00 0.40 0.04 0.36 0.20
#> TCGA.06.5856.01 4 0.0000 0.807 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.06.0211.02 4 0.3864 0.412 0.00 0.00 0.48 0.52 0.00 0.00
#> TCGA.14.1402.02 2 0.1092 0.775 0.02 0.96 0.02 0.00 0.00 0.00
#> TCGA.RR.A6KC.01 3 0.6596 0.400 0.00 0.00 0.42 0.04 0.34 0.20
#> TCGA.FG.A4MW.01 4 0.3864 0.412 0.00 0.00 0.48 0.52 0.00 0.00
#> TCGA.06.6695.01 4 0.0000 0.807 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.19.A60I.01 4 0.0000 0.807 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.32.5222.01 4 0.0000 0.807 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.6406.01 2 0.3156 0.798 0.02 0.80 0.00 0.00 0.00 0.18
#> TCGA.76.6661.01 5 0.0937 0.824 0.00 0.00 0.00 0.04 0.96 0.00
#> TCGA.28.5209.01 6 0.6417 0.000 0.02 0.32 0.24 0.00 0.00 0.42
#> TCGA.19.5951.01 2 0.4723 0.671 0.14 0.68 0.00 0.00 0.00 0.18
#> TCGA.HT.8104.01 2 0.3460 0.731 0.00 0.76 0.00 0.00 0.02 0.22
#> TCGA.FG.A4MU.01 5 0.0937 0.824 0.00 0.00 0.00 0.04 0.96 0.00
#> TCGA.74.6581.01 5 0.6364 0.182 0.02 0.00 0.18 0.04 0.58 0.18
#> TCGA.S9.A6WM.01 1 0.3076 1.000 0.76 0.24 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YJ.01 4 0.4637 0.548 0.02 0.00 0.36 0.60 0.00 0.02
#> TCGA.06.5414.01 4 0.0000 0.807 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.76.6656.01 3 0.5422 0.434 0.00 0.00 0.62 0.24 0.02 0.12
#> TCGA.76.4925.01 4 0.0000 0.807 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FG.6692.01 3 0.4690 0.325 0.04 0.00 0.70 0.22 0.04 0.00
#> TCGA.KT.A7W1.01 1 0.3076 1.000 0.76 0.24 0.00 0.00 0.00 0.00
#> TCGA.28.5204.01 3 0.7213 0.361 0.02 0.00 0.36 0.04 0.30 0.28
#> TCGA.06.1804.01 2 0.3156 0.798 0.02 0.80 0.00 0.00 0.00 0.18
#> TCGA.DU.A7TJ.01 5 0.0937 0.824 0.00 0.00 0.00 0.04 0.96 0.00
#> TCGA.76.4931.01 1 0.3076 1.000 0.76 0.24 0.00 0.00 0.00 0.00
#> TCGA.87.5896.01 2 0.0547 0.769 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.06.6699.01 2 0.1807 0.755 0.06 0.92 0.02 0.00 0.00 0.00
#> TCGA.19.5959.01 2 0.0547 0.769 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.19.5960.01 4 0.5679 0.585 0.12 0.00 0.18 0.64 0.00 0.06
#> TCGA.28.5208.01 4 0.3660 0.695 0.06 0.00 0.16 0.78 0.00 0.00
#> TCGA.DU.6405.01 2 0.3156 0.790 0.00 0.80 0.00 0.00 0.02 0.18
#> TCGA.26.5132.01 4 0.0000 0.807 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.12.5299.01 1 0.3076 1.000 0.76 0.24 0.00 0.00 0.00 0.00
#> TCGA.26.5139.01 1 0.3076 1.000 0.76 0.24 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.76.4932.01 1 0.1886 1.000 0.88 0.12 0.00 0.00 0.00 0.00 0.00
#> TCGA.12.5295.01 2 0.4100 0.787 0.04 0.76 0.00 0.10 0.10 0.00 0.00
#> TCGA.06.0125.01 2 0.0000 0.825 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VW.A8FI.01 3 0.1363 0.758 0.00 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.06.5856.01 4 0.3496 0.917 0.00 0.00 0.00 0.58 0.00 0.00 0.42
#> TCGA.06.0211.02 7 0.0504 0.670 0.00 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.14.1402.02 2 0.3284 0.804 0.00 0.80 0.00 0.10 0.10 0.00 0.00
#> TCGA.RR.A6KC.01 3 0.1363 0.758 0.00 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.FG.A4MW.01 7 0.0504 0.670 0.00 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.06.6695.01 4 0.3496 0.917 0.00 0.00 0.00 0.58 0.00 0.00 0.42
#> TCGA.19.A60I.01 4 0.3496 0.917 0.00 0.00 0.00 0.58 0.00 0.00 0.42
#> TCGA.32.5222.01 4 0.3546 0.889 0.00 0.00 0.00 0.54 0.00 0.00 0.46
#> TCGA.DU.6406.01 2 0.0504 0.818 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.76.6661.01 5 0.2422 0.954 0.00 0.00 0.18 0.00 0.82 0.00 0.00
#> TCGA.28.5209.01 6 0.2259 0.000 0.00 0.16 0.00 0.00 0.00 0.84 0.00
#> TCGA.19.5951.01 2 0.3691 0.677 0.12 0.80 0.02 0.02 0.04 0.00 0.00
#> TCGA.HT.8104.01 2 0.2722 0.744 0.00 0.84 0.04 0.12 0.00 0.00 0.00
#> TCGA.FG.A4MU.01 5 0.2912 0.939 0.04 0.00 0.14 0.00 0.82 0.00 0.00
#> TCGA.74.6581.01 3 0.3519 0.477 0.04 0.00 0.74 0.00 0.22 0.00 0.00
#> TCGA.S9.A6WM.01 1 0.1886 1.000 0.88 0.12 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YJ.01 7 0.0863 0.602 0.00 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.06.5414.01 4 0.3546 0.889 0.00 0.00 0.00 0.54 0.00 0.00 0.46
#> TCGA.76.6656.01 3 0.3496 0.276 0.00 0.00 0.58 0.00 0.00 0.00 0.42
#> TCGA.76.4925.01 4 0.3496 0.917 0.00 0.00 0.00 0.58 0.00 0.00 0.42
#> TCGA.FG.6692.01 7 0.5386 0.164 0.00 0.00 0.24 0.10 0.00 0.06 0.60
#> TCGA.KT.A7W1.01 1 0.1886 1.000 0.88 0.12 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5204.01 3 0.2278 0.739 0.00 0.00 0.88 0.00 0.00 0.04 0.08
#> TCGA.06.1804.01 2 0.0000 0.825 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A7TJ.01 5 0.2259 0.959 0.00 0.00 0.16 0.00 0.84 0.00 0.00
#> TCGA.76.4931.01 1 0.1886 1.000 0.88 0.12 0.00 0.00 0.00 0.00 0.00
#> TCGA.87.5896.01 2 0.3263 0.804 0.00 0.80 0.00 0.12 0.08 0.00 0.00
#> TCGA.06.6699.01 2 0.3879 0.797 0.04 0.78 0.00 0.10 0.08 0.00 0.00
#> TCGA.19.5959.01 2 0.3058 0.812 0.00 0.82 0.00 0.10 0.08 0.00 0.00
#> TCGA.19.5960.01 7 0.4718 0.124 0.02 0.00 0.00 0.32 0.00 0.06 0.60
#> TCGA.28.5208.01 4 0.4421 0.439 0.02 0.00 0.00 0.50 0.00 0.02 0.46
#> TCGA.DU.6405.01 2 0.1860 0.787 0.00 0.92 0.02 0.02 0.04 0.00 0.00
#> TCGA.26.5132.01 4 0.3496 0.917 0.00 0.00 0.00 0.58 0.00 0.00 0.42
#> TCGA.12.5299.01 1 0.1886 1.000 0.88 0.12 0.00 0.00 0.00 0.00 0.00
#> TCGA.26.5139.01 1 0.1886 1.000 0.88 0.12 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.76.4932.01 1 0.0808 1.0000 0.96 0.04 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.12.5295.01 2 0.0000 0.4909 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.0125.01 2 0.3299 0.0420 0.00 0.56 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.VW.A8FI.01 3 0.2350 0.7671 0.00 0.00 0.86 0.00 0.04 0.00 0.10 0.00
#> TCGA.06.5856.01 4 0.3299 1.0000 0.00 0.00 0.00 0.56 0.00 0.00 0.44 0.00
#> TCGA.06.0211.02 7 0.0471 0.6359 0.00 0.00 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.14.1402.02 2 0.0000 0.4909 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RR.A6KC.01 3 0.2350 0.7671 0.00 0.00 0.86 0.00 0.04 0.00 0.10 0.00
#> TCGA.FG.A4MW.01 7 0.0471 0.6359 0.00 0.00 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.06.6695.01 4 0.3299 1.0000 0.00 0.00 0.00 0.56 0.00 0.00 0.44 0.00
#> TCGA.19.A60I.01 4 0.3299 1.0000 0.00 0.00 0.00 0.56 0.00 0.00 0.44 0.00
#> TCGA.32.5222.01 4 0.3299 1.0000 0.00 0.00 0.00 0.56 0.00 0.00 0.44 0.00
#> TCGA.DU.6406.01 2 0.3318 -0.0238 0.00 0.54 0.00 0.00 0.00 0.00 0.00 0.46
#> TCGA.76.6661.01 5 0.2404 0.9541 0.00 0.00 0.14 0.00 0.84 0.00 0.02 0.00
#> TCGA.28.5209.01 6 0.2406 0.0000 0.00 0.20 0.00 0.00 0.00 0.80 0.00 0.00
#> TCGA.19.5951.01 8 0.5644 0.0000 0.16 0.34 0.02 0.02 0.00 0.00 0.00 0.46
#> TCGA.HT.8104.01 2 0.6190 -0.1765 0.00 0.46 0.02 0.16 0.08 0.00 0.00 0.28
#> TCGA.FG.A4MU.01 5 0.3311 0.9407 0.00 0.00 0.14 0.02 0.80 0.00 0.02 0.02
#> TCGA.74.6581.01 3 0.3471 0.6151 0.00 0.00 0.78 0.02 0.16 0.02 0.02 0.00
#> TCGA.S9.A6WM.01 1 0.0808 1.0000 0.96 0.04 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YJ.01 7 0.0941 0.5972 0.00 0.00 0.00 0.02 0.00 0.00 0.96 0.02
#> TCGA.06.5414.01 4 0.3299 1.0000 0.00 0.00 0.00 0.56 0.00 0.00 0.44 0.00
#> TCGA.76.6656.01 3 0.3237 0.4330 0.00 0.00 0.60 0.00 0.00 0.00 0.40 0.00
#> TCGA.76.4925.01 4 0.3299 1.0000 0.00 0.00 0.00 0.56 0.00 0.00 0.44 0.00
#> TCGA.FG.6692.01 7 0.5864 0.2509 0.00 0.00 0.20 0.04 0.00 0.14 0.56 0.06
#> TCGA.KT.A7W1.01 1 0.0808 1.0000 0.96 0.04 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5204.01 3 0.4030 0.6649 0.02 0.00 0.78 0.04 0.00 0.02 0.04 0.10
#> TCGA.06.1804.01 2 0.3299 0.0420 0.00 0.56 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.DU.A7TJ.01 5 0.2224 0.9608 0.00 0.00 0.12 0.00 0.86 0.00 0.02 0.00
#> TCGA.76.4931.01 1 0.0808 1.0000 0.96 0.04 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.87.5896.01 2 0.2025 0.4838 0.00 0.88 0.00 0.10 0.00 0.00 0.00 0.02
#> TCGA.06.6699.01 2 0.1341 0.4677 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.19.5959.01 2 0.2025 0.4838 0.00 0.88 0.00 0.10 0.00 0.00 0.00 0.02
#> TCGA.19.5960.01 7 0.4833 0.3883 0.00 0.00 0.00 0.12 0.02 0.00 0.58 0.28
#> TCGA.28.5208.01 7 0.5440 -0.1801 0.02 0.00 0.00 0.30 0.00 0.10 0.54 0.04
#> TCGA.DU.6405.01 2 0.4407 -0.2728 0.00 0.48 0.00 0.02 0.04 0.00 0.00 0.46
#> TCGA.26.5132.01 4 0.3299 1.0000 0.00 0.00 0.00 0.56 0.00 0.00 0.44 0.00
#> TCGA.12.5299.01 1 0.0808 1.0000 0.96 0.04 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.26.5139.01 1 0.0808 1.0000 0.96 0.04 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: Node011. Child nodes: Node01111-leaf , Node01112-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01211-leaf , Node01212-leaf , Node01213 , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node01224-leaf , Node01225-leaf , Node01311-leaf , Node01312-leaf , Node01313-leaf , Node01411-leaf , Node01412-leaf , Node01431-leaf , Node01432-leaf , Node02211-leaf , Node02212 , Node02221 , Node02222-leaf , Node02223-leaf , Node02231 , Node02232-leaf , Node02233-leaf , Node02234-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0112"]
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 '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 0.983 0.990 0.4407 0.557 0.557
#> 3 3 1.000 1.000 1.000 0.4898 0.644 0.434
#> 4 4 1.000 0.997 0.998 0.1079 0.905 0.733
#> 5 5 1.000 0.920 0.981 0.0179 0.988 0.957
#> 6 6 0.943 0.848 0.950 0.0182 0.992 0.970
#> 7 7 0.905 0.749 0.908 0.0318 1.000 1.000
#> 8 8 0.897 0.728 0.905 0.0256 0.957 0.828
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.06.6694.01 1 0.000 0.992 1.00 0.00
#> TCGA.76.6285.01 1 0.141 0.986 0.98 0.02
#> TCGA.DU.6403.01 1 0.000 0.992 1.00 0.00
#> TCGA.26.5135.01 1 0.000 0.992 1.00 0.00
#> TCGA.28.5219.01 1 0.000 0.992 1.00 0.00
#> TCGA.76.4934.01 1 0.000 0.992 1.00 0.00
#> TCGA.76.6191.01 1 0.141 0.986 0.98 0.02
#> TCGA.28.5215.01 1 0.000 0.992 1.00 0.00
#> TCGA.76.4929.01 1 0.000 0.992 1.00 0.00
#> TCGA.76.4935.01 1 0.000 0.992 1.00 0.00
#> TCGA.HT.A61C.01 2 0.000 0.983 0.00 1.00
#> TCGA.4W.AA9R.01 1 0.141 0.986 0.98 0.02
#> TCGA.26.5134.01 2 0.000 0.983 0.00 1.00
#> TCGA.76.6660.01 1 0.141 0.986 0.98 0.02
#> TCGA.HT.8011.01 2 0.469 0.887 0.10 0.90
#> TCGA.19.0957.01 1 0.000 0.992 1.00 0.00
#> TCGA.06.0210.02 1 0.000 0.992 1.00 0.00
#> TCGA.19.5956.01 2 0.000 0.983 0.00 1.00
#> TCGA.28.5216.01 2 0.000 0.983 0.00 1.00
#> TCGA.14.0740.01 2 0.000 0.983 0.00 1.00
#> TCGA.E1.A7YD.01 1 0.141 0.986 0.98 0.02
#> TCGA.12.5301.01 1 0.141 0.986 0.98 0.02
#> TCGA.TM.A84J.01 2 0.000 0.983 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.06.6694.01 1 0 1 1 0 0
#> TCGA.76.6285.01 3 0 1 0 0 1
#> TCGA.DU.6403.01 1 0 1 1 0 0
#> TCGA.26.5135.01 1 0 1 1 0 0
#> TCGA.28.5219.01 1 0 1 1 0 0
#> TCGA.76.4934.01 1 0 1 1 0 0
#> TCGA.76.6191.01 3 0 1 0 0 1
#> TCGA.28.5215.01 1 0 1 1 0 0
#> TCGA.76.4929.01 1 0 1 1 0 0
#> TCGA.76.4935.01 1 0 1 1 0 0
#> TCGA.HT.A61C.01 3 0 1 0 0 1
#> TCGA.4W.AA9R.01 3 0 1 0 0 1
#> TCGA.26.5134.01 2 0 1 0 1 0
#> TCGA.76.6660.01 3 0 1 0 0 1
#> TCGA.HT.8011.01 3 0 1 0 0 1
#> TCGA.19.0957.01 1 0 1 1 0 0
#> TCGA.06.0210.02 1 0 1 1 0 0
#> TCGA.19.5956.01 2 0 1 0 1 0
#> TCGA.28.5216.01 3 0 1 0 0 1
#> TCGA.14.0740.01 2 0 1 0 1 0
#> TCGA.E1.A7YD.01 3 0 1 0 0 1
#> TCGA.12.5301.01 3 0 1 0 0 1
#> TCGA.TM.A84J.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.06.6694.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.76.6285.01 3 0.0000 1.000 0 0.00 1.00 0.00
#> TCGA.DU.6403.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.26.5135.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.28.5219.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.76.4934.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.76.6191.01 3 0.0000 1.000 0 0.00 1.00 0.00
#> TCGA.28.5215.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.76.4929.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.76.4935.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.HT.A61C.01 4 0.0000 0.985 0 0.00 0.00 1.00
#> TCGA.4W.AA9R.01 3 0.0000 1.000 0 0.00 1.00 0.00
#> TCGA.26.5134.01 4 0.0707 0.976 0 0.02 0.00 0.98
#> TCGA.76.6660.01 3 0.0000 1.000 0 0.00 1.00 0.00
#> TCGA.HT.8011.01 4 0.0707 0.973 0 0.00 0.02 0.98
#> TCGA.19.0957.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.06.0210.02 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.19.5956.01 2 0.0000 1.000 0 1.00 0.00 0.00
#> TCGA.28.5216.01 4 0.0000 0.985 0 0.00 0.00 1.00
#> TCGA.14.0740.01 2 0.0000 1.000 0 1.00 0.00 0.00
#> TCGA.E1.A7YD.01 3 0.0000 1.000 0 0.00 1.00 0.00
#> TCGA.12.5301.01 3 0.0000 1.000 0 0.00 1.00 0.00
#> TCGA.TM.A84J.01 2 0.0000 1.000 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.06.6694.01 1 0.0000 1.000 1 0.0 0.00 0.00 0.00
#> TCGA.76.6285.01 3 0.0000 0.970 0 0.0 1.00 0.00 0.00
#> TCGA.DU.6403.01 1 0.0000 1.000 1 0.0 0.00 0.00 0.00
#> TCGA.26.5135.01 1 0.0000 1.000 1 0.0 0.00 0.00 0.00
#> TCGA.28.5219.01 1 0.0000 1.000 1 0.0 0.00 0.00 0.00
#> TCGA.76.4934.01 1 0.0000 1.000 1 0.0 0.00 0.00 0.00
#> TCGA.76.6191.01 3 0.1410 0.961 0 0.0 0.94 0.00 0.06
#> TCGA.28.5215.01 1 0.0000 1.000 1 0.0 0.00 0.00 0.00
#> TCGA.76.4929.01 1 0.0000 1.000 1 0.0 0.00 0.00 0.00
#> TCGA.76.4935.01 1 0.0000 1.000 1 0.0 0.00 0.00 0.00
#> TCGA.HT.A61C.01 4 0.1410 0.926 0 0.0 0.00 0.94 0.06
#> TCGA.4W.AA9R.01 3 0.0000 0.970 0 0.0 1.00 0.00 0.00
#> TCGA.26.5134.01 4 0.0000 0.964 0 0.0 0.00 1.00 0.00
#> TCGA.76.6660.01 3 0.0000 0.970 0 0.0 1.00 0.00 0.00
#> TCGA.HT.8011.01 5 0.0609 0.000 0 0.0 0.00 0.02 0.98
#> TCGA.19.0957.01 1 0.0000 1.000 1 0.0 0.00 0.00 0.00
#> TCGA.06.0210.02 1 0.0000 1.000 1 0.0 0.00 0.00 0.00
#> TCGA.19.5956.01 2 0.3109 0.744 0 0.8 0.00 0.20 0.00
#> TCGA.28.5216.01 4 0.0000 0.964 0 0.0 0.00 1.00 0.00
#> TCGA.14.0740.01 2 0.0000 0.877 0 1.0 0.00 0.00 0.00
#> TCGA.E1.A7YD.01 3 0.1410 0.961 0 0.0 0.94 0.00 0.06
#> TCGA.12.5301.01 3 0.1043 0.967 0 0.0 0.96 0.00 0.04
#> TCGA.TM.A84J.01 2 0.0000 0.877 0 1.0 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.06.6694.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6285.01 3 0.2454 0.897 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.DU.6403.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.26.5135.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5219.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.4934.01 1 0.0547 0.981 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.76.6191.01 3 0.0000 0.897 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.28.5215.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.4929.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.4935.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A61C.01 4 0.2190 0.764 0.00 0.00 0.04 0.90 0.06 0.00
#> TCGA.4W.AA9R.01 3 0.2631 0.897 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.26.5134.01 4 0.3198 0.604 0.00 0.00 0.00 0.74 0.00 0.26
#> TCGA.76.6660.01 3 0.2631 0.897 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.HT.8011.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.19.0957.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.0210.02 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.5956.01 6 0.3523 0.000 0.00 0.18 0.00 0.04 0.00 0.78
#> TCGA.28.5216.01 4 0.0000 0.793 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.14.0740.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YD.01 3 0.0000 0.897 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.12.5301.01 3 0.0547 0.897 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.TM.A84J.01 2 0.0000 1.000 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.06.6694.01 1 0.000 0.950 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6285.01 3 0.391 0.802 0.00 0.20 0.72 0.00 0.00 0.08 0.00
#> TCGA.DU.6403.01 1 0.000 0.950 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.26.5135.01 1 0.000 0.950 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5219.01 1 0.000 0.950 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.4934.01 1 0.355 0.324 0.54 0.46 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6191.01 3 0.136 0.811 0.00 0.04 0.94 0.00 0.00 0.02 0.00
#> TCGA.28.5215.01 1 0.000 0.950 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.4929.01 1 0.000 0.950 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.4935.01 1 0.000 0.950 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A61C.01 4 0.172 0.651 0.00 0.04 0.04 0.92 0.00 0.00 0.00
#> TCGA.4W.AA9R.01 3 0.345 0.822 0.00 0.14 0.78 0.00 0.00 0.08 0.00
#> TCGA.26.5134.01 4 0.545 0.158 0.00 0.24 0.00 0.46 0.00 0.30 0.00
#> TCGA.76.6660.01 3 0.345 0.822 0.00 0.14 0.78 0.00 0.00 0.08 0.00
#> TCGA.HT.8011.01 5 0.000 0.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.19.0957.01 1 0.000 0.950 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.0210.02 1 0.000 0.950 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.5956.01 6 0.189 0.000 0.00 0.00 0.00 0.00 0.00 0.88 0.12
#> TCGA.28.5216.01 4 0.000 0.668 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.14.0740.01 7 0.000 1.000 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.E1.A7YD.01 3 0.193 0.798 0.00 0.08 0.90 0.00 0.00 0.02 0.00
#> TCGA.12.5301.01 3 0.101 0.813 0.00 0.02 0.96 0.00 0.02 0.00 0.00
#> TCGA.TM.A84J.01 7 0.000 1.000 0.00 0.00 0.00 0.00 0.00 0.00 1.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.06.6694.01 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.76.6285.01 3 0.4559 0.663 0.00 0.02 0.60 0.00 0.00 0.30 0 0.08
#> TCGA.DU.6403.01 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.26.5135.01 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.28.5219.01 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.76.4934.01 8 0.2852 0.000 0.28 0.00 0.00 0.00 0.00 0.00 0 0.72
#> TCGA.76.6191.01 3 0.2020 0.692 0.00 0.02 0.90 0.02 0.00 0.00 0 0.06
#> TCGA.28.5215.01 1 0.0471 0.971 0.98 0.00 0.00 0.00 0.00 0.00 0 0.02
#> TCGA.76.4929.01 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.76.4935.01 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.HT.A61C.01 4 0.1557 0.810 0.00 0.02 0.00 0.92 0.06 0.00 0 0.00
#> TCGA.4W.AA9R.01 3 0.3083 0.723 0.00 0.00 0.66 0.00 0.00 0.34 0 0.00
#> TCGA.26.5134.01 2 0.2406 0.000 0.00 0.80 0.00 0.20 0.00 0.00 0 0.00
#> TCGA.76.6660.01 3 0.3083 0.723 0.00 0.00 0.66 0.00 0.00 0.34 0 0.00
#> TCGA.HT.8011.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1.00 0.00 0 0.00
#> TCGA.19.0957.01 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.06.0210.02 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.19.5956.01 6 0.4247 0.000 0.00 0.28 0.00 0.00 0.00 0.62 0 0.10
#> TCGA.28.5216.01 4 0.1557 0.805 0.00 0.06 0.00 0.92 0.00 0.00 0 0.02
#> TCGA.14.0740.01 7 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 0.00 1 0.00
#> TCGA.E1.A7YD.01 3 0.1408 0.706 0.00 0.00 0.94 0.02 0.00 0.02 0 0.02
#> TCGA.12.5301.01 3 0.2674 0.681 0.00 0.04 0.86 0.00 0.00 0.04 0 0.06
#> TCGA.TM.A84J.01 7 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 0.00 1 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: Node011. Child nodes: Node01111-leaf , Node01112-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01211-leaf , Node01212-leaf , Node01213 , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node01224-leaf , Node01225-leaf , Node01311-leaf , Node01312-leaf , Node01313-leaf , Node01411-leaf , Node01412-leaf , Node01431-leaf , Node01432-leaf , Node02211-leaf , Node02212 , Node02221 , Node02222-leaf , Node02223-leaf , Node02231 , Node02232-leaf , Node02233-leaf , Node02234-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0113"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 24 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.987 0.994 0.4598 0.536 0.536
#> 3 3 1.000 0.997 0.998 0.4595 0.757 0.562
#> 4 4 1.000 0.929 0.969 0.1542 0.899 0.692
#> 5 5 0.835 0.785 0.899 0.0283 0.989 0.952
#> 6 6 0.805 0.711 0.874 0.0321 0.967 0.857
#> 7 7 0.818 0.587 0.835 0.0274 0.949 0.770
#> 8 8 0.819 0.627 0.805 0.0239 0.917 0.589
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.26.A7UX.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.6388.01 1 0.000 0.980 1.00 0.00
#> TCGA.28.5220.01 2 0.000 1.000 0.00 1.00
#> TCGA.OX.A56R.01 2 0.000 1.000 0.00 1.00
#> TCGA.76.4926.01 2 0.000 1.000 0.00 1.00
#> TCGA.28.5207.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.5408.01 1 0.000 0.980 1.00 0.00
#> TCGA.14.1395.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.5418.01 1 0.000 0.980 1.00 0.00
#> TCGA.06.6693.01 1 0.000 0.980 1.00 0.00
#> TCGA.06.A6S0.01 2 0.000 1.000 0.00 1.00
#> TCGA.81.5910.01 2 0.000 1.000 0.00 1.00
#> TCGA.DU.7013.01 2 0.000 1.000 0.00 1.00
#> TCGA.HT.A5RA.01 1 0.000 0.980 1.00 0.00
#> TCGA.76.6286.01 2 0.000 1.000 0.00 1.00
#> TCGA.19.5954.01 1 0.000 0.980 1.00 0.00
#> TCGA.DU.5852.01 1 0.000 0.980 1.00 0.00
#> TCGA.06.5859.01 2 0.000 1.000 0.00 1.00
#> TCGA.41.5651.01 1 0.584 0.837 0.86 0.14
#> TCGA.74.6573.01 2 0.000 1.000 0.00 1.00
#> TCGA.HT.7469.01 2 0.000 1.000 0.00 1.00
#> TCGA.DU.A7TD.01 2 0.000 1.000 0.00 1.00
#> TCGA.06.0152.01 2 0.000 1.000 0.00 1.00
#> TCGA.TM.A84B.01 2 0.000 1.000 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.26.A7UX.01 2 0.0000 0.996 0 1.00 0.00
#> TCGA.06.6388.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.28.5220.01 2 0.0000 0.996 0 1.00 0.00
#> TCGA.OX.A56R.01 2 0.0000 0.996 0 1.00 0.00
#> TCGA.76.4926.01 2 0.0000 0.996 0 1.00 0.00
#> TCGA.28.5207.01 2 0.0000 0.996 0 1.00 0.00
#> TCGA.06.5408.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.14.1395.01 2 0.0000 0.996 0 1.00 0.00
#> TCGA.06.5418.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.06.6693.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.06.A6S0.01 2 0.0892 0.982 0 0.98 0.02
#> TCGA.81.5910.01 2 0.0000 0.996 0 1.00 0.00
#> TCGA.DU.7013.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.HT.A5RA.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.76.6286.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.19.5954.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DU.5852.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.06.5859.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.41.5651.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.74.6573.01 2 0.0000 0.996 0 1.00 0.00
#> TCGA.HT.7469.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.DU.A7TD.01 2 0.0000 0.996 0 1.00 0.00
#> TCGA.06.0152.01 2 0.0892 0.982 0 0.98 0.02
#> TCGA.TM.A84B.01 3 0.0000 1.000 0 0.00 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.26.A7UX.01 2 0.0000 0.891 0 1.00 0.00 0.00
#> TCGA.06.6388.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.28.5220.01 4 0.0000 0.976 0 0.00 0.00 1.00
#> TCGA.OX.A56R.01 4 0.1211 0.953 0 0.04 0.00 0.96
#> TCGA.76.4926.01 2 0.4907 0.322 0 0.58 0.00 0.42
#> TCGA.28.5207.01 4 0.0707 0.971 0 0.02 0.00 0.98
#> TCGA.06.5408.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.14.1395.01 2 0.0000 0.891 0 1.00 0.00 0.00
#> TCGA.06.5418.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.06.6693.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.06.A6S0.01 4 0.0000 0.976 0 0.00 0.00 1.00
#> TCGA.81.5910.01 2 0.0000 0.891 0 1.00 0.00 0.00
#> TCGA.DU.7013.01 3 0.0000 0.988 0 0.00 1.00 0.00
#> TCGA.HT.A5RA.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.76.6286.01 3 0.0000 0.988 0 0.00 1.00 0.00
#> TCGA.19.5954.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.DU.5852.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.06.5859.01 3 0.0000 0.988 0 0.00 1.00 0.00
#> TCGA.41.5651.01 3 0.0000 0.988 0 0.00 1.00 0.00
#> TCGA.74.6573.01 2 0.0000 0.891 0 1.00 0.00 0.00
#> TCGA.HT.7469.01 3 0.0000 0.988 0 0.00 1.00 0.00
#> TCGA.DU.A7TD.01 2 0.1211 0.876 0 0.96 0.00 0.04
#> TCGA.06.0152.01 2 0.3172 0.784 0 0.84 0.00 0.16
#> TCGA.TM.A84B.01 3 0.1637 0.938 0 0.00 0.94 0.06
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.26.A7UX.01 2 0.0000 0.843 0.00 1.00 0.00 0.00 0.00
#> TCGA.06.6388.01 1 0.0000 0.926 1.00 0.00 0.00 0.00 0.00
#> TCGA.28.5220.01 4 0.0000 0.814 0.00 0.00 0.00 1.00 0.00
#> TCGA.OX.A56R.01 4 0.3521 0.677 0.00 0.04 0.00 0.82 0.14
#> TCGA.76.4926.01 2 0.4287 0.241 0.00 0.54 0.00 0.46 0.00
#> TCGA.28.5207.01 4 0.0609 0.821 0.00 0.02 0.00 0.98 0.00
#> TCGA.06.5408.01 1 0.0000 0.926 1.00 0.00 0.00 0.00 0.00
#> TCGA.14.1395.01 2 0.0000 0.843 0.00 1.00 0.00 0.00 0.00
#> TCGA.06.5418.01 1 0.3684 0.747 0.72 0.00 0.00 0.00 0.28
#> TCGA.06.6693.01 1 0.0000 0.926 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.A6S0.01 5 0.5157 0.000 0.00 0.04 0.00 0.44 0.52
#> TCGA.81.5910.01 2 0.0000 0.843 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7013.01 3 0.0000 0.916 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.A5RA.01 1 0.0000 0.926 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.6286.01 3 0.0000 0.916 0.00 0.00 1.00 0.00 0.00
#> TCGA.19.5954.01 1 0.3109 0.815 0.80 0.00 0.00 0.00 0.20
#> TCGA.DU.5852.01 1 0.0000 0.926 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.5859.01 3 0.0000 0.916 0.00 0.00 1.00 0.00 0.00
#> TCGA.41.5651.01 3 0.2929 0.824 0.00 0.00 0.82 0.00 0.18
#> TCGA.74.6573.01 2 0.0000 0.843 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7469.01 3 0.0000 0.916 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.A7TD.01 2 0.2516 0.787 0.00 0.86 0.00 0.14 0.00
#> TCGA.06.0152.01 2 0.4094 0.727 0.00 0.78 0.02 0.18 0.02
#> TCGA.TM.A84B.01 3 0.4872 0.708 0.00 0.00 0.72 0.16 0.12
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.26.A7UX.01 6 0.0547 0.842 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.06.6388.01 1 0.0547 0.870 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.28.5220.01 4 0.1267 0.761 0.00 0.00 0.00 0.94 0.06 0.00
#> TCGA.OX.A56R.01 4 0.4066 0.700 0.00 0.08 0.00 0.78 0.12 0.02
#> TCGA.76.4926.01 4 0.4094 0.652 0.00 0.08 0.00 0.74 0.00 0.18
#> TCGA.28.5207.01 4 0.0547 0.777 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.06.5408.01 1 0.0000 0.881 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.14.1395.01 6 0.0937 0.848 0.00 0.00 0.00 0.04 0.00 0.96
#> TCGA.06.5418.01 1 0.3706 0.615 0.62 0.38 0.00 0.00 0.00 0.00
#> TCGA.06.6693.01 1 0.0000 0.881 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.A6S0.01 5 0.0937 0.000 0.00 0.00 0.00 0.04 0.96 0.00
#> TCGA.81.5910.01 6 0.0547 0.849 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.DU.7013.01 3 0.0000 0.804 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.A5RA.01 1 0.0000 0.881 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6286.01 3 0.0000 0.804 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.19.5954.01 1 0.3578 0.658 0.66 0.34 0.00 0.00 0.00 0.00
#> TCGA.DU.5852.01 1 0.0000 0.881 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5859.01 3 0.0000 0.804 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.41.5651.01 3 0.3869 0.355 0.00 0.50 0.50 0.00 0.00 0.00
#> TCGA.74.6573.01 6 0.0547 0.842 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.HT.7469.01 3 0.0000 0.804 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.A7TD.01 6 0.3163 0.770 0.00 0.00 0.00 0.14 0.04 0.82
#> TCGA.06.0152.01 6 0.6308 0.427 0.00 0.06 0.02 0.28 0.08 0.56
#> TCGA.TM.A84B.01 3 0.5896 0.364 0.00 0.10 0.54 0.32 0.04 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.26.A7UX.01 6 0.2278 0.8220 0.00 0.00 0.00 0.00 0.04 0.88 0.08
#> TCGA.06.6388.01 1 0.0000 0.8597 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5220.01 4 0.2159 0.4970 0.00 0.02 0.00 0.90 0.06 0.00 0.02
#> TCGA.OX.A56R.01 4 0.5655 0.1822 0.00 0.16 0.00 0.44 0.38 0.02 0.00
#> TCGA.76.4926.01 4 0.5880 0.4500 0.00 0.02 0.00 0.54 0.22 0.20 0.02
#> TCGA.28.5207.01 4 0.0504 0.5175 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.06.5408.01 1 0.0000 0.8597 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.14.1395.01 6 0.0863 0.8300 0.00 0.00 0.00 0.00 0.04 0.96 0.00
#> TCGA.06.5418.01 1 0.4669 0.4668 0.52 0.08 0.00 0.00 0.00 0.00 0.40
#> TCGA.06.6693.01 1 0.0504 0.8534 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.06.A6S0.01 2 0.0000 0.0000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.81.5910.01 6 0.0000 0.8400 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.7013.01 3 0.0000 0.7948 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A5RA.01 1 0.0000 0.8597 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6286.01 3 0.0000 0.7948 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.19.5954.01 1 0.3755 0.6141 0.64 0.00 0.00 0.00 0.02 0.00 0.34
#> TCGA.DU.5852.01 1 0.0000 0.8597 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5859.01 3 0.0000 0.7948 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.41.5651.01 7 0.5567 0.0000 0.00 0.02 0.18 0.00 0.28 0.00 0.52
#> TCGA.74.6573.01 6 0.2016 0.8304 0.00 0.00 0.00 0.00 0.04 0.90 0.06
#> TCGA.HT.7469.01 3 0.0504 0.7796 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.DU.A7TD.01 6 0.4121 0.5047 0.00 0.00 0.00 0.20 0.10 0.70 0.00
#> TCGA.06.0152.01 4 0.6794 0.0959 0.00 0.00 0.06 0.36 0.24 0.32 0.02
#> TCGA.TM.A84B.01 3 0.6264 -0.0225 0.00 0.00 0.40 0.38 0.10 0.00 0.12
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.26.A7UX.01 6 0.2407 0.696 0.00 0.00 0.08 0.00 0.00 0.86 0.00 0.06
#> TCGA.06.6388.01 1 0.0941 0.945 0.96 0.00 0.02 0.00 0.00 0.00 0.02 0.00
#> TCGA.28.5220.01 4 0.6574 0.449 0.00 0.02 0.14 0.40 0.34 0.00 0.02 0.08
#> TCGA.OX.A56R.01 4 0.1887 0.227 0.00 0.06 0.00 0.90 0.00 0.00 0.04 0.00
#> TCGA.76.4926.01 4 0.6219 0.387 0.00 0.00 0.18 0.54 0.08 0.16 0.02 0.02
#> TCGA.28.5207.01 4 0.5983 0.474 0.00 0.00 0.18 0.40 0.34 0.00 0.00 0.08
#> TCGA.06.5408.01 1 0.0471 0.959 0.98 0.00 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.14.1395.01 6 0.1408 0.714 0.00 0.00 0.00 0.02 0.02 0.94 0.00 0.02
#> TCGA.06.5418.01 8 0.4655 0.746 0.34 0.02 0.02 0.00 0.00 0.00 0.04 0.58
#> TCGA.06.6693.01 1 0.0808 0.926 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.06.A6S0.01 2 0.0471 0.000 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.81.5910.01 6 0.2020 0.708 0.00 0.00 0.06 0.00 0.00 0.90 0.02 0.02
#> TCGA.DU.7013.01 3 0.3690 0.927 0.00 0.00 0.56 0.00 0.42 0.02 0.00 0.00
#> TCGA.HT.A5RA.01 1 0.0000 0.964 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6286.01 3 0.3299 0.949 0.00 0.00 0.56 0.00 0.44 0.00 0.00 0.00
#> TCGA.19.5954.01 8 0.3449 0.754 0.32 0.00 0.00 0.00 0.00 0.00 0.02 0.66
#> TCGA.DU.5852.01 1 0.0000 0.964 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5859.01 3 0.3272 0.965 0.00 0.00 0.58 0.00 0.42 0.00 0.00 0.00
#> TCGA.41.5651.01 7 0.1741 0.000 0.00 0.02 0.04 0.00 0.02 0.00 0.92 0.00
#> TCGA.74.6573.01 6 0.1887 0.713 0.00 0.00 0.06 0.00 0.00 0.90 0.00 0.04
#> TCGA.HT.7469.01 3 0.3272 0.965 0.00 0.00 0.58 0.00 0.42 0.00 0.00 0.00
#> TCGA.DU.A7TD.01 6 0.6387 0.473 0.00 0.02 0.16 0.04 0.12 0.58 0.04 0.04
#> TCGA.06.0152.01 6 0.8090 0.144 0.00 0.02 0.14 0.18 0.16 0.36 0.04 0.10
#> TCGA.TM.A84B.01 5 0.0471 0.000 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node01. Child nodes: Node0111 , Node0112 , Node0113 , Node0121 , Node0122 , Node0123-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0141 , Node0142-leaf , Node0143 , Node0211-leaf , Node0212-leaf , Node0213-leaf , Node0214-leaf , Node0221 , Node0222 , Node0223 , Node0231 , Node0232-leaf , Node0233-leaf , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0323-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 74 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 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 0.5040 0.496 0.496
#> 3 3 0.909 0.960 0.966 0.1582 0.935 0.870
#> 4 4 0.704 0.667 0.839 0.1359 0.954 0.894
#> 5 5 0.641 0.591 0.744 0.0937 0.917 0.787
#> 6 6 0.622 0.592 0.770 0.0509 0.903 0.694
#> 7 7 0.636 0.498 0.759 0.0392 0.910 0.656
#> 8 8 0.669 0.472 0.722 0.0166 0.931 0.710
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.FG.6688.01 2 0 1 0 1
#> TCGA.28.5213.01 1 0 1 1 0
#> TCGA.19.1389.01 1 0 1 1 0
#> TCGA.19.5953.01 1 0 1 1 0
#> TCGA.4W.AA9T.01 2 0 1 0 1
#> TCGA.S9.A7IX.01 1 0 1 1 0
#> TCGA.06.6700.01 1 0 1 1 0
#> TCGA.28.5218.01 1 0 1 1 0
#> TCGA.DU.8165.01 2 0 1 0 1
#> TCGA.76.6663.01 2 0 1 0 1
#> TCGA.19.4065.01 1 0 1 1 0
#> TCGA.CS.4941.01 1 0 1 1 0
#> TCGA.S9.A6U0.01 1 0 1 1 0
#> TCGA.FG.5963.02 1 0 1 1 0
#> TCGA.HT.A5RC.01 2 0 1 0 1
#> TCGA.28.5211.01 1 0 1 1 0
#> TCGA.QH.A6CX.01 1 0 1 1 0
#> TCGA.06.A6S1.01 2 0 1 0 1
#> TCGA.CS.6186.01 1 0 1 1 0
#> TCGA.S9.A6UA.01 1 0 1 1 0
#> TCGA.DU.A7TB.01 1 0 1 1 0
#> TCGA.DU.A76K.01 1 0 1 1 0
#> TCGA.E1.A7YQ.01 2 0 1 0 1
#> TCGA.19.1389.02 1 0 1 1 0
#> TCGA.26.6174.01 2 0 1 0 1
#> TCGA.DU.7012.01 2 0 1 0 1
#> TCGA.DU.6402.01 1 0 1 1 0
#> TCGA.FG.A87Q.01 2 0 1 0 1
#> TCGA.14.0862.01 1 0 1 1 0
#> TCGA.19.5955.01 1 0 1 1 0
#> TCGA.DU.A5TT.01 1 0 1 1 0
#> TCGA.76.6662.01 1 0 1 1 0
#> TCGA.RR.A6KA.01 2 0 1 0 1
#> TCGA.CS.5397.01 2 0 1 0 1
#> TCGA.S9.A7R2.01 1 0 1 1 0
#> TCGA.76.6193.01 1 0 1 1 0
#> TCGA.14.1043.01 1 0 1 1 0
#> TCGA.HT.8110.01 1 0 1 1 0
#> TCGA.06.6391.01 2 0 1 0 1
#> TCGA.06.0190.01 1 0 1 1 0
#> TCGA.06.0190.02 1 0 1 1 0
#> TCGA.28.2501.01 1 0 1 1 0
#> TCGA.14.1450.01 2 0 1 0 1
#> TCGA.DU.A5TY.01 2 0 1 0 1
#> TCGA.DU.5847.01 2 0 1 0 1
#> TCGA.76.4928.01 2 0 1 0 1
#> TCGA.26.6173.01 1 0 1 1 0
#> TCGA.HT.7882.01 1 0 1 1 0
#> TCGA.DU.5854.01 2 0 1 0 1
#> TCGA.76.6282.01 1 0 1 1 0
#> TCGA.P5.A72U.01 2 0 1 0 1
#> TCGA.DU.6404.02 2 0 1 0 1
#> TCGA.DU.6404.01 2 0 1 0 1
#> TCGA.E1.A7YN.01 2 0 1 0 1
#> TCGA.76.6192.01 1 0 1 1 0
#> TCGA.74.6575.01 2 0 1 0 1
#> TCGA.E1.A7Z2.01 2 0 1 0 1
#> TCGA.VM.A8CD.01 1 0 1 1 0
#> TCGA.06.A5U1.01 2 0 1 0 1
#> TCGA.HT.8564.01 1 0 1 1 0
#> TCGA.06.5858.01 2 0 1 0 1
#> TCGA.HT.7860.01 2 0 1 0 1
#> TCGA.81.5911.01 1 0 1 1 0
#> TCGA.DU.7006.01 2 0 1 0 1
#> TCGA.E1.A7YM.01 1 0 1 1 0
#> TCGA.19.5947.01 2 0 1 0 1
#> TCGA.14.0736.02 1 0 1 1 0
#> TCGA.HT.A74H.01 1 0 1 1 0
#> TCGA.DU.7290.01 2 0 1 0 1
#> TCGA.HT.A4DS.01 2 0 1 0 1
#> TCGA.RR.A6KB.01 1 0 1 1 0
#> TCGA.06.5416.01 2 0 1 0 1
#> TCGA.DU.8158.01 2 0 1 0 1
#> TCGA.41.6646.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.FG.6688.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.28.5213.01 1 0.0000 0.931 1.00 0 0.00
#> TCGA.19.1389.01 1 0.4002 0.882 0.84 0 0.16
#> TCGA.19.5953.01 1 0.0000 0.931 1.00 0 0.00
#> TCGA.4W.AA9T.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.S9.A7IX.01 1 0.2537 0.924 0.92 0 0.08
#> TCGA.06.6700.01 1 0.2959 0.922 0.90 0 0.10
#> TCGA.28.5218.01 3 0.0000 0.988 0.00 0 1.00
#> TCGA.DU.8165.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.76.6663.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.19.4065.01 1 0.2066 0.923 0.94 0 0.06
#> TCGA.CS.4941.01 1 0.0000 0.931 1.00 0 0.00
#> TCGA.S9.A6U0.01 1 0.2066 0.923 0.94 0 0.06
#> TCGA.FG.5963.02 3 0.0000 0.988 0.00 0 1.00
#> TCGA.HT.A5RC.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.28.5211.01 1 0.4002 0.882 0.84 0 0.16
#> TCGA.QH.A6CX.01 1 0.2537 0.924 0.92 0 0.08
#> TCGA.06.A6S1.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.CS.6186.01 1 0.0892 0.932 0.98 0 0.02
#> TCGA.S9.A6UA.01 3 0.0000 0.988 0.00 0 1.00
#> TCGA.DU.A7TB.01 3 0.0892 0.982 0.02 0 0.98
#> TCGA.DU.A76K.01 1 0.0892 0.932 0.98 0 0.02
#> TCGA.E1.A7YQ.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.19.1389.02 1 0.4002 0.882 0.84 0 0.16
#> TCGA.26.6174.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.DU.7012.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.DU.6402.01 1 0.0000 0.931 1.00 0 0.00
#> TCGA.FG.A87Q.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.14.0862.01 1 0.0000 0.931 1.00 0 0.00
#> TCGA.19.5955.01 1 0.2066 0.923 0.94 0 0.06
#> TCGA.DU.A5TT.01 1 0.2537 0.924 0.92 0 0.08
#> TCGA.76.6662.01 1 0.0000 0.931 1.00 0 0.00
#> TCGA.RR.A6KA.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.CS.5397.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.S9.A7R2.01 1 0.2537 0.924 0.92 0 0.08
#> TCGA.76.6193.01 1 0.2537 0.924 0.92 0 0.08
#> TCGA.14.1043.01 1 0.4796 0.847 0.78 0 0.22
#> TCGA.HT.8110.01 1 0.4555 0.866 0.80 0 0.20
#> TCGA.06.6391.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.06.0190.01 1 0.1529 0.928 0.96 0 0.04
#> TCGA.06.0190.02 1 0.1529 0.928 0.96 0 0.04
#> TCGA.28.2501.01 1 0.0000 0.931 1.00 0 0.00
#> TCGA.14.1450.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.DU.A5TY.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.DU.5847.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.76.4928.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.26.6173.01 1 0.0000 0.931 1.00 0 0.00
#> TCGA.HT.7882.01 1 0.2066 0.923 0.94 0 0.06
#> TCGA.DU.5854.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.76.6282.01 1 0.2959 0.903 0.90 0 0.10
#> TCGA.P5.A72U.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.DU.6404.02 2 0.0000 1.000 0.00 1 0.00
#> TCGA.DU.6404.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.E1.A7YN.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.76.6192.01 1 0.2066 0.923 0.94 0 0.06
#> TCGA.74.6575.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.E1.A7Z2.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.VM.A8CD.01 1 0.2537 0.924 0.92 0 0.08
#> TCGA.06.A5U1.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.HT.8564.01 3 0.0892 0.982 0.02 0 0.98
#> TCGA.06.5858.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.HT.7860.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.81.5911.01 1 0.0000 0.931 1.00 0 0.00
#> TCGA.DU.7006.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.E1.A7YM.01 1 0.2537 0.924 0.92 0 0.08
#> TCGA.19.5947.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.14.0736.02 1 0.4555 0.866 0.80 0 0.20
#> TCGA.HT.A74H.01 1 0.2537 0.924 0.92 0 0.08
#> TCGA.DU.7290.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.HT.A4DS.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.RR.A6KB.01 1 0.2537 0.924 0.92 0 0.08
#> TCGA.06.5416.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.DU.8158.01 2 0.0000 1.000 0.00 1 0.00
#> TCGA.41.6646.01 2 0.0000 1.000 0.00 1 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.FG.6688.01 2 0.1211 0.897 0.00 0.96 0.04 0.00
#> TCGA.28.5213.01 1 0.2647 0.550 0.88 0.00 0.00 0.12
#> TCGA.19.1389.01 4 0.5570 0.931 0.44 0.00 0.02 0.54
#> TCGA.19.5953.01 1 0.1211 0.608 0.96 0.00 0.00 0.04
#> TCGA.4W.AA9T.01 2 0.0000 0.901 0.00 1.00 0.00 0.00
#> TCGA.S9.A7IX.01 1 0.3400 0.565 0.82 0.00 0.00 0.18
#> TCGA.06.6700.01 1 0.4079 0.485 0.80 0.00 0.02 0.18
#> TCGA.28.5218.01 3 0.5000 0.964 0.00 0.00 0.50 0.50
#> TCGA.DU.8165.01 2 0.0707 0.899 0.00 0.98 0.02 0.00
#> TCGA.76.6663.01 2 0.0000 0.901 0.00 1.00 0.00 0.00
#> TCGA.19.4065.01 1 0.3975 0.316 0.76 0.00 0.00 0.24
#> TCGA.CS.4941.01 1 0.0707 0.622 0.98 0.00 0.00 0.02
#> TCGA.S9.A6U0.01 1 0.4790 -0.204 0.62 0.00 0.00 0.38
#> TCGA.FG.5963.02 3 0.4948 0.972 0.00 0.00 0.56 0.44
#> TCGA.HT.A5RC.01 2 0.0000 0.901 0.00 1.00 0.00 0.00
#> TCGA.28.5211.01 4 0.5535 0.936 0.42 0.00 0.02 0.56
#> TCGA.QH.A6CX.01 1 0.3610 0.545 0.80 0.00 0.00 0.20
#> TCGA.06.A6S1.01 2 0.4624 0.712 0.00 0.66 0.34 0.00
#> TCGA.CS.6186.01 1 0.1637 0.614 0.94 0.00 0.00 0.06
#> TCGA.S9.A6UA.01 3 0.4994 0.976 0.00 0.00 0.52 0.48
#> TCGA.DU.A7TB.01 3 0.4977 0.982 0.00 0.00 0.54 0.46
#> TCGA.DU.A76K.01 1 0.1637 0.614 0.94 0.00 0.00 0.06
#> TCGA.E1.A7YQ.01 2 0.0000 0.901 0.00 1.00 0.00 0.00
#> TCGA.19.1389.02 4 0.5594 0.924 0.46 0.00 0.02 0.52
#> TCGA.26.6174.01 2 0.4855 0.657 0.00 0.60 0.40 0.00
#> TCGA.DU.7012.01 2 0.2345 0.881 0.00 0.90 0.10 0.00
#> TCGA.DU.6402.01 1 0.1637 0.612 0.94 0.00 0.00 0.06
#> TCGA.FG.A87Q.01 2 0.0000 0.901 0.00 1.00 0.00 0.00
#> TCGA.14.0862.01 1 0.1637 0.596 0.94 0.00 0.00 0.06
#> TCGA.19.5955.01 1 0.4134 0.253 0.74 0.00 0.00 0.26
#> TCGA.DU.A5TT.01 1 0.4755 0.482 0.76 0.00 0.04 0.20
#> TCGA.76.6662.01 1 0.2011 0.581 0.92 0.00 0.00 0.08
#> TCGA.RR.A6KA.01 2 0.0000 0.901 0.00 1.00 0.00 0.00
#> TCGA.CS.5397.01 2 0.0707 0.900 0.00 0.98 0.02 0.00
#> TCGA.S9.A7R2.01 1 0.4284 0.525 0.78 0.00 0.02 0.20
#> TCGA.76.6193.01 1 0.3606 0.534 0.84 0.00 0.02 0.14
#> TCGA.14.1043.01 1 0.5535 -0.405 0.56 0.00 0.02 0.42
#> TCGA.HT.8110.01 1 0.5915 -0.465 0.56 0.00 0.04 0.40
#> TCGA.06.6391.01 2 0.4907 0.635 0.00 0.58 0.42 0.00
#> TCGA.06.0190.01 1 0.3801 0.366 0.78 0.00 0.00 0.22
#> TCGA.06.0190.02 1 0.3801 0.366 0.78 0.00 0.00 0.22
#> TCGA.28.2501.01 1 0.0707 0.623 0.98 0.00 0.00 0.02
#> TCGA.14.1450.01 2 0.0000 0.901 0.00 1.00 0.00 0.00
#> TCGA.DU.A5TY.01 2 0.2011 0.887 0.00 0.92 0.08 0.00
#> TCGA.DU.5847.01 2 0.0000 0.901 0.00 1.00 0.00 0.00
#> TCGA.76.4928.01 2 0.0000 0.901 0.00 1.00 0.00 0.00
#> TCGA.26.6173.01 1 0.1637 0.606 0.94 0.00 0.00 0.06
#> TCGA.HT.7882.01 1 0.4134 0.253 0.74 0.00 0.00 0.26
#> TCGA.DU.5854.01 2 0.0000 0.901 0.00 1.00 0.00 0.00
#> TCGA.76.6282.01 1 0.5000 -0.654 0.50 0.00 0.00 0.50
#> TCGA.P5.A72U.01 2 0.0000 0.901 0.00 1.00 0.00 0.00
#> TCGA.DU.6404.02 2 0.4948 0.612 0.00 0.56 0.44 0.00
#> TCGA.DU.6404.01 2 0.4948 0.612 0.00 0.56 0.44 0.00
#> TCGA.E1.A7YN.01 2 0.2345 0.881 0.00 0.90 0.10 0.00
#> TCGA.76.6192.01 1 0.3975 0.316 0.76 0.00 0.00 0.24
#> TCGA.74.6575.01 2 0.2345 0.881 0.00 0.90 0.10 0.00
#> TCGA.E1.A7Z2.01 2 0.2345 0.882 0.00 0.90 0.10 0.00
#> TCGA.VM.A8CD.01 1 0.3975 0.487 0.76 0.00 0.00 0.24
#> TCGA.06.A5U1.01 2 0.0000 0.901 0.00 1.00 0.00 0.00
#> TCGA.HT.8564.01 3 0.4977 0.982 0.00 0.00 0.54 0.46
#> TCGA.06.5858.01 2 0.3037 0.870 0.00 0.88 0.10 0.02
#> TCGA.HT.7860.01 2 0.0000 0.901 0.00 1.00 0.00 0.00
#> TCGA.81.5911.01 1 0.2011 0.612 0.92 0.00 0.00 0.08
#> TCGA.DU.7006.01 2 0.2345 0.881 0.00 0.90 0.10 0.00
#> TCGA.E1.A7YM.01 1 0.3400 0.565 0.82 0.00 0.00 0.18
#> TCGA.19.5947.01 2 0.1211 0.896 0.00 0.96 0.04 0.00
#> TCGA.14.0736.02 4 0.5570 0.923 0.44 0.00 0.02 0.54
#> TCGA.HT.A74H.01 1 0.4284 0.523 0.78 0.00 0.02 0.20
#> TCGA.DU.7290.01 2 0.0000 0.901 0.00 1.00 0.00 0.00
#> TCGA.HT.A4DS.01 2 0.4624 0.715 0.00 0.66 0.34 0.00
#> TCGA.RR.A6KB.01 1 0.4079 0.548 0.80 0.00 0.02 0.18
#> TCGA.06.5416.01 2 0.4855 0.657 0.00 0.60 0.40 0.00
#> TCGA.DU.8158.01 2 0.1637 0.890 0.00 0.94 0.06 0.00
#> TCGA.41.6646.01 2 0.0000 0.901 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.FG.6688.01 2 0.3513 0.7041 0.00 0.80 0.00 0.02 0.18
#> TCGA.28.5213.01 1 0.2516 0.4885 0.86 0.00 0.00 0.14 0.00
#> TCGA.19.1389.01 4 0.6929 0.7572 0.32 0.00 0.04 0.50 0.14
#> TCGA.19.5953.01 1 0.1732 0.5192 0.92 0.00 0.00 0.08 0.00
#> TCGA.4W.AA9T.01 2 0.0000 0.8136 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A7IX.01 1 0.3684 0.4551 0.72 0.00 0.00 0.28 0.00
#> TCGA.06.6700.01 1 0.4966 0.3920 0.70 0.00 0.04 0.24 0.02
#> TCGA.28.5218.01 3 0.1648 0.9436 0.00 0.00 0.94 0.02 0.04
#> TCGA.DU.8165.01 2 0.1410 0.8037 0.00 0.94 0.00 0.00 0.06
#> TCGA.76.6663.01 2 0.0000 0.8136 0.00 1.00 0.00 0.00 0.00
#> TCGA.19.4065.01 1 0.4921 0.1986 0.62 0.00 0.00 0.34 0.04
#> TCGA.CS.4941.01 1 0.3513 0.5202 0.80 0.00 0.00 0.18 0.02
#> TCGA.S9.A6U0.01 1 0.4262 -0.0721 0.56 0.00 0.00 0.44 0.00
#> TCGA.FG.5963.02 3 0.1216 0.9551 0.00 0.00 0.96 0.02 0.02
#> TCGA.HT.A5RC.01 2 0.0000 0.8136 0.00 1.00 0.00 0.00 0.00
#> TCGA.28.5211.01 4 0.7535 0.6909 0.34 0.00 0.10 0.44 0.12
#> TCGA.QH.A6CX.01 1 0.4132 0.4592 0.72 0.00 0.00 0.26 0.02
#> TCGA.06.A6S1.01 5 0.4840 0.7995 0.00 0.32 0.00 0.04 0.64
#> TCGA.CS.6186.01 1 0.2516 0.5331 0.86 0.00 0.00 0.14 0.00
#> TCGA.S9.A6UA.01 3 0.0609 0.9630 0.00 0.00 0.98 0.00 0.02
#> TCGA.DU.A7TB.01 3 0.0609 0.9650 0.00 0.00 0.98 0.02 0.00
#> TCGA.DU.A76K.01 1 0.2516 0.5304 0.86 0.00 0.00 0.14 0.00
#> TCGA.E1.A7YQ.01 2 0.0609 0.8146 0.00 0.98 0.00 0.00 0.02
#> TCGA.19.1389.02 4 0.6929 0.7572 0.32 0.00 0.04 0.50 0.14
#> TCGA.26.6174.01 5 0.3684 0.8705 0.00 0.28 0.00 0.00 0.72
#> TCGA.DU.7012.01 2 0.4840 0.4254 0.00 0.64 0.00 0.04 0.32
#> TCGA.DU.6402.01 1 0.2020 0.5168 0.90 0.00 0.00 0.10 0.00
#> TCGA.FG.A87Q.01 2 0.0000 0.8136 0.00 1.00 0.00 0.00 0.00
#> TCGA.14.0862.01 1 0.3513 0.4445 0.80 0.00 0.00 0.18 0.02
#> TCGA.19.5955.01 1 0.4360 0.3103 0.68 0.00 0.00 0.30 0.02
#> TCGA.DU.A5TT.01 1 0.4360 0.4195 0.68 0.00 0.00 0.30 0.02
#> TCGA.76.6662.01 1 0.2616 0.5032 0.88 0.00 0.00 0.10 0.02
#> TCGA.RR.A6KA.01 2 0.0609 0.8146 0.00 0.98 0.00 0.00 0.02
#> TCGA.CS.5397.01 2 0.1648 0.8064 0.00 0.94 0.00 0.02 0.04
#> TCGA.S9.A7R2.01 1 0.4613 0.3348 0.62 0.00 0.00 0.36 0.02
#> TCGA.76.6193.01 1 0.3521 0.5235 0.82 0.00 0.00 0.14 0.04
#> TCGA.14.1043.01 1 0.6727 -0.4919 0.46 0.00 0.10 0.40 0.04
#> TCGA.HT.8110.01 4 0.6539 0.3577 0.42 0.00 0.08 0.46 0.04
#> TCGA.06.6391.01 5 0.4254 0.8630 0.00 0.22 0.00 0.04 0.74
#> TCGA.06.0190.01 1 0.4360 0.3103 0.68 0.00 0.00 0.30 0.02
#> TCGA.06.0190.02 1 0.4360 0.3103 0.68 0.00 0.00 0.30 0.02
#> TCGA.28.2501.01 1 0.2732 0.5424 0.84 0.00 0.00 0.16 0.00
#> TCGA.14.1450.01 2 0.0000 0.8136 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.A5TY.01 2 0.4254 0.6391 0.00 0.74 0.00 0.04 0.22
#> TCGA.DU.5847.01 2 0.0000 0.8136 0.00 1.00 0.00 0.00 0.00
#> TCGA.76.4928.01 2 0.1410 0.8001 0.00 0.94 0.00 0.00 0.06
#> TCGA.26.6173.01 1 0.2516 0.5008 0.86 0.00 0.00 0.14 0.00
#> TCGA.HT.7882.01 1 0.4540 0.2516 0.64 0.00 0.00 0.34 0.02
#> TCGA.DU.5854.01 2 0.1410 0.8001 0.00 0.94 0.00 0.00 0.06
#> TCGA.76.6282.01 1 0.5695 -0.3240 0.48 0.00 0.02 0.46 0.04
#> TCGA.P5.A72U.01 2 0.0000 0.8136 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.6404.02 5 0.4254 0.8630 0.00 0.22 0.00 0.04 0.74
#> TCGA.DU.6404.01 5 0.4254 0.8630 0.00 0.22 0.00 0.04 0.74
#> TCGA.E1.A7YN.01 2 0.4840 0.4237 0.00 0.64 0.00 0.04 0.32
#> TCGA.76.6192.01 1 0.4360 0.3103 0.68 0.00 0.00 0.30 0.02
#> TCGA.74.6575.01 2 0.4527 0.5725 0.00 0.70 0.00 0.04 0.26
#> TCGA.E1.A7Z2.01 2 0.4840 0.4007 0.00 0.64 0.00 0.04 0.32
#> TCGA.VM.A8CD.01 1 0.4456 0.4013 0.66 0.00 0.00 0.32 0.02
#> TCGA.06.A5U1.01 2 0.2020 0.7866 0.00 0.90 0.00 0.00 0.10
#> TCGA.HT.8564.01 3 0.0609 0.9607 0.00 0.00 0.98 0.02 0.00
#> TCGA.06.5858.01 2 0.5597 0.3750 0.00 0.64 0.00 0.16 0.20
#> TCGA.HT.7860.01 2 0.0000 0.8136 0.00 1.00 0.00 0.00 0.00
#> TCGA.81.5911.01 1 0.1410 0.5470 0.94 0.00 0.00 0.06 0.00
#> TCGA.DU.7006.01 2 0.4527 0.5712 0.00 0.70 0.00 0.04 0.26
#> TCGA.E1.A7YM.01 1 0.4360 0.4253 0.68 0.00 0.00 0.30 0.02
#> TCGA.19.5947.01 2 0.4433 0.6487 0.00 0.74 0.00 0.06 0.20
#> TCGA.14.0736.02 4 0.7399 0.7201 0.30 0.00 0.14 0.48 0.08
#> TCGA.HT.A74H.01 1 0.4920 0.3928 0.66 0.00 0.02 0.30 0.02
#> TCGA.DU.7290.01 2 0.0609 0.8146 0.00 0.98 0.00 0.00 0.02
#> TCGA.HT.A4DS.01 5 0.4613 0.7355 0.00 0.36 0.00 0.02 0.62
#> TCGA.RR.A6KB.01 1 0.3903 0.4938 0.80 0.00 0.02 0.16 0.02
#> TCGA.06.5416.01 5 0.3684 0.8705 0.00 0.28 0.00 0.00 0.72
#> TCGA.DU.8158.01 2 0.3561 0.5521 0.00 0.74 0.00 0.00 0.26
#> TCGA.41.6646.01 2 0.0000 0.8136 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.FG.6688.01 2 0.3460 0.69911 0.00 0.76 0.00 0.02 0.22 0.00
#> TCGA.28.5213.01 1 0.3819 0.36202 0.70 0.00 0.00 0.02 0.00 0.28
#> TCGA.19.1389.01 4 0.5150 0.81030 0.16 0.00 0.00 0.62 0.00 0.22
#> TCGA.19.5953.01 1 0.4502 0.12642 0.64 0.00 0.00 0.02 0.02 0.32
#> TCGA.4W.AA9T.01 2 0.0000 0.81861 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IX.01 6 0.3076 0.68346 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.06.6700.01 6 0.6109 0.47553 0.40 0.00 0.06 0.04 0.02 0.48
#> TCGA.28.5218.01 3 0.3795 0.81554 0.12 0.00 0.80 0.06 0.00 0.02
#> TCGA.DU.8165.01 2 0.2728 0.76343 0.00 0.86 0.00 0.04 0.10 0.00
#> TCGA.76.6663.01 2 0.0000 0.81861 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.19.4065.01 1 0.2725 0.61769 0.88 0.00 0.00 0.04 0.02 0.06
#> TCGA.CS.4941.01 6 0.3851 0.39030 0.46 0.00 0.00 0.00 0.00 0.54
#> TCGA.S9.A6U0.01 1 0.3045 0.56717 0.86 0.00 0.00 0.06 0.02 0.06
#> TCGA.FG.5963.02 3 0.1267 0.86880 0.00 0.00 0.94 0.06 0.00 0.00
#> TCGA.HT.A5RC.01 2 0.0000 0.81861 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.28.5211.01 1 0.5586 -0.52509 0.44 0.00 0.00 0.42 0.00 0.14
#> TCGA.QH.A6CX.01 6 0.3711 0.67742 0.26 0.00 0.00 0.00 0.02 0.72
#> TCGA.06.A6S1.01 5 0.3819 0.66791 0.00 0.28 0.00 0.02 0.70 0.00
#> TCGA.CS.6186.01 6 0.4637 0.53779 0.36 0.00 0.00 0.02 0.02 0.60
#> TCGA.S9.A6UA.01 3 0.3600 0.84059 0.08 0.00 0.82 0.08 0.00 0.02
#> TCGA.DU.A7TB.01 3 0.1480 0.87371 0.00 0.00 0.94 0.04 0.00 0.02
#> TCGA.DU.A76K.01 6 0.4731 0.50894 0.40 0.00 0.00 0.02 0.02 0.56
#> TCGA.E1.A7YQ.01 2 0.0937 0.81525 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.19.1389.02 4 0.5150 0.81030 0.16 0.00 0.00 0.62 0.00 0.22
#> TCGA.26.6174.01 5 0.2048 0.82267 0.00 0.12 0.00 0.00 0.88 0.00
#> TCGA.DU.7012.01 2 0.4282 0.31190 0.00 0.56 0.00 0.02 0.42 0.00
#> TCGA.DU.6402.01 1 0.4913 0.16255 0.60 0.00 0.00 0.04 0.02 0.34
#> TCGA.FG.A87Q.01 2 0.0000 0.81861 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.14.0862.01 1 0.2094 0.59269 0.90 0.00 0.00 0.02 0.00 0.08
#> TCGA.19.5955.01 1 0.0547 0.62341 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DU.A5TT.01 6 0.2631 0.66805 0.18 0.00 0.00 0.00 0.00 0.82
#> TCGA.76.6662.01 1 0.4502 0.20607 0.64 0.00 0.00 0.02 0.02 0.32
#> TCGA.RR.A6KA.01 2 0.0000 0.81861 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.5397.01 2 0.2350 0.78894 0.00 0.88 0.00 0.02 0.10 0.00
#> TCGA.S9.A7R2.01 6 0.3460 0.68468 0.22 0.00 0.00 0.02 0.00 0.76
#> TCGA.76.6193.01 6 0.5213 0.53139 0.40 0.00 0.02 0.02 0.02 0.54
#> TCGA.14.1043.01 6 0.7048 -0.29854 0.24 0.00 0.12 0.18 0.00 0.46
#> TCGA.HT.8110.01 6 0.6584 0.03697 0.24 0.00 0.06 0.20 0.00 0.50
#> TCGA.06.6391.01 5 0.3258 0.80442 0.00 0.10 0.00 0.04 0.84 0.02
#> TCGA.06.0190.01 1 0.2725 0.60488 0.88 0.00 0.00 0.04 0.02 0.06
#> TCGA.06.0190.02 1 0.2345 0.60863 0.90 0.00 0.00 0.02 0.02 0.06
#> TCGA.28.2501.01 6 0.5106 0.38804 0.44 0.00 0.00 0.04 0.02 0.50
#> TCGA.14.1450.01 2 0.0000 0.81861 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TY.01 2 0.3711 0.65200 0.00 0.72 0.00 0.02 0.26 0.00
#> TCGA.DU.5847.01 2 0.0000 0.81861 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.4928.01 2 0.1267 0.80991 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.26.6173.01 1 0.4845 0.05361 0.54 0.00 0.00 0.06 0.00 0.40
#> TCGA.HT.7882.01 1 0.0547 0.62132 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DU.5854.01 2 0.0937 0.81625 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.76.6282.01 1 0.4838 0.22853 0.70 0.00 0.00 0.18 0.02 0.10
#> TCGA.P5.A72U.01 2 0.0000 0.81861 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6404.02 5 0.4519 0.77311 0.00 0.10 0.00 0.08 0.76 0.06
#> TCGA.DU.6404.01 5 0.4519 0.77311 0.00 0.10 0.00 0.08 0.76 0.06
#> TCGA.E1.A7YN.01 2 0.4144 0.48556 0.00 0.62 0.00 0.02 0.36 0.00
#> TCGA.76.6192.01 1 0.1480 0.61990 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.74.6575.01 2 0.3076 0.69297 0.00 0.76 0.00 0.00 0.24 0.00
#> TCGA.E1.A7Z2.01 2 0.4482 0.44623 0.00 0.60 0.00 0.04 0.36 0.00
#> TCGA.VM.A8CD.01 6 0.4179 0.63691 0.16 0.00 0.02 0.06 0.00 0.76
#> TCGA.06.A5U1.01 2 0.0937 0.81601 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.HT.8564.01 3 0.1807 0.87475 0.00 0.00 0.92 0.06 0.00 0.02
#> TCGA.06.5858.01 2 0.6646 -0.00873 0.00 0.42 0.00 0.32 0.22 0.04
#> TCGA.HT.7860.01 2 0.0000 0.81861 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.81.5911.01 1 0.5347 -0.15607 0.50 0.00 0.00 0.06 0.02 0.42
#> TCGA.DU.7006.01 2 0.4078 0.52492 0.00 0.64 0.00 0.02 0.34 0.00
#> TCGA.E1.A7YM.01 6 0.3076 0.68387 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.19.5947.01 2 0.3460 0.70140 0.00 0.76 0.00 0.02 0.22 0.00
#> TCGA.14.0736.02 4 0.6965 0.53325 0.26 0.00 0.06 0.38 0.00 0.30
#> TCGA.HT.A74H.01 6 0.4917 0.64884 0.18 0.00 0.04 0.02 0.04 0.72
#> TCGA.DU.7290.01 2 0.1092 0.81542 0.00 0.96 0.00 0.02 0.02 0.00
#> TCGA.HT.A4DS.01 5 0.4172 0.64522 0.00 0.28 0.00 0.04 0.68 0.00
#> TCGA.RR.A6KB.01 6 0.5672 0.60994 0.32 0.00 0.02 0.04 0.04 0.58
#> TCGA.06.5416.01 5 0.2981 0.81373 0.00 0.16 0.00 0.02 0.82 0.00
#> TCGA.DU.8158.01 2 0.3198 0.60978 0.00 0.74 0.00 0.00 0.26 0.00
#> TCGA.41.6646.01 2 0.0547 0.80647 0.00 0.98 0.00 0.00 0.02 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.FG.6688.01 2 0.2945 0.52440 0.00 0.74 0.00 0.00 0.26 0.00 0.00
#> TCGA.28.5213.01 1 0.4070 0.42775 0.62 0.00 0.00 0.00 0.00 0.34 0.04
#> TCGA.19.1389.01 4 0.3667 0.68489 0.20 0.00 0.00 0.74 0.00 0.06 0.00
#> TCGA.19.5953.01 1 0.3546 0.14776 0.54 0.00 0.00 0.00 0.00 0.46 0.00
#> TCGA.4W.AA9T.01 2 0.0000 0.73479 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IX.01 6 0.1363 0.72745 0.00 0.00 0.00 0.00 0.02 0.94 0.04
#> TCGA.06.6700.01 6 0.6106 -0.02038 0.42 0.00 0.04 0.08 0.00 0.42 0.04
#> TCGA.28.5218.01 3 0.4963 0.59095 0.16 0.00 0.64 0.18 0.00 0.00 0.02
#> TCGA.DU.8165.01 2 0.3744 0.56797 0.00 0.78 0.00 0.02 0.12 0.00 0.08
#> TCGA.76.6663.01 2 0.0000 0.73479 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.4065.01 1 0.1664 0.60655 0.92 0.00 0.00 0.02 0.00 0.06 0.00
#> TCGA.CS.4941.01 6 0.4974 0.31254 0.34 0.00 0.02 0.00 0.04 0.58 0.02
#> TCGA.S9.A6U0.01 1 0.2769 0.51756 0.86 0.00 0.00 0.08 0.00 0.04 0.02
#> TCGA.FG.5963.02 3 0.3058 0.66140 0.00 0.00 0.82 0.10 0.00 0.00 0.08
#> TCGA.HT.A5RC.01 2 0.0000 0.73479 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.5211.01 1 0.4710 -0.49430 0.48 0.00 0.04 0.46 0.00 0.00 0.02
#> TCGA.QH.A6CX.01 6 0.3485 0.70212 0.10 0.00 0.02 0.02 0.00 0.82 0.04
#> TCGA.06.A6S1.01 5 0.2259 0.52532 0.00 0.16 0.00 0.00 0.84 0.00 0.00
#> TCGA.CS.6186.01 6 0.3142 0.69655 0.06 0.00 0.02 0.02 0.02 0.86 0.02
#> TCGA.S9.A6UA.01 3 0.4478 0.61632 0.14 0.00 0.66 0.20 0.00 0.00 0.00
#> TCGA.DU.A7TB.01 3 0.4340 0.67647 0.00 0.00 0.72 0.12 0.00 0.02 0.14
#> TCGA.DU.A76K.01 6 0.2355 0.71175 0.04 0.00 0.00 0.02 0.02 0.90 0.02
#> TCGA.E1.A7YQ.01 2 0.3061 0.66231 0.00 0.84 0.00 0.02 0.06 0.00 0.08
#> TCGA.19.1389.02 4 0.3667 0.68489 0.20 0.00 0.00 0.74 0.00 0.06 0.00
#> TCGA.26.6174.01 5 0.1928 0.51549 0.00 0.08 0.00 0.00 0.90 0.00 0.02
#> TCGA.DU.7012.01 5 0.3546 0.15934 0.00 0.46 0.00 0.00 0.54 0.00 0.00
#> TCGA.DU.6402.01 6 0.4269 0.25226 0.36 0.00 0.00 0.02 0.00 0.60 0.02
#> TCGA.FG.A87Q.01 2 0.0000 0.73479 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.14.0862.01 1 0.4530 0.47655 0.64 0.00 0.00 0.02 0.02 0.30 0.02
#> TCGA.19.5955.01 1 0.2278 0.62396 0.88 0.00 0.00 0.00 0.00 0.08 0.04
#> TCGA.DU.A5TT.01 6 0.1860 0.71284 0.00 0.00 0.02 0.00 0.04 0.92 0.02
#> TCGA.76.6662.01 1 0.3867 0.35367 0.60 0.00 0.00 0.00 0.00 0.38 0.02
#> TCGA.RR.A6KA.01 2 0.0504 0.72516 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CS.5397.01 2 0.2422 0.63484 0.00 0.82 0.00 0.00 0.18 0.00 0.00
#> TCGA.S9.A7R2.01 6 0.2159 0.71131 0.02 0.00 0.00 0.02 0.00 0.90 0.06
#> TCGA.76.6193.01 6 0.3086 0.66930 0.16 0.00 0.00 0.00 0.00 0.80 0.04
#> TCGA.14.1043.01 4 0.6947 0.36480 0.30 0.00 0.08 0.36 0.00 0.24 0.02
#> TCGA.HT.8110.01 1 0.7051 -0.23380 0.36 0.00 0.06 0.26 0.00 0.28 0.04
#> TCGA.06.6391.01 5 0.3617 0.46008 0.00 0.08 0.00 0.00 0.76 0.00 0.16
#> TCGA.06.0190.01 1 0.3876 0.62224 0.78 0.00 0.00 0.04 0.02 0.14 0.02
#> TCGA.06.0190.02 1 0.3876 0.62224 0.78 0.00 0.00 0.04 0.02 0.14 0.02
#> TCGA.28.2501.01 6 0.3745 0.57703 0.26 0.00 0.00 0.00 0.00 0.70 0.04
#> TCGA.14.1450.01 2 0.0000 0.73479 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TY.01 2 0.3496 0.19908 0.00 0.58 0.00 0.00 0.42 0.00 0.00
#> TCGA.DU.5847.01 2 0.1664 0.69171 0.00 0.92 0.00 0.02 0.00 0.00 0.06
#> TCGA.76.4928.01 2 0.0863 0.72478 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.26.6173.01 6 0.5560 0.01350 0.44 0.00 0.02 0.02 0.02 0.46 0.04
#> TCGA.HT.7882.01 1 0.1166 0.60956 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.DU.5854.01 2 0.1433 0.70796 0.00 0.92 0.00 0.00 0.08 0.00 0.00
#> TCGA.76.6282.01 1 0.4589 0.24488 0.68 0.00 0.00 0.22 0.00 0.06 0.04
#> TCGA.P5.A72U.01 2 0.0000 0.73479 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6404.02 5 0.4191 0.32331 0.00 0.06 0.00 0.00 0.64 0.00 0.30
#> TCGA.DU.6404.01 5 0.4191 0.32331 0.00 0.06 0.00 0.00 0.64 0.00 0.30
#> TCGA.E1.A7YN.01 5 0.3558 0.09086 0.00 0.48 0.00 0.00 0.52 0.00 0.00
#> TCGA.76.6192.01 1 0.2081 0.63044 0.86 0.00 0.00 0.00 0.00 0.14 0.00
#> TCGA.74.6575.01 2 0.3562 -0.12512 0.00 0.50 0.00 0.00 0.50 0.00 0.00
#> TCGA.E1.A7Z2.01 5 0.4901 0.20767 0.00 0.40 0.00 0.02 0.52 0.00 0.06
#> TCGA.VM.A8CD.01 6 0.2509 0.68236 0.00 0.00 0.06 0.02 0.00 0.88 0.04
#> TCGA.06.A5U1.01 2 0.1433 0.70671 0.00 0.92 0.00 0.00 0.08 0.00 0.00
#> TCGA.HT.8564.01 3 0.1718 0.71187 0.00 0.00 0.92 0.04 0.00 0.04 0.00
#> TCGA.06.5858.01 7 0.6947 0.00000 0.00 0.34 0.02 0.10 0.18 0.00 0.36
#> TCGA.HT.7860.01 2 0.0000 0.73479 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.81.5911.01 6 0.3386 0.61974 0.18 0.00 0.00 0.02 0.00 0.78 0.02
#> TCGA.DU.7006.01 2 0.3546 -0.00929 0.00 0.54 0.00 0.00 0.46 0.00 0.00
#> TCGA.E1.A7YM.01 6 0.0504 0.72289 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.19.5947.01 2 0.3867 0.25993 0.00 0.60 0.00 0.00 0.38 0.00 0.02
#> TCGA.14.0736.02 4 0.6261 0.61029 0.30 0.00 0.08 0.50 0.00 0.10 0.02
#> TCGA.HT.A74H.01 6 0.3257 0.68366 0.02 0.00 0.04 0.02 0.00 0.84 0.08
#> TCGA.DU.7290.01 2 0.2804 0.66881 0.00 0.86 0.00 0.02 0.06 0.00 0.06
#> TCGA.HT.A4DS.01 5 0.2832 0.46318 0.00 0.24 0.00 0.00 0.76 0.00 0.00
#> TCGA.RR.A6KB.01 6 0.2654 0.71064 0.10 0.00 0.00 0.02 0.00 0.86 0.02
#> TCGA.06.5416.01 5 0.2163 0.52271 0.00 0.10 0.00 0.00 0.88 0.00 0.02
#> TCGA.DU.8158.01 2 0.4908 0.24767 0.00 0.62 0.00 0.02 0.26 0.00 0.10
#> TCGA.41.6646.01 2 0.1363 0.68657 0.00 0.94 0.00 0.00 0.02 0.00 0.04
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.FG.6688.01 2 0.4144 0.4282 0.00 0.66 0.00 0.00 0.12 0.00 0.00 0.22
#> TCGA.28.5213.01 1 0.4162 0.5083 0.66 0.00 0.00 0.02 0.00 0.28 0.02 0.02
#> TCGA.19.1389.01 4 0.1887 0.5285 0.04 0.00 0.00 0.90 0.00 0.06 0.00 0.00
#> TCGA.19.5953.01 1 0.3907 0.3181 0.58 0.00 0.00 0.00 0.00 0.38 0.00 0.04
#> TCGA.4W.AA9T.01 2 0.0471 0.7080 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.S9.A7IX.01 6 0.2348 0.6815 0.06 0.00 0.00 0.02 0.00 0.88 0.00 0.04
#> TCGA.06.6700.01 6 0.6955 0.2381 0.26 0.00 0.04 0.04 0.00 0.44 0.14 0.08
#> TCGA.28.5218.01 3 0.2864 0.6662 0.08 0.00 0.84 0.06 0.00 0.02 0.00 0.00
#> TCGA.DU.8165.01 2 0.2399 0.6586 0.00 0.88 0.00 0.00 0.04 0.00 0.04 0.04
#> TCGA.76.6663.01 2 0.0000 0.7092 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.4065.01 1 0.3048 0.6432 0.84 0.00 0.00 0.02 0.00 0.04 0.02 0.08
#> TCGA.CS.4941.01 6 0.3907 0.2688 0.38 0.00 0.00 0.00 0.00 0.58 0.00 0.04
#> TCGA.S9.A6U0.01 1 0.3758 0.4551 0.76 0.00 0.00 0.14 0.00 0.00 0.04 0.06
#> TCGA.FG.5963.02 3 0.5159 0.5698 0.02 0.00 0.52 0.00 0.00 0.00 0.30 0.16
#> TCGA.HT.A5RC.01 2 0.0471 0.7080 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.28.5211.01 4 0.4672 0.4954 0.26 0.00 0.04 0.64 0.00 0.00 0.04 0.02
#> TCGA.QH.A6CX.01 6 0.2591 0.6625 0.04 0.00 0.00 0.08 0.00 0.86 0.00 0.02
#> TCGA.06.A6S1.01 8 0.4971 0.8014 0.00 0.18 0.00 0.00 0.36 0.00 0.00 0.46
#> TCGA.CS.6186.01 6 0.4272 0.6017 0.16 0.00 0.00 0.02 0.00 0.72 0.02 0.08
#> TCGA.S9.A6UA.01 3 0.5155 0.6549 0.08 0.00 0.72 0.04 0.02 0.06 0.04 0.04
#> TCGA.DU.A7TB.01 3 0.5428 0.6470 0.02 0.00 0.60 0.02 0.02 0.00 0.22 0.12
#> TCGA.DU.A76K.01 6 0.3002 0.6517 0.12 0.00 0.00 0.02 0.00 0.82 0.00 0.04
#> TCGA.E1.A7YQ.01 2 0.1275 0.6989 0.00 0.94 0.00 0.00 0.04 0.00 0.00 0.02
#> TCGA.19.1389.02 4 0.1887 0.5285 0.04 0.00 0.00 0.90 0.00 0.06 0.00 0.00
#> TCGA.26.6174.01 5 0.4554 -0.3943 0.00 0.10 0.00 0.00 0.48 0.00 0.00 0.42
#> TCGA.DU.7012.01 2 0.4943 -0.1095 0.00 0.48 0.00 0.00 0.18 0.00 0.00 0.34
#> TCGA.DU.6402.01 1 0.4803 0.0227 0.46 0.00 0.00 0.02 0.00 0.44 0.00 0.08
#> TCGA.FG.A87Q.01 2 0.0000 0.7092 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.14.0862.01 1 0.4700 0.5071 0.62 0.00 0.00 0.04 0.00 0.26 0.00 0.08
#> TCGA.19.5955.01 1 0.1887 0.6623 0.90 0.00 0.00 0.00 0.00 0.04 0.00 0.06
#> TCGA.DU.A5TT.01 6 0.3264 0.6611 0.02 0.00 0.02 0.02 0.00 0.84 0.04 0.06
#> TCGA.76.6662.01 1 0.4028 0.5142 0.66 0.00 0.00 0.02 0.00 0.28 0.00 0.04
#> TCGA.RR.A6KA.01 2 0.0000 0.7092 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.5397.01 2 0.2994 0.6347 0.00 0.80 0.00 0.00 0.06 0.00 0.00 0.14
#> TCGA.S9.A7R2.01 6 0.2807 0.6614 0.02 0.00 0.02 0.06 0.00 0.86 0.00 0.04
#> TCGA.76.6193.01 6 0.5151 0.2378 0.38 0.00 0.02 0.02 0.00 0.52 0.04 0.02
#> TCGA.14.1043.01 4 0.7769 0.3491 0.18 0.00 0.12 0.32 0.00 0.26 0.06 0.06
#> TCGA.HT.8110.01 4 0.7366 0.2934 0.28 0.00 0.10 0.30 0.00 0.18 0.14 0.00
#> TCGA.06.6391.01 5 0.3504 0.3521 0.00 0.04 0.00 0.00 0.70 0.00 0.00 0.26
#> TCGA.06.0190.01 1 0.2532 0.6580 0.88 0.00 0.00 0.04 0.00 0.04 0.02 0.02
#> TCGA.06.0190.02 1 0.2532 0.6580 0.88 0.00 0.00 0.04 0.00 0.04 0.02 0.02
#> TCGA.28.2501.01 6 0.4417 0.3690 0.36 0.00 0.00 0.02 0.00 0.58 0.02 0.02
#> TCGA.14.1450.01 2 0.0000 0.7092 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TY.01 2 0.4482 0.2831 0.00 0.60 0.00 0.00 0.14 0.00 0.00 0.26
#> TCGA.DU.5847.01 2 0.0000 0.7092 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.4928.01 2 0.0808 0.7097 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.26.6173.01 1 0.5943 0.2805 0.48 0.00 0.00 0.06 0.00 0.30 0.02 0.14
#> TCGA.HT.7882.01 1 0.1275 0.6592 0.94 0.00 0.00 0.02 0.00 0.04 0.00 0.00
#> TCGA.DU.5854.01 2 0.0941 0.7108 0.00 0.96 0.00 0.00 0.02 0.00 0.00 0.02
#> TCGA.76.6282.01 1 0.6493 -0.1513 0.46 0.00 0.06 0.32 0.00 0.08 0.04 0.04
#> TCGA.P5.A72U.01 2 0.0471 0.7080 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DU.6404.02 5 0.0471 0.4897 0.00 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.DU.6404.01 5 0.0471 0.4897 0.00 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.E1.A7YN.01 2 0.4897 0.0433 0.00 0.52 0.00 0.00 0.20 0.00 0.00 0.28
#> TCGA.76.6192.01 1 0.3397 0.6424 0.80 0.00 0.00 0.04 0.00 0.10 0.00 0.06
#> TCGA.74.6575.01 2 0.4943 -0.1247 0.00 0.48 0.00 0.00 0.18 0.00 0.00 0.34
#> TCGA.E1.A7Z2.01 2 0.5103 -0.3598 0.00 0.44 0.00 0.00 0.22 0.00 0.00 0.34
#> TCGA.VM.A8CD.01 6 0.3585 0.6694 0.04 0.00 0.02 0.04 0.00 0.82 0.02 0.06
#> TCGA.06.A5U1.01 2 0.2407 0.6683 0.00 0.86 0.00 0.00 0.06 0.00 0.00 0.08
#> TCGA.HT.8564.01 3 0.2348 0.6954 0.00 0.00 0.88 0.00 0.00 0.04 0.02 0.06
#> TCGA.06.5858.01 7 0.5750 0.0000 0.00 0.28 0.00 0.06 0.06 0.00 0.54 0.06
#> TCGA.HT.7860.01 2 0.0000 0.7092 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.81.5911.01 6 0.5028 0.2558 0.36 0.00 0.00 0.06 0.00 0.52 0.00 0.06
#> TCGA.DU.7006.01 2 0.4841 -0.0483 0.00 0.50 0.00 0.00 0.16 0.00 0.00 0.34
#> TCGA.E1.A7YM.01 6 0.2399 0.6892 0.04 0.00 0.00 0.04 0.00 0.88 0.00 0.04
#> TCGA.19.5947.01 2 0.5257 0.1836 0.00 0.54 0.00 0.00 0.14 0.00 0.04 0.28
#> TCGA.14.0736.02 4 0.6970 0.4203 0.16 0.00 0.16 0.48 0.00 0.08 0.10 0.02
#> TCGA.HT.A74H.01 6 0.4087 0.6321 0.02 0.00 0.04 0.02 0.00 0.78 0.06 0.08
#> TCGA.DU.7290.01 2 0.1091 0.7014 0.00 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.HT.A4DS.01 8 0.5103 0.8259 0.00 0.22 0.00 0.00 0.34 0.00 0.00 0.44
#> TCGA.RR.A6KB.01 6 0.5254 0.6133 0.14 0.00 0.04 0.04 0.00 0.68 0.04 0.06
#> TCGA.06.5416.01 5 0.4562 -0.4577 0.00 0.10 0.00 0.00 0.46 0.00 0.00 0.44
#> TCGA.DU.8158.01 2 0.3434 0.5499 0.00 0.76 0.00 0.00 0.14 0.00 0.00 0.10
#> TCGA.41.6646.01 2 0.0808 0.6701 0.00 0.96 0.00 0.00 0.00 0.00 0.04 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node012. Child nodes: Node01111-leaf , Node01112-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01211-leaf , Node01212-leaf , Node01213 , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node01224-leaf , Node01225-leaf , Node01311-leaf , Node01312-leaf , Node01313-leaf , Node01411-leaf , Node01412-leaf , Node01431-leaf , Node01432-leaf , Node02211-leaf , Node02212 , Node02221 , Node02222-leaf , Node02223-leaf , Node02231 , Node02232-leaf , Node02233-leaf , Node02234-leaf , Node02311-leaf , Node02312-leaf , Node02313-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 35 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 0.4443 0.556 0.556
#> 3 3 1.000 0.969 0.966 0.4832 0.664 0.451
#> 4 4 0.793 0.753 0.852 0.1337 0.845 0.568
#> 5 5 0.710 0.418 0.639 0.0520 0.874 0.566
#> 6 6 0.830 0.823 0.863 0.0433 0.872 0.522
#> 7 7 0.841 0.825 0.838 0.0371 0.966 0.815
#> 8 8 0.841 0.601 0.722 0.0233 0.948 0.684
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.28.5213.01 1 0 1 1 0
#> TCGA.19.1389.01 1 0 1 1 0
#> TCGA.19.5953.01 1 0 1 1 0
#> TCGA.S9.A7IX.01 2 0 1 0 1
#> TCGA.06.6700.01 1 0 1 1 0
#> TCGA.19.4065.01 1 0 1 1 0
#> TCGA.CS.4941.01 1 0 1 1 0
#> TCGA.S9.A6U0.01 1 0 1 1 0
#> TCGA.28.5211.01 1 0 1 1 0
#> TCGA.QH.A6CX.01 2 0 1 0 1
#> TCGA.CS.6186.01 2 0 1 0 1
#> TCGA.DU.A76K.01 2 0 1 0 1
#> TCGA.19.1389.02 1 0 1 1 0
#> TCGA.DU.6402.01 2 0 1 0 1
#> TCGA.14.0862.01 1 0 1 1 0
#> TCGA.19.5955.01 1 0 1 1 0
#> TCGA.DU.A5TT.01 2 0 1 0 1
#> TCGA.76.6662.01 1 0 1 1 0
#> TCGA.S9.A7R2.01 2 0 1 0 1
#> TCGA.76.6193.01 1 0 1 1 0
#> TCGA.14.1043.01 1 0 1 1 0
#> TCGA.HT.8110.01 1 0 1 1 0
#> TCGA.06.0190.01 1 0 1 1 0
#> TCGA.06.0190.02 1 0 1 1 0
#> TCGA.28.2501.01 1 0 1 1 0
#> TCGA.26.6173.01 1 0 1 1 0
#> TCGA.HT.7882.01 1 0 1 1 0
#> TCGA.76.6282.01 1 0 1 1 0
#> TCGA.76.6192.01 1 0 1 1 0
#> TCGA.VM.A8CD.01 2 0 1 0 1
#> TCGA.81.5911.01 2 0 1 0 1
#> TCGA.E1.A7YM.01 2 0 1 0 1
#> TCGA.14.0736.02 1 0 1 1 0
#> TCGA.HT.A74H.01 2 0 1 0 1
#> TCGA.RR.A6KB.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.28.5213.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.19.1389.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.19.5953.01 3 0.207 0.955 0.06 0.00 0.94
#> TCGA.S9.A7IX.01 2 0.254 0.981 0.00 0.92 0.08
#> TCGA.06.6700.01 3 0.254 0.950 0.08 0.00 0.92
#> TCGA.19.4065.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.CS.4941.01 3 0.207 0.955 0.06 0.00 0.94
#> TCGA.S9.A6U0.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.28.5211.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.QH.A6CX.01 3 0.254 0.857 0.00 0.08 0.92
#> TCGA.CS.6186.01 2 0.000 0.943 0.00 1.00 0.00
#> TCGA.DU.A76K.01 2 0.254 0.981 0.00 0.92 0.08
#> TCGA.19.1389.02 3 0.254 0.950 0.08 0.00 0.92
#> TCGA.DU.6402.01 3 0.000 0.929 0.00 0.00 1.00
#> TCGA.14.0862.01 3 0.207 0.955 0.06 0.00 0.94
#> TCGA.19.5955.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.DU.A5TT.01 2 0.254 0.981 0.00 0.92 0.08
#> TCGA.76.6662.01 3 0.254 0.950 0.08 0.00 0.92
#> TCGA.S9.A7R2.01 2 0.254 0.981 0.00 0.92 0.08
#> TCGA.76.6193.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.14.1043.01 3 0.207 0.955 0.06 0.00 0.94
#> TCGA.HT.8110.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.06.0190.01 3 0.254 0.950 0.08 0.00 0.92
#> TCGA.06.0190.02 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.28.2501.01 3 0.000 0.929 0.00 0.00 1.00
#> TCGA.26.6173.01 3 0.254 0.950 0.08 0.00 0.92
#> TCGA.HT.7882.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.76.6282.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.76.6192.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.VM.A8CD.01 2 0.254 0.981 0.00 0.92 0.08
#> TCGA.81.5911.01 2 0.000 0.943 0.00 1.00 0.00
#> TCGA.E1.A7YM.01 2 0.254 0.981 0.00 0.92 0.08
#> TCGA.14.0736.02 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.HT.A74H.01 3 0.000 0.929 0.00 0.00 1.00
#> TCGA.RR.A6KB.01 3 0.000 0.929 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.28.5213.01 4 0.479 0.425 0.38 0.00 0.00 0.62
#> TCGA.19.1389.01 4 0.479 0.425 0.38 0.00 0.00 0.62
#> TCGA.19.5953.01 3 0.462 0.862 0.00 0.00 0.66 0.34
#> TCGA.S9.A7IX.01 2 0.000 0.923 0.00 1.00 0.00 0.00
#> TCGA.06.6700.01 3 0.462 0.862 0.00 0.00 0.66 0.34
#> TCGA.19.4065.01 1 0.000 0.952 1.00 0.00 0.00 0.00
#> TCGA.CS.4941.01 3 0.462 0.862 0.00 0.00 0.66 0.34
#> TCGA.S9.A6U0.01 1 0.201 0.938 0.92 0.00 0.00 0.08
#> TCGA.28.5211.01 1 0.000 0.952 1.00 0.00 0.00 0.00
#> TCGA.QH.A6CX.01 3 0.428 0.579 0.00 0.28 0.72 0.00
#> TCGA.CS.6186.01 2 0.428 0.775 0.00 0.72 0.28 0.00
#> TCGA.DU.A76K.01 2 0.000 0.923 0.00 1.00 0.00 0.00
#> TCGA.19.1389.02 4 0.201 0.420 0.00 0.00 0.08 0.92
#> TCGA.DU.6402.01 3 0.479 0.843 0.00 0.00 0.62 0.38
#> TCGA.14.0862.01 3 0.479 0.843 0.00 0.00 0.62 0.38
#> TCGA.19.5955.01 1 0.000 0.952 1.00 0.00 0.00 0.00
#> TCGA.DU.A5TT.01 2 0.000 0.923 0.00 1.00 0.00 0.00
#> TCGA.76.6662.01 4 0.201 0.420 0.00 0.00 0.08 0.92
#> TCGA.S9.A7R2.01 2 0.164 0.886 0.00 0.94 0.06 0.00
#> TCGA.76.6193.01 4 0.479 0.425 0.38 0.00 0.00 0.62
#> TCGA.14.1043.01 3 0.471 0.855 0.00 0.00 0.64 0.36
#> TCGA.HT.8110.01 1 0.201 0.938 0.92 0.00 0.00 0.08
#> TCGA.06.0190.01 4 0.164 0.442 0.00 0.00 0.06 0.94
#> TCGA.06.0190.02 1 0.000 0.952 1.00 0.00 0.00 0.00
#> TCGA.28.2501.01 3 0.428 0.844 0.00 0.00 0.72 0.28
#> TCGA.26.6173.01 4 0.428 -0.147 0.00 0.00 0.28 0.72
#> TCGA.HT.7882.01 1 0.000 0.952 1.00 0.00 0.00 0.00
#> TCGA.76.6282.01 1 0.201 0.938 0.92 0.00 0.00 0.08
#> TCGA.76.6192.01 1 0.201 0.938 0.92 0.00 0.00 0.08
#> TCGA.VM.A8CD.01 2 0.000 0.923 0.00 1.00 0.00 0.00
#> TCGA.81.5911.01 2 0.428 0.775 0.00 0.72 0.28 0.00
#> TCGA.E1.A7YM.01 2 0.000 0.923 0.00 1.00 0.00 0.00
#> TCGA.14.0736.02 4 0.479 0.425 0.38 0.00 0.00 0.62
#> TCGA.HT.A74H.01 3 0.428 0.579 0.00 0.28 0.72 0.00
#> TCGA.RR.A6KB.01 3 0.428 0.844 0.00 0.00 0.72 0.28
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.28.5213.01 4 0.473 0.194 0.40 0.00 0.00 0.58 0.02
#> TCGA.19.1389.01 4 0.406 0.283 0.36 0.00 0.00 0.64 0.00
#> TCGA.19.5953.01 4 0.682 -0.360 0.00 0.00 0.32 0.36 0.32
#> TCGA.S9.A7IX.01 2 0.477 0.725 0.00 0.56 0.42 0.00 0.02
#> TCGA.06.6700.01 4 0.682 -0.360 0.00 0.00 0.32 0.36 0.32
#> TCGA.19.4065.01 1 0.311 0.903 0.80 0.00 0.00 0.00 0.20
#> TCGA.CS.4941.01 4 0.682 -0.360 0.00 0.00 0.32 0.36 0.32
#> TCGA.S9.A6U0.01 1 0.000 0.875 1.00 0.00 0.00 0.00 0.00
#> TCGA.28.5211.01 1 0.311 0.903 0.80 0.00 0.00 0.00 0.20
#> TCGA.QH.A6CX.01 3 0.000 0.406 0.00 0.00 1.00 0.00 0.00
#> TCGA.CS.6186.01 2 0.228 0.489 0.00 0.88 0.00 0.00 0.12
#> TCGA.DU.A76K.01 2 0.413 0.781 0.00 0.62 0.38 0.00 0.00
#> TCGA.19.1389.02 4 0.000 0.251 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.6402.01 5 0.596 0.913 0.00 0.00 0.16 0.26 0.58
#> TCGA.14.0862.01 5 0.586 0.910 0.00 0.00 0.12 0.32 0.56
#> TCGA.19.5955.01 1 0.311 0.903 0.80 0.00 0.00 0.00 0.20
#> TCGA.DU.A5TT.01 2 0.413 0.781 0.00 0.62 0.38 0.00 0.00
#> TCGA.76.6662.01 4 0.141 0.215 0.00 0.00 0.00 0.94 0.06
#> TCGA.S9.A7R2.01 3 0.429 -0.666 0.00 0.46 0.54 0.00 0.00
#> TCGA.76.6193.01 4 0.454 0.306 0.34 0.00 0.00 0.64 0.02
#> TCGA.14.1043.01 4 0.679 -0.379 0.00 0.00 0.30 0.38 0.32
#> TCGA.HT.8110.01 1 0.000 0.875 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.0190.01 4 0.000 0.251 0.00 0.00 0.00 1.00 0.00
#> TCGA.06.0190.02 1 0.311 0.903 0.80 0.00 0.00 0.00 0.20
#> TCGA.28.2501.01 3 0.611 -0.147 0.00 0.00 0.56 0.18 0.26
#> TCGA.26.6173.01 4 0.464 -0.277 0.00 0.00 0.04 0.68 0.28
#> TCGA.HT.7882.01 1 0.311 0.903 0.80 0.00 0.00 0.00 0.20
#> TCGA.76.6282.01 1 0.000 0.875 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.6192.01 1 0.000 0.875 1.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8CD.01 2 0.413 0.781 0.00 0.62 0.38 0.00 0.00
#> TCGA.81.5911.01 2 0.141 0.518 0.00 0.94 0.00 0.00 0.06
#> TCGA.E1.A7YM.01 2 0.413 0.781 0.00 0.62 0.38 0.00 0.00
#> TCGA.14.0736.02 4 0.406 0.283 0.36 0.00 0.00 0.64 0.00
#> TCGA.HT.A74H.01 3 0.000 0.406 0.00 0.00 1.00 0.00 0.00
#> TCGA.RR.A6KB.01 3 0.605 -0.110 0.00 0.00 0.56 0.16 0.28
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.28.5213.01 4 0.3321 0.868 0.08 0.00 0.00 0.82 0.00 0.10
#> TCGA.19.1389.01 4 0.1807 0.901 0.06 0.00 0.02 0.92 0.00 0.00
#> TCGA.19.5953.01 3 0.0937 0.861 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.S9.A7IX.01 2 0.0000 0.838 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.6700.01 3 0.0937 0.861 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.19.4065.01 1 0.0000 0.829 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.4941.01 3 0.0937 0.861 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.S9.A6U0.01 1 0.4002 0.779 0.66 0.00 0.00 0.02 0.32 0.00
#> TCGA.28.5211.01 1 0.0000 0.829 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CX.01 2 0.5363 0.573 0.00 0.64 0.20 0.00 0.14 0.02
#> TCGA.CS.6186.01 6 0.2793 0.892 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.DU.A76K.01 2 0.0000 0.838 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.19.1389.02 4 0.0937 0.882 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.DU.6402.01 5 0.5693 0.959 0.00 0.00 0.32 0.04 0.56 0.08
#> TCGA.14.0862.01 5 0.5898 0.960 0.00 0.00 0.30 0.06 0.56 0.08
#> TCGA.19.5955.01 1 0.0000 0.829 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TT.01 2 0.0000 0.838 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.6662.01 4 0.3321 0.853 0.00 0.00 0.08 0.82 0.00 0.10
#> TCGA.S9.A7R2.01 2 0.1807 0.799 0.00 0.92 0.00 0.00 0.06 0.02
#> TCGA.76.6193.01 4 0.3572 0.886 0.06 0.00 0.02 0.82 0.00 0.10
#> TCGA.14.1043.01 3 0.0937 0.861 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.HT.8110.01 1 0.4002 0.779 0.66 0.00 0.00 0.02 0.32 0.00
#> TCGA.06.0190.01 4 0.0937 0.882 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.06.0190.02 1 0.0000 0.829 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.2501.01 3 0.2350 0.745 0.00 0.00 0.88 0.00 0.10 0.02
#> TCGA.26.6173.01 3 0.2941 0.579 0.00 0.00 0.78 0.22 0.00 0.00
#> TCGA.HT.7882.01 1 0.0000 0.829 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6282.01 1 0.4002 0.779 0.66 0.00 0.00 0.02 0.32 0.00
#> TCGA.76.6192.01 1 0.4002 0.779 0.66 0.00 0.00 0.02 0.32 0.00
#> TCGA.VM.A8CD.01 2 0.0000 0.838 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.81.5911.01 6 0.3819 0.894 0.00 0.28 0.00 0.02 0.00 0.70
#> TCGA.E1.A7YM.01 2 0.0000 0.838 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.14.0736.02 4 0.1807 0.901 0.06 0.00 0.02 0.92 0.00 0.00
#> TCGA.HT.A74H.01 2 0.5363 0.573 0.00 0.64 0.20 0.00 0.14 0.02
#> TCGA.RR.A6KB.01 3 0.2350 0.744 0.00 0.00 0.88 0.00 0.10 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.28.5213.01 4 0.3985 0.739 0.00 0.00 0.00 0.72 0.10 0.00 0.18
#> TCGA.19.1389.01 4 0.0504 0.794 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.19.5953.01 3 0.0000 0.788 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IX.01 2 0.2081 0.834 0.00 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.06.6700.01 3 0.0000 0.788 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.19.4065.01 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.4941.01 3 0.0863 0.769 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.S9.A6U0.01 7 0.3909 1.000 0.40 0.00 0.00 0.02 0.00 0.00 0.58
#> TCGA.28.5211.01 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CX.01 2 0.3680 0.622 0.00 0.78 0.02 0.00 0.06 0.00 0.14
#> TCGA.CS.6186.01 6 0.0504 0.885 0.00 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.DU.A76K.01 2 0.2081 0.834 0.00 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.19.1389.02 4 0.1505 0.792 0.00 0.00 0.02 0.94 0.02 0.00 0.02
#> TCGA.DU.6402.01 5 0.2708 1.000 0.00 0.00 0.22 0.00 0.78 0.00 0.00
#> TCGA.14.0862.01 5 0.2708 1.000 0.00 0.00 0.22 0.00 0.78 0.00 0.00
#> TCGA.19.5955.01 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TT.01 2 0.2081 0.834 0.00 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.76.6662.01 4 0.6828 0.526 0.00 0.00 0.18 0.44 0.10 0.02 0.26
#> TCGA.S9.A7R2.01 2 0.0504 0.764 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.76.6193.01 4 0.3985 0.739 0.00 0.00 0.00 0.72 0.10 0.00 0.18
#> TCGA.14.1043.01 3 0.0000 0.788 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8110.01 7 0.3909 1.000 0.40 0.00 0.00 0.02 0.00 0.00 0.58
#> TCGA.06.0190.01 4 0.2159 0.776 0.00 0.00 0.02 0.90 0.00 0.02 0.06
#> TCGA.06.0190.02 1 0.0504 0.981 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.28.2501.01 3 0.4766 0.592 0.00 0.12 0.70 0.00 0.06 0.00 0.12
#> TCGA.26.6173.01 3 0.3965 0.548 0.00 0.00 0.76 0.12 0.00 0.02 0.10
#> TCGA.HT.7882.01 1 0.0504 0.981 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.76.6282.01 7 0.3909 1.000 0.40 0.00 0.00 0.02 0.00 0.00 0.58
#> TCGA.76.6192.01 7 0.3909 1.000 0.40 0.00 0.00 0.02 0.00 0.00 0.58
#> TCGA.VM.A8CD.01 2 0.2081 0.834 0.00 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.81.5911.01 6 0.2163 0.887 0.00 0.10 0.00 0.00 0.02 0.88 0.00
#> TCGA.E1.A7YM.01 2 0.2081 0.834 0.00 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.14.0736.02 4 0.0000 0.799 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.A74H.01 2 0.4016 0.601 0.00 0.76 0.04 0.00 0.06 0.00 0.14
#> TCGA.RR.A6KB.01 3 0.4937 0.573 0.00 0.14 0.68 0.00 0.06 0.00 0.12
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.28.5213.01 4 0.3658 -0.138 0.00 0.00 0.00 0.58 0.00 0.40 0.02 0.00
#> TCGA.19.1389.01 4 0.0941 0.631 0.00 0.00 0.00 0.96 0.00 0.02 0.02 0.00
#> TCGA.19.5953.01 3 0.0000 0.760 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IX.01 2 0.3299 0.453 0.00 0.56 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.06.6700.01 3 0.0000 0.760 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.4065.01 1 0.0000 0.960 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.4941.01 3 0.2132 0.702 0.00 0.00 0.88 0.00 0.00 0.08 0.04 0.00
#> TCGA.S9.A6U0.01 7 0.2650 0.981 0.24 0.00 0.00 0.00 0.00 0.00 0.76 0.00
#> TCGA.28.5211.01 1 0.0000 0.960 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CX.01 8 0.0808 0.685 0.00 0.00 0.04 0.00 0.00 0.00 0.00 0.96
#> TCGA.CS.6186.01 2 0.4511 -0.112 0.00 0.52 0.00 0.00 0.00 0.38 0.10 0.00
#> TCGA.DU.A76K.01 2 0.3272 0.458 0.00 0.58 0.00 0.00 0.00 0.00 0.00 0.42
#> TCGA.19.1389.02 4 0.1408 0.612 0.00 0.00 0.00 0.94 0.00 0.02 0.02 0.02
#> TCGA.DU.6402.01 5 0.2020 0.986 0.00 0.00 0.06 0.02 0.90 0.00 0.02 0.00
#> TCGA.14.0862.01 5 0.1557 0.986 0.00 0.00 0.06 0.02 0.92 0.00 0.00 0.00
#> TCGA.19.5955.01 1 0.0000 0.960 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TT.01 2 0.3299 0.453 0.00 0.56 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.76.6662.01 6 0.4841 0.000 0.00 0.00 0.16 0.34 0.00 0.50 0.00 0.00
#> TCGA.S9.A7R2.01 8 0.2938 0.134 0.00 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.76.6193.01 4 0.3907 -0.123 0.00 0.00 0.00 0.58 0.00 0.38 0.04 0.00
#> TCGA.14.1043.01 3 0.0000 0.760 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8110.01 7 0.2534 0.981 0.22 0.00 0.00 0.00 0.00 0.00 0.78 0.00
#> TCGA.06.0190.01 4 0.2020 0.554 0.00 0.00 0.00 0.90 0.00 0.06 0.02 0.02
#> TCGA.06.0190.02 1 0.1741 0.940 0.92 0.00 0.00 0.00 0.04 0.02 0.00 0.02
#> TCGA.28.2501.01 3 0.3015 0.592 0.00 0.00 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.26.6173.01 3 0.5675 0.265 0.00 0.00 0.56 0.22 0.00 0.14 0.06 0.02
#> TCGA.HT.7882.01 1 0.1741 0.940 0.92 0.00 0.00 0.00 0.04 0.02 0.00 0.02
#> TCGA.76.6282.01 7 0.2650 0.981 0.24 0.00 0.00 0.00 0.00 0.00 0.76 0.00
#> TCGA.76.6192.01 7 0.2534 0.981 0.22 0.00 0.00 0.00 0.00 0.00 0.78 0.00
#> TCGA.VM.A8CD.01 2 0.3272 0.458 0.00 0.58 0.00 0.00 0.00 0.00 0.00 0.42
#> TCGA.81.5911.01 2 0.3837 0.135 0.00 0.76 0.00 0.00 0.04 0.10 0.10 0.00
#> TCGA.E1.A7YM.01 2 0.3299 0.453 0.00 0.56 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.14.0736.02 4 0.0471 0.631 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.HT.A74H.01 8 0.1341 0.666 0.00 0.00 0.08 0.00 0.00 0.00 0.00 0.92
#> TCGA.RR.A6KB.01 3 0.3015 0.592 0.00 0.00 0.68 0.00 0.00 0.00 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: Node0121. Child nodes: Node012131-leaf , Node012132-leaf , Node012133-leaf , Node012134-leaf , Node022121-leaf , Node022122-leaf , Node022123-leaf , Node022211-leaf , Node022212-leaf , Node022311-leaf , Node022312-leaf , Node022313-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["01213"]
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 14 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.637 0.972 0.979 0.5116 0.473 0.473
#> 3 3 0.703 0.787 0.871 0.3066 0.615 0.364
#> 4 4 1.000 0.986 0.989 0.1795 0.791 0.457
#> 5 5 0.835 0.711 0.811 0.0482 0.956 0.789
#> 6 6 0.835 0.735 0.839 0.0426 0.923 0.588
#> 7 7 0.824 0.718 0.876 0.0337 0.967 0.750
#> 8 8 0.824 0.606 0.813 0.0212 0.978 0.778
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
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.19.5953.01 1 0.000 1.000 1.0 0.0
#> TCGA.06.6700.01 1 0.000 1.000 1.0 0.0
#> TCGA.CS.4941.01 1 0.000 1.000 1.0 0.0
#> TCGA.QH.A6CX.01 1 0.000 1.000 1.0 0.0
#> TCGA.19.1389.02 2 0.469 0.933 0.1 0.9
#> TCGA.DU.6402.01 2 0.000 0.938 0.0 1.0
#> TCGA.14.0862.01 2 0.000 0.938 0.0 1.0
#> TCGA.76.6662.01 2 0.000 0.938 0.0 1.0
#> TCGA.14.1043.01 1 0.000 1.000 1.0 0.0
#> TCGA.06.0190.01 2 0.469 0.933 0.1 0.9
#> TCGA.28.2501.01 1 0.000 1.000 1.0 0.0
#> TCGA.26.6173.01 2 0.469 0.933 0.1 0.9
#> TCGA.HT.A74H.01 1 0.000 1.000 1.0 0.0
#> TCGA.RR.A6KB.01 1 0.000 1.000 1.0 0.0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.19.5953.01 2 0.595 0.675 0.36 0.64 0.00
#> TCGA.06.6700.01 1 0.000 0.568 1.00 0.00 0.00
#> TCGA.CS.4941.01 2 0.595 0.675 0.36 0.64 0.00
#> TCGA.QH.A6CX.01 1 0.595 0.903 0.64 0.00 0.36
#> TCGA.19.1389.02 2 0.000 0.704 0.00 1.00 0.00
#> TCGA.DU.6402.01 3 0.595 1.000 0.00 0.36 0.64
#> TCGA.14.0862.01 3 0.595 1.000 0.00 0.36 0.64
#> TCGA.76.6662.01 2 0.000 0.704 0.00 1.00 0.00
#> TCGA.14.1043.01 2 0.595 0.675 0.36 0.64 0.00
#> TCGA.06.0190.01 2 0.000 0.704 0.00 1.00 0.00
#> TCGA.28.2501.01 1 0.595 0.903 0.64 0.00 0.36
#> TCGA.26.6173.01 2 0.000 0.704 0.00 1.00 0.00
#> TCGA.HT.A74H.01 1 0.595 0.903 0.64 0.00 0.36
#> TCGA.RR.A6KB.01 1 0.595 0.903 0.64 0.00 0.36
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.19.5953.01 4 0.000 0.982 0.00 0.00 0 1.00
#> TCGA.06.6700.01 4 0.121 0.945 0.04 0.00 0 0.96
#> TCGA.CS.4941.01 4 0.000 0.982 0.00 0.00 0 1.00
#> TCGA.QH.A6CX.01 1 0.000 1.000 1.00 0.00 0 0.00
#> TCGA.19.1389.02 2 0.121 0.986 0.00 0.96 0 0.04
#> TCGA.DU.6402.01 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.14.0862.01 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.76.6662.01 2 0.000 0.956 0.00 1.00 0 0.00
#> TCGA.14.1043.01 4 0.000 0.982 0.00 0.00 0 1.00
#> TCGA.06.0190.01 2 0.121 0.986 0.00 0.96 0 0.04
#> TCGA.28.2501.01 1 0.000 1.000 1.00 0.00 0 0.00
#> TCGA.26.6173.01 2 0.121 0.986 0.00 0.96 0 0.04
#> TCGA.HT.A74H.01 1 0.000 1.000 1.00 0.00 0 0.00
#> TCGA.RR.A6KB.01 1 0.000 1.000 1.00 0.00 0 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.19.5953.01 4 0.468 1.000 0.00 0.02 0.0 0.60 0.38
#> TCGA.06.6700.01 5 0.454 -0.289 0.02 0.00 0.0 0.34 0.64
#> TCGA.CS.4941.01 5 0.413 -0.297 0.00 0.02 0.0 0.26 0.72
#> TCGA.QH.A6CX.01 1 0.356 0.814 0.74 0.00 0.0 0.00 0.26
#> TCGA.19.1389.02 2 0.000 0.907 0.00 1.00 0.0 0.00 0.00
#> TCGA.DU.6402.01 3 0.233 0.929 0.00 0.00 0.9 0.08 0.02
#> TCGA.14.0862.01 3 0.000 0.929 0.00 0.00 1.0 0.00 0.00
#> TCGA.76.6662.01 2 0.389 0.687 0.00 0.68 0.0 0.32 0.00
#> TCGA.14.1043.01 4 0.468 1.000 0.00 0.02 0.0 0.60 0.38
#> TCGA.06.0190.01 2 0.000 0.907 0.00 1.00 0.0 0.00 0.00
#> TCGA.28.2501.01 1 0.356 0.814 0.74 0.00 0.0 0.00 0.26
#> TCGA.26.6173.01 2 0.000 0.907 0.00 1.00 0.0 0.00 0.00
#> TCGA.HT.A74H.01 1 0.000 0.823 1.00 0.00 0.0 0.00 0.00
#> TCGA.RR.A6KB.01 1 0.000 0.823 1.00 0.00 0.0 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.19.5953.01 4 0.0547 0.963 0.00 0.00 0.0 0.98 0.02 0.00
#> TCGA.06.6700.01 5 0.3499 0.404 0.00 0.00 0.0 0.32 0.68 0.00
#> TCGA.CS.4941.01 6 0.3851 0.000 0.00 0.00 0.0 0.46 0.00 0.54
#> TCGA.QH.A6CX.01 5 0.3578 0.689 0.34 0.00 0.0 0.00 0.66 0.00
#> TCGA.19.1389.02 2 0.0000 0.844 0.00 1.00 0.0 0.00 0.00 0.00
#> TCGA.DU.6402.01 3 0.3351 0.839 0.00 0.00 0.8 0.00 0.04 0.16
#> TCGA.14.0862.01 3 0.0000 0.839 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.76.6662.01 2 0.5721 0.482 0.00 0.52 0.0 0.00 0.24 0.24
#> TCGA.14.1043.01 4 0.0000 0.963 0.00 0.00 0.0 1.00 0.00 0.00
#> TCGA.06.0190.01 2 0.0547 0.841 0.00 0.98 0.0 0.00 0.02 0.00
#> TCGA.28.2501.01 5 0.3578 0.689 0.34 0.00 0.0 0.00 0.66 0.00
#> TCGA.26.6173.01 2 0.0547 0.841 0.00 0.98 0.0 0.00 0.02 0.00
#> TCGA.HT.A74H.01 1 0.0000 0.946 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.RR.A6KB.01 1 0.1267 0.946 0.94 0.00 0.0 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.19.5953.01 4 0.4305 0.915 0.00 0.00 0.00 0.66 0.02 0.28 0.04
#> TCGA.06.6700.01 5 0.4905 0.571 0.00 0.00 0.00 0.10 0.68 0.06 0.16
#> TCGA.CS.4941.01 6 0.0000 0.000 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.QH.A6CX.01 5 0.2422 0.799 0.18 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.19.1389.02 2 0.0504 0.888 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DU.6402.01 3 0.0000 0.794 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.14.0862.01 3 0.3848 0.794 0.00 0.00 0.76 0.16 0.06 0.00 0.02
#> TCGA.76.6662.01 7 0.2708 0.000 0.00 0.22 0.00 0.00 0.00 0.00 0.78
#> TCGA.14.1043.01 4 0.3047 0.915 0.00 0.00 0.00 0.72 0.00 0.28 0.00
#> TCGA.06.0190.01 2 0.0000 0.888 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.2501.01 5 0.2422 0.799 0.18 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.26.6173.01 2 0.3058 0.784 0.00 0.82 0.00 0.10 0.08 0.00 0.00
#> TCGA.HT.A74H.01 1 0.1363 0.952 0.94 0.00 0.00 0.02 0.00 0.00 0.04
#> TCGA.RR.A6KB.01 1 0.0000 0.952 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.19.5953.01 4 0.3198 0.677 0.00 0.00 0.00 0.72 0.00 0.00 0.02 0.26
#> TCGA.06.6700.01 8 0.4562 0.000 0.00 0.00 0.00 0.10 0.44 0.00 0.00 0.46
#> TCGA.CS.4941.01 6 0.1341 0.000 0.00 0.00 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.QH.A6CX.01 5 0.0000 0.973 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.19.1389.02 2 0.0808 0.771 0.04 0.96 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6402.01 3 0.0000 0.693 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.14.0862.01 3 0.5205 0.693 0.08 0.00 0.66 0.00 0.00 0.08 0.14 0.04
#> TCGA.76.6662.01 7 0.2650 0.000 0.00 0.24 0.00 0.00 0.00 0.00 0.76 0.00
#> TCGA.14.1043.01 4 0.0000 0.701 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.0190.01 2 0.0000 0.771 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.2501.01 5 0.0471 0.973 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.26.6173.01 2 0.3675 0.538 0.04 0.66 0.00 0.00 0.00 0.00 0.00 0.30
#> TCGA.HT.A74H.01 1 0.4764 0.845 0.66 0.00 0.00 0.00 0.16 0.00 0.06 0.12
#> TCGA.RR.A6KB.01 1 0.2114 0.845 0.84 0.00 0.00 0.00 0.16 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: Node01111-leaf , Node01112-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01211-leaf , Node01212-leaf , Node01213 , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node01224-leaf , Node01225-leaf , Node01311-leaf , Node01312-leaf , Node01313-leaf , Node01411-leaf , Node01412-leaf , Node01431-leaf , Node01432-leaf , Node02211-leaf , Node02212 , Node02221 , Node02222-leaf , Node02223-leaf , Node02231 , Node02232-leaf , Node02233-leaf , Node02234-leaf , Node02311-leaf , Node02312-leaf , Node02313-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 34 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 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 0.623 0.833 0.903 0.4859 0.492 0.492
#> 3 3 0.774 0.882 0.932 0.2209 0.939 0.877
#> 4 4 0.720 0.588 0.516 0.1582 0.715 0.452
#> 5 5 0.948 0.965 0.958 0.1004 0.911 0.725
#> 6 6 0.885 0.880 0.935 0.0455 0.980 0.917
#> 7 7 0.825 0.745 0.869 0.0359 1.000 1.000
#> 8 8 0.782 0.692 0.829 0.0280 0.993 0.967
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
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.FG.6688.01 2 0.999 0.413 0.48 0.52
#> TCGA.4W.AA9T.01 1 0.000 0.994 1.00 0.00
#> TCGA.DU.8165.01 1 0.242 0.947 0.96 0.04
#> TCGA.76.6663.01 1 0.000 0.994 1.00 0.00
#> TCGA.HT.A5RC.01 1 0.000 0.994 1.00 0.00
#> TCGA.06.A6S1.01 2 0.000 0.804 0.00 1.00
#> TCGA.E1.A7YQ.01 1 0.000 0.994 1.00 0.00
#> TCGA.26.6174.01 2 0.000 0.804 0.00 1.00
#> TCGA.DU.7012.01 2 0.760 0.748 0.22 0.78
#> TCGA.FG.A87Q.01 1 0.000 0.994 1.00 0.00
#> TCGA.RR.A6KA.01 1 0.000 0.994 1.00 0.00
#> TCGA.CS.5397.01 2 0.981 0.535 0.42 0.58
#> TCGA.06.6391.01 2 0.000 0.804 0.00 1.00
#> TCGA.14.1450.01 1 0.000 0.994 1.00 0.00
#> TCGA.DU.A5TY.01 2 0.855 0.718 0.28 0.72
#> TCGA.DU.5847.01 1 0.000 0.994 1.00 0.00
#> TCGA.76.4928.01 1 0.000 0.994 1.00 0.00
#> TCGA.DU.5854.01 2 0.999 0.413 0.48 0.52
#> TCGA.P5.A72U.01 1 0.000 0.994 1.00 0.00
#> TCGA.DU.6404.02 2 0.000 0.804 0.00 1.00
#> TCGA.DU.6404.01 2 0.000 0.804 0.00 1.00
#> TCGA.E1.A7YN.01 2 0.855 0.718 0.28 0.72
#> TCGA.74.6575.01 2 0.327 0.796 0.06 0.94
#> TCGA.E1.A7Z2.01 2 0.000 0.804 0.00 1.00
#> TCGA.06.A5U1.01 2 0.995 0.458 0.46 0.54
#> TCGA.06.5858.01 2 0.000 0.804 0.00 1.00
#> TCGA.HT.7860.01 1 0.000 0.994 1.00 0.00
#> TCGA.DU.7006.01 2 0.855 0.718 0.28 0.72
#> TCGA.19.5947.01 2 0.855 0.718 0.28 0.72
#> TCGA.DU.7290.01 1 0.000 0.994 1.00 0.00
#> TCGA.HT.A4DS.01 2 0.000 0.804 0.00 1.00
#> TCGA.06.5416.01 2 0.000 0.804 0.00 1.00
#> TCGA.DU.8158.01 1 0.141 0.973 0.98 0.02
#> TCGA.41.6646.01 1 0.000 0.994 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.FG.6688.01 2 0.2066 0.854 0.06 0.94 0.00
#> TCGA.4W.AA9T.01 1 0.0000 0.948 1.00 0.00 0.00
#> TCGA.DU.8165.01 1 0.7298 0.657 0.70 0.20 0.10
#> TCGA.76.6663.01 1 0.0000 0.948 1.00 0.00 0.00
#> TCGA.HT.A5RC.01 1 0.0000 0.948 1.00 0.00 0.00
#> TCGA.06.A6S1.01 2 0.4796 0.746 0.00 0.78 0.22
#> TCGA.E1.A7YQ.01 1 0.2959 0.907 0.90 0.00 0.10
#> TCGA.26.6174.01 2 0.4796 0.746 0.00 0.78 0.22
#> TCGA.DU.7012.01 2 0.0000 0.891 0.00 1.00 0.00
#> TCGA.FG.A87Q.01 1 0.0000 0.948 1.00 0.00 0.00
#> TCGA.RR.A6KA.01 1 0.0000 0.948 1.00 0.00 0.00
#> TCGA.CS.5397.01 2 0.2066 0.854 0.06 0.94 0.00
#> TCGA.06.6391.01 2 0.5016 0.719 0.00 0.76 0.24
#> TCGA.14.1450.01 1 0.0000 0.948 1.00 0.00 0.00
#> TCGA.DU.A5TY.01 2 0.0000 0.891 0.00 1.00 0.00
#> TCGA.DU.5847.01 1 0.2959 0.907 0.90 0.00 0.10
#> TCGA.76.4928.01 1 0.0892 0.934 0.98 0.02 0.00
#> TCGA.DU.5854.01 2 0.2066 0.854 0.06 0.94 0.00
#> TCGA.P5.A72U.01 1 0.0000 0.948 1.00 0.00 0.00
#> TCGA.DU.6404.02 3 0.3340 1.000 0.00 0.12 0.88
#> TCGA.DU.6404.01 3 0.3340 1.000 0.00 0.12 0.88
#> TCGA.E1.A7YN.01 2 0.0000 0.891 0.00 1.00 0.00
#> TCGA.74.6575.01 2 0.0000 0.891 0.00 1.00 0.00
#> TCGA.E1.A7Z2.01 2 0.0000 0.891 0.00 1.00 0.00
#> TCGA.06.A5U1.01 2 0.1529 0.869 0.04 0.96 0.00
#> TCGA.06.5858.01 2 0.0000 0.891 0.00 1.00 0.00
#> TCGA.HT.7860.01 1 0.0000 0.948 1.00 0.00 0.00
#> TCGA.DU.7006.01 2 0.0000 0.891 0.00 1.00 0.00
#> TCGA.19.5947.01 2 0.0000 0.891 0.00 1.00 0.00
#> TCGA.DU.7290.01 1 0.2959 0.907 0.90 0.00 0.10
#> TCGA.HT.A4DS.01 2 0.4796 0.746 0.00 0.78 0.22
#> TCGA.06.5416.01 2 0.4796 0.746 0.00 0.78 0.22
#> TCGA.DU.8158.01 1 0.3832 0.894 0.88 0.02 0.10
#> TCGA.41.6646.01 1 0.0000 0.948 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.FG.6688.01 2 0.0707 0.964 0.02 0.98 0.00 0.00
#> TCGA.4W.AA9T.01 1 0.5487 0.395 0.58 0.02 0.00 0.40
#> TCGA.DU.8165.01 4 0.5062 0.362 0.02 0.30 0.00 0.68
#> TCGA.76.6663.01 1 0.5487 0.395 0.58 0.02 0.00 0.40
#> TCGA.HT.A5RC.01 1 0.5487 0.395 0.58 0.02 0.00 0.40
#> TCGA.06.A6S1.01 1 0.7832 -0.231 0.38 0.36 0.26 0.00
#> TCGA.E1.A7YQ.01 4 0.0000 0.854 0.00 0.00 0.00 1.00
#> TCGA.26.6174.01 1 0.7832 -0.231 0.38 0.36 0.26 0.00
#> TCGA.DU.7012.01 2 0.0000 0.975 0.00 1.00 0.00 0.00
#> TCGA.FG.A87Q.01 1 0.5487 0.395 0.58 0.02 0.00 0.40
#> TCGA.RR.A6KA.01 1 0.5487 0.395 0.58 0.02 0.00 0.40
#> TCGA.CS.5397.01 2 0.0707 0.964 0.02 0.98 0.00 0.00
#> TCGA.06.6391.01 1 0.7832 -0.231 0.38 0.36 0.26 0.00
#> TCGA.14.1450.01 1 0.5487 0.395 0.58 0.02 0.00 0.40
#> TCGA.DU.A5TY.01 2 0.0000 0.975 0.00 1.00 0.00 0.00
#> TCGA.DU.5847.01 4 0.0000 0.854 0.00 0.00 0.00 1.00
#> TCGA.76.4928.01 1 0.6836 0.283 0.58 0.14 0.00 0.28
#> TCGA.DU.5854.01 2 0.0707 0.964 0.02 0.98 0.00 0.00
#> TCGA.P5.A72U.01 1 0.5487 0.395 0.58 0.02 0.00 0.40
#> TCGA.DU.6404.02 3 0.0707 1.000 0.00 0.02 0.98 0.00
#> TCGA.DU.6404.01 3 0.0707 1.000 0.00 0.02 0.98 0.00
#> TCGA.E1.A7YN.01 2 0.0000 0.975 0.00 1.00 0.00 0.00
#> TCGA.74.6575.01 2 0.0707 0.960 0.02 0.98 0.00 0.00
#> TCGA.E1.A7Z2.01 2 0.1211 0.950 0.04 0.96 0.00 0.00
#> TCGA.06.A5U1.01 2 0.0000 0.975 0.00 1.00 0.00 0.00
#> TCGA.06.5858.01 2 0.3037 0.883 0.10 0.88 0.02 0.00
#> TCGA.HT.7860.01 1 0.5487 0.395 0.58 0.02 0.00 0.40
#> TCGA.DU.7006.01 2 0.0000 0.975 0.00 1.00 0.00 0.00
#> TCGA.19.5947.01 2 0.0000 0.975 0.00 1.00 0.00 0.00
#> TCGA.DU.7290.01 4 0.0000 0.854 0.00 0.00 0.00 1.00
#> TCGA.HT.A4DS.01 1 0.7832 -0.231 0.38 0.36 0.26 0.00
#> TCGA.06.5416.01 1 0.7832 -0.231 0.38 0.36 0.26 0.00
#> TCGA.DU.8158.01 4 0.0000 0.854 0.00 0.00 0.00 1.00
#> TCGA.41.6646.01 1 0.5487 0.395 0.58 0.02 0.00 0.40
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.FG.6688.01 2 0.0000 0.978 0.00 1.00 0.00 0.00 0.00
#> TCGA.4W.AA9T.01 1 0.0609 0.976 0.98 0.00 0.02 0.00 0.00
#> TCGA.DU.8165.01 4 0.1648 0.847 0.00 0.04 0.00 0.94 0.02
#> TCGA.76.6663.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A5RC.01 1 0.0609 0.976 0.98 0.00 0.02 0.00 0.00
#> TCGA.06.A6S1.01 5 0.1410 1.000 0.00 0.06 0.00 0.00 0.94
#> TCGA.E1.A7YQ.01 4 0.4115 0.889 0.08 0.00 0.06 0.82 0.04
#> TCGA.26.6174.01 5 0.1410 1.000 0.00 0.06 0.00 0.00 0.94
#> TCGA.DU.7012.01 2 0.0000 0.978 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.A87Q.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.RR.A6KA.01 1 0.0000 0.975 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.5397.01 2 0.0609 0.970 0.02 0.98 0.00 0.00 0.00
#> TCGA.06.6391.01 5 0.1410 1.000 0.00 0.06 0.00 0.00 0.94
#> TCGA.14.1450.01 1 0.0609 0.976 0.98 0.00 0.02 0.00 0.00
#> TCGA.DU.A5TY.01 2 0.0000 0.978 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.5847.01 4 0.1732 0.943 0.08 0.00 0.00 0.92 0.00
#> TCGA.76.4928.01 1 0.1732 0.873 0.92 0.08 0.00 0.00 0.00
#> TCGA.DU.5854.01 2 0.0609 0.970 0.02 0.98 0.00 0.00 0.00
#> TCGA.P5.A72U.01 1 0.0609 0.976 0.98 0.00 0.02 0.00 0.00
#> TCGA.DU.6404.02 3 0.2280 1.000 0.00 0.00 0.88 0.00 0.12
#> TCGA.DU.6404.01 3 0.2280 1.000 0.00 0.00 0.88 0.00 0.12
#> TCGA.E1.A7YN.01 2 0.0000 0.978 0.00 1.00 0.00 0.00 0.00
#> TCGA.74.6575.01 2 0.0000 0.978 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.A7Z2.01 2 0.1043 0.952 0.00 0.96 0.00 0.04 0.00
#> TCGA.06.A5U1.01 2 0.0609 0.970 0.02 0.98 0.00 0.00 0.00
#> TCGA.06.5858.01 2 0.3110 0.862 0.00 0.86 0.06 0.08 0.00
#> TCGA.HT.7860.01 1 0.0609 0.976 0.98 0.00 0.02 0.00 0.00
#> TCGA.DU.7006.01 2 0.0000 0.978 0.00 1.00 0.00 0.00 0.00
#> TCGA.19.5947.01 2 0.0000 0.978 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7290.01 4 0.1732 0.943 0.08 0.00 0.00 0.92 0.00
#> TCGA.HT.A4DS.01 5 0.1410 1.000 0.00 0.06 0.00 0.00 0.94
#> TCGA.06.5416.01 5 0.1410 1.000 0.00 0.06 0.00 0.00 0.94
#> TCGA.DU.8158.01 4 0.1732 0.943 0.08 0.00 0.00 0.92 0.00
#> TCGA.41.6646.01 1 0.0000 0.975 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.FG.6688.01 2 0.2790 0.797 0.00 0.84 0.00 0.00 0.02 0.14
#> TCGA.4W.AA9T.01 1 0.0547 0.943 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DU.8165.01 4 0.0000 0.922 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.76.6663.01 1 0.1814 0.913 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.HT.A5RC.01 1 0.1480 0.926 0.94 0.00 0.02 0.00 0.00 0.04
#> TCGA.06.A6S1.01 5 0.0547 1.000 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.E1.A7YQ.01 4 0.4222 0.690 0.02 0.00 0.02 0.70 0.00 0.26
#> TCGA.26.6174.01 5 0.0547 1.000 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.DU.7012.01 2 0.1092 0.876 0.00 0.96 0.02 0.00 0.00 0.02
#> TCGA.FG.A87Q.01 1 0.1267 0.935 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.RR.A6KA.01 1 0.2094 0.907 0.90 0.00 0.00 0.00 0.02 0.08
#> TCGA.CS.5397.01 2 0.2260 0.798 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.06.6391.01 5 0.0547 1.000 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.14.1450.01 1 0.0000 0.944 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TY.01 2 0.0937 0.877 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.DU.5847.01 4 0.0547 0.921 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.76.4928.01 1 0.2094 0.885 0.90 0.08 0.00 0.00 0.00 0.02
#> TCGA.DU.5854.01 2 0.2260 0.798 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.P5.A72U.01 1 0.0000 0.944 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6404.02 3 0.1480 0.987 0.00 0.00 0.94 0.00 0.04 0.02
#> TCGA.DU.6404.01 3 0.0937 0.987 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.E1.A7YN.01 2 0.0547 0.882 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.74.6575.01 2 0.0000 0.884 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7Z2.01 2 0.2581 0.744 0.00 0.86 0.00 0.00 0.02 0.12
#> TCGA.06.A5U1.01 2 0.0547 0.881 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.06.5858.01 6 0.4199 0.000 0.00 0.38 0.00 0.00 0.02 0.60
#> TCGA.HT.7860.01 1 0.1092 0.935 0.96 0.00 0.02 0.00 0.00 0.02
#> TCGA.DU.7006.01 2 0.0937 0.874 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.19.5947.01 2 0.0547 0.881 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.DU.7290.01 4 0.0547 0.921 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.HT.A4DS.01 5 0.0547 1.000 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.06.5416.01 5 0.0547 1.000 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.DU.8158.01 4 0.0000 0.922 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.41.6646.01 1 0.0547 0.943 0.98 0.00 0.00 0.00 0.00 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.FG.6688.01 7 0.4127 0.590 0.00 0.36 0.00 0.00 0.00 0.04 0.60
#> TCGA.4W.AA9T.01 1 0.1166 0.846 0.94 0.06 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.8165.01 4 0.3244 0.684 0.00 0.18 0.00 0.78 0.00 0.04 0.00
#> TCGA.76.6663.01 1 0.3139 0.691 0.70 0.30 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A5RC.01 1 0.1166 0.846 0.94 0.06 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.A6S1.01 5 0.0504 0.943 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.E1.A7YQ.01 4 0.6415 0.370 0.08 0.30 0.02 0.48 0.00 0.12 0.00
#> TCGA.26.6174.01 5 0.0000 0.954 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.7012.01 7 0.0863 0.754 0.00 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.FG.A87Q.01 1 0.2422 0.790 0.82 0.18 0.00 0.00 0.00 0.00 0.00
#> TCGA.RR.A6KA.01 1 0.3841 0.664 0.68 0.28 0.00 0.04 0.00 0.00 0.00
#> TCGA.CS.5397.01 7 0.3413 0.576 0.00 0.38 0.00 0.00 0.00 0.00 0.62
#> TCGA.06.6391.01 5 0.0000 0.954 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.14.1450.01 1 0.0504 0.853 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TY.01 7 0.2278 0.760 0.00 0.08 0.00 0.00 0.00 0.04 0.88
#> TCGA.DU.5847.01 4 0.0504 0.802 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.76.4928.01 1 0.3835 0.706 0.74 0.10 0.00 0.00 0.00 0.00 0.16
#> TCGA.DU.5854.01 7 0.3358 0.596 0.00 0.36 0.00 0.00 0.00 0.00 0.64
#> TCGA.P5.A72U.01 1 0.0000 0.853 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6404.02 3 0.0504 0.969 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.DU.6404.01 3 0.1363 0.969 0.00 0.00 0.94 0.00 0.02 0.04 0.00
#> TCGA.E1.A7YN.01 7 0.0863 0.754 0.00 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.74.6575.01 7 0.1166 0.768 0.00 0.06 0.00 0.00 0.00 0.00 0.94
#> TCGA.E1.A7Z2.01 7 0.5923 0.197 0.00 0.24 0.00 0.00 0.08 0.14 0.54
#> TCGA.06.A5U1.01 7 0.0504 0.760 0.00 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.06.5858.01 6 0.3244 0.000 0.00 0.00 0.00 0.00 0.04 0.78 0.18
#> TCGA.HT.7860.01 1 0.0000 0.853 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7006.01 7 0.1671 0.762 0.00 0.10 0.00 0.00 0.00 0.00 0.90
#> TCGA.19.5947.01 7 0.0000 0.760 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.7290.01 4 0.0504 0.802 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.HT.A4DS.01 5 0.1433 0.938 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.06.5416.01 5 0.1433 0.938 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.DU.8158.01 4 0.1505 0.791 0.00 0.02 0.02 0.94 0.00 0.02 0.00
#> TCGA.41.6646.01 1 0.1433 0.845 0.92 0.08 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.FG.6688.01 7 0.435 0.581 0.00 0.02 0.0 0.00 0.00 0.06 0.62 0.30
#> TCGA.4W.AA9T.01 1 0.286 0.739 0.78 0.02 0.0 0.00 0.00 0.00 0.00 0.20
#> TCGA.DU.8165.01 4 0.403 0.624 0.00 0.10 0.0 0.72 0.00 0.02 0.00 0.16
#> TCGA.76.6663.01 1 0.265 0.673 0.76 0.00 0.0 0.00 0.00 0.00 0.00 0.24
#> TCGA.HT.A5RC.01 1 0.340 0.706 0.72 0.04 0.0 0.00 0.00 0.00 0.00 0.24
#> TCGA.06.A6S1.01 5 0.000 0.962 0.00 0.00 0.0 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YQ.01 2 0.366 0.000 0.06 0.70 0.0 0.24 0.00 0.00 0.00 0.00
#> TCGA.26.6174.01 5 0.000 0.962 0.00 0.00 0.0 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7012.01 7 0.235 0.701 0.00 0.02 0.0 0.00 0.00 0.04 0.88 0.06
#> TCGA.FG.A87Q.01 1 0.211 0.752 0.84 0.00 0.0 0.00 0.00 0.00 0.00 0.16
#> TCGA.RR.A6KA.01 1 0.253 0.680 0.78 0.00 0.0 0.00 0.00 0.00 0.00 0.22
#> TCGA.CS.5397.01 7 0.417 0.562 0.00 0.02 0.0 0.00 0.00 0.04 0.62 0.32
#> TCGA.06.6391.01 5 0.000 0.962 0.00 0.00 0.0 0.00 1.00 0.00 0.00 0.00
#> TCGA.14.1450.01 1 0.000 0.780 1.00 0.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TY.01 7 0.207 0.695 0.00 0.02 0.0 0.00 0.00 0.04 0.90 0.04
#> TCGA.DU.5847.01 4 0.000 0.855 0.00 0.00 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.4928.01 1 0.489 0.578 0.58 0.04 0.0 0.00 0.00 0.02 0.04 0.32
#> TCGA.DU.5854.01 7 0.417 0.562 0.00 0.02 0.0 0.00 0.00 0.04 0.62 0.32
#> TCGA.P5.A72U.01 1 0.000 0.780 1.00 0.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6404.02 3 0.000 0.917 0.00 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6404.01 3 0.156 0.917 0.00 0.10 0.9 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YN.01 7 0.235 0.701 0.00 0.02 0.0 0.00 0.00 0.04 0.88 0.06
#> TCGA.74.6575.01 7 0.000 0.708 0.00 0.00 0.0 0.00 0.00 0.00 1.00 0.00
#> TCGA.E1.A7Z2.01 7 0.621 0.160 0.00 0.14 0.0 0.00 0.00 0.20 0.44 0.22
#> TCGA.06.A5U1.01 7 0.459 0.537 0.00 0.04 0.0 0.00 0.00 0.10 0.66 0.20
#> TCGA.06.5858.01 6 0.222 0.000 0.00 0.00 0.0 0.00 0.02 0.86 0.12 0.00
#> TCGA.HT.7860.01 1 0.180 0.758 0.90 0.02 0.0 0.00 0.00 0.00 0.00 0.08
#> TCGA.DU.7006.01 7 0.134 0.701 0.00 0.00 0.0 0.00 0.00 0.00 0.92 0.08
#> TCGA.19.5947.01 7 0.176 0.676 0.00 0.00 0.0 0.00 0.00 0.00 0.88 0.12
#> TCGA.DU.7290.01 4 0.000 0.855 0.00 0.00 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A4DS.01 5 0.174 0.943 0.00 0.02 0.0 0.00 0.92 0.02 0.00 0.04
#> TCGA.06.5416.01 5 0.174 0.943 0.00 0.02 0.0 0.00 0.92 0.02 0.00 0.04
#> TCGA.DU.8158.01 4 0.128 0.837 0.00 0.02 0.0 0.94 0.00 0.00 0.00 0.04
#> TCGA.41.6646.01 1 0.329 0.736 0.74 0.04 0.0 0.00 0.00 0.00 0.00 0.22
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 , Node0112 , Node0113 , Node0121 , Node0122 , Node0123-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0141 , Node0142-leaf , Node0143 , Node0211-leaf , Node0212-leaf , Node0213-leaf , Node0214-leaf , Node0221 , Node0222 , Node0223 , Node0231 , Node0232-leaf , Node0233-leaf , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0323-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["013"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 41 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 8.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4883 0.512 0.512
#> 3 3 1.000 0.997 0.999 0.3937 0.776 0.575
#> 4 4 1.000 0.984 0.975 0.0988 0.932 0.786
#> 5 5 0.955 0.933 0.949 0.0535 0.943 0.775
#> 6 6 0.858 0.830 0.897 0.0393 1.000 1.000
#> 7 7 0.856 0.809 0.916 0.0238 0.926 0.663
#> 8 8 0.912 0.780 0.918 0.0154 0.980 0.883
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 8
#> attr(,"optional")
#> [1] 2 3 4 5
There is also optional best \(k\) = 2 3 4 5 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.06.AABW.11 1 0 1 1 0
#> TCGA.TQ.A7RP.01 1 0 1 1 0
#> TCGA.06.5412.01 2 0 1 0 1
#> TCGA.06.0171.02 2 0 1 0 1
#> TCGA.FG.7643.01 1 0 1 1 0
#> TCGA.FG.8181.01 1 0 1 1 0
#> TCGA.FG.5963.01 1 0 1 1 0
#> TCGA.06.5410.01 2 0 1 0 1
#> TCGA.TM.A84C.01 1 0 1 1 0
#> TCGA.DB.A75P.01 1 0 1 1 0
#> TCGA.S9.A89V.01 1 0 1 1 0
#> TCGA.06.1806.01 2 0 1 0 1
#> TCGA.06.6697.01 2 0 1 0 1
#> TCGA.DU.8162.01 1 0 1 1 0
#> TCGA.QH.A6CS.01 1 0 1 1 0
#> TCGA.HT.7691.01 1 0 1 1 0
#> TCGA.32.1980.01 1 0 1 1 0
#> TCGA.DB.A64O.01 2 0 1 0 1
#> TCGA.FG.8189.01 1 0 1 1 0
#> TCGA.HT.8019.01 1 0 1 1 0
#> TCGA.P5.A5EY.01 1 0 1 1 0
#> TCGA.DU.5872.02 2 0 1 0 1
#> TCGA.74.6573.11 1 0 1 1 0
#> TCGA.HW.A5KK.01 1 0 1 1 0
#> TCGA.06.0650.01 2 0 1 0 1
#> TCGA.CS.6669.01 1 0 1 1 0
#> TCGA.HT.7680.01 1 0 1 1 0
#> TCGA.06.6698.01 2 0 1 0 1
#> TCGA.P5.A5F6.01 2 0 1 0 1
#> TCGA.HT.8558.01 1 0 1 1 0
#> TCGA.HT.8107.01 1 0 1 1 0
#> TCGA.HT.7854.01 2 0 1 0 1
#> TCGA.VM.A8C9.01 1 0 1 1 0
#> TCGA.06.6390.01 2 0 1 0 1
#> TCGA.DU.8161.01 2 0 1 0 1
#> TCGA.HT.8015.01 1 0 1 1 0
#> TCGA.28.2510.01 1 0 1 1 0
#> TCGA.19.A6J4.01 2 0 1 0 1
#> TCGA.14.0781.01 2 0 1 0 1
#> TCGA.HT.A617.01 2 0 1 0 1
#> TCGA.HT.7857.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.06.AABW.11 3 0.000 0.995 0.00 0 1.00
#> TCGA.TQ.A7RP.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.06.5412.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.06.0171.02 2 0.000 1.000 0.00 1 0.00
#> TCGA.FG.7643.01 3 0.000 0.995 0.00 0 1.00
#> TCGA.FG.8181.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.FG.5963.01 3 0.207 0.936 0.06 0 0.94
#> TCGA.06.5410.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.TM.A84C.01 3 0.000 0.995 0.00 0 1.00
#> TCGA.DB.A75P.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.S9.A89V.01 3 0.000 0.995 0.00 0 1.00
#> TCGA.06.1806.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.06.6697.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DU.8162.01 3 0.000 0.995 0.00 0 1.00
#> TCGA.QH.A6CS.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.HT.7691.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.32.1980.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.DB.A64O.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.FG.8189.01 3 0.000 0.995 0.00 0 1.00
#> TCGA.HT.8019.01 3 0.000 0.995 0.00 0 1.00
#> TCGA.P5.A5EY.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.DU.5872.02 2 0.000 1.000 0.00 1 0.00
#> TCGA.74.6573.11 3 0.000 0.995 0.00 0 1.00
#> TCGA.HW.A5KK.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.06.0650.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.CS.6669.01 3 0.000 0.995 0.00 0 1.00
#> TCGA.HT.7680.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.06.6698.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.P5.A5F6.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.HT.8558.01 3 0.000 0.995 0.00 0 1.00
#> TCGA.HT.8107.01 3 0.000 0.995 0.00 0 1.00
#> TCGA.HT.7854.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.VM.A8C9.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.06.6390.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DU.8161.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.HT.8015.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.28.2510.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.19.A6J4.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.14.0781.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.HT.A617.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.HT.7857.01 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.06.AABW.11 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.TQ.A7RP.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.06.5412.01 2 0.2011 1.000 0.00 0.92 0.00 0.08
#> TCGA.06.0171.02 2 0.2011 1.000 0.00 0.92 0.00 0.08
#> TCGA.FG.7643.01 3 0.0707 0.981 0.00 0.02 0.98 0.00
#> TCGA.FG.8181.01 1 0.0707 0.974 0.98 0.02 0.00 0.00
#> TCGA.FG.5963.01 3 0.1913 0.943 0.02 0.04 0.94 0.00
#> TCGA.06.5410.01 2 0.2011 1.000 0.00 0.92 0.00 0.08
#> TCGA.TM.A84C.01 3 0.2335 0.928 0.02 0.06 0.92 0.00
#> TCGA.DB.A75P.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.S9.A89V.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.06.1806.01 4 0.0000 1.000 0.00 0.00 0.00 1.00
#> TCGA.06.6697.01 2 0.2011 1.000 0.00 0.92 0.00 0.08
#> TCGA.DU.8162.01 3 0.0707 0.981 0.00 0.02 0.98 0.00
#> TCGA.QH.A6CS.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.HT.7691.01 1 0.1637 0.955 0.94 0.06 0.00 0.00
#> TCGA.32.1980.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.DB.A64O.01 4 0.0000 1.000 0.00 0.00 0.00 1.00
#> TCGA.FG.8189.01 3 0.0707 0.981 0.00 0.02 0.98 0.00
#> TCGA.HT.8019.01 3 0.0707 0.981 0.00 0.02 0.98 0.00
#> TCGA.P5.A5EY.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.DU.5872.02 2 0.2011 1.000 0.00 0.92 0.00 0.08
#> TCGA.74.6573.11 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.HW.A5KK.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.06.0650.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.CS.6669.01 3 0.0707 0.981 0.00 0.02 0.98 0.00
#> TCGA.HT.7680.01 1 0.1637 0.955 0.94 0.06 0.00 0.00
#> TCGA.06.6698.01 4 0.0000 1.000 0.00 0.00 0.00 1.00
#> TCGA.P5.A5F6.01 4 0.0000 1.000 0.00 0.00 0.00 1.00
#> TCGA.HT.8558.01 3 0.0000 0.979 0.00 0.00 1.00 0.00
#> TCGA.HT.8107.01 3 0.0707 0.981 0.00 0.02 0.98 0.00
#> TCGA.HT.7854.01 4 0.0000 1.000 0.00 0.00 0.00 1.00
#> TCGA.VM.A8C9.01 1 0.1637 0.955 0.94 0.06 0.00 0.00
#> TCGA.06.6390.01 4 0.0000 1.000 0.00 0.00 0.00 1.00
#> TCGA.DU.8161.01 4 0.0000 1.000 0.00 0.00 0.00 1.00
#> TCGA.HT.8015.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.28.2510.01 1 0.0707 0.974 0.98 0.02 0.00 0.00
#> TCGA.19.A6J4.01 2 0.2011 1.000 0.00 0.92 0.00 0.08
#> TCGA.14.0781.01 2 0.2011 1.000 0.00 0.92 0.00 0.08
#> TCGA.HT.A617.01 2 0.2011 1.000 0.00 0.92 0.00 0.08
#> TCGA.HT.7857.01 1 0.0000 0.985 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.06.AABW.11 3 0.1648 0.930 0.00 0.00 0.94 0.02 0.04
#> TCGA.TQ.A7RP.01 1 0.0000 0.980 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.5412.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.06.0171.02 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.7643.01 3 0.0000 0.939 0.00 0.00 1.00 0.00 0.00
#> TCGA.FG.8181.01 1 0.1043 0.935 0.96 0.00 0.04 0.00 0.00
#> TCGA.FG.5963.01 3 0.5068 0.450 0.06 0.00 0.64 0.00 0.30
#> TCGA.06.5410.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.TM.A84C.01 5 0.0000 0.494 0.00 0.00 0.00 0.00 1.00
#> TCGA.DB.A75P.01 1 0.0000 0.980 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A89V.01 3 0.1732 0.914 0.00 0.00 0.92 0.00 0.08
#> TCGA.06.1806.01 4 0.0609 1.000 0.00 0.02 0.00 0.98 0.00
#> TCGA.06.6697.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.8162.01 3 0.0000 0.939 0.00 0.00 1.00 0.00 0.00
#> TCGA.QH.A6CS.01 1 0.0000 0.980 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7691.01 5 0.4182 0.778 0.40 0.00 0.00 0.00 0.60
#> TCGA.32.1980.01 1 0.0000 0.980 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64O.01 4 0.0609 1.000 0.00 0.02 0.00 0.98 0.00
#> TCGA.FG.8189.01 3 0.0000 0.939 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.8019.01 3 0.0000 0.939 0.00 0.00 1.00 0.00 0.00
#> TCGA.P5.A5EY.01 1 0.0000 0.980 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5872.02 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.74.6573.11 3 0.1648 0.930 0.00 0.00 0.94 0.02 0.04
#> TCGA.HW.A5KK.01 1 0.0000 0.980 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.0650.01 1 0.0000 0.980 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6669.01 3 0.0000 0.939 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7680.01 5 0.4182 0.778 0.40 0.00 0.00 0.00 0.60
#> TCGA.06.6698.01 4 0.0609 1.000 0.00 0.02 0.00 0.98 0.00
#> TCGA.P5.A5F6.01 4 0.0609 1.000 0.00 0.02 0.00 0.98 0.00
#> TCGA.HT.8558.01 3 0.1648 0.930 0.00 0.00 0.94 0.02 0.04
#> TCGA.HT.8107.01 3 0.0609 0.937 0.00 0.00 0.98 0.00 0.02
#> TCGA.HT.7854.01 4 0.0609 1.000 0.00 0.02 0.00 0.98 0.00
#> TCGA.VM.A8C9.01 5 0.4182 0.778 0.40 0.00 0.00 0.00 0.60
#> TCGA.06.6390.01 4 0.0609 1.000 0.00 0.02 0.00 0.98 0.00
#> TCGA.DU.8161.01 4 0.0609 1.000 0.00 0.02 0.00 0.98 0.00
#> TCGA.HT.8015.01 1 0.0000 0.980 1.00 0.00 0.00 0.00 0.00
#> TCGA.28.2510.01 1 0.1043 0.935 0.96 0.00 0.04 0.00 0.00
#> TCGA.19.A6J4.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.14.0781.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.A617.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7857.01 1 0.1043 0.930 0.96 0.00 0.00 0.00 0.04
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.06.AABW.11 3 0.3864 0.617 0.00 0.48 0.52 0.0 0.00 0
#> TCGA.TQ.A7RP.01 1 0.0000 0.888 1.00 0.00 0.00 0.0 0.00 0
#> TCGA.06.5412.01 6 0.0000 1.000 0.00 0.00 0.00 0.0 0.00 1
#> TCGA.06.0171.02 6 0.0000 1.000 0.00 0.00 0.00 0.0 0.00 1
#> TCGA.FG.7643.01 3 0.0000 0.775 0.00 0.00 1.00 0.0 0.00 0
#> TCGA.FG.8181.01 1 0.3076 0.661 0.76 0.00 0.24 0.0 0.00 0
#> TCGA.FG.5963.01 3 0.6088 0.142 0.06 0.08 0.48 0.0 0.38 0
#> TCGA.06.5410.01 6 0.0000 1.000 0.00 0.00 0.00 0.0 0.00 1
#> TCGA.TM.A84C.01 5 0.3756 0.515 0.00 0.40 0.00 0.0 0.60 0
#> TCGA.DB.A75P.01 1 0.0000 0.888 1.00 0.00 0.00 0.0 0.00 0
#> TCGA.S9.A89V.01 3 0.3787 0.707 0.00 0.12 0.78 0.0 0.10 0
#> TCGA.06.1806.01 4 0.0000 0.986 0.00 0.00 0.00 1.0 0.00 0
#> TCGA.06.6697.01 6 0.0000 1.000 0.00 0.00 0.00 0.0 0.00 1
#> TCGA.DU.8162.01 3 0.0000 0.775 0.00 0.00 1.00 0.0 0.00 0
#> TCGA.QH.A6CS.01 1 0.0000 0.888 1.00 0.00 0.00 0.0 0.00 0
#> TCGA.HT.7691.01 5 0.2454 0.847 0.16 0.00 0.00 0.0 0.84 0
#> TCGA.32.1980.01 1 0.0000 0.888 1.00 0.00 0.00 0.0 0.00 0
#> TCGA.DB.A64O.01 4 0.0000 0.986 0.00 0.00 0.00 1.0 0.00 0
#> TCGA.FG.8189.01 3 0.0000 0.775 0.00 0.00 1.00 0.0 0.00 0
#> TCGA.HT.8019.01 3 0.0000 0.775 0.00 0.00 1.00 0.0 0.00 0
#> TCGA.P5.A5EY.01 1 0.0000 0.888 1.00 0.00 0.00 0.0 0.00 0
#> TCGA.DU.5872.02 6 0.0000 1.000 0.00 0.00 0.00 0.0 0.00 1
#> TCGA.74.6573.11 3 0.3864 0.617 0.00 0.48 0.52 0.0 0.00 0
#> TCGA.HW.A5KK.01 1 0.0547 0.880 0.98 0.02 0.00 0.0 0.00 0
#> TCGA.06.0650.01 1 0.0547 0.880 0.98 0.02 0.00 0.0 0.00 0
#> TCGA.CS.6669.01 3 0.0000 0.775 0.00 0.00 1.00 0.0 0.00 0
#> TCGA.HT.7680.01 5 0.2454 0.847 0.16 0.00 0.00 0.0 0.84 0
#> TCGA.06.6698.01 4 0.0000 0.986 0.00 0.00 0.00 1.0 0.00 0
#> TCGA.P5.A5F6.01 4 0.1814 0.912 0.00 0.10 0.00 0.9 0.00 0
#> TCGA.HT.8558.01 3 0.3864 0.617 0.00 0.48 0.52 0.0 0.00 0
#> TCGA.HT.8107.01 3 0.2631 0.744 0.00 0.18 0.82 0.0 0.00 0
#> TCGA.HT.7854.01 4 0.0000 0.986 0.00 0.00 0.00 1.0 0.00 0
#> TCGA.VM.A8C9.01 5 0.2454 0.847 0.16 0.00 0.00 0.0 0.84 0
#> TCGA.06.6390.01 4 0.0000 0.986 0.00 0.00 0.00 1.0 0.00 0
#> TCGA.DU.8161.01 4 0.0000 0.986 0.00 0.00 0.00 1.0 0.00 0
#> TCGA.HT.8015.01 1 0.0000 0.888 1.00 0.00 0.00 0.0 0.00 0
#> TCGA.28.2510.01 1 0.3578 0.520 0.66 0.00 0.34 0.0 0.00 0
#> TCGA.19.A6J4.01 6 0.0000 1.000 0.00 0.00 0.00 0.0 0.00 1
#> TCGA.14.0781.01 6 0.0000 1.000 0.00 0.00 0.00 0.0 0.00 1
#> TCGA.HT.A617.01 6 0.0000 1.000 0.00 0.00 0.00 0.0 0.00 1
#> TCGA.HT.7857.01 1 0.3592 0.559 0.74 0.02 0.00 0.0 0.24 0
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.06.AABW.11 2 0.1671 1.0000 0.00 0.90 0.10 0.00 0.00 0 0.00
#> TCGA.TQ.A7RP.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.06.5412.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1 0.00
#> TCGA.06.0171.02 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1 0.00
#> TCGA.FG.7643.01 3 0.0504 0.6698 0.02 0.00 0.98 0.00 0.00 0 0.00
#> TCGA.FG.8181.01 3 0.3459 0.3318 0.40 0.00 0.60 0.00 0.00 0 0.00
#> TCGA.FG.5963.01 3 0.6507 0.0448 0.06 0.16 0.44 0.00 0.32 0 0.02
#> TCGA.06.5410.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1 0.00
#> TCGA.TM.A84C.01 7 0.0504 0.0000 0.00 0.00 0.00 0.00 0.02 0 0.98
#> TCGA.DB.A75P.01 1 0.0504 0.9549 0.98 0.00 0.00 0.00 0.02 0 0.00
#> TCGA.S9.A89V.01 3 0.6120 0.0367 0.00 0.30 0.48 0.00 0.08 0 0.14
#> TCGA.06.1806.01 4 0.0000 0.9746 0.00 0.00 0.00 1.00 0.00 0 0.00
#> TCGA.06.6697.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1 0.00
#> TCGA.DU.8162.01 3 0.0000 0.6759 0.00 0.00 1.00 0.00 0.00 0 0.00
#> TCGA.QH.A6CS.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.HT.7691.01 5 0.2376 1.0000 0.12 0.00 0.02 0.00 0.86 0 0.00
#> TCGA.32.1980.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.DB.A64O.01 4 0.0000 0.9746 0.00 0.00 0.00 1.00 0.00 0 0.00
#> TCGA.FG.8189.01 3 0.0000 0.6759 0.00 0.00 1.00 0.00 0.00 0 0.00
#> TCGA.HT.8019.01 3 0.0000 0.6759 0.00 0.00 1.00 0.00 0.00 0 0.00
#> TCGA.P5.A5EY.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.DU.5872.02 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1 0.00
#> TCGA.74.6573.11 2 0.1671 1.0000 0.00 0.90 0.10 0.00 0.00 0 0.00
#> TCGA.HW.A5KK.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.06.0650.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.CS.6669.01 3 0.0504 0.6658 0.00 0.02 0.98 0.00 0.00 0 0.00
#> TCGA.HT.7680.01 5 0.2376 1.0000 0.12 0.00 0.02 0.00 0.86 0 0.00
#> TCGA.06.6698.01 4 0.0000 0.9746 0.00 0.00 0.00 1.00 0.00 0 0.00
#> TCGA.P5.A5F6.01 4 0.2803 0.8307 0.00 0.06 0.00 0.84 0.10 0 0.00
#> TCGA.HT.8558.01 2 0.1671 1.0000 0.00 0.90 0.10 0.00 0.00 0 0.00
#> TCGA.HT.8107.01 3 0.3562 -0.2189 0.00 0.50 0.50 0.00 0.00 0 0.00
#> TCGA.HT.7854.01 4 0.0000 0.9746 0.00 0.00 0.00 1.00 0.00 0 0.00
#> TCGA.VM.A8C9.01 5 0.2376 1.0000 0.12 0.00 0.02 0.00 0.86 0 0.00
#> TCGA.06.6390.01 4 0.0000 0.9746 0.00 0.00 0.00 1.00 0.00 0 0.00
#> TCGA.DU.8161.01 4 0.0000 0.9746 0.00 0.00 0.00 1.00 0.00 0 0.00
#> TCGA.HT.8015.01 1 0.0000 0.9706 1.00 0.00 0.00 0.00 0.00 0 0.00
#> TCGA.28.2510.01 3 0.3221 0.4460 0.32 0.00 0.68 0.00 0.00 0 0.00
#> TCGA.19.A6J4.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1 0.00
#> TCGA.14.0781.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1 0.00
#> TCGA.HT.A617.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1 0.00
#> TCGA.HT.7857.01 1 0.2422 0.7431 0.82 0.00 0.00 0.00 0.18 0 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.06.AABW.11 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.TQ.A7RP.01 1 0.0471 0.9541 0.98 0.00 0.00 0.00 0.00 0 0.00 0.02
#> TCGA.06.5412.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.06.0171.02 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.FG.7643.01 3 0.0000 0.6881 0.00 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.FG.8181.01 3 0.3237 0.3504 0.40 0.00 0.60 0.00 0.00 0 0.00 0.00
#> TCGA.FG.5963.01 3 0.6668 -0.1007 0.04 0.14 0.38 0.00 0.36 0 0.02 0.06
#> TCGA.06.5410.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.TM.A84C.01 7 0.0808 0.0000 0.00 0.00 0.00 0.00 0.04 0 0.96 0.00
#> TCGA.DB.A75P.01 1 0.0000 0.9597 1.00 0.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.S9.A89V.01 8 0.6909 -0.2040 0.00 0.18 0.30 0.00 0.06 0 0.10 0.36
#> TCGA.06.1806.01 4 0.0471 0.9751 0.00 0.00 0.00 0.98 0.00 0 0.00 0.02
#> TCGA.06.6697.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.DU.8162.01 3 0.0000 0.6881 0.00 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.QH.A6CS.01 1 0.0000 0.9597 1.00 0.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.HT.7691.01 5 0.0808 1.0000 0.04 0.00 0.00 0.00 0.96 0 0.00 0.00
#> TCGA.32.1980.01 1 0.0000 0.9597 1.00 0.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.DB.A64O.01 4 0.0000 0.9859 0.00 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.FG.8189.01 3 0.0000 0.6881 0.00 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.HT.8019.01 3 0.0000 0.6881 0.00 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.P5.A5EY.01 1 0.0000 0.9597 1.00 0.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.DU.5872.02 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.74.6573.11 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.HW.A5KK.01 1 0.0471 0.9541 0.98 0.00 0.00 0.00 0.00 0 0.00 0.02
#> TCGA.06.0650.01 1 0.0941 0.9382 0.96 0.00 0.00 0.02 0.00 0 0.00 0.02
#> TCGA.CS.6669.01 3 0.0000 0.6881 0.00 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.HT.7680.01 5 0.0808 1.0000 0.04 0.00 0.00 0.00 0.96 0 0.00 0.00
#> TCGA.06.6698.01 4 0.0808 0.9576 0.00 0.00 0.00 0.96 0.00 0 0.00 0.04
#> TCGA.P5.A5F6.01 8 0.3272 -0.2509 0.00 0.00 0.00 0.42 0.00 0 0.00 0.58
#> TCGA.HT.8558.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.HT.8107.01 3 0.3318 0.0426 0.00 0.46 0.54 0.00 0.00 0 0.00 0.00
#> TCGA.HT.7854.01 4 0.0000 0.9859 0.00 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.VM.A8C9.01 5 0.0808 1.0000 0.04 0.00 0.00 0.00 0.96 0 0.00 0.00
#> TCGA.06.6390.01 4 0.0000 0.9859 0.00 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.DU.8161.01 4 0.0000 0.9859 0.00 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.HT.8015.01 1 0.0000 0.9597 1.00 0.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.28.2510.01 3 0.3291 0.4747 0.28 0.00 0.70 0.00 0.00 0 0.00 0.02
#> TCGA.19.A6J4.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.14.0781.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.HT.A617.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.HT.7857.01 1 0.3036 0.7231 0.78 0.00 0.00 0.00 0.18 0 0.00 0.04
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node013. Child nodes: Node01111-leaf , Node01112-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01211-leaf , Node01212-leaf , Node01213 , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node01224-leaf , Node01225-leaf , Node01311-leaf , Node01312-leaf , Node01313-leaf , Node01411-leaf , Node01412-leaf , Node01431-leaf , Node01432-leaf , Node02211-leaf , Node02212 , Node02221 , Node02222-leaf , Node02223-leaf , Node02231 , Node02232-leaf , Node02233-leaf , Node02234-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0131"]
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 14 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 0.5389 0.462 0.462
#> 3 3 1.000 1.000 1.000 0.2444 0.868 0.714
#> 4 4 1.000 0.929 1.000 0.0491 0.967 0.900
#> 5 5 1.000 0.855 0.997 0.0312 0.978 0.926
#> 6 6 0.967 0.722 0.930 0.0327 0.978 0.920
#> 7 7 0.923 0.616 0.970 0.0288 0.989 0.957
#> 8 8 0.802 0.425 0.906 0.1224 0.868 0.455
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.TQ.A7RP.01 1 0 1 1 0
#> TCGA.FG.8181.01 1 0 1 1 0
#> TCGA.DB.A75P.01 2 0 1 0 1
#> TCGA.QH.A6CS.01 1 0 1 1 0
#> TCGA.HT.7691.01 2 0 1 0 1
#> TCGA.32.1980.01 1 0 1 1 0
#> TCGA.P5.A5EY.01 1 0 1 1 0
#> TCGA.HW.A5KK.01 1 0 1 1 0
#> TCGA.06.0650.01 2 0 1 0 1
#> TCGA.HT.7680.01 2 0 1 0 1
#> TCGA.VM.A8C9.01 2 0 1 0 1
#> TCGA.HT.8015.01 1 0 1 1 0
#> TCGA.28.2510.01 2 0 1 0 1
#> TCGA.HT.7857.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.TQ.A7RP.01 1 0 1 1 0 0
#> TCGA.FG.8181.01 1 0 1 1 0 0
#> TCGA.DB.A75P.01 2 0 1 0 1 0
#> TCGA.QH.A6CS.01 1 0 1 1 0 0
#> TCGA.HT.7691.01 3 0 1 0 0 1
#> TCGA.32.1980.01 1 0 1 1 0 0
#> TCGA.P5.A5EY.01 1 0 1 1 0 0
#> TCGA.HW.A5KK.01 1 0 1 1 0 0
#> TCGA.06.0650.01 2 0 1 0 1 0
#> TCGA.HT.7680.01 3 0 1 0 0 1
#> TCGA.VM.A8C9.01 2 0 1 0 1 0
#> TCGA.HT.8015.01 1 0 1 1 0 0
#> TCGA.28.2510.01 2 0 1 0 1 0
#> TCGA.HT.7857.01 3 0 1 0 0 1
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.TQ.A7RP.01 1 0 1 1 0 0 0
#> TCGA.FG.8181.01 1 0 1 1 0 0 0
#> TCGA.DB.A75P.01 2 0 1 0 1 0 0
#> TCGA.QH.A6CS.01 1 0 1 1 0 0 0
#> TCGA.HT.7691.01 3 0 1 0 0 1 0
#> TCGA.32.1980.01 1 0 1 1 0 0 0
#> TCGA.P5.A5EY.01 1 0 1 1 0 0 0
#> TCGA.HW.A5KK.01 1 0 1 1 0 0 0
#> TCGA.06.0650.01 2 0 1 0 1 0 0
#> TCGA.HT.7680.01 3 0 1 0 0 1 0
#> TCGA.VM.A8C9.01 4 0 0 0 0 0 1
#> TCGA.HT.8015.01 1 0 1 1 0 0 0
#> TCGA.28.2510.01 2 0 1 0 1 0 0
#> TCGA.HT.7857.01 3 0 1 0 0 1 0
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.TQ.A7RP.01 1 0.0000 1.000 1 0.00 0.00 0 0.00
#> TCGA.FG.8181.01 1 0.0000 1.000 1 0.00 0.00 0 0.00
#> TCGA.DB.A75P.01 5 0.0609 0.000 0 0.02 0.00 0 0.98
#> TCGA.QH.A6CS.01 1 0.0000 1.000 1 0.00 0.00 0 0.00
#> TCGA.HT.7691.01 3 0.0000 0.991 0 0.00 1.00 0 0.00
#> TCGA.32.1980.01 1 0.0000 1.000 1 0.00 0.00 0 0.00
#> TCGA.P5.A5EY.01 1 0.0000 1.000 1 0.00 0.00 0 0.00
#> TCGA.HW.A5KK.01 1 0.0000 1.000 1 0.00 0.00 0 0.00
#> TCGA.06.0650.01 2 0.0000 1.000 0 1.00 0.00 0 0.00
#> TCGA.HT.7680.01 3 0.0609 0.983 0 0.00 0.98 0 0.02
#> TCGA.VM.A8C9.01 4 0.0000 0.000 0 0.00 0.00 1 0.00
#> TCGA.HT.8015.01 1 0.0000 1.000 1 0.00 0.00 0 0.00
#> TCGA.28.2510.01 2 0.0000 1.000 0 1.00 0.00 0 0.00
#> TCGA.HT.7857.01 3 0.0000 0.991 0 0.00 1.00 0 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.TQ.A7RP.01 1 0.0937 0.966 0.96 0.00 0.00 0 0 0.04
#> TCGA.FG.8181.01 1 0.0547 0.974 0.98 0.00 0.00 0 0 0.02
#> TCGA.DB.A75P.01 5 0.0000 0.000 0.00 0.00 0.00 0 1 0.00
#> TCGA.QH.A6CS.01 1 0.0937 0.966 0.96 0.00 0.00 0 0 0.04
#> TCGA.HT.7691.01 3 0.0000 1.000 0.00 0.00 1.00 0 0 0.00
#> TCGA.32.1980.01 1 0.0000 0.975 1.00 0.00 0.00 0 0 0.00
#> TCGA.P5.A5EY.01 1 0.0547 0.974 0.98 0.00 0.00 0 0 0.02
#> TCGA.HW.A5KK.01 1 0.0547 0.973 0.98 0.00 0.00 0 0 0.02
#> TCGA.06.0650.01 2 0.3706 0.652 0.00 0.62 0.00 0 0 0.38
#> TCGA.HT.7680.01 6 0.3828 0.000 0.00 0.00 0.44 0 0 0.56
#> TCGA.VM.A8C9.01 4 0.0000 0.000 0.00 0.00 0.00 1 0 0.00
#> TCGA.HT.8015.01 1 0.0547 0.974 0.98 0.00 0.00 0 0 0.02
#> TCGA.28.2510.01 2 0.0000 0.652 0.00 1.00 0.00 0 0 0.00
#> TCGA.HT.7857.01 3 0.0000 1.000 0.00 0.00 1.00 0 0 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.TQ.A7RP.01 1 0.1363 0.941 0.94 0.0 0.00 0 0 0.02 0.04
#> TCGA.FG.8181.01 1 0.0863 0.951 0.96 0.0 0.00 0 0 0.00 0.04
#> TCGA.DB.A75P.01 5 0.0000 0.000 0.00 0.0 0.00 0 1 0.00 0.00
#> TCGA.QH.A6CS.01 1 0.1664 0.930 0.92 0.0 0.00 0 0 0.02 0.06
#> TCGA.HT.7691.01 3 0.0000 1.000 0.00 0.0 1.00 0 0 0.00 0.00
#> TCGA.32.1980.01 1 0.0000 0.954 1.00 0.0 0.00 0 0 0.00 0.00
#> TCGA.P5.A5EY.01 1 0.0863 0.951 0.96 0.0 0.00 0 0 0.00 0.04
#> TCGA.HW.A5KK.01 1 0.1006 0.948 0.96 0.0 0.00 0 0 0.02 0.02
#> TCGA.06.0650.01 2 0.0000 0.000 0.00 1.0 0.00 0 0 0.00 0.00
#> TCGA.HT.7680.01 6 0.0504 0.000 0.00 0.0 0.02 0 0 0.98 0.00
#> TCGA.VM.A8C9.01 4 0.0000 0.000 0.00 0.0 0.00 1 0 0.00 0.00
#> TCGA.HT.8015.01 1 0.0863 0.951 0.96 0.0 0.00 0 0 0.00 0.04
#> TCGA.28.2510.01 7 0.1671 0.000 0.00 0.1 0.00 0 0 0.00 0.90
#> TCGA.HT.7857.01 3 0.0000 1.000 0.00 0.0 1.00 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.TQ.A7RP.01 8 0.265 0.576 0.24 0 0 0 0 0 0 0.76
#> TCGA.FG.8181.01 1 0.195 0.678 0.86 0 0 0 0 0 0 0.14
#> TCGA.DB.A75P.01 5 0.000 0.000 0.00 0 0 0 1 0 0 0.00
#> TCGA.QH.A6CS.01 8 0.000 0.514 0.00 0 0 0 0 0 0 1.00
#> TCGA.HT.7691.01 3 0.000 1.000 0.00 0 1 0 0 0 0 0.00
#> TCGA.32.1980.01 1 0.301 0.412 0.68 0 0 0 0 0 0 0.32
#> TCGA.P5.A5EY.01 1 0.109 0.777 0.94 0 0 0 0 0 0 0.06
#> TCGA.HW.A5KK.01 8 0.330 0.215 0.44 0 0 0 0 0 0 0.56
#> TCGA.06.0650.01 2 0.000 0.000 0.00 1 0 0 0 0 0 0.00
#> TCGA.HT.7680.01 6 0.000 0.000 0.00 0 0 0 0 1 0 0.00
#> TCGA.VM.A8C9.01 4 0.000 0.000 0.00 0 0 1 0 0 0 0.00
#> TCGA.HT.8015.01 1 0.109 0.777 0.94 0 0 0 0 0 0 0.06
#> TCGA.28.2510.01 7 0.000 0.000 0.00 0 0 0 0 0 1 0.00
#> TCGA.HT.7857.01 3 0.000 1.000 0.00 0 1 0 0 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: Node01. Child nodes: Node0111 , Node0112 , Node0113 , Node0121 , Node0122 , Node0123-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0141 , Node0142-leaf , Node0143 , Node0211-leaf , Node0212-leaf , Node0213-leaf , Node0214-leaf , Node0221 , Node0222 , Node0223 , Node0231 , Node0232-leaf , Node0233-leaf , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0323-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["014"]
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 42 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 0.979 0.991 0.5123 0.488 0.488
#> 3 3 1.000 0.998 0.999 0.3248 0.729 0.499
#> 4 4 0.740 0.676 0.814 0.1045 0.894 0.685
#> 5 5 0.734 0.661 0.783 0.0572 0.913 0.671
#> 6 6 0.719 0.485 0.701 0.0332 0.883 0.514
#> 7 7 0.831 0.793 0.829 0.0350 0.936 0.650
#> 8 8 0.803 0.788 0.848 0.0258 0.985 0.890
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.74.6577.01 2 0.000 0.984 0.00 1.00
#> TCGA.06.0125.02 1 0.000 0.998 1.00 0.00
#> TCGA.06.0171.01 2 0.000 0.984 0.00 1.00
#> TCGA.26.5136.01 2 0.000 0.984 0.00 1.00
#> TCGA.DU.A76L.01 2 0.000 0.984 0.00 1.00
#> TCGA.14.1402.01 1 0.000 0.998 1.00 0.00
#> TCGA.06.0211.01 1 0.000 0.998 1.00 0.00
#> TCGA.19.4065.02 2 0.000 0.984 0.00 1.00
#> TCGA.19.5950.01 1 0.000 0.998 1.00 0.00
#> TCGA.CS.5395.01 2 0.000 0.984 0.00 1.00
#> TCGA.DU.7292.01 1 0.000 0.998 1.00 0.00
#> TCGA.19.5958.01 1 0.000 0.998 1.00 0.00
#> TCGA.06.5415.01 1 0.000 0.998 1.00 0.00
#> TCGA.4W.AA9S.01 1 0.242 0.957 0.96 0.04
#> TCGA.76.6283.01 1 0.000 0.998 1.00 0.00
#> TCGA.DU.6392.01 2 0.000 0.984 0.00 1.00
#> TCGA.FG.A70Z.01 2 0.000 0.984 0.00 1.00
#> TCGA.QH.A6XC.01 1 0.000 0.998 1.00 0.00
#> TCGA.TM.A7C3.01 1 0.000 0.998 1.00 0.00
#> TCGA.06.A7TK.01 2 0.000 0.984 0.00 1.00
#> TCGA.06.5411.01 2 0.000 0.984 0.00 1.00
#> TCGA.E1.A7YL.01 2 0.000 0.984 0.00 1.00
#> TCGA.QH.A6CV.01 1 0.000 0.998 1.00 0.00
#> TCGA.28.5214.01 1 0.000 0.998 1.00 0.00
#> TCGA.74.6584.01 2 0.000 0.984 0.00 1.00
#> TCGA.76.6664.01 2 0.000 0.984 0.00 1.00
#> TCGA.CS.6188.01 1 0.000 0.998 1.00 0.00
#> TCGA.28.6450.01 1 0.000 0.998 1.00 0.00
#> TCGA.32.1979.01 1 0.000 0.998 1.00 0.00
#> TCGA.19.0957.02 2 0.000 0.984 0.00 1.00
#> TCGA.76.6657.01 1 0.000 0.998 1.00 0.00
#> TCGA.06.0210.01 2 0.000 0.984 0.00 1.00
#> TCGA.06.A5U0.01 2 0.000 0.984 0.00 1.00
#> TCGA.06.5413.01 2 0.904 0.527 0.32 0.68
#> TCGA.14.1034.02 1 0.000 0.998 1.00 0.00
#> TCGA.19.5952.01 2 0.000 0.984 0.00 1.00
#> TCGA.DH.5140.01 2 0.000 0.984 0.00 1.00
#> TCGA.76.6280.01 1 0.000 0.998 1.00 0.00
#> TCGA.14.0736.01 2 0.000 0.984 0.00 1.00
#> TCGA.06.0152.02 1 0.000 0.998 1.00 0.00
#> TCGA.76.4927.01 1 0.000 0.998 1.00 0.00
#> TCGA.74.6578.01 2 0.000 0.984 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.74.6577.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.06.0125.02 3 0.000 1.000 0.00 0 1.00
#> TCGA.06.0171.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.26.5136.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DU.A76L.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.14.1402.01 1 0.000 0.997 1.00 0 0.00
#> TCGA.06.0211.01 1 0.000 0.997 1.00 0 0.00
#> TCGA.19.4065.02 3 0.000 1.000 0.00 0 1.00
#> TCGA.19.5950.01 1 0.000 0.997 1.00 0 0.00
#> TCGA.CS.5395.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DU.7292.01 1 0.000 0.997 1.00 0 0.00
#> TCGA.19.5958.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.06.5415.01 1 0.000 0.997 1.00 0 0.00
#> TCGA.4W.AA9S.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.76.6283.01 1 0.153 0.958 0.96 0 0.04
#> TCGA.DU.6392.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.FG.A70Z.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.QH.A6XC.01 1 0.000 0.997 1.00 0 0.00
#> TCGA.TM.A7C3.01 1 0.000 0.997 1.00 0 0.00
#> TCGA.06.A7TK.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.06.5411.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.E1.A7YL.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.QH.A6CV.01 1 0.000 0.997 1.00 0 0.00
#> TCGA.28.5214.01 1 0.000 0.997 1.00 0 0.00
#> TCGA.74.6584.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.76.6664.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.CS.6188.01 1 0.000 0.997 1.00 0 0.00
#> TCGA.28.6450.01 1 0.000 0.997 1.00 0 0.00
#> TCGA.32.1979.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.19.0957.02 2 0.000 1.000 0.00 1 0.00
#> TCGA.76.6657.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.06.0210.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.06.A5U0.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.06.5413.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.14.1034.02 1 0.000 0.997 1.00 0 0.00
#> TCGA.19.5952.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.DH.5140.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.76.6280.01 1 0.000 0.997 1.00 0 0.00
#> TCGA.14.0736.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.06.0152.02 1 0.000 0.997 1.00 0 0.00
#> TCGA.76.4927.01 1 0.000 0.997 1.00 0 0.00
#> TCGA.74.6578.01 3 0.000 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.74.6577.01 2 0.000 0.779 0.00 1.00 0.00 0.00
#> TCGA.06.0125.02 4 0.380 0.169 0.00 0.00 0.22 0.78
#> TCGA.06.0171.01 3 0.479 0.705 0.00 0.00 0.62 0.38
#> TCGA.26.5136.01 2 0.498 0.679 0.00 0.54 0.46 0.00
#> TCGA.DU.A76L.01 3 0.121 0.586 0.00 0.00 0.96 0.04
#> TCGA.14.1402.01 1 0.340 0.871 0.82 0.00 0.00 0.18
#> TCGA.06.0211.01 4 0.491 0.011 0.42 0.00 0.00 0.58
#> TCGA.19.4065.02 3 0.413 0.657 0.00 0.00 0.74 0.26
#> TCGA.19.5950.01 1 0.340 0.871 0.82 0.00 0.00 0.18
#> TCGA.CS.5395.01 2 0.498 0.679 0.00 0.54 0.46 0.00
#> TCGA.DU.7292.01 1 0.340 0.871 0.82 0.00 0.00 0.18
#> TCGA.19.5958.01 4 0.121 0.514 0.00 0.00 0.04 0.96
#> TCGA.06.5415.01 1 0.000 0.881 1.00 0.00 0.00 0.00
#> TCGA.4W.AA9S.01 3 0.498 0.640 0.00 0.00 0.54 0.46
#> TCGA.76.6283.01 4 0.201 0.548 0.08 0.00 0.00 0.92
#> TCGA.DU.6392.01 2 0.000 0.779 0.00 1.00 0.00 0.00
#> TCGA.FG.A70Z.01 2 0.498 0.679 0.00 0.54 0.46 0.00
#> TCGA.QH.A6XC.01 1 0.340 0.871 0.82 0.00 0.00 0.18
#> TCGA.TM.A7C3.01 1 0.000 0.881 1.00 0.00 0.00 0.00
#> TCGA.06.A7TK.01 3 0.479 0.705 0.00 0.00 0.62 0.38
#> TCGA.06.5411.01 2 0.000 0.779 0.00 1.00 0.00 0.00
#> TCGA.E1.A7YL.01 3 0.479 0.705 0.00 0.00 0.62 0.38
#> TCGA.QH.A6CV.01 1 0.000 0.881 1.00 0.00 0.00 0.00
#> TCGA.28.5214.01 1 0.000 0.881 1.00 0.00 0.00 0.00
#> TCGA.74.6584.01 2 0.000 0.779 0.00 1.00 0.00 0.00
#> TCGA.76.6664.01 3 0.000 0.562 0.00 0.00 1.00 0.00
#> TCGA.CS.6188.01 4 0.498 -0.133 0.46 0.00 0.00 0.54
#> TCGA.28.6450.01 1 0.340 0.871 0.82 0.00 0.00 0.18
#> TCGA.32.1979.01 4 0.380 0.169 0.00 0.00 0.22 0.78
#> TCGA.19.0957.02 2 0.499 0.656 0.00 0.52 0.48 0.00
#> TCGA.76.6657.01 4 0.000 0.531 0.00 0.00 0.00 1.00
#> TCGA.06.0210.01 2 0.498 0.679 0.00 0.54 0.46 0.00
#> TCGA.06.A5U0.01 2 0.000 0.779 0.00 1.00 0.00 0.00
#> TCGA.06.5413.01 3 0.498 0.640 0.00 0.00 0.54 0.46
#> TCGA.14.1034.02 1 0.000 0.881 1.00 0.00 0.00 0.00
#> TCGA.19.5952.01 3 0.000 0.562 0.00 0.00 1.00 0.00
#> TCGA.DH.5140.01 2 0.000 0.779 0.00 1.00 0.00 0.00
#> TCGA.76.6280.01 1 0.201 0.883 0.92 0.00 0.00 0.08
#> TCGA.14.0736.01 2 0.317 0.761 0.00 0.84 0.16 0.00
#> TCGA.06.0152.02 1 0.000 0.881 1.00 0.00 0.00 0.00
#> TCGA.76.4927.01 1 0.340 0.871 0.82 0.00 0.00 0.18
#> TCGA.74.6578.01 3 0.498 0.640 0.00 0.00 0.54 0.46
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.74.6577.01 2 0.3983 0.99585 0.00 0.66 0.00 0.00 0.34
#> TCGA.06.0125.02 4 0.6447 0.41414 0.00 0.18 0.38 0.44 0.00
#> TCGA.06.0171.01 3 0.0000 0.86738 0.00 0.00 1.00 0.00 0.00
#> TCGA.26.5136.01 5 0.1648 0.61451 0.00 0.00 0.02 0.04 0.94
#> TCGA.DU.A76L.01 5 0.6539 0.06304 0.00 0.04 0.42 0.08 0.46
#> TCGA.14.1402.01 1 0.4227 0.69579 0.58 0.00 0.00 0.42 0.00
#> TCGA.06.0211.01 4 0.2516 0.41714 0.14 0.00 0.00 0.86 0.00
#> TCGA.19.4065.02 3 0.7280 -0.13071 0.00 0.04 0.40 0.18 0.38
#> TCGA.19.5950.01 1 0.4227 0.69579 0.58 0.00 0.00 0.42 0.00
#> TCGA.CS.5395.01 5 0.0000 0.62281 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.7292.01 1 0.4227 0.69579 0.58 0.00 0.00 0.42 0.00
#> TCGA.19.5958.01 4 0.5273 0.68815 0.00 0.16 0.16 0.68 0.00
#> TCGA.06.5415.01 1 0.0000 0.72232 1.00 0.00 0.00 0.00 0.00
#> TCGA.4W.AA9S.01 3 0.0609 0.86298 0.00 0.00 0.98 0.02 0.00
#> TCGA.76.6283.01 4 0.6329 0.66706 0.02 0.30 0.12 0.56 0.00
#> TCGA.DU.6392.01 2 0.4540 0.97908 0.00 0.64 0.00 0.02 0.34
#> TCGA.FG.A70Z.01 5 0.0000 0.62281 0.00 0.00 0.00 0.00 1.00
#> TCGA.QH.A6XC.01 1 0.4227 0.69579 0.58 0.00 0.00 0.42 0.00
#> TCGA.TM.A7C3.01 1 0.0000 0.72232 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.A7TK.01 3 0.0000 0.86738 0.00 0.00 1.00 0.00 0.00
#> TCGA.06.5411.01 2 0.3983 0.99585 0.00 0.66 0.00 0.00 0.34
#> TCGA.E1.A7YL.01 3 0.0000 0.86738 0.00 0.00 1.00 0.00 0.00
#> TCGA.QH.A6CV.01 1 0.0000 0.72232 1.00 0.00 0.00 0.00 0.00
#> TCGA.28.5214.01 1 0.0000 0.72232 1.00 0.00 0.00 0.00 0.00
#> TCGA.74.6584.01 2 0.3983 0.99585 0.00 0.66 0.00 0.00 0.34
#> TCGA.76.6664.01 5 0.6338 0.35083 0.00 0.04 0.32 0.08 0.56
#> TCGA.CS.6188.01 4 0.2732 0.37148 0.16 0.00 0.00 0.84 0.00
#> TCGA.28.6450.01 1 0.4227 0.69579 0.58 0.00 0.00 0.42 0.00
#> TCGA.32.1979.01 4 0.6447 0.41414 0.00 0.18 0.38 0.44 0.00
#> TCGA.19.0957.02 5 0.2754 0.63193 0.00 0.00 0.08 0.04 0.88
#> TCGA.76.6657.01 4 0.5414 0.69022 0.00 0.20 0.14 0.66 0.00
#> TCGA.06.0210.01 5 0.1648 0.61451 0.00 0.00 0.02 0.04 0.94
#> TCGA.06.A5U0.01 2 0.3983 0.99585 0.00 0.66 0.00 0.00 0.34
#> TCGA.06.5413.01 3 0.0609 0.86298 0.00 0.00 0.98 0.02 0.00
#> TCGA.14.1034.02 1 0.0000 0.72232 1.00 0.00 0.00 0.00 0.00
#> TCGA.19.5952.01 5 0.6263 0.35415 0.00 0.04 0.30 0.08 0.58
#> TCGA.DH.5140.01 2 0.3983 0.99585 0.00 0.66 0.00 0.00 0.34
#> TCGA.76.6280.01 1 0.3684 0.71592 0.72 0.00 0.00 0.28 0.00
#> TCGA.14.0736.01 5 0.3561 -0.00919 0.00 0.26 0.00 0.00 0.74
#> TCGA.06.0152.02 1 0.0000 0.72232 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.4927.01 1 0.4227 0.69579 0.58 0.00 0.00 0.42 0.00
#> TCGA.74.6578.01 3 0.1216 0.85353 0.00 0.02 0.96 0.02 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.74.6577.01 2 0.0547 0.963 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.06.0125.02 4 0.6331 0.232 0.02 0.00 0.38 0.40 0.00 0.20
#> TCGA.06.0171.01 3 0.0547 0.946 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.26.5136.01 5 0.2454 0.761 0.00 0.16 0.00 0.00 0.84 0.00
#> TCGA.DU.A76L.01 4 0.4845 -0.137 0.00 0.00 0.06 0.54 0.40 0.00
#> TCGA.14.1402.01 1 0.0000 0.610 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.0211.01 1 0.4989 0.303 0.64 0.00 0.00 0.14 0.00 0.22
#> TCGA.19.4065.02 4 0.4244 0.186 0.00 0.00 0.08 0.72 0.20 0.00
#> TCGA.19.5950.01 1 0.0547 0.599 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CS.5395.01 5 0.4838 0.750 0.00 0.18 0.00 0.10 0.70 0.02
#> TCGA.DU.7292.01 1 0.0547 0.607 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.19.5958.01 4 0.7424 0.372 0.18 0.00 0.20 0.40 0.00 0.22
#> TCGA.06.5415.01 1 0.3864 -0.479 0.52 0.00 0.00 0.00 0.00 0.48
#> TCGA.4W.AA9S.01 3 0.0547 0.954 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.76.6283.01 6 0.8055 -0.493 0.08 0.00 0.12 0.32 0.12 0.36
#> TCGA.DU.6392.01 2 0.2048 0.880 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.FG.A70Z.01 5 0.4838 0.750 0.00 0.18 0.00 0.10 0.70 0.02
#> TCGA.QH.A6XC.01 1 0.0547 0.607 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.TM.A7C3.01 6 0.3869 0.309 0.50 0.00 0.00 0.00 0.00 0.50
#> TCGA.06.A7TK.01 3 0.0547 0.946 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.06.5411.01 2 0.0000 0.968 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YL.01 3 0.0000 0.954 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.QH.A6CV.01 6 0.3869 0.309 0.50 0.00 0.00 0.00 0.00 0.50
#> TCGA.28.5214.01 1 0.3869 -0.525 0.50 0.00 0.00 0.00 0.00 0.50
#> TCGA.74.6584.01 2 0.0547 0.963 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.76.6664.01 5 0.5406 0.185 0.00 0.00 0.12 0.38 0.50 0.00
#> TCGA.CS.6188.01 1 0.4989 0.303 0.64 0.00 0.00 0.14 0.00 0.22
#> TCGA.28.6450.01 1 0.0937 0.606 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.32.1979.01 4 0.6331 0.232 0.02 0.00 0.38 0.40 0.00 0.20
#> TCGA.19.0957.02 5 0.3321 0.717 0.00 0.10 0.08 0.00 0.82 0.00
#> TCGA.76.6657.01 4 0.7507 0.376 0.18 0.00 0.12 0.44 0.02 0.24
#> TCGA.06.0210.01 5 0.2981 0.758 0.00 0.16 0.02 0.00 0.82 0.00
#> TCGA.06.A5U0.01 2 0.0000 0.968 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.5413.01 3 0.0547 0.954 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.14.1034.02 6 0.3869 0.309 0.50 0.00 0.00 0.00 0.00 0.50
#> TCGA.19.5952.01 4 0.4609 -0.168 0.00 0.00 0.04 0.54 0.42 0.00
#> TCGA.DH.5140.01 2 0.0000 0.968 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.6280.01 1 0.1814 0.507 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.14.0736.01 5 0.4337 0.255 0.00 0.48 0.00 0.00 0.50 0.02
#> TCGA.06.0152.02 1 0.3851 -0.432 0.54 0.00 0.00 0.00 0.00 0.46
#> TCGA.76.4927.01 1 0.0000 0.610 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.74.6578.01 3 0.1556 0.888 0.00 0.00 0.92 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.74.6577.01 2 0.0000 0.978 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.0125.02 4 0.2572 0.787 0.00 0.00 0.20 0.80 0.00 0.00 0.00
#> TCGA.06.0171.01 3 0.0000 0.883 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.26.5136.01 5 0.2159 0.740 0.02 0.06 0.00 0.02 0.90 0.00 0.00
#> TCGA.DU.A76L.01 7 0.4821 0.787 0.00 0.00 0.08 0.04 0.22 0.00 0.66
#> TCGA.14.1402.01 1 0.3685 0.832 0.66 0.00 0.00 0.00 0.02 0.32 0.00
#> TCGA.06.0211.01 1 0.4388 0.494 0.64 0.00 0.00 0.30 0.02 0.04 0.00
#> TCGA.19.4065.02 7 0.4969 0.681 0.00 0.00 0.08 0.20 0.06 0.00 0.66
#> TCGA.19.5950.01 1 0.4461 0.829 0.62 0.00 0.00 0.04 0.00 0.32 0.02
#> TCGA.CS.5395.01 5 0.3940 0.718 0.08 0.06 0.00 0.00 0.78 0.00 0.08
#> TCGA.DU.7292.01 1 0.3685 0.838 0.66 0.00 0.00 0.02 0.00 0.32 0.00
#> TCGA.19.5958.01 4 0.2376 0.797 0.02 0.00 0.12 0.86 0.00 0.00 0.00
#> TCGA.06.5415.01 6 0.0504 0.971 0.02 0.00 0.00 0.00 0.00 0.98 0.00
#> TCGA.4W.AA9S.01 3 0.0863 0.882 0.00 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.76.6283.01 4 0.5612 0.529 0.12 0.00 0.02 0.56 0.00 0.02 0.28
#> TCGA.DU.6392.01 2 0.2159 0.911 0.06 0.90 0.00 0.02 0.00 0.00 0.02
#> TCGA.FG.A70Z.01 5 0.3691 0.720 0.06 0.06 0.00 0.00 0.80 0.00 0.08
#> TCGA.QH.A6XC.01 1 0.4003 0.834 0.64 0.00 0.00 0.04 0.00 0.32 0.00
#> TCGA.TM.A7C3.01 6 0.0000 0.984 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.06.A7TK.01 3 0.3485 0.826 0.10 0.00 0.82 0.02 0.04 0.00 0.02
#> TCGA.06.5411.01 2 0.0000 0.978 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YL.01 3 0.3485 0.826 0.10 0.00 0.82 0.02 0.04 0.00 0.02
#> TCGA.QH.A6CV.01 6 0.0000 0.984 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.28.5214.01 6 0.0000 0.984 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.74.6584.01 2 0.0504 0.965 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.76.6664.01 5 0.4461 -0.236 0.00 0.00 0.06 0.00 0.54 0.00 0.40
#> TCGA.CS.6188.01 1 0.4524 0.479 0.60 0.00 0.00 0.34 0.00 0.04 0.02
#> TCGA.28.6450.01 1 0.4146 0.837 0.64 0.00 0.00 0.02 0.00 0.32 0.02
#> TCGA.32.1979.01 4 0.2572 0.787 0.00 0.00 0.20 0.80 0.00 0.00 0.00
#> TCGA.19.0957.02 5 0.3054 0.684 0.04 0.04 0.04 0.00 0.86 0.00 0.02
#> TCGA.76.6657.01 4 0.2563 0.757 0.04 0.00 0.04 0.88 0.04 0.00 0.00
#> TCGA.06.0210.01 5 0.1166 0.740 0.00 0.06 0.00 0.00 0.94 0.00 0.00
#> TCGA.06.A5U0.01 2 0.0000 0.978 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5413.01 3 0.0863 0.882 0.00 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.14.1034.02 6 0.0000 0.984 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.19.5952.01 7 0.4305 0.722 0.00 0.00 0.04 0.02 0.28 0.00 0.66
#> TCGA.DH.5140.01 2 0.0000 0.978 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6280.01 1 0.4146 0.833 0.64 0.00 0.00 0.00 0.02 0.32 0.02
#> TCGA.14.0736.01 5 0.4264 0.520 0.06 0.32 0.00 0.00 0.62 0.00 0.00
#> TCGA.06.0152.02 6 0.0863 0.948 0.04 0.00 0.00 0.00 0.00 0.96 0.00
#> TCGA.76.4927.01 1 0.3685 0.832 0.66 0.00 0.00 0.00 0.02 0.32 0.00
#> TCGA.74.6578.01 3 0.1671 0.824 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.74.6577.01 2 0.0000 0.986 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.0125.02 4 0.1557 0.869 0.02 0.00 0.06 0.92 0.00 0.00 0.00 0.00
#> TCGA.06.0171.01 3 0.2484 0.822 0.02 0.00 0.86 0.10 0.00 0.00 0.00 0.02
#> TCGA.26.5136.01 5 0.3873 0.717 0.06 0.02 0.00 0.00 0.72 0.00 0.00 0.20
#> TCGA.DU.A76L.01 7 0.2020 0.808 0.00 0.00 0.02 0.02 0.06 0.00 0.90 0.00
#> TCGA.14.1402.01 1 0.4276 0.828 0.70 0.00 0.00 0.00 0.00 0.18 0.04 0.08
#> TCGA.06.0211.01 1 0.4578 0.668 0.70 0.00 0.00 0.16 0.00 0.02 0.04 0.08
#> TCGA.19.4065.02 7 0.1765 0.721 0.00 0.00 0.00 0.12 0.00 0.00 0.88 0.00
#> TCGA.19.5950.01 1 0.3748 0.816 0.74 0.00 0.00 0.00 0.02 0.20 0.02 0.02
#> TCGA.CS.5395.01 5 0.3002 0.673 0.00 0.02 0.00 0.00 0.82 0.00 0.12 0.04
#> TCGA.DU.7292.01 1 0.2114 0.838 0.84 0.00 0.00 0.00 0.00 0.16 0.00 0.00
#> TCGA.19.5958.01 4 0.1607 0.860 0.04 0.00 0.04 0.92 0.00 0.00 0.00 0.00
#> TCGA.06.5415.01 6 0.1408 0.912 0.02 0.00 0.00 0.00 0.00 0.94 0.02 0.02
#> TCGA.4W.AA9S.01 3 0.2114 0.827 0.00 0.00 0.84 0.16 0.00 0.00 0.00 0.00
#> TCGA.76.6283.01 8 0.3862 0.000 0.04 0.00 0.00 0.36 0.00 0.00 0.00 0.60
#> TCGA.DU.6392.01 2 0.1741 0.925 0.04 0.92 0.00 0.02 0.00 0.00 0.00 0.02
#> TCGA.FG.A70Z.01 5 0.2224 0.678 0.00 0.02 0.00 0.00 0.86 0.00 0.12 0.00
#> TCGA.QH.A6XC.01 1 0.2114 0.838 0.84 0.00 0.00 0.00 0.00 0.16 0.00 0.00
#> TCGA.TM.A7C3.01 6 0.0941 0.942 0.00 0.00 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.06.A7TK.01 3 0.0941 0.782 0.02 0.00 0.96 0.00 0.00 0.00 0.02 0.00
#> TCGA.06.5411.01 2 0.0000 0.986 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YL.01 3 0.0941 0.782 0.02 0.00 0.96 0.00 0.00 0.00 0.02 0.00
#> TCGA.QH.A6CV.01 6 0.0941 0.942 0.00 0.00 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.28.5214.01 6 0.0000 0.939 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.74.6584.01 2 0.0000 0.986 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6664.01 7 0.5224 0.495 0.04 0.00 0.02 0.00 0.24 0.00 0.60 0.10
#> TCGA.CS.6188.01 1 0.2569 0.680 0.82 0.00 0.00 0.16 0.00 0.02 0.00 0.00
#> TCGA.28.6450.01 1 0.3868 0.813 0.72 0.00 0.00 0.00 0.02 0.22 0.02 0.02
#> TCGA.32.1979.01 4 0.1557 0.869 0.02 0.00 0.06 0.92 0.00 0.00 0.00 0.00
#> TCGA.19.0957.02 5 0.5024 0.630 0.04 0.00 0.10 0.00 0.64 0.00 0.02 0.20
#> TCGA.76.6657.01 4 0.2648 0.594 0.08 0.00 0.00 0.84 0.00 0.00 0.00 0.08
#> TCGA.06.0210.01 5 0.3615 0.710 0.04 0.02 0.00 0.00 0.74 0.00 0.00 0.20
#> TCGA.06.A5U0.01 2 0.0000 0.986 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5413.01 3 0.2114 0.827 0.00 0.00 0.84 0.16 0.00 0.00 0.00 0.00
#> TCGA.14.1034.02 6 0.0941 0.942 0.00 0.00 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.19.5952.01 7 0.1563 0.804 0.00 0.00 0.00 0.00 0.10 0.00 0.90 0.00
#> TCGA.DH.5140.01 2 0.0000 0.986 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6280.01 1 0.5462 0.776 0.58 0.00 0.00 0.00 0.02 0.24 0.06 0.10
#> TCGA.14.0736.01 5 0.2719 0.630 0.00 0.18 0.00 0.00 0.80 0.00 0.02 0.00
#> TCGA.06.0152.02 6 0.2020 0.884 0.02 0.00 0.00 0.00 0.00 0.90 0.02 0.06
#> TCGA.76.4927.01 1 0.4276 0.828 0.70 0.00 0.00 0.00 0.00 0.18 0.04 0.08
#> TCGA.74.6578.01 3 0.4040 0.500 0.02 0.00 0.58 0.38 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: Node014. Child nodes: Node01111-leaf , Node01112-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01211-leaf , Node01212-leaf , Node01213 , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node01224-leaf , Node01225-leaf , Node01311-leaf , Node01312-leaf , Node01313-leaf , Node01411-leaf , Node01412-leaf , Node01431-leaf , Node01432-leaf , Node02211-leaf , Node02212 , Node02221 , Node02222-leaf , Node02223-leaf , Node02231 , Node02232-leaf , Node02233-leaf , Node02234-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0141"]
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 '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 0.4589 0.542 0.542
#> 3 3 0.800 0.936 0.920 0.2497 0.850 0.723
#> 4 4 0.750 0.507 0.829 0.1945 0.917 0.792
#> 5 5 0.767 0.695 0.824 0.0854 0.808 0.465
#> 6 6 0.683 0.747 0.843 0.0609 0.983 0.917
#> 7 7 0.808 0.657 0.819 0.0696 1.000 1.000
#> 8 8 0.800 0.680 0.839 0.0478 0.908 0.500
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.14.1402.01 2 0 1 0 1
#> TCGA.06.0211.01 1 0 1 1 0
#> TCGA.19.5950.01 2 0 1 0 1
#> TCGA.DU.7292.01 1 0 1 1 0
#> TCGA.06.5415.01 1 0 1 1 0
#> TCGA.76.6283.01 2 0 1 0 1
#> TCGA.QH.A6XC.01 1 0 1 1 0
#> TCGA.TM.A7C3.01 2 0 1 0 1
#> TCGA.QH.A6CV.01 1 0 1 1 0
#> TCGA.28.5214.01 1 0 1 1 0
#> TCGA.CS.6188.01 1 0 1 1 0
#> TCGA.28.6450.01 1 0 1 1 0
#> TCGA.14.1034.02 2 0 1 0 1
#> TCGA.76.6280.01 1 0 1 1 0
#> TCGA.06.0152.02 1 0 1 1 0
#> TCGA.76.4927.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.14.1402.01 2 0.556 0.801 0.00 0.7 0.30
#> TCGA.06.0211.01 1 0.000 1.000 1.00 0.0 0.00
#> TCGA.19.5950.01 2 0.556 0.801 0.00 0.7 0.30
#> TCGA.DU.7292.01 1 0.000 1.000 1.00 0.0 0.00
#> TCGA.06.5415.01 1 0.000 1.000 1.00 0.0 0.00
#> TCGA.76.6283.01 2 0.000 0.872 0.00 1.0 0.00
#> TCGA.QH.A6XC.01 1 0.000 1.000 1.00 0.0 0.00
#> TCGA.TM.A7C3.01 2 0.000 0.872 0.00 1.0 0.00
#> TCGA.QH.A6CV.01 3 0.556 0.884 0.30 0.0 0.70
#> TCGA.28.5214.01 3 0.604 0.871 0.38 0.0 0.62
#> TCGA.CS.6188.01 1 0.000 1.000 1.00 0.0 0.00
#> TCGA.28.6450.01 1 0.000 1.000 1.00 0.0 0.00
#> TCGA.14.1034.02 2 0.000 0.872 0.00 1.0 0.00
#> TCGA.76.6280.01 1 0.000 1.000 1.00 0.0 0.00
#> TCGA.06.0152.02 1 0.000 1.000 1.00 0.0 0.00
#> TCGA.76.4927.01 1 0.000 1.000 1.00 0.0 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.14.1402.01 2 0.4624 0.736 0.00 0.66 0.00 0.34
#> TCGA.06.0211.01 1 0.0000 0.825 1.00 0.00 0.00 0.00
#> TCGA.19.5950.01 2 0.5173 0.736 0.00 0.66 0.02 0.32
#> TCGA.DU.7292.01 1 0.0707 0.819 0.98 0.00 0.00 0.02
#> TCGA.06.5415.01 1 0.5000 -0.336 0.50 0.00 0.00 0.50
#> TCGA.76.6283.01 2 0.0000 0.832 0.00 1.00 0.00 0.00
#> TCGA.QH.A6XC.01 1 0.0000 0.825 1.00 0.00 0.00 0.00
#> TCGA.TM.A7C3.01 2 0.0000 0.832 0.00 1.00 0.00 0.00
#> TCGA.QH.A6CV.01 3 0.1211 0.000 0.04 0.00 0.96 0.00
#> TCGA.28.5214.01 4 0.6611 -0.506 0.08 0.00 0.46 0.46
#> TCGA.CS.6188.01 1 0.0707 0.819 0.98 0.00 0.00 0.02
#> TCGA.28.6450.01 4 0.5000 -0.342 0.50 0.00 0.00 0.50
#> TCGA.14.1034.02 2 0.0707 0.829 0.00 0.98 0.02 0.00
#> TCGA.76.6280.01 1 0.4406 0.390 0.70 0.00 0.00 0.30
#> TCGA.06.0152.02 1 0.0000 0.825 1.00 0.00 0.00 0.00
#> TCGA.76.4927.01 1 0.0000 0.825 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.14.1402.01 5 0.426 0.145 0.00 0.44 0.00 0.00 0.56
#> TCGA.06.0211.01 1 0.000 0.962 1.00 0.00 0.00 0.00 0.00
#> TCGA.19.5950.01 5 0.545 0.145 0.00 0.44 0.00 0.06 0.50
#> TCGA.DU.7292.01 1 0.165 0.950 0.94 0.00 0.00 0.02 0.04
#> TCGA.06.5415.01 4 0.368 0.936 0.28 0.00 0.00 0.72 0.00
#> TCGA.76.6283.01 2 0.104 0.940 0.00 0.96 0.04 0.00 0.00
#> TCGA.QH.A6XC.01 1 0.104 0.958 0.96 0.00 0.00 0.00 0.04
#> TCGA.TM.A7C3.01 2 0.000 0.940 0.00 1.00 0.00 0.00 0.00
#> TCGA.QH.A6CV.01 3 0.104 0.000 0.04 0.00 0.96 0.00 0.00
#> TCGA.28.5214.01 5 0.770 -0.452 0.06 0.00 0.24 0.30 0.40
#> TCGA.CS.6188.01 1 0.165 0.950 0.94 0.00 0.00 0.02 0.04
#> TCGA.28.6450.01 4 0.368 0.936 0.28 0.00 0.00 0.72 0.00
#> TCGA.14.1034.02 2 0.173 0.918 0.00 0.92 0.00 0.08 0.00
#> TCGA.76.6280.01 4 0.406 0.863 0.36 0.00 0.00 0.64 0.00
#> TCGA.06.0152.02 1 0.000 0.962 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.4927.01 1 0.000 0.962 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.14.1402.01 5 0.3076 0.924 0.00 0.24 0.00 0.00 0.76 0.00
#> TCGA.06.0211.01 1 0.2454 0.877 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.19.5950.01 5 0.4754 0.924 0.00 0.24 0.00 0.06 0.68 0.02
#> TCGA.DU.7292.01 1 0.0000 0.879 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.5415.01 4 0.2941 0.927 0.22 0.00 0.00 0.78 0.00 0.00
#> TCGA.76.6283.01 2 0.0547 0.790 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.QH.A6XC.01 1 0.0000 0.879 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A7C3.01 2 0.0000 0.790 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CV.01 3 0.0000 0.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.28.5214.01 6 0.7234 0.000 0.00 0.00 0.18 0.22 0.16 0.44
#> TCGA.CS.6188.01 1 0.0000 0.879 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.28.6450.01 4 0.2941 0.927 0.22 0.00 0.00 0.78 0.00 0.00
#> TCGA.14.1034.02 2 0.3647 0.560 0.00 0.64 0.00 0.00 0.00 0.36
#> TCGA.76.6280.01 4 0.4711 0.853 0.28 0.00 0.00 0.64 0.08 0.00
#> TCGA.06.0152.02 1 0.2631 0.871 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.76.4927.01 1 0.2631 0.871 0.82 0.00 0.00 0.00 0.00 0.18
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.14.1402.01 7 0.414 0.928 0.00 0.20 0 0.02 0.06 0.00 0.72
#> TCGA.06.0211.01 1 0.000 0.686 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.19.5950.01 7 0.257 0.928 0.00 0.20 0 0.00 0.00 0.00 0.80
#> TCGA.DU.7292.01 1 0.355 0.694 0.54 0.00 0 0.00 0.46 0.00 0.00
#> TCGA.06.5415.01 4 0.566 0.793 0.06 0.00 0 0.58 0.18 0.00 0.18
#> TCGA.76.6283.01 2 0.000 0.820 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.QH.A6XC.01 1 0.355 0.694 0.54 0.00 0 0.00 0.46 0.00 0.00
#> TCGA.TM.A7C3.01 2 0.202 0.820 0.00 0.90 0 0.04 0.00 0.06 0.00
#> TCGA.QH.A6CV.01 3 0.000 0.000 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.28.5214.01 6 0.117 0.000 0.00 0.00 0 0.06 0.00 0.94 0.00
#> TCGA.CS.6188.01 1 0.355 0.694 0.54 0.00 0 0.00 0.46 0.00 0.00
#> TCGA.28.6450.01 4 0.554 0.798 0.06 0.00 0 0.60 0.18 0.00 0.16
#> TCGA.14.1034.02 2 0.305 0.716 0.00 0.72 0 0.00 0.28 0.00 0.00
#> TCGA.76.6280.01 4 0.193 0.577 0.08 0.00 0 0.90 0.02 0.00 0.00
#> TCGA.06.0152.02 1 0.000 0.686 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.76.4927.01 1 0.101 0.672 0.96 0.00 0 0.00 0.02 0.00 0.02
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.14.1402.01 7 0.5077 0.835 0.12 0.18 0.02 0.00 0.04 0.00 0.64 0.00
#> TCGA.06.0211.01 1 0.3015 0.868 0.68 0.00 0.00 0.00 0.00 0.00 0.00 0.32
#> TCGA.19.5950.01 7 0.2267 0.835 0.00 0.18 0.00 0.00 0.00 0.00 0.82 0.00
#> TCGA.DU.7292.01 8 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.06.5415.01 4 0.0000 0.845 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.76.6283.01 2 0.0000 0.756 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6XC.01 8 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.TM.A7C3.01 2 0.0471 0.756 0.00 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CV.01 3 0.0808 0.000 0.00 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.28.5214.01 6 0.0000 0.000 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CS.6188.01 8 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.28.6450.01 4 0.2020 0.838 0.02 0.00 0.00 0.90 0.06 0.00 0.02 0.00
#> TCGA.14.1034.02 2 0.4538 0.475 0.12 0.56 0.00 0.00 0.32 0.00 0.00 0.00
#> TCGA.76.6280.01 5 0.3193 0.000 0.00 0.00 0.00 0.38 0.62 0.00 0.00 0.00
#> TCGA.06.0152.02 1 0.3757 0.836 0.68 0.00 0.00 0.00 0.00 0.00 0.06 0.26
#> TCGA.76.4927.01 1 0.4740 0.837 0.58 0.00 0.00 0.00 0.02 0.00 0.10 0.30
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: Node014. Child nodes: Node01111-leaf , Node01112-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01211-leaf , Node01212-leaf , Node01213 , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node01224-leaf , Node01225-leaf , Node01311-leaf , Node01312-leaf , Node01313-leaf , Node01411-leaf , Node01412-leaf , Node01431-leaf , Node01432-leaf , Node02211-leaf , Node02212 , Node02221 , Node02222-leaf , Node02223-leaf , Node02231 , Node02232-leaf , Node02233-leaf , Node02234-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0143"]
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 14 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 0.3633 0.637 0.637
#> 3 3 0.659 0.909 0.917 0.7750 0.692 0.517
#> 4 4 0.703 0.872 0.864 0.1942 0.868 0.600
#> 5 5 0.747 0.769 0.837 0.0790 0.923 0.632
#> 6 6 0.802 0.763 0.870 0.0465 0.978 0.846
#> 7 7 0.813 0.605 0.739 0.0308 0.967 0.750
#> 8 8 0.879 0.566 0.801 0.0271 0.934 0.455
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.06.0125.02 2 0 1 0 1
#> TCGA.06.0171.01 1 0 1 1 0
#> TCGA.DU.A76L.01 1 0 1 1 0
#> TCGA.19.4065.02 1 0 1 1 0
#> TCGA.19.5958.01 1 0 1 1 0
#> TCGA.4W.AA9S.01 1 0 1 1 0
#> TCGA.06.A7TK.01 1 0 1 1 0
#> TCGA.E1.A7YL.01 1 0 1 1 0
#> TCGA.76.6664.01 2 0 1 0 1
#> TCGA.32.1979.01 2 0 1 0 1
#> TCGA.76.6657.01 1 0 1 1 0
#> TCGA.06.5413.01 1 0 1 1 0
#> TCGA.19.5952.01 1 0 1 1 0
#> TCGA.74.6578.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.06.0125.02 2 0.000 0.974 0.00 1.00 0.00
#> TCGA.06.0171.01 3 0.254 1.000 0.08 0.00 0.92
#> TCGA.DU.A76L.01 1 0.334 0.862 0.88 0.00 0.12
#> TCGA.19.4065.02 3 0.254 1.000 0.08 0.00 0.92
#> TCGA.19.5958.01 1 0.429 0.844 0.82 0.00 0.18
#> TCGA.4W.AA9S.01 1 0.540 0.721 0.72 0.00 0.28
#> TCGA.06.A7TK.01 1 0.000 0.854 1.00 0.00 0.00
#> TCGA.E1.A7YL.01 1 0.000 0.854 1.00 0.00 0.00
#> TCGA.76.6664.01 2 0.254 0.948 0.00 0.92 0.08
#> TCGA.32.1979.01 2 0.000 0.974 0.00 1.00 0.00
#> TCGA.76.6657.01 1 0.000 0.854 1.00 0.00 0.00
#> TCGA.06.5413.01 1 0.429 0.844 0.82 0.00 0.18
#> TCGA.19.5952.01 3 0.254 1.000 0.08 0.00 0.92
#> TCGA.74.6578.01 3 0.254 1.000 0.08 0.00 0.92
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.06.0125.02 2 0.0000 0.935 0.00 1.00 0.00 0.00
#> TCGA.06.0171.01 3 0.5271 0.704 0.34 0.00 0.64 0.02
#> TCGA.DU.A76L.01 1 0.3610 0.840 0.80 0.00 0.00 0.20
#> TCGA.19.4065.02 3 0.0707 0.851 0.02 0.00 0.98 0.00
#> TCGA.19.5958.01 1 0.3400 0.863 0.82 0.00 0.00 0.18
#> TCGA.4W.AA9S.01 1 0.1211 0.661 0.96 0.00 0.04 0.00
#> TCGA.06.A7TK.01 4 0.3400 1.000 0.18 0.00 0.00 0.82
#> TCGA.E1.A7YL.01 4 0.3400 1.000 0.18 0.00 0.00 0.82
#> TCGA.76.6664.01 2 0.3853 0.866 0.00 0.82 0.02 0.16
#> TCGA.32.1979.01 2 0.0000 0.935 0.00 1.00 0.00 0.00
#> TCGA.76.6657.01 4 0.3400 1.000 0.18 0.00 0.00 0.82
#> TCGA.06.5413.01 1 0.3400 0.863 0.82 0.00 0.00 0.18
#> TCGA.19.5952.01 3 0.0707 0.851 0.02 0.00 0.98 0.00
#> TCGA.74.6578.01 3 0.3853 0.836 0.16 0.00 0.82 0.02
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.06.0125.02 2 0.0000 0.887 0.00 1.00 0.00 0.00 0.00
#> TCGA.06.0171.01 5 0.3999 0.238 0.02 0.00 0.24 0.00 0.74
#> TCGA.DU.A76L.01 1 0.3922 0.948 0.78 0.00 0.00 0.18 0.04
#> TCGA.19.4065.02 3 0.0000 0.780 0.00 0.00 1.00 0.00 0.00
#> TCGA.19.5958.01 1 0.2929 0.974 0.82 0.00 0.00 0.18 0.00
#> TCGA.4W.AA9S.01 5 0.5232 0.284 0.34 0.00 0.00 0.06 0.60
#> TCGA.06.A7TK.01 4 0.0000 0.941 0.00 0.00 0.00 1.00 0.00
#> TCGA.E1.A7YL.01 4 0.0000 0.941 0.00 0.00 0.00 1.00 0.00
#> TCGA.76.6664.01 2 0.4263 0.808 0.06 0.76 0.00 0.00 0.18
#> TCGA.32.1979.01 2 0.1410 0.887 0.06 0.94 0.00 0.00 0.00
#> TCGA.76.6657.01 4 0.2754 0.875 0.04 0.00 0.00 0.88 0.08
#> TCGA.06.5413.01 1 0.2929 0.974 0.82 0.00 0.00 0.18 0.00
#> TCGA.19.5952.01 3 0.0609 0.777 0.02 0.00 0.98 0.00 0.00
#> TCGA.74.6578.01 3 0.5068 0.447 0.06 0.00 0.64 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.06.0125.02 2 0.0000 0.846 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.0171.01 5 0.2094 0.605 0.00 0.00 0.08 0.00 0.90 0.02
#> TCGA.DU.A76L.01 1 0.2350 0.872 0.88 0.00 0.00 0.00 0.02 0.10
#> TCGA.19.4065.02 3 0.0000 0.830 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.19.5958.01 1 0.0000 0.929 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.4W.AA9S.01 5 0.2793 0.662 0.20 0.00 0.00 0.00 0.80 0.00
#> TCGA.06.A7TK.01 4 0.1556 0.908 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.E1.A7YL.01 4 0.1556 0.908 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.76.6664.01 2 0.4574 0.702 0.00 0.68 0.00 0.02 0.04 0.26
#> TCGA.32.1979.01 2 0.1092 0.846 0.00 0.96 0.00 0.02 0.02 0.00
#> TCGA.76.6657.01 4 0.4377 0.808 0.12 0.00 0.00 0.72 0.00 0.16
#> TCGA.06.5413.01 1 0.0547 0.925 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.19.5952.01 3 0.2474 0.840 0.00 0.00 0.88 0.04 0.00 0.08
#> TCGA.74.6578.01 6 0.6296 0.000 0.02 0.00 0.34 0.00 0.20 0.44
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.06.0125.02 2 0.2376 0.847 0.02 0.86 0.00 0.00 0.00 0.00 0.12
#> TCGA.06.0171.01 5 0.3228 0.643 0.02 0.00 0.00 0.00 0.80 0.02 0.16
#> TCGA.DU.A76L.01 1 0.0863 0.611 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.19.4065.02 3 0.2569 0.829 0.00 0.00 0.84 0.00 0.00 0.14 0.02
#> TCGA.19.5958.01 1 0.5370 0.788 0.56 0.00 0.00 0.04 0.10 0.00 0.30
#> TCGA.4W.AA9S.01 5 0.1671 0.661 0.10 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.06.A7TK.01 4 0.0000 0.821 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YL.01 4 0.0000 0.821 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.76.6664.01 6 0.3558 -0.483 0.00 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.32.1979.01 2 0.0000 0.847 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6657.01 4 0.4763 0.607 0.18 0.00 0.00 0.62 0.00 0.00 0.20
#> TCGA.06.5413.01 1 0.5220 0.793 0.60 0.00 0.00 0.04 0.10 0.00 0.26
#> TCGA.19.5952.01 3 0.0000 0.833 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.74.6578.01 6 0.5947 -0.146 0.00 0.00 0.10 0.00 0.08 0.46 0.36
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.06.0125.02 2 0.2020 0.840 0.00 0.90 0.00 0.00 0.02 0.00 0.02 0.06
#> TCGA.06.0171.01 5 0.3337 0.794 0.00 0.00 0.00 0.00 0.78 0.16 0.04 0.02
#> TCGA.DU.A76L.01 8 0.3083 -0.190 0.34 0.00 0.00 0.00 0.00 0.00 0.00 0.66
#> TCGA.19.4065.02 3 0.4180 0.638 0.00 0.00 0.70 0.00 0.00 0.06 0.20 0.04
#> TCGA.19.5958.01 1 0.1091 0.938 0.94 0.00 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.4W.AA9S.01 5 0.0808 0.798 0.04 0.00 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.06.A7TK.01 4 0.0000 0.940 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YL.01 4 0.1275 0.940 0.00 0.00 0.00 0.94 0.02 0.04 0.00 0.00
#> TCGA.76.6664.01 6 0.3318 0.000 0.00 0.46 0.00 0.00 0.00 0.54 0.00 0.00
#> TCGA.32.1979.01 2 0.0000 0.840 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.76.6657.01 8 0.5455 -0.227 0.00 0.00 0.00 0.38 0.00 0.20 0.02 0.40
#> TCGA.06.5413.01 1 0.0000 0.938 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.19.5952.01 3 0.0000 0.681 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.74.6578.01 7 0.0941 0.000 0.00 0.00 0.02 0.00 0.02 0.00 0.96 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node014 , Node021 , Node022 , Node023 , Node031 , Node032 , Node033-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 328 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 0.989 0.996 0.4883 0.513 0.513
#> 3 3 1.000 0.991 0.996 0.2279 0.879 0.766
#> 4 4 0.801 0.897 0.880 0.1409 0.914 0.786
#> 5 5 0.990 0.948 0.980 0.1225 0.886 0.657
#> 6 6 0.866 0.850 0.929 0.0358 0.967 0.859
#> 7 7 0.797 0.701 0.833 0.0306 0.961 0.821
#> 8 8 0.791 0.653 0.755 0.0145 0.982 0.906
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.HT.7693.01 1 0.000 0.9941 1.00 0.00
#> TCGA.S9.A7J2.01 2 0.000 0.9981 0.00 1.00
#> TCGA.S9.A6TX.01 2 0.000 0.9981 0.00 1.00
#> TCGA.VM.A8C8.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.A74L.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.A5TS.01 1 0.000 0.9941 1.00 0.00
#> TCGA.06.A7TL.01 1 0.000 0.9941 1.00 0.00
#> TCGA.E1.5311.01 2 0.000 0.9981 0.00 1.00
#> TCGA.E1.A7YI.01 1 0.141 0.9748 0.98 0.02
#> TCGA.E1.5305.01 1 0.000 0.9941 1.00 0.00
#> TCGA.F6.A8O4.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DH.A66G.01 1 0.000 0.9941 1.00 0.00
#> TCGA.P5.A731.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.7480.01 2 0.000 0.9981 0.00 1.00
#> TCGA.S9.A7R1.01 2 0.000 0.9981 0.00 1.00
#> TCGA.FG.A710.01 2 0.000 0.9981 0.00 1.00
#> TCGA.S9.A7J0.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.A6S6.01 2 0.000 0.9981 0.00 1.00
#> TCGA.FG.7634.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.6407.01 1 0.000 0.9941 1.00 0.00
#> TCGA.P5.A5F1.01 1 0.000 0.9941 1.00 0.00
#> TCGA.VM.A8CF.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.6542.01 1 0.000 0.9941 1.00 0.00
#> TCGA.FG.7638.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DH.5143.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.7299.01 1 0.000 0.9941 1.00 0.00
#> TCGA.CS.5393.01 1 0.000 0.9941 1.00 0.00
#> TCGA.TM.A84Q.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DB.5281.01 1 0.000 0.9941 1.00 0.00
#> TCGA.FG.A6J1.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HT.7608.01 2 0.000 0.9981 0.00 1.00
#> TCGA.E1.A7YU.01 1 0.000 0.9941 1.00 0.00
#> TCGA.W9.A837.01 2 0.000 0.9981 0.00 1.00
#> TCGA.TM.A7C5.01 2 0.000 0.9981 0.00 1.00
#> TCGA.QH.A6CW.01 1 0.000 0.9941 1.00 0.00
#> TCGA.S9.A6WO.01 1 0.000 0.9941 1.00 0.00
#> TCGA.IK.7675.01 1 0.000 0.9941 1.00 0.00
#> TCGA.P5.A5ET.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HT.7472.01 1 0.000 0.9941 1.00 0.00
#> TCGA.19.A6J5.01 2 0.000 0.9981 0.00 1.00
#> TCGA.P5.A77X.01 2 0.000 0.9981 0.00 1.00
#> TCGA.FG.A6IZ.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HT.7873.01 1 0.000 0.9941 1.00 0.00
#> TCGA.CS.4938.01 1 0.000 0.9941 1.00 0.00
#> TCGA.KT.A74X.01 2 0.000 0.9981 0.00 1.00
#> TCGA.VM.A8CH.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.7476.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DB.A75L.01 1 0.000 0.9941 1.00 0.00
#> TCGA.S9.A7IS.01 1 0.000 0.9941 1.00 0.00
#> TCGA.TQ.A8XE.02 1 0.000 0.9941 1.00 0.00
#> TCGA.E1.A7YO.01 2 0.000 0.9981 0.00 1.00
#> TCGA.TQ.A7RG.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HW.7493.01 1 0.000 0.9941 1.00 0.00
#> TCGA.RY.A847.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.8166.01 1 0.000 0.9941 1.00 0.00
#> TCGA.VM.A8CA.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HT.7855.01 1 0.000 0.9941 1.00 0.00
#> TCGA.S9.A89Z.01 1 0.999 0.0839 0.52 0.48
#> TCGA.DB.A4XG.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.7015.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.A616.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.7611.01 1 0.000 0.9941 1.00 0.00
#> TCGA.FG.A60K.01 2 0.000 0.9981 0.00 1.00
#> TCGA.S9.A6TY.01 2 0.000 0.9981 0.00 1.00
#> TCGA.WY.A85C.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DB.A4XC.01 1 0.000 0.9941 1.00 0.00
#> TCGA.P5.A72W.01 1 0.000 0.9941 1.00 0.00
#> TCGA.S9.A6TU.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.5855.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.7884.01 1 0.000 0.9941 1.00 0.00
#> TCGA.TQ.A7RQ.01 2 0.000 0.9981 0.00 1.00
#> TCGA.IK.8125.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HT.A74K.01 2 0.000 0.9981 0.00 1.00
#> TCGA.WH.A86K.01 1 0.000 0.9941 1.00 0.00
#> TCGA.QH.A6X8.01 2 0.000 0.9981 0.00 1.00
#> TCGA.WY.A85E.01 1 0.000 0.9941 1.00 0.00
#> TCGA.FG.6691.01 1 0.000 0.9941 1.00 0.00
#> TCGA.S9.A7R3.01 1 0.000 0.9941 1.00 0.00
#> TCGA.FG.A4MX.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.7681.01 2 0.000 0.9981 0.00 1.00
#> TCGA.S9.A7IZ.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.A6S7.01 1 0.000 0.9941 1.00 0.00
#> TCGA.06.0221.01 1 0.000 0.9941 1.00 0.00
#> TCGA.P5.A72Z.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HT.8114.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.8168.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HW.8321.01 1 0.000 0.9941 1.00 0.00
#> TCGA.TQ.A7RN.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DH.5141.01 2 0.000 0.9981 0.00 1.00
#> TCGA.EZ.7264.01 2 0.000 0.9981 0.00 1.00
#> TCGA.P5.A5F4.01 1 0.000 0.9941 1.00 0.00
#> TCGA.QH.A65V.01 2 0.000 0.9981 0.00 1.00
#> TCGA.FG.8191.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DH.5142.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.A6S8.01 2 0.000 0.9981 0.00 1.00
#> TCGA.E1.A7YW.01 1 0.000 0.9941 1.00 0.00
#> TCGA.CS.6666.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.7298.01 2 0.242 0.9568 0.04 0.96
#> TCGA.DB.A64R.01 2 0.000 0.9981 0.00 1.00
#> TCGA.CS.5390.01 2 0.000 0.9981 0.00 1.00
#> TCGA.S9.A6WP.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DB.5280.01 1 0.000 0.9941 1.00 0.00
#> TCGA.TM.A84T.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DH.A66D.01 1 0.000 0.9941 1.00 0.00
#> TCGA.RY.A83Z.01 1 0.000 0.9941 1.00 0.00
#> TCGA.TQ.A7RH.01 1 0.000 0.9941 1.00 0.00
#> TCGA.E1.A7YS.01 2 0.000 0.9981 0.00 1.00
#> TCGA.P5.A735.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.7294.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HT.7695.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DB.A64X.01 1 0.402 0.9103 0.92 0.08
#> TCGA.FG.7637.01 2 0.000 0.9981 0.00 1.00
#> TCGA.S9.A6U5.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HT.7609.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DB.5274.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HW.7487.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HW.7491.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DB.A75M.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HW.A5KM.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.7477.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.8012.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.8167.01 1 0.000 0.9941 1.00 0.00
#> TCGA.S9.A6U1.01 1 0.000 0.9941 1.00 0.00
#> TCGA.FG.5965.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.A614.01 1 0.000 0.9941 1.00 0.00
#> TCGA.S9.A7QZ.01 2 0.000 0.9981 0.00 1.00
#> TCGA.QH.A6X4.01 2 0.000 0.9981 0.00 1.00
#> TCGA.P5.A77W.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.7302.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.6399.01 1 0.000 0.9941 1.00 0.00
#> TCGA.E1.5307.01 1 0.000 0.9941 1.00 0.00
#> TCGA.S9.A7QW.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.7604.01 1 0.000 0.9941 1.00 0.00
#> TCGA.P5.A733.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.7684.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HW.7495.01 2 0.000 0.9981 0.00 1.00
#> TCGA.QH.A65R.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DH.A7UV.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.7879.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.A7TC.01 1 0.000 0.9941 1.00 0.00
#> TCGA.FG.A60J.01 1 0.000 0.9941 1.00 0.00
#> TCGA.E1.5303.01 1 0.000 0.9941 1.00 0.00
#> TCGA.FN.7833.01 1 0.000 0.9941 1.00 0.00
#> TCGA.E1.A7Z4.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.7875.01 2 0.000 0.9981 0.00 1.00
#> TCGA.06.5417.01 1 0.141 0.9748 0.98 0.02
#> TCGA.HT.7473.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.7008.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DB.A75O.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.7304.02 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.6394.01 2 0.000 0.9981 0.00 1.00
#> TCGA.S9.A6WD.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.5872.01 1 0.000 0.9941 1.00 0.00
#> TCGA.FG.8185.01 1 0.000 0.9941 1.00 0.00
#> TCGA.TQ.A7RU.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.5874.01 2 0.000 0.9981 0.00 1.00
#> TCGA.S9.A6WE.01 2 0.760 0.7167 0.22 0.78
#> TCGA.FG.6690.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HW.8320.01 1 0.000 0.9941 1.00 0.00
#> TCGA.R8.A6MK.01 2 0.000 0.9981 0.00 1.00
#> TCGA.S9.A7J1.01 2 0.000 0.9981 0.00 1.00
#> TCGA.E1.5322.01 1 0.000 0.9941 1.00 0.00
#> TCGA.P5.A5F0.01 2 0.000 0.9981 0.00 1.00
#> TCGA.R8.A73M.01 2 0.000 0.9981 0.00 1.00
#> TCGA.CS.4942.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DB.A4X9.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DB.A4XF.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.A74O.01 1 0.000 0.9941 1.00 0.00
#> TCGA.FG.8188.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.A6S3.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DB.A4XH.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HT.7485.01 1 0.000 0.9941 1.00 0.00
#> TCGA.VW.A7QS.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.8164.01 2 0.000 0.9981 0.00 1.00
#> TCGA.S9.A6TS.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DB.A64S.01 1 0.000 0.9941 1.00 0.00
#> TCGA.VV.A86M.01 1 0.000 0.9941 1.00 0.00
#> TCGA.TQ.A8XE.01 1 0.000 0.9941 1.00 0.00
#> TCGA.CS.6667.01 1 0.000 0.9941 1.00 0.00
#> TCGA.E1.A7YV.01 1 0.000 0.9941 1.00 0.00
#> TCGA.TQ.A7RW.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.A7TI.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.7468.01 2 0.000 0.9981 0.00 1.00
#> TCGA.TQ.A7RI.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DB.5279.01 2 0.000 0.9981 0.00 1.00
#> TCGA.S9.A6U8.01 1 0.000 0.9941 1.00 0.00
#> TCGA.R8.A6YH.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.7018.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HT.7677.01 2 0.000 0.9981 0.00 1.00
#> TCGA.TM.A7CA.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.7690.01 1 0.000 0.9941 1.00 0.00
#> TCGA.FG.6689.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.7007.01 1 0.000 0.9941 1.00 0.00
#> TCGA.TQ.A7RF.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DB.5277.01 1 0.000 0.9941 1.00 0.00
#> TCGA.TM.A84M.01 2 0.000 0.9981 0.00 1.00
#> TCGA.F6.A8O3.01 2 0.000 0.9981 0.00 1.00
#> TCGA.QH.A86X.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HT.8013.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HW.7490.01 1 0.000 0.9941 1.00 0.00
#> TCGA.QH.A65S.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.A76R.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DH.5144.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HT.7606.01 1 0.000 0.9941 1.00 0.00
#> TCGA.RY.A840.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HW.A5KJ.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HT.8105.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HT.7471.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.6395.01 1 0.000 0.9941 1.00 0.00
#> TCGA.S9.A6TV.01 1 0.000 0.9941 1.00 0.00
#> TCGA.P5.A5EW.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.6408.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DB.A4XB.01 1 0.000 0.9941 1.00 0.00
#> TCGA.FG.A4MT.01 1 0.000 0.9941 1.00 0.00
#> TCGA.FG.A4MT.02 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.A619.01 2 0.000 0.9981 0.00 1.00
#> TCGA.QH.A870.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.A5R9.01 2 0.000 0.9981 0.00 1.00
#> TCGA.CS.5396.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.A7TA.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HW.8319.01 1 0.000 0.9941 1.00 0.00
#> TCGA.TM.A84H.01 1 0.000 0.9941 1.00 0.00
#> TCGA.S9.A6TZ.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.6400.01 2 0.000 0.9981 0.00 1.00
#> TCGA.S9.A6WL.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DB.A75K.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DB.A4XD.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DB.A64Q.01 2 0.000 0.9981 0.00 1.00
#> TCGA.P5.A737.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DB.5275.01 1 0.000 0.9941 1.00 0.00
#> TCGA.S9.A6WH.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.A5TU.01 1 0.981 0.2811 0.58 0.42
#> TCGA.HT.A5RB.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.7616.01 2 0.000 0.9981 0.00 1.00
#> TCGA.S9.A7R8.01 1 0.000 0.9941 1.00 0.00
#> TCGA.QH.A6XA.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.A5TP.01 1 0.000 0.9941 1.00 0.00
#> TCGA.RY.A83Y.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HT.7482.01 1 0.000 0.9941 1.00 0.00
#> TCGA.TQ.A7RK.02 1 0.000 0.9941 1.00 0.00
#> TCGA.TQ.A7RK.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.7475.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DB.A64U.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DB.A64W.01 2 0.000 0.9981 0.00 1.00
#> TCGA.R8.A6MO.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.A7T8.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HW.8322.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.5870.02 2 0.000 0.9981 0.00 1.00
#> TCGA.CS.6668.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.5870.01 2 0.000 0.9981 0.00 1.00
#> TCGA.FG.7636.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.7692.01 2 0.000 0.9981 0.00 1.00
#> TCGA.WY.A859.01 1 0.000 0.9941 1.00 0.00
#> TCGA.R8.A6ML.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.6410.01 2 0.000 0.9981 0.00 1.00
#> TCGA.S9.A6U9.01 1 0.000 0.9941 1.00 0.00
#> TCGA.TQ.A7RO.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.7019.01 1 0.000 0.9941 1.00 0.00
#> TCGA.TQ.A7RM.01 1 0.141 0.9748 0.98 0.02
#> TCGA.S9.A7R4.01 1 0.000 0.9941 1.00 0.00
#> TCGA.E1.5318.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HT.7676.01 1 0.000 0.9941 1.00 0.00
#> TCGA.S9.A7J3.01 2 0.000 0.9981 0.00 1.00
#> TCGA.06.6701.01 1 0.000 0.9941 1.00 0.00
#> TCGA.P5.A5F2.01 1 0.000 0.9941 1.00 0.00
#> TCGA.E1.5304.01 1 0.402 0.9103 0.92 0.08
#> TCGA.WY.A85B.01 1 0.000 0.9941 1.00 0.00
#> TCGA.TQ.A7RS.01 2 0.000 0.9981 0.00 1.00
#> TCGA.S9.A7QX.01 1 0.000 0.9941 1.00 0.00
#> TCGA.CS.4943.01 1 0.000 0.9941 1.00 0.00
#> TCGA.QH.A65Z.01 2 0.000 0.9981 0.00 1.00
#> TCGA.P5.A730.01 2 0.000 0.9981 0.00 1.00
#> TCGA.WY.A85D.01 1 0.000 0.9941 1.00 0.00
#> TCGA.RY.A83X.01 2 0.000 0.9981 0.00 1.00
#> TCGA.S9.A6UB.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DH.A66F.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.6393.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HT.8108.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.7304.01 1 0.000 0.9941 1.00 0.00
#> TCGA.S9.A7IY.01 2 0.000 0.9981 0.00 1.00
#> TCGA.FG.7641.01 2 0.000 0.9981 0.00 1.00
#> TCGA.P5.A5EV.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.7301.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.7009.01 2 0.000 0.9981 0.00 1.00
#> TCGA.FG.A4MY.01 1 0.000 0.9941 1.00 0.00
#> TCGA.TM.A7CF.01 1 0.000 0.9941 1.00 0.00
#> TCGA.FG.8186.01 2 0.000 0.9981 0.00 1.00
#> TCGA.S9.A6U6.01 1 0.000 0.9941 1.00 0.00
#> TCGA.RY.A845.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.7010.01 1 0.000 0.9941 1.00 0.00
#> TCGA.FG.8182.01 1 0.000 0.9941 1.00 0.00
#> TCGA.QH.A6X3.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.6401.01 1 0.000 0.9941 1.00 0.00
#> TCGA.E1.A7YH.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.7306.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.A74J.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DB.A4XE.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DB.A64L.01 2 0.000 0.9981 0.00 1.00
#> TCGA.VV.A829.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HT.A61B.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DH.A66B.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.6397.02 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.6397.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.5853.01 1 0.000 0.9941 1.00 0.00
#> TCGA.CS.6670.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.7014.01 1 0.000 0.9941 1.00 0.00
#> TCGA.QH.A65X.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DB.A64P.01 2 0.000 0.9981 0.00 1.00
#> TCGA.TQ.A7RV.01 1 0.000 0.9941 1.00 0.00
#> TCGA.06.6389.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HW.A5KL.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DH.A7UU.01 1 0.000 0.9941 1.00 0.00
#> TCGA.QH.A6CZ.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DH.A669.02 2 0.000 0.9981 0.00 1.00
#> TCGA.DH.A669.01 2 0.000 0.9981 0.00 1.00
#> TCGA.QH.A6X9.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.5871.01 1 0.000 0.9941 1.00 0.00
#> TCGA.TQ.A7RJ.01 1 0.000 0.9941 1.00 0.00
#> TCGA.VM.A8CB.01 2 0.000 0.9981 0.00 1.00
#> TCGA.HT.7483.01 1 0.000 0.9941 1.00 0.00
#> TCGA.HT.7687.01 2 0.000 0.9981 0.00 1.00
#> TCGA.TM.A84G.01 2 0.000 0.9981 0.00 1.00
#> TCGA.E1.A7Z6.01 1 0.000 0.9941 1.00 0.00
#> TCGA.TM.A84I.01 1 0.000 0.9941 1.00 0.00
#> TCGA.CS.5394.01 2 0.000 0.9981 0.00 1.00
#> TCGA.DU.A76O.01 1 0.000 0.9941 1.00 0.00
#> TCGA.DU.A5TW.01 1 0.000 0.9941 1.00 0.00
#> TCGA.FG.5962.01 2 0.000 0.9981 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.HT.7693.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.S9.A7J2.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.S9.A6TX.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.VM.A8C8.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HT.A74L.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DU.A5TS.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.06.A7TL.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.E1.5311.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.E1.A7YI.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.E1.5305.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.F6.A8O4.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DH.A66G.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.P5.A731.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HT.7480.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.S9.A7R1.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.FG.A710.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.S9.A7J0.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.DU.A6S6.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.FG.7634.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DU.6407.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.P5.A5F1.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.VM.A8CF.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.6542.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.FG.7638.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DH.5143.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.7299.01 1 0.4002 0.807 0.84 0.00 0.16
#> TCGA.CS.5393.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.TM.A84Q.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DB.5281.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.FG.A6J1.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HT.7608.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.E1.A7YU.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.W9.A837.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.TM.A7C5.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.QH.A6CW.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.S9.A6WO.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.IK.7675.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.P5.A5ET.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HT.7472.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.19.A6J5.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.P5.A77X.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.FG.A6IZ.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HT.7873.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.CS.4938.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.KT.A74X.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.VM.A8CH.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HT.7476.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DB.A75L.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.S9.A7IS.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.TQ.A8XE.02 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.E1.A7YO.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.TQ.A7RG.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HW.7493.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.RY.A847.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DU.8166.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.VM.A8CA.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HT.7855.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.S9.A89Z.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.DB.A4XG.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DU.7015.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HT.A616.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HT.7611.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.FG.A60K.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.S9.A6TY.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.WY.A85C.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DB.A4XC.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.P5.A72W.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.S9.A6TU.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.5855.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HT.7884.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.TQ.A7RQ.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.IK.8125.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HT.A74K.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.WH.A86K.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.QH.A6X8.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.WY.A85E.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.FG.6691.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.S9.A7R3.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.FG.A4MX.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HT.7681.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.S9.A7IZ.01 1 0.4002 0.807 0.84 0.00 0.16
#> TCGA.DU.A6S7.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.06.0221.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.P5.A72Z.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HT.8114.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.8168.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HW.8321.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.TQ.A7RN.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DH.5141.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.EZ.7264.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.P5.A5F4.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.QH.A65V.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.FG.8191.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DH.5142.01 3 0.4291 0.783 0.18 0.00 0.82
#> TCGA.DU.A6S8.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.E1.A7YW.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CS.6666.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.7298.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DB.A64R.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.CS.5390.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.S9.A6WP.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DB.5280.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.TM.A84T.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DH.A66D.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.RY.A83Z.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.TQ.A7RH.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.E1.A7YS.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.P5.A735.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.7294.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HT.7695.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DB.A64X.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.FG.7637.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.S9.A6U5.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HT.7609.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DB.5274.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HW.7487.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HW.7491.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DB.A75M.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HW.A5KM.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HT.7477.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.HT.8012.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DU.8167.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.S9.A6U1.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.FG.5965.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HT.A614.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.S9.A7QZ.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.QH.A6X4.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.P5.A77W.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DU.7302.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DU.6399.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.E1.5307.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.S9.A7QW.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HT.7604.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.P5.A733.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HT.7684.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HW.7495.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.QH.A65R.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DH.A7UV.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HT.7879.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.A7TC.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.FG.A60J.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.E1.5303.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.FN.7833.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.E1.A7Z4.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HT.7875.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.06.5417.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.HT.7473.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.7008.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DB.A75O.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.7304.02 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.DU.6394.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.S9.A6WD.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DU.5872.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.FG.8185.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.TQ.A7RU.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DU.5874.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.S9.A6WE.01 1 0.6045 0.389 0.62 0.38 0.00
#> TCGA.FG.6690.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HW.8320.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.R8.A6MK.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.S9.A7J1.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.E1.5322.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.P5.A5F0.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.R8.A73M.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.CS.4942.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DB.A4X9.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DB.A4XF.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HT.A74O.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.FG.8188.01 3 0.5016 0.690 0.24 0.00 0.76
#> TCGA.DU.A6S3.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DB.A4XH.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HT.7485.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.VW.A7QS.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DU.8164.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.S9.A6TS.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.DB.A64S.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.VV.A86M.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.TQ.A8XE.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CS.6667.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.E1.A7YV.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.TQ.A7RW.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.A7TI.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HT.7468.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.TQ.A7RI.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DB.5279.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.S9.A6U8.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.R8.A6YH.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.7018.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HT.7677.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.TM.A7CA.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HT.7690.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.FG.6689.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.7007.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.TQ.A7RF.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DB.5277.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.TM.A84M.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.F6.A8O3.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.QH.A86X.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HT.8013.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HW.7490.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.QH.A65S.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.A76R.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DH.5144.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HT.7606.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.RY.A840.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HW.A5KJ.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HT.8105.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HT.7471.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DU.6395.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.S9.A6TV.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.P5.A5EW.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.6408.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.DB.A4XB.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.FG.A4MT.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.FG.A4MT.02 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HT.A619.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.QH.A870.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HT.A5R9.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.CS.5396.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DU.A7TA.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HW.8319.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.TM.A84H.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.S9.A6TZ.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.6400.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.S9.A6WL.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DB.A75K.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DB.A4XD.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DB.A64Q.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.P5.A737.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DB.5275.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.S9.A6WH.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DU.A5TU.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.HT.A5RB.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HT.7616.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.S9.A7R8.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.QH.A6XA.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.A5TP.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.RY.A83Y.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HT.7482.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.TQ.A7RK.02 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.TQ.A7RK.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HT.7475.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DB.A64U.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DB.A64W.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.R8.A6MO.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DU.A7T8.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HW.8322.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DU.5870.02 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.CS.6668.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DU.5870.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.FG.7636.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HT.7692.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.WY.A859.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.R8.A6ML.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DU.6410.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.S9.A6U9.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.TQ.A7RO.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DU.7019.01 1 0.0892 0.975 0.98 0.00 0.02
#> TCGA.TQ.A7RM.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.S9.A7R4.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.E1.5318.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HT.7676.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.S9.A7J3.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.06.6701.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.P5.A5F2.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.E1.5304.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.WY.A85B.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.TQ.A7RS.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.S9.A7QX.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CS.4943.01 1 0.0892 0.975 0.98 0.00 0.02
#> TCGA.QH.A65Z.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.P5.A730.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.WY.A85D.01 1 0.0892 0.975 0.98 0.00 0.02
#> TCGA.RY.A83X.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.S9.A6UB.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DH.A66F.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DU.6393.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HT.8108.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.7304.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.S9.A7IY.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.FG.7641.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.P5.A5EV.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.7301.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.7009.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.FG.A4MY.01 3 0.1529 0.950 0.04 0.00 0.96
#> TCGA.TM.A7CF.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.FG.8186.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.S9.A6U6.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.RY.A845.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.7010.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.FG.8182.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.QH.A6X3.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.6401.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.E1.A7YH.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.7306.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HT.A74J.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DB.A4XE.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DB.A64L.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.VV.A829.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HT.A61B.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.DH.A66B.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.6397.02 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DU.6397.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DU.5853.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.CS.6670.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DU.7014.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.QH.A65X.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DB.A64P.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.TQ.A7RV.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.06.6389.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.HW.A5KL.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DH.A7UU.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.QH.A6CZ.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DH.A669.02 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DH.A669.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.QH.A6X9.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.5871.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.TQ.A7RJ.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.VM.A8CB.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.HT.7483.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.HT.7687.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.TM.A84G.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.E1.A7Z6.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.TM.A84I.01 3 0.0000 0.988 0.00 0.00 1.00
#> TCGA.CS.5394.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.DU.A76O.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.DU.A5TW.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.FG.5962.01 2 0.0000 1.000 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.HT.7693.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.S9.A7J2.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.S9.A6TX.01 4 0.2345 0.829 0.00 0.10 0.00 0.90
#> TCGA.VM.A8C8.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.HT.A74L.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.DU.A5TS.01 3 0.4522 0.769 0.00 0.32 0.68 0.00
#> TCGA.06.A7TL.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.E1.5311.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.E1.A7YI.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.E1.5305.01 3 0.4522 0.769 0.00 0.32 0.68 0.00
#> TCGA.F6.A8O4.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DH.A66G.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.P5.A731.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.HT.7480.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.S9.A7R1.01 2 0.4977 0.738 0.00 0.54 0.00 0.46
#> TCGA.FG.A710.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.S9.A7J0.01 3 0.2345 0.881 0.00 0.10 0.90 0.00
#> TCGA.DU.A6S6.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.FG.7634.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.DU.6407.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.P5.A5F1.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.VM.A8CF.01 1 0.4406 0.736 0.70 0.30 0.00 0.00
#> TCGA.DU.6542.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.FG.7638.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.DH.5143.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DU.7299.01 1 0.5986 0.647 0.62 0.32 0.06 0.00
#> TCGA.CS.5393.01 3 0.3975 0.816 0.00 0.24 0.76 0.00
#> TCGA.TM.A84Q.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DB.5281.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.FG.A6J1.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.HT.7608.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.E1.A7YU.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.W9.A837.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.TM.A7C5.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.QH.A6CW.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.S9.A6WO.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.IK.7675.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.P5.A5ET.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.HT.7472.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.19.A6J5.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.P5.A77X.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.FG.A6IZ.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.HT.7873.01 3 0.3172 0.789 0.16 0.00 0.84 0.00
#> TCGA.CS.4938.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.KT.A74X.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.VM.A8CH.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.HT.7476.01 1 0.4624 0.702 0.66 0.34 0.00 0.00
#> TCGA.DB.A75L.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.S9.A7IS.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.TQ.A8XE.02 1 0.0707 0.895 0.98 0.02 0.00 0.00
#> TCGA.E1.A7YO.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.TQ.A7RG.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.HW.7493.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.RY.A847.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.DU.8166.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.VM.A8CA.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.HT.7855.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.S9.A89Z.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.DB.A4XG.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.DU.7015.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.HT.A616.01 1 0.0707 0.895 0.98 0.02 0.00 0.00
#> TCGA.HT.7611.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.FG.A60K.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.S9.A6TY.01 4 0.2647 0.789 0.00 0.12 0.00 0.88
#> TCGA.WY.A85C.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.DB.A4XC.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.P5.A72W.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.S9.A6TU.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.DU.5855.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.HT.7884.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RQ.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.IK.8125.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.HT.A74K.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.WH.A86K.01 3 0.5173 0.754 0.02 0.32 0.66 0.00
#> TCGA.QH.A6X8.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.WY.A85E.01 1 0.0707 0.895 0.98 0.02 0.00 0.00
#> TCGA.FG.6691.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.S9.A7R3.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.FG.A4MX.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.HT.7681.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.S9.A7IZ.01 1 0.2706 0.832 0.90 0.02 0.08 0.00
#> TCGA.DU.A6S7.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.06.0221.01 3 0.3400 0.847 0.00 0.18 0.82 0.00
#> TCGA.P5.A72Z.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.HT.8114.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DU.8168.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.HW.8321.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RN.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.DH.5141.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.EZ.7264.01 4 0.0707 0.961 0.00 0.02 0.00 0.98
#> TCGA.P5.A5F4.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.QH.A65V.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.FG.8191.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DH.5142.01 3 0.5062 0.605 0.30 0.02 0.68 0.00
#> TCGA.DU.A6S8.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.E1.A7YW.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.CS.6666.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.DU.7298.01 2 0.0000 0.452 0.00 1.00 0.00 0.00
#> TCGA.DB.A64R.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.CS.5390.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.S9.A6WP.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.DB.5280.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.TM.A84T.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DH.A66D.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.RY.A83Z.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.TQ.A7RH.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YS.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.P5.A735.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DU.7294.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.HT.7695.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.DB.A64X.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.FG.7637.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.S9.A6U5.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.HT.7609.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DB.5274.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.HW.7487.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.HW.7491.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.DB.A75M.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.HW.A5KM.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.HT.7477.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.HT.8012.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.DU.8167.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.S9.A6U1.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.FG.5965.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.HT.A614.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.S9.A7QZ.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.QH.A6X4.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.P5.A77W.01 4 0.1211 0.932 0.00 0.04 0.00 0.96
#> TCGA.DU.7302.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.DU.6399.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.E1.5307.01 3 0.4522 0.769 0.00 0.32 0.68 0.00
#> TCGA.S9.A7QW.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.HT.7604.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.P5.A733.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.HT.7684.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.HW.7495.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.QH.A65R.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.DH.A7UV.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.HT.7879.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DU.A7TC.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.FG.A60J.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.E1.5303.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.FN.7833.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.E1.A7Z4.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.HT.7875.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.06.5417.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.HT.7473.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DU.7008.01 1 0.4277 0.749 0.72 0.28 0.00 0.00
#> TCGA.DB.A75O.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DU.7304.02 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.DU.6394.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.S9.A6WD.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.DU.5872.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.FG.8185.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.TQ.A7RU.01 2 0.4713 0.922 0.00 0.64 0.00 0.36
#> TCGA.DU.5874.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.S9.A6WE.01 2 0.6104 0.716 0.14 0.68 0.00 0.18
#> TCGA.FG.6690.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.HW.8320.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.R8.A6MK.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.S9.A7J1.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.E1.5322.01 1 0.0707 0.895 0.98 0.02 0.00 0.00
#> TCGA.P5.A5F0.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.R8.A73M.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.CS.4942.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DB.A4X9.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DB.A4XF.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.HT.A74O.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.FG.8188.01 3 0.7016 0.609 0.14 0.32 0.54 0.00
#> TCGA.DU.A6S3.01 4 0.0707 0.961 0.00 0.02 0.00 0.98
#> TCGA.DB.A4XH.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.HT.7485.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.VW.A7QS.01 4 0.3975 0.458 0.00 0.24 0.00 0.76
#> TCGA.DU.8164.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.S9.A6TS.01 3 0.2921 0.866 0.00 0.14 0.86 0.00
#> TCGA.DB.A64S.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.VV.A86M.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.TQ.A8XE.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.CS.6667.01 1 0.0707 0.896 0.98 0.02 0.00 0.00
#> TCGA.E1.A7YV.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.TQ.A7RW.01 1 0.3172 0.822 0.84 0.16 0.00 0.00
#> TCGA.DU.A7TI.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.HT.7468.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.TQ.A7RI.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.DB.5279.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.S9.A6U8.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.R8.A6YH.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DU.7018.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.HT.7677.01 2 0.4907 0.821 0.00 0.58 0.00 0.42
#> TCGA.TM.A7CA.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.HT.7690.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.FG.6689.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DU.7007.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.TQ.A7RF.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DB.5277.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.TM.A84M.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.F6.A8O3.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.QH.A86X.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.HT.8013.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.HW.7490.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.QH.A65S.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DU.A76R.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.DH.5144.01 4 0.0707 0.961 0.00 0.02 0.00 0.98
#> TCGA.HT.7606.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.RY.A840.01 2 0.4713 0.921 0.00 0.64 0.00 0.36
#> TCGA.HW.A5KJ.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.HT.8105.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.HT.7471.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.DU.6395.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.S9.A6TV.01 3 0.1637 0.894 0.00 0.06 0.94 0.00
#> TCGA.P5.A5EW.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DU.6408.01 3 0.1637 0.874 0.06 0.00 0.94 0.00
#> TCGA.DB.A4XB.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.FG.A4MT.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.FG.A4MT.02 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.HT.A619.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.QH.A870.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.HT.A5R9.01 2 0.4948 0.781 0.00 0.56 0.00 0.44
#> TCGA.CS.5396.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.DU.A7TA.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.HW.8319.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.TM.A84H.01 1 0.0707 0.895 0.98 0.02 0.00 0.00
#> TCGA.S9.A6TZ.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DU.6400.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.S9.A6WL.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.DB.A75K.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.DB.A4XD.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.DB.A64Q.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.P5.A737.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.DB.5275.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.S9.A6WH.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.DU.A5TU.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.HT.A5RB.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.HT.7616.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.S9.A7R8.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.QH.A6XA.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DU.A5TP.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.RY.A83Y.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.HT.7482.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RK.02 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.TQ.A7RK.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.HT.7475.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DB.A64U.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.DB.A64W.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.R8.A6MO.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.DU.A7T8.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.HW.8322.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.DU.5870.02 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.CS.6668.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.DU.5870.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.FG.7636.01 1 0.0707 0.895 0.98 0.02 0.00 0.00
#> TCGA.HT.7692.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.WY.A859.01 1 0.0707 0.895 0.98 0.02 0.00 0.00
#> TCGA.R8.A6ML.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.DU.6410.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.S9.A6U9.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RO.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.DU.7019.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.TQ.A7RM.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.S9.A7R4.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.E1.5318.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.HT.7676.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.S9.A7J3.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.06.6701.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.P5.A5F2.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.E1.5304.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.WY.A85B.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RS.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.S9.A7QX.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.CS.4943.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.QH.A65Z.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.P5.A730.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.WY.A85D.01 1 0.5619 0.674 0.64 0.32 0.04 0.00
#> TCGA.RY.A83X.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.S9.A6UB.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.DH.A66F.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.DU.6393.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.HT.8108.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DU.7304.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.S9.A7IY.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.FG.7641.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.P5.A5EV.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.DU.7301.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.DU.7009.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.FG.A4MY.01 3 0.5173 0.754 0.02 0.32 0.66 0.00
#> TCGA.TM.A7CF.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.FG.8186.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.S9.A6U6.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.RY.A845.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DU.7010.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.FG.8182.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.QH.A6X3.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DU.6401.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YH.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DU.7306.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.HT.A74J.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DB.A4XE.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DB.A64L.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.VV.A829.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.HT.A61B.01 3 0.1411 0.898 0.02 0.02 0.96 0.00
#> TCGA.DH.A66B.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.DU.6397.02 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.DU.6397.01 2 0.4977 0.738 0.00 0.54 0.00 0.46
#> TCGA.DU.5853.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.CS.6670.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.DU.7014.01 3 0.4522 0.769 0.00 0.32 0.68 0.00
#> TCGA.QH.A65X.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.DB.A64P.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.TQ.A7RV.01 1 0.2011 0.866 0.92 0.08 0.00 0.00
#> TCGA.06.6389.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.HW.A5KL.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.DH.A7UU.01 3 0.3172 0.856 0.00 0.16 0.84 0.00
#> TCGA.QH.A6CZ.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.DH.A669.02 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.DH.A669.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.QH.A6X9.01 1 0.5173 0.700 0.66 0.32 0.02 0.00
#> TCGA.DU.5871.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.TQ.A7RJ.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.VM.A8CB.01 2 0.4522 0.976 0.00 0.68 0.00 0.32
#> TCGA.HT.7483.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.HT.7687.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.TM.A84G.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.E1.A7Z6.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.TM.A84I.01 3 0.0000 0.909 0.00 0.00 1.00 0.00
#> TCGA.CS.5394.01 4 0.0000 0.986 0.00 0.00 0.00 1.00
#> TCGA.DU.A76O.01 1 0.0000 0.904 1.00 0.00 0.00 0.00
#> TCGA.DU.A5TW.01 1 0.4522 0.723 0.68 0.32 0.00 0.00
#> TCGA.FG.5962.01 4 0.0000 0.986 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.HT.7693.01 5 0.0000 0.9417 0.00 0.00 0.00 0.00 1.00
#> TCGA.S9.A7J2.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6TX.01 4 0.1043 0.9379 0.00 0.04 0.00 0.96 0.00
#> TCGA.VM.A8C8.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A74L.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.A5TS.01 5 0.0000 0.9417 0.00 0.00 0.00 0.00 1.00
#> TCGA.06.A7TL.01 3 0.0000 0.9565 0.00 0.00 1.00 0.00 0.00
#> TCGA.E1.5311.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YI.01 3 0.0000 0.9565 0.00 0.00 1.00 0.00 0.00
#> TCGA.E1.5305.01 5 0.0000 0.9417 0.00 0.00 0.00 0.00 1.00
#> TCGA.F6.A8O4.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A66G.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A731.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7480.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A7R1.01 2 0.3796 0.5788 0.00 0.70 0.00 0.30 0.00
#> TCGA.FG.A710.01 4 0.0000 0.9832 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A7J0.01 5 0.4287 0.1846 0.00 0.00 0.46 0.00 0.54
#> TCGA.DU.A6S6.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.7634.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.6407.01 5 0.0000 0.9417 0.00 0.00 0.00 0.00 1.00
#> TCGA.P5.A5F1.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8CF.01 5 0.2732 0.7471 0.16 0.00 0.00 0.00 0.84
#> TCGA.DU.6542.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7638.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.DH.5143.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7299.01 5 0.0000 0.9417 0.00 0.00 0.00 0.00 1.00
#> TCGA.CS.5393.01 5 0.2732 0.7923 0.00 0.00 0.16 0.00 0.84
#> TCGA.TM.A84Q.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5281.01 5 0.0000 0.9417 0.00 0.00 0.00 0.00 1.00
#> TCGA.FG.A6J1.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7608.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YU.01 3 0.0000 0.9565 0.00 0.00 1.00 0.00 0.00
#> TCGA.W9.A837.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
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#> TCGA.DU.5870.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.7636.01 1 0.0609 0.9709 0.98 0.00 0.00 0.00 0.02
#> TCGA.HT.7692.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.WY.A859.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.R8.A6ML.01 4 0.0000 0.9832 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.6410.01 4 0.0000 0.9832 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A6U9.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RO.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7019.01 5 0.0000 0.9417 0.00 0.00 0.00 0.00 1.00
#> TCGA.TQ.A7RM.01 3 0.0000 0.9565 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A7R4.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5318.01 4 0.0000 0.9832 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7676.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7J3.01 4 0.0000 0.9832 0.00 0.00 0.00 1.00 0.00
#> TCGA.06.6701.01 5 0.0000 0.9417 0.00 0.00 0.00 0.00 1.00
#> TCGA.P5.A5F2.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5304.01 3 0.0000 0.9565 0.00 0.00 1.00 0.00 0.00
#> TCGA.WY.A85B.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RS.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A7QX.01 5 0.3109 0.6857 0.20 0.00 0.00 0.00 0.80
#> TCGA.CS.4943.01 5 0.0000 0.9417 0.00 0.00 0.00 0.00 1.00
#> TCGA.QH.A65Z.01 4 0.0000 0.9832 0.00 0.00 0.00 1.00 0.00
#> TCGA.P5.A730.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.WY.A85D.01 5 0.0000 0.9417 0.00 0.00 0.00 0.00 1.00
#> TCGA.RY.A83X.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6UB.01 4 0.0000 0.9832 0.00 0.00 0.00 1.00 0.00
#> TCGA.DH.A66F.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.6393.01 4 0.0000 0.9832 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.8108.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7304.01 5 0.0000 0.9417 0.00 0.00 0.00 0.00 1.00
#> TCGA.S9.A7IY.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.7641.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A5EV.01 5 0.1043 0.9040 0.04 0.00 0.00 0.00 0.96
#> TCGA.DU.7301.01 5 0.0000 0.9417 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.7009.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.A4MY.01 5 0.0000 0.9417 0.00 0.00 0.00 0.00 1.00
#> TCGA.TM.A7CF.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8186.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6U6.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.RY.A845.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7010.01 3 0.0000 0.9565 0.00 0.00 1.00 0.00 0.00
#> TCGA.FG.8182.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6X3.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6401.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YH.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7306.01 5 0.0000 0.9417 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.A74J.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4XE.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64L.01 4 0.0000 0.9832 0.00 0.00 0.00 1.00 0.00
#> TCGA.VV.A829.01 4 0.0000 0.9832 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.A61B.01 3 0.1410 0.8948 0.06 0.00 0.94 0.00 0.00
#> TCGA.DH.A66B.01 5 0.0000 0.9417 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.6397.02 4 0.0000 0.9832 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.6397.01 2 0.4126 0.3984 0.00 0.62 0.00 0.38 0.00
#> TCGA.DU.5853.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6670.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7014.01 5 0.0000 0.9417 0.00 0.00 0.00 0.00 1.00
#> TCGA.QH.A65X.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.A64P.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RV.01 1 0.2516 0.8269 0.86 0.00 0.00 0.00 0.14
#> TCGA.06.6389.01 3 0.0000 0.9565 0.00 0.00 1.00 0.00 0.00
#> TCGA.HW.A5KL.01 5 0.0000 0.9417 0.00 0.00 0.00 0.00 1.00
#> TCGA.DH.A7UU.01 5 0.4060 0.4559 0.00 0.00 0.36 0.00 0.64
#> TCGA.QH.A6CZ.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.DH.A669.02 4 0.0000 0.9832 0.00 0.00 0.00 1.00 0.00
#> TCGA.DH.A669.01 4 0.0000 0.9832 0.00 0.00 0.00 1.00 0.00
#> TCGA.QH.A6X9.01 5 0.0000 0.9417 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.5871.01 5 0.0000 0.9417 0.00 0.00 0.00 0.00 1.00
#> TCGA.TQ.A7RJ.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8CB.01 2 0.0000 0.9797 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7483.01 1 0.0609 0.9709 0.98 0.00 0.00 0.00 0.02
#> TCGA.HT.7687.01 4 0.0000 0.9832 0.00 0.00 0.00 1.00 0.00
#> TCGA.TM.A84G.01 4 0.0000 0.9832 0.00 0.00 0.00 1.00 0.00
#> TCGA.E1.A7Z6.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84I.01 3 0.0000 0.9565 0.00 0.00 1.00 0.00 0.00
#> TCGA.CS.5394.01 4 0.0000 0.9832 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.A76O.01 1 0.0000 0.9903 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TW.01 5 0.1043 0.9036 0.04 0.00 0.00 0.00 0.96
#> TCGA.FG.5962.01 4 0.0000 0.9832 0.00 0.00 0.00 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.HT.7693.01 5 0.0547 0.8689 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.S9.A7J2.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TX.01 4 0.0937 0.9415 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.VM.A8C8.01 1 0.0547 0.9028 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.HT.A74L.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TS.01 5 0.3163 0.7742 0.00 0.00 0.04 0.00 0.82 0.14
#> TCGA.06.A7TL.01 6 0.3309 0.3360 0.00 0.00 0.28 0.00 0.00 0.72
#> TCGA.E1.5311.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YI.01 3 0.0937 0.8954 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.E1.5305.01 5 0.4576 0.3719 0.00 0.00 0.04 0.00 0.56 0.40
#> TCGA.F6.A8O4.01 1 0.0937 0.8900 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.DH.A66G.01 6 0.3828 0.2729 0.44 0.00 0.00 0.00 0.00 0.56
#> TCGA.P5.A731.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7480.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7R1.01 2 0.3409 0.5602 0.00 0.70 0.00 0.30 0.00 0.00
#> TCGA.FG.A710.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A7J0.01 6 0.5555 0.0563 0.00 0.00 0.14 0.00 0.38 0.48
#> TCGA.DU.A6S6.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7634.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6407.01 5 0.0000 0.8681 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.P5.A5F1.01 1 0.1092 0.9012 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.VM.A8CF.01 6 0.4503 0.5012 0.08 0.00 0.00 0.00 0.24 0.68
#> TCGA.DU.6542.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7638.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.5143.01 1 0.2260 0.8185 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.DU.7299.01 6 0.3409 0.4131 0.00 0.00 0.00 0.00 0.30 0.70
#> TCGA.CS.5393.01 6 0.2190 0.5721 0.00 0.00 0.04 0.00 0.06 0.90
#> TCGA.TM.A84Q.01 1 0.2260 0.8147 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.DB.5281.01 5 0.0547 0.8689 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.FG.A6J1.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7608.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YU.01 6 0.0937 0.6016 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.W9.A837.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A7C5.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CW.01 5 0.0547 0.8689 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.S9.A6WO.01 1 0.0547 0.9028 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.IK.7675.01 3 0.3756 0.4899 0.00 0.00 0.60 0.00 0.00 0.40
#> TCGA.P5.A5ET.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7472.01 1 0.1267 0.8830 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.19.A6J5.01 3 0.0000 0.8934 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A77X.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A6IZ.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7873.01 6 0.0937 0.6024 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.CS.4938.01 1 0.0547 0.9028 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.KT.A74X.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8CH.01 1 0.2790 0.7987 0.84 0.00 0.00 0.00 0.14 0.02
#> TCGA.HT.7476.01 5 0.0547 0.8640 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.DB.A75L.01 5 0.0547 0.8689 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.S9.A7IS.01 3 0.3409 0.6702 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.TQ.A8XE.02 6 0.4078 0.5068 0.34 0.00 0.00 0.00 0.02 0.64
#> TCGA.E1.A7YO.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RG.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HW.7493.01 1 0.0547 0.9028 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.RY.A847.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.8166.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8CA.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7855.01 5 0.0547 0.8640 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.S9.A89Z.01 3 0.0547 0.8895 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.DB.A4XG.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7015.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A616.01 6 0.4576 0.3649 0.40 0.00 0.00 0.00 0.04 0.56
#> TCGA.HT.7611.01 5 0.3460 0.5965 0.22 0.00 0.00 0.00 0.76 0.02
#> TCGA.FG.A60K.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TY.01 4 0.1556 0.8864 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.WY.A85C.01 5 0.0547 0.8640 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.DB.A4XC.01 1 0.2048 0.8377 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.P5.A72W.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TU.01 5 0.0000 0.8681 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.5855.01 5 0.1267 0.8539 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.HT.7884.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RQ.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.IK.8125.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.A74K.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.WH.A86K.01 5 0.4067 0.6379 0.00 0.00 0.04 0.00 0.70 0.26
#> TCGA.QH.A6X8.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.WY.A85E.01 1 0.3950 0.6383 0.72 0.00 0.00 0.00 0.04 0.24
#> TCGA.FG.6691.01 1 0.0547 0.9002 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.S9.A7R3.01 1 0.2260 0.8185 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.FG.A4MX.01 1 0.1267 0.8797 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.HT.7681.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IZ.01 6 0.1814 0.6243 0.10 0.00 0.00 0.00 0.00 0.90
#> TCGA.DU.A6S7.01 5 0.0547 0.8640 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.06.0221.01 5 0.4380 0.6570 0.00 0.00 0.08 0.00 0.70 0.22
#> TCGA.P5.A72Z.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.8114.01 1 0.1480 0.8798 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.DU.8168.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HW.8321.01 1 0.3156 0.7517 0.80 0.00 0.00 0.00 0.18 0.02
#> TCGA.TQ.A7RN.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.5141.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EZ.7264.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.P5.A5F4.01 1 0.2790 0.7987 0.84 0.00 0.00 0.00 0.14 0.02
#> TCGA.QH.A65V.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8191.01 1 0.0547 0.9028 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DH.5142.01 6 0.1092 0.6140 0.02 0.00 0.02 0.00 0.00 0.96
#> TCGA.DU.A6S8.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E1.A7YW.01 1 0.2048 0.8377 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.CS.6666.01 5 0.0547 0.8640 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.DU.7298.01 5 0.2094 0.8073 0.00 0.08 0.00 0.00 0.90 0.02
#> TCGA.DB.A64R.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.5390.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6WP.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DB.5280.01 1 0.0547 0.9028 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.TM.A84T.01 1 0.1814 0.8547 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.DH.A66D.01 1 0.0547 0.9028 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.RY.A83Z.01 3 0.0937 0.8954 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.TQ.A7RH.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YS.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.P5.A735.01 1 0.0547 0.9028 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DU.7294.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7695.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64X.01 3 0.1267 0.8655 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.FG.7637.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6U5.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7609.01 1 0.2094 0.8510 0.90 0.00 0.00 0.00 0.08 0.02
#> TCGA.DB.5274.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HW.7487.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HW.7491.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A75M.01 1 0.0547 0.9028 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.HW.A5KM.01 1 0.0937 0.8902 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.HT.7477.01 3 0.3309 0.6974 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.HT.8012.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.8167.01 5 0.0547 0.8689 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.S9.A6U1.01 1 0.2790 0.7987 0.84 0.00 0.00 0.00 0.14 0.02
#> TCGA.FG.5965.01 6 0.3076 0.5728 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.HT.A614.01 6 0.2454 0.6077 0.16 0.00 0.00 0.00 0.00 0.84
#> TCGA.S9.A7QZ.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.QH.A6X4.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A77W.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.7302.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.6399.01 5 0.1267 0.8545 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.E1.5307.01 5 0.2728 0.8089 0.00 0.00 0.04 0.00 0.86 0.10
#> TCGA.S9.A7QW.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7604.01 5 0.0547 0.8640 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.P5.A733.01 1 0.3315 0.7249 0.78 0.00 0.00 0.00 0.20 0.02
#> TCGA.HT.7684.01 1 0.1267 0.8849 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.HW.7495.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A65R.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DH.A7UV.01 5 0.0000 0.8681 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7879.01 1 0.0547 0.9028 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DU.A7TC.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A60J.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5303.01 1 0.3706 0.3748 0.62 0.00 0.00 0.00 0.00 0.38
#> TCGA.FN.7833.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7Z4.01 1 0.0547 0.9028 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.HT.7875.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.5417.01 3 0.0937 0.8954 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.HT.7473.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7008.01 5 0.4199 0.3003 0.38 0.00 0.00 0.00 0.60 0.02
#> TCGA.DB.A75O.01 1 0.0547 0.9028 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DU.7304.02 3 0.0547 0.8895 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.DU.6394.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6WD.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.5872.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8185.01 5 0.0547 0.8640 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.TQ.A7RU.01 2 0.1814 0.8546 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.DU.5874.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6WE.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.6690.01 5 0.2350 0.7635 0.10 0.00 0.00 0.00 0.88 0.02
#> TCGA.HW.8320.01 5 0.0547 0.8689 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.R8.A6MK.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7J1.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5322.01 1 0.2956 0.8154 0.84 0.00 0.00 0.00 0.12 0.04
#> TCGA.P5.A5F0.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.R8.A73M.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.4942.01 1 0.1814 0.8549 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.DB.A4X9.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4XF.01 5 0.0547 0.8640 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.HT.A74O.01 5 0.0000 0.8681 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FG.8188.01 5 0.2350 0.8202 0.00 0.00 0.02 0.00 0.88 0.10
#> TCGA.DU.A6S3.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DB.A4XH.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7485.01 1 0.2048 0.8377 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.VW.A7QS.01 4 0.3076 0.6333 0.00 0.24 0.00 0.76 0.00 0.00
#> TCGA.DU.8164.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6TS.01 5 0.4798 0.5258 0.00 0.00 0.08 0.00 0.62 0.30
#> TCGA.DB.A64S.01 1 0.1807 0.8667 0.92 0.00 0.00 0.00 0.06 0.02
#> TCGA.VV.A86M.01 5 0.1807 0.8537 0.02 0.00 0.00 0.00 0.92 0.06
#> TCGA.TQ.A8XE.01 1 0.4078 0.4454 0.64 0.00 0.00 0.00 0.02 0.34
#> TCGA.CS.6667.01 1 0.3315 0.7251 0.78 0.00 0.00 0.00 0.20 0.02
#> TCGA.E1.A7YV.01 3 0.0937 0.8954 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.TQ.A7RW.01 6 0.5202 0.5201 0.26 0.00 0.00 0.00 0.14 0.60
#> TCGA.DU.A7TI.01 1 0.0547 0.9028 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.HT.7468.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RI.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5279.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6U8.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.R8.A6YH.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7018.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7677.01 2 0.3409 0.5621 0.00 0.70 0.00 0.30 0.00 0.00
#> TCGA.TM.A7CA.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7690.01 1 0.0547 0.9006 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.FG.6689.01 1 0.0937 0.8943 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.DU.7007.01 6 0.3076 0.3689 0.00 0.00 0.24 0.00 0.00 0.76
#> TCGA.TQ.A7RF.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5277.01 6 0.3499 0.2672 0.00 0.00 0.32 0.00 0.00 0.68
#> TCGA.TM.A84M.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.F6.A8O3.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A86X.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8013.01 1 0.2048 0.8377 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.HW.7490.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A65S.01 6 0.2941 0.5852 0.22 0.00 0.00 0.00 0.00 0.78
#> TCGA.DU.A76R.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.5144.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7606.01 3 0.2260 0.8067 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.RY.A840.01 2 0.2260 0.8018 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.HW.A5KJ.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.8105.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7471.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6395.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TV.01 6 0.0937 0.6017 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.P5.A5EW.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6408.01 6 0.0937 0.6024 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.DB.A4XB.01 1 0.3797 0.2405 0.58 0.00 0.00 0.00 0.00 0.42
#> TCGA.FG.A4MT.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A4MT.02 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A619.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.QH.A870.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A5R9.01 2 0.3828 0.2388 0.00 0.56 0.00 0.44 0.00 0.00
#> TCGA.CS.5396.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.A7TA.01 1 0.2790 0.7987 0.84 0.00 0.00 0.00 0.14 0.02
#> TCGA.HW.8319.01 6 0.1807 0.5969 0.02 0.00 0.06 0.00 0.00 0.92
#> TCGA.TM.A84H.01 1 0.2956 0.7916 0.84 0.00 0.00 0.00 0.12 0.04
#> TCGA.S9.A6TZ.01 1 0.1865 0.8798 0.92 0.00 0.00 0.00 0.04 0.04
#> TCGA.DU.6400.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6WL.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DB.A75K.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4XD.01 5 0.0000 0.8681 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DB.A64Q.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.P5.A737.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5275.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WH.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.A5TU.01 3 0.0547 0.8895 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.HT.A5RB.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7616.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A7R8.01 5 0.2512 0.8099 0.06 0.00 0.00 0.00 0.88 0.06
#> TCGA.QH.A6XA.01 1 0.2048 0.8377 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.DU.A5TP.01 1 0.2260 0.8194 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.RY.A83Y.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7482.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RK.02 5 0.2790 0.7238 0.14 0.00 0.00 0.00 0.84 0.02
#> TCGA.TQ.A7RK.01 1 0.3315 0.7256 0.78 0.00 0.00 0.00 0.20 0.02
#> TCGA.HT.7475.01 1 0.2048 0.8417 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.DB.A64U.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64W.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.R8.A6MO.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.A7T8.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HW.8322.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5870.02 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CS.6668.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.5870.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7636.01 6 0.4144 0.4725 0.36 0.00 0.00 0.00 0.02 0.62
#> TCGA.HT.7692.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.WY.A859.01 6 0.3198 0.5636 0.26 0.00 0.00 0.00 0.00 0.74
#> TCGA.R8.A6ML.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.6410.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6U9.01 1 0.2790 0.7987 0.84 0.00 0.00 0.00 0.14 0.02
#> TCGA.TQ.A7RO.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7019.01 5 0.0547 0.8689 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.TQ.A7RM.01 3 0.0547 0.8895 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.S9.A7R4.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5318.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7676.01 1 0.2048 0.8377 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.S9.A7J3.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.06.6701.01 5 0.0937 0.8623 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.P5.A5F2.01 1 0.3198 0.6564 0.74 0.00 0.00 0.00 0.00 0.26
#> TCGA.E1.5304.01 3 0.0937 0.8954 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.WY.A85B.01 1 0.2790 0.7987 0.84 0.00 0.00 0.00 0.14 0.02
#> TCGA.TQ.A7RS.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7QX.01 5 0.3592 0.5546 0.24 0.00 0.00 0.00 0.74 0.02
#> TCGA.CS.4943.01 5 0.3851 0.2537 0.00 0.00 0.00 0.00 0.54 0.46
#> TCGA.QH.A65Z.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.P5.A730.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.WY.A85D.01 5 0.2350 0.8202 0.00 0.00 0.02 0.00 0.88 0.10
#> TCGA.RY.A83X.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6UB.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DH.A66F.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6393.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.8108.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7304.01 5 0.0547 0.8689 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.S9.A7IY.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7641.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A5EV.01 5 0.3544 0.7168 0.12 0.00 0.00 0.00 0.80 0.08
#> TCGA.DU.7301.01 5 0.0000 0.8681 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.7009.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A4MY.01 5 0.4067 0.6382 0.00 0.00 0.04 0.00 0.70 0.26
#> TCGA.TM.A7CF.01 1 0.0547 0.9028 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.FG.8186.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6U6.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RY.A845.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7010.01 3 0.0937 0.8954 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.FG.8182.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6X3.01 1 0.2790 0.7987 0.84 0.00 0.00 0.00 0.14 0.02
#> TCGA.DU.6401.01 1 0.2790 0.7987 0.84 0.00 0.00 0.00 0.14 0.02
#> TCGA.E1.A7YH.01 1 0.1092 0.8917 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.DU.7306.01 5 0.0547 0.8615 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.HT.A74J.01 1 0.2941 0.7176 0.78 0.00 0.00 0.00 0.00 0.22
#> TCGA.DB.A4XE.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64L.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.VV.A829.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.A61B.01 6 0.0937 0.6024 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.DH.A66B.01 5 0.0547 0.8689 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.DU.6397.02 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.6397.01 2 0.3647 0.4590 0.00 0.64 0.00 0.36 0.00 0.00
#> TCGA.DU.5853.01 1 0.2454 0.7972 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.CS.6670.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7014.01 5 0.2474 0.8231 0.00 0.00 0.04 0.00 0.88 0.08
#> TCGA.QH.A65X.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64P.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RV.01 1 0.5027 0.5743 0.64 0.00 0.00 0.00 0.20 0.16
#> TCGA.06.6389.01 6 0.3499 0.2254 0.00 0.00 0.32 0.00 0.00 0.68
#> TCGA.HW.A5KL.01 5 0.0547 0.8689 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.DH.A7UU.01 5 0.5324 0.3520 0.00 0.00 0.34 0.00 0.54 0.12
#> TCGA.QH.A6CZ.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A669.02 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DH.A669.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.QH.A6X9.01 5 0.2350 0.8202 0.00 0.00 0.02 0.00 0.88 0.10
#> TCGA.DU.5871.01 5 0.0547 0.8640 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.TQ.A7RJ.01 1 0.2790 0.8023 0.84 0.00 0.00 0.00 0.14 0.02
#> TCGA.VM.A8CB.01 2 0.0000 0.9712 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7483.01 1 0.3315 0.7279 0.78 0.00 0.00 0.00 0.20 0.02
#> TCGA.HT.7687.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.TM.A84G.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E1.A7Z6.01 1 0.0547 0.9028 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.TM.A84I.01 6 0.3797 -0.0649 0.00 0.00 0.42 0.00 0.00 0.58
#> TCGA.CS.5394.01 4 0.0000 0.9921 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.A76O.01 1 0.0000 0.9068 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TW.01 5 0.2350 0.7754 0.10 0.00 0.00 0.00 0.88 0.02
#> TCGA.FG.5962.01 4 0.0000 0.9921 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.HT.7693.01 5 0.2832 0.6983 0.00 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.S9.A7J2.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.S9.A6TX.01 4 0.3284 0.8219 0.00 0.10 0.00 0.80 0.00 0.00 0.10
#> TCGA.VM.A8C8.01 1 0.0504 0.7413 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.HT.A74L.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.DU.A5TS.01 5 0.3208 0.6456 0.00 0.00 0.02 0.00 0.82 0.04 0.12
#> TCGA.06.A7TL.01 6 0.6149 0.2451 0.00 0.00 0.22 0.00 0.16 0.52 0.10
#> TCGA.E1.5311.01 2 0.1671 0.8822 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.E1.A7YI.01 3 0.0504 0.8276 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.E1.5305.01 5 0.4309 0.5059 0.00 0.00 0.00 0.00 0.68 0.12 0.20
#> TCGA.F6.A8O4.01 1 0.3517 0.2695 0.70 0.00 0.00 0.00 0.02 0.00 0.28
#> TCGA.DH.A66G.01 1 0.3909 0.2755 0.58 0.00 0.00 0.00 0.00 0.40 0.02
#> TCGA.P5.A731.01 1 0.0504 0.7411 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.HT.7480.01 2 0.1671 0.8822 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.S9.A7R1.01 2 0.4243 0.6195 0.00 0.68 0.00 0.22 0.00 0.00 0.10
#> TCGA.FG.A710.01 4 0.1166 0.9106 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.S9.A7J0.01 5 0.5604 0.1291 0.00 0.00 0.02 0.00 0.48 0.34 0.16
#> TCGA.DU.A6S6.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.FG.7634.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.DU.6407.01 5 0.2259 0.7294 0.00 0.00 0.00 0.00 0.84 0.00 0.16
#> TCGA.P5.A5F1.01 1 0.2163 0.7110 0.88 0.00 0.00 0.00 0.00 0.02 0.10
#> TCGA.VM.A8CF.01 5 0.6586 -0.1441 0.14 0.00 0.00 0.00 0.40 0.32 0.14
#> TCGA.DU.6542.01 1 0.1928 0.7211 0.90 0.00 0.00 0.00 0.00 0.02 0.08
#> TCGA.FG.7638.01 2 0.0863 0.8928 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.DH.5143.01 1 0.3370 0.6104 0.78 0.00 0.00 0.00 0.00 0.16 0.06
#> TCGA.DU.7299.01 6 0.3388 0.5671 0.00 0.00 0.00 0.00 0.20 0.76 0.04
#> TCGA.CS.5393.01 6 0.3835 0.5731 0.00 0.00 0.00 0.00 0.16 0.74 0.10
#> TCGA.TM.A84Q.01 7 0.3994 0.6558 0.48 0.00 0.00 0.00 0.02 0.00 0.50
#> TCGA.DB.5281.01 5 0.1671 0.7414 0.00 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.FG.A6J1.01 2 0.0504 0.8910 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.HT.7608.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.E1.A7YU.01 6 0.1433 0.6724 0.00 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.W9.A837.01 2 0.1671 0.8822 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.TM.A7C5.01 2 0.1671 0.8822 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.QH.A6CW.01 5 0.2832 0.7139 0.00 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.S9.A6WO.01 1 0.0504 0.7369 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.IK.7675.01 3 0.3994 0.1651 0.00 0.00 0.50 0.00 0.00 0.48 0.02
#> TCGA.P5.A5ET.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.HT.7472.01 1 0.1166 0.7304 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.19.A6J5.01 3 0.1006 0.8238 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.P5.A77X.01 2 0.0863 0.8931 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.FG.A6IZ.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7873.01 6 0.1006 0.6867 0.00 0.00 0.02 0.00 0.00 0.96 0.02
#> TCGA.CS.4938.01 1 0.0504 0.7413 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.KT.A74X.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.VM.A8CH.01 7 0.4278 0.6891 0.46 0.00 0.00 0.00 0.04 0.00 0.50
#> TCGA.HT.7476.01 5 0.3221 0.6427 0.00 0.00 0.00 0.00 0.68 0.00 0.32
#> TCGA.DB.A75L.01 5 0.2422 0.7245 0.00 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.S9.A7IS.01 3 0.3943 0.3192 0.00 0.00 0.56 0.00 0.00 0.42 0.02
#> TCGA.TQ.A8XE.02 1 0.5429 -0.0719 0.46 0.00 0.00 0.00 0.02 0.40 0.12
#> TCGA.E1.A7YO.01 2 0.1671 0.8822 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.TQ.A7RG.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.HW.7493.01 1 0.0504 0.7413 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.RY.A847.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.DU.8166.01 1 0.1886 0.6863 0.88 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.VM.A8CA.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.HT.7855.01 5 0.3358 0.6025 0.00 0.00 0.00 0.00 0.64 0.00 0.36
#> TCGA.S9.A89Z.01 3 0.1928 0.7899 0.00 0.00 0.90 0.00 0.00 0.02 0.08
#> TCGA.DB.A4XG.01 2 0.1671 0.8822 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.DU.7015.01 1 0.2259 0.6845 0.84 0.00 0.00 0.00 0.00 0.00 0.16
#> TCGA.HT.A616.01 1 0.4994 0.2794 0.56 0.00 0.00 0.00 0.02 0.34 0.08
#> TCGA.HT.7611.01 7 0.4978 0.1673 0.12 0.00 0.00 0.00 0.38 0.00 0.50
#> TCGA.FG.A60K.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.S9.A6TY.01 4 0.3670 0.7706 0.00 0.14 0.00 0.76 0.00 0.00 0.10
#> TCGA.WY.A85C.01 5 0.3358 0.6025 0.00 0.00 0.00 0.00 0.64 0.00 0.36
#> TCGA.DB.A4XC.01 1 0.1886 0.6959 0.88 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.P5.A72W.01 1 0.1886 0.6828 0.88 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.S9.A6TU.01 5 0.3139 0.6740 0.00 0.00 0.00 0.00 0.70 0.00 0.30
#> TCGA.DU.5855.01 5 0.2376 0.6921 0.00 0.00 0.00 0.00 0.86 0.02 0.12
#> TCGA.HT.7884.01 1 0.1671 0.7198 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.TQ.A7RQ.01 2 0.0863 0.8931 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.IK.8125.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.A74K.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.WH.A86K.01 5 0.3908 0.5675 0.00 0.00 0.00 0.00 0.72 0.08 0.20
#> TCGA.QH.A6X8.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.WY.A85E.01 1 0.5086 0.4317 0.62 0.00 0.00 0.00 0.02 0.16 0.20
#> TCGA.FG.6691.01 1 0.2945 0.4484 0.74 0.00 0.00 0.00 0.00 0.00 0.26
#> TCGA.S9.A7R3.01 1 0.3244 0.6092 0.78 0.00 0.00 0.00 0.00 0.18 0.04
#> TCGA.FG.A4MX.01 1 0.3459 -0.2128 0.60 0.00 0.00 0.00 0.00 0.00 0.40
#> TCGA.HT.7681.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.S9.A7IZ.01 6 0.1718 0.6795 0.04 0.00 0.00 0.00 0.00 0.92 0.04
#> TCGA.DU.A6S7.01 5 0.3294 0.6255 0.00 0.00 0.00 0.00 0.66 0.00 0.34
#> TCGA.06.0221.01 5 0.4162 0.5702 0.00 0.00 0.02 0.00 0.74 0.12 0.12
#> TCGA.P5.A72Z.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.8114.01 1 0.2832 0.4826 0.76 0.00 0.00 0.00 0.00 0.00 0.24
#> TCGA.DU.8168.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HW.8321.01 7 0.4505 0.7049 0.44 0.00 0.00 0.00 0.06 0.00 0.50
#> TCGA.TQ.A7RN.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.DH.5141.01 2 0.1671 0.8822 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.EZ.7264.01 4 0.3058 0.8433 0.00 0.08 0.00 0.82 0.00 0.00 0.10
#> TCGA.P5.A5F4.01 7 0.4278 0.6891 0.46 0.00 0.00 0.00 0.04 0.00 0.50
#> TCGA.QH.A65V.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.FG.8191.01 1 0.0504 0.7413 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DH.5142.01 6 0.1006 0.6894 0.02 0.00 0.00 0.00 0.00 0.96 0.02
#> TCGA.DU.A6S8.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YW.01 1 0.1886 0.6959 0.88 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.CS.6666.01 5 0.3413 0.5769 0.00 0.00 0.00 0.00 0.62 0.00 0.38
#> TCGA.DU.7298.01 5 0.2722 0.6731 0.00 0.04 0.00 0.00 0.84 0.00 0.12
#> TCGA.DB.A64R.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.CS.5390.01 4 0.0504 0.9246 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.S9.A6WP.01 4 0.3058 0.8433 0.00 0.08 0.00 0.82 0.00 0.00 0.10
#> TCGA.DB.5280.01 1 0.0504 0.7369 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.TM.A84T.01 1 0.1433 0.7207 0.92 0.00 0.00 0.00 0.00 0.08 0.00
#> TCGA.DH.A66D.01 1 0.0863 0.7381 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.RY.A83Z.01 3 0.0504 0.8276 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.TQ.A7RH.01 1 0.0863 0.7378 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.E1.A7YS.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A735.01 1 0.0504 0.7413 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DU.7294.01 2 0.1671 0.8822 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.HT.7695.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.DB.A64X.01 3 0.3541 0.7102 0.00 0.00 0.80 0.00 0.08 0.02 0.10
#> TCGA.FG.7637.01 2 0.1166 0.8914 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.S9.A6U5.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.HT.7609.01 1 0.3525 -0.3964 0.56 0.00 0.00 0.00 0.00 0.00 0.44
#> TCGA.DB.5274.01 4 0.3058 0.8433 0.00 0.08 0.00 0.82 0.00 0.00 0.10
#> TCGA.HW.7487.01 4 0.3058 0.8433 0.00 0.08 0.00 0.82 0.00 0.00 0.10
#> TCGA.HW.7491.01 2 0.1671 0.8822 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.DB.A75M.01 1 0.1006 0.7378 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.HW.A5KM.01 1 0.2572 0.5751 0.80 0.00 0.00 0.00 0.00 0.00 0.20
#> TCGA.HT.7477.01 3 0.3815 0.4440 0.00 0.00 0.62 0.00 0.00 0.36 0.02
#> TCGA.HT.8012.01 2 0.1433 0.8872 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.DU.8167.01 5 0.0863 0.7255 0.00 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.S9.A6U1.01 7 0.3994 0.6558 0.48 0.00 0.00 0.00 0.02 0.00 0.50
#> TCGA.FG.5965.01 6 0.3047 0.5095 0.28 0.00 0.00 0.00 0.00 0.72 0.00
#> TCGA.HT.A614.01 6 0.2259 0.6125 0.16 0.00 0.00 0.00 0.00 0.84 0.00
#> TCGA.S9.A7QZ.01 4 0.0504 0.9246 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.QH.A6X4.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.P5.A77W.01 4 0.3058 0.8433 0.00 0.08 0.00 0.82 0.00 0.00 0.10
#> TCGA.DU.7302.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.6399.01 5 0.0000 0.7187 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E1.5307.01 5 0.3052 0.6208 0.00 0.00 0.00 0.00 0.78 0.02 0.20
#> TCGA.S9.A7QW.01 1 0.0504 0.7378 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.HT.7604.01 5 0.3221 0.6446 0.00 0.00 0.00 0.00 0.68 0.00 0.32
#> TCGA.P5.A733.01 7 0.4514 0.6686 0.46 0.00 0.00 0.00 0.06 0.00 0.48
#> TCGA.HT.7684.01 1 0.1664 0.7248 0.92 0.00 0.00 0.00 0.00 0.06 0.02
#> TCGA.HW.7495.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.QH.A65R.01 4 0.3058 0.8433 0.00 0.08 0.00 0.82 0.00 0.00 0.10
#> TCGA.DH.A7UV.01 5 0.2832 0.6983 0.00 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.HT.7879.01 1 0.0863 0.7313 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.DU.A7TC.01 1 0.2708 0.5861 0.78 0.00 0.00 0.00 0.00 0.00 0.22
#> TCGA.FG.A60J.01 1 0.1886 0.7031 0.88 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.E1.5303.01 1 0.4003 0.4402 0.64 0.00 0.00 0.00 0.00 0.32 0.04
#> TCGA.FN.7833.01 1 0.0504 0.7413 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.E1.A7Z4.01 1 0.0504 0.7413 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.HT.7875.01 2 0.0863 0.8931 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.06.5417.01 3 0.0504 0.8276 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.HT.7473.01 1 0.0504 0.7413 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DU.7008.01 7 0.5190 0.4239 0.18 0.00 0.00 0.00 0.30 0.00 0.52
#> TCGA.DB.A75O.01 1 0.1006 0.7378 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.DU.7304.02 3 0.1006 0.8156 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.DU.6394.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6WD.01 4 0.1433 0.9015 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.DU.5872.01 1 0.0863 0.7336 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.FG.8185.01 5 0.3413 0.5769 0.00 0.00 0.00 0.00 0.62 0.00 0.38
#> TCGA.TQ.A7RU.01 2 0.3284 0.7861 0.00 0.80 0.00 0.10 0.00 0.00 0.10
#> TCGA.DU.5874.01 4 0.0504 0.9246 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.S9.A6WE.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.FG.6690.01 5 0.4998 0.5005 0.14 0.00 0.00 0.00 0.54 0.00 0.32
#> TCGA.HW.8320.01 5 0.2572 0.7164 0.00 0.00 0.00 0.00 0.80 0.00 0.20
#> TCGA.R8.A6MK.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.S9.A7J1.01 2 0.1671 0.8822 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.E1.5322.01 7 0.4941 0.5139 0.46 0.00 0.00 0.00 0.02 0.06 0.46
#> TCGA.P5.A5F0.01 2 0.1671 0.8822 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.R8.A73M.01 2 0.1671 0.8822 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.CS.4942.01 1 0.1671 0.7094 0.90 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.DB.A4X9.01 1 0.0504 0.7413 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DB.A4XF.01 5 0.3413 0.5710 0.00 0.00 0.00 0.00 0.62 0.00 0.38
#> TCGA.HT.A74O.01 5 0.2572 0.7177 0.00 0.00 0.00 0.00 0.80 0.00 0.20
#> TCGA.FG.8188.01 5 0.2163 0.6711 0.00 0.00 0.00 0.00 0.88 0.02 0.10
#> TCGA.DU.A6S3.01 4 0.3058 0.8433 0.00 0.08 0.00 0.82 0.00 0.00 0.10
#> TCGA.DB.A4XH.01 4 0.0504 0.9246 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.HT.7485.01 1 0.1671 0.7090 0.90 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.VW.A7QS.01 4 0.4538 0.5494 0.00 0.28 0.00 0.62 0.00 0.00 0.10
#> TCGA.DU.8164.01 4 0.1166 0.9106 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.S9.A6TS.01 5 0.4308 0.5462 0.00 0.00 0.02 0.00 0.72 0.16 0.10
#> TCGA.DB.A64S.01 1 0.3558 -0.5503 0.52 0.00 0.00 0.00 0.00 0.00 0.48
#> TCGA.VV.A86M.01 5 0.4487 0.5571 0.00 0.00 0.00 0.00 0.52 0.06 0.42
#> TCGA.TQ.A8XE.01 1 0.5052 0.4164 0.62 0.00 0.00 0.00 0.02 0.22 0.14
#> TCGA.CS.6667.01 7 0.4820 0.7165 0.38 0.00 0.00 0.00 0.10 0.00 0.52
#> TCGA.E1.A7YV.01 3 0.0504 0.8276 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.TQ.A7RW.01 6 0.6848 0.3231 0.28 0.00 0.00 0.00 0.22 0.36 0.14
#> TCGA.DU.A7TI.01 1 0.0863 0.7328 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.HT.7468.01 2 0.2163 0.8675 0.00 0.88 0.00 0.02 0.00 0.00 0.10
#> TCGA.TQ.A7RI.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.DB.5279.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6U8.01 1 0.2259 0.6392 0.84 0.00 0.00 0.00 0.00 0.00 0.16
#> TCGA.R8.A6YH.01 1 0.1886 0.6828 0.88 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.DU.7018.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7677.01 2 0.4121 0.6507 0.00 0.70 0.00 0.20 0.00 0.00 0.10
#> TCGA.TM.A7CA.01 1 0.2081 0.6641 0.86 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.HT.7690.01 1 0.2572 0.5767 0.80 0.00 0.00 0.00 0.00 0.00 0.20
#> TCGA.FG.6689.01 1 0.0504 0.7413 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DU.7007.01 6 0.3617 0.5347 0.00 0.00 0.16 0.00 0.00 0.76 0.08
#> TCGA.TQ.A7RF.01 1 0.1886 0.6852 0.88 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.DB.5277.01 6 0.5130 0.3928 0.00 0.00 0.18 0.00 0.04 0.64 0.14
#> TCGA.TM.A84M.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.F6.A8O3.01 2 0.0863 0.8926 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.QH.A86X.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.HT.8013.01 1 0.1886 0.6959 0.88 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.HW.7490.01 1 0.2422 0.6081 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.QH.A65S.01 6 0.2945 0.5294 0.26 0.00 0.00 0.00 0.00 0.74 0.00
#> TCGA.DU.A76R.01 2 0.1671 0.8822 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.DH.5144.01 4 0.3058 0.8433 0.00 0.08 0.00 0.82 0.00 0.00 0.10
#> TCGA.HT.7606.01 3 0.6300 0.3597 0.00 0.00 0.48 0.00 0.26 0.16 0.10
#> TCGA.RY.A840.01 2 0.3985 0.6801 0.00 0.72 0.00 0.18 0.00 0.00 0.10
#> TCGA.HW.A5KJ.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.8105.01 4 0.0504 0.9246 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.HT.7471.01 2 0.1671 0.8822 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.DU.6395.01 1 0.2259 0.6392 0.84 0.00 0.00 0.00 0.00 0.00 0.16
#> TCGA.S9.A6TV.01 6 0.1166 0.6727 0.00 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.P5.A5EW.01 1 0.0504 0.7413 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DU.6408.01 6 0.1006 0.6867 0.00 0.00 0.02 0.00 0.00 0.96 0.02
#> TCGA.DB.A4XB.01 1 0.3525 0.2219 0.56 0.00 0.00 0.00 0.00 0.44 0.00
#> TCGA.FG.A4MT.01 1 0.2081 0.6696 0.86 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.FG.A4MT.02 1 0.2081 0.6696 0.86 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.HT.A619.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.QH.A870.01 1 0.0504 0.7413 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.HT.A5R9.01 2 0.4866 0.0721 0.00 0.48 0.00 0.42 0.00 0.00 0.10
#> TCGA.CS.5396.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.A7TA.01 1 0.3994 -0.6184 0.50 0.00 0.00 0.00 0.02 0.00 0.48
#> TCGA.HW.8319.01 6 0.1363 0.6803 0.00 0.00 0.04 0.00 0.00 0.94 0.02
#> TCGA.TM.A84H.01 1 0.3289 0.6730 0.82 0.00 0.00 0.00 0.02 0.06 0.10
#> TCGA.S9.A6TZ.01 1 0.3770 0.5344 0.74 0.00 0.00 0.00 0.08 0.00 0.18
#> TCGA.DU.6400.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6WL.01 4 0.3058 0.8433 0.00 0.08 0.00 0.82 0.00 0.00 0.10
#> TCGA.DB.A75K.01 2 0.1671 0.8822 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.DB.A4XD.01 5 0.2945 0.6863 0.00 0.00 0.00 0.00 0.74 0.00 0.26
#> TCGA.DB.A64Q.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A737.01 2 0.1671 0.8822 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.DB.5275.01 1 0.3370 0.6409 0.78 0.00 0.00 0.00 0.00 0.06 0.16
#> TCGA.S9.A6WH.01 4 0.0504 0.9246 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.DU.A5TU.01 3 0.1718 0.8169 0.00 0.00 0.92 0.00 0.00 0.04 0.04
#> TCGA.HT.A5RB.01 1 0.1886 0.6852 0.88 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.HT.7616.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A7R8.01 5 0.3991 0.6802 0.04 0.00 0.00 0.00 0.72 0.02 0.22
#> TCGA.QH.A6XA.01 1 0.1886 0.6959 0.88 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.DU.A5TP.01 1 0.1886 0.6959 0.88 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.RY.A83Y.01 4 0.3058 0.8433 0.00 0.08 0.00 0.82 0.00 0.00 0.10
#> TCGA.HT.7482.01 1 0.1433 0.7126 0.92 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.TQ.A7RK.02 7 0.5128 0.3757 0.16 0.00 0.00 0.00 0.32 0.00 0.52
#> TCGA.TQ.A7RK.01 7 0.4820 0.7165 0.38 0.00 0.00 0.00 0.10 0.00 0.52
#> TCGA.HT.7475.01 1 0.3284 0.6573 0.80 0.00 0.00 0.00 0.00 0.10 0.10
#> TCGA.DB.A64U.01 2 0.0863 0.8931 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.DB.A64W.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.R8.A6MO.01 4 0.3058 0.8433 0.00 0.08 0.00 0.82 0.00 0.00 0.10
#> TCGA.DU.A7T8.01 1 0.1886 0.6828 0.88 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.HW.8322.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.DU.5870.02 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CS.6668.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.5870.01 2 0.1671 0.8822 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.FG.7636.01 1 0.5132 -0.0515 0.46 0.00 0.00 0.00 0.02 0.44 0.08
#> TCGA.HT.7692.01 2 0.0504 0.8910 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.WY.A859.01 6 0.4146 0.4827 0.24 0.00 0.00 0.00 0.00 0.68 0.08
#> TCGA.R8.A6ML.01 4 0.0504 0.9246 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.DU.6410.01 4 0.3058 0.8433 0.00 0.08 0.00 0.82 0.00 0.00 0.10
#> TCGA.S9.A6U9.01 7 0.4278 0.6891 0.46 0.00 0.00 0.00 0.04 0.00 0.50
#> TCGA.TQ.A7RO.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.DU.7019.01 5 0.0504 0.7135 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.TQ.A7RM.01 3 0.1433 0.8024 0.00 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.S9.A7R4.01 1 0.1671 0.7015 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.E1.5318.01 4 0.0504 0.9246 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.HT.7676.01 1 0.1886 0.6959 0.88 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.S9.A7J3.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.06.6701.01 5 0.1433 0.7402 0.00 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.P5.A5F2.01 1 0.3795 0.5436 0.72 0.00 0.00 0.00 0.00 0.22 0.06
#> TCGA.E1.5304.01 3 0.0504 0.8276 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.WY.A85B.01 7 0.3994 0.6558 0.48 0.00 0.00 0.00 0.02 0.00 0.50
#> TCGA.TQ.A7RS.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.S9.A7QX.01 7 0.4978 0.1506 0.12 0.00 0.00 0.00 0.38 0.00 0.50
#> TCGA.CS.4943.01 5 0.4737 0.2963 0.00 0.00 0.00 0.00 0.56 0.34 0.10
#> TCGA.QH.A65Z.01 4 0.3058 0.8433 0.00 0.08 0.00 0.82 0.00 0.00 0.10
#> TCGA.P5.A730.01 2 0.1166 0.8913 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.WY.A85D.01 5 0.2906 0.6359 0.00 0.00 0.00 0.00 0.80 0.02 0.18
#> TCGA.RY.A83X.01 2 0.1433 0.8872 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.S9.A6UB.01 4 0.1433 0.9015 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.DH.A66F.01 2 0.1671 0.8822 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.DU.6393.01 4 0.1166 0.9106 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.HT.8108.01 1 0.1886 0.6828 0.88 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.DU.7304.01 5 0.1166 0.7348 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.S9.A7IY.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.FG.7641.01 2 0.1433 0.8872 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.P5.A5EV.01 5 0.4640 0.5302 0.18 0.00 0.00 0.00 0.64 0.00 0.18
#> TCGA.DU.7301.01 5 0.3047 0.6770 0.00 0.00 0.00 0.00 0.72 0.00 0.28
#> TCGA.DU.7009.01 2 0.1166 0.8912 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.FG.A4MY.01 5 0.4177 0.5305 0.00 0.00 0.00 0.00 0.70 0.12 0.18
#> TCGA.TM.A7CF.01 1 0.0863 0.7313 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.FG.8186.01 2 0.1433 0.8808 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.S9.A6U6.01 1 0.2081 0.6641 0.86 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.RY.A845.01 1 0.2081 0.6641 0.86 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.DU.7010.01 3 0.0504 0.8276 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.FG.8182.01 1 0.0504 0.7411 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.QH.A6X3.01 7 0.4705 0.6907 0.44 0.00 0.00 0.00 0.08 0.00 0.48
#> TCGA.DU.6401.01 7 0.3994 0.6558 0.48 0.00 0.00 0.00 0.02 0.00 0.50
#> TCGA.E1.A7YH.01 1 0.3047 0.3598 0.72 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.DU.7306.01 5 0.3294 0.6285 0.00 0.00 0.00 0.00 0.66 0.00 0.34
#> TCGA.HT.A74J.01 1 0.2708 0.6046 0.78 0.00 0.00 0.00 0.00 0.22 0.00
#> TCGA.DB.A4XE.01 1 0.2259 0.6392 0.84 0.00 0.00 0.00 0.00 0.00 0.16
#> TCGA.DB.A64L.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VV.A829.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.A61B.01 6 0.1664 0.6847 0.00 0.00 0.02 0.00 0.00 0.92 0.06
#> TCGA.DH.A66B.01 5 0.0504 0.7254 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DU.6397.02 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.6397.01 2 0.4353 0.5871 0.00 0.66 0.00 0.24 0.00 0.00 0.10
#> TCGA.DU.5853.01 1 0.2422 0.6440 0.82 0.00 0.00 0.00 0.00 0.18 0.00
#> TCGA.CS.6670.01 2 0.1166 0.8912 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.DU.7014.01 5 0.1928 0.6783 0.00 0.00 0.00 0.00 0.90 0.02 0.08
#> TCGA.QH.A65X.01 2 0.1166 0.8914 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.DB.A64P.01 2 0.1433 0.8872 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.TQ.A7RV.01 1 0.6301 -0.2454 0.38 0.00 0.00 0.00 0.06 0.20 0.36
#> TCGA.06.6389.01 6 0.3519 0.4667 0.00 0.00 0.22 0.00 0.00 0.74 0.04
#> TCGA.HW.A5KL.01 5 0.2081 0.7377 0.00 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.DH.A7UU.01 5 0.4965 0.4351 0.00 0.00 0.18 0.00 0.66 0.04 0.12
#> TCGA.QH.A6CZ.01 2 0.1671 0.8822 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.DH.A669.02 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DH.A669.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.QH.A6X9.01 5 0.2163 0.6787 0.00 0.00 0.00 0.00 0.88 0.02 0.10
#> TCGA.DU.5871.01 5 0.3496 0.5021 0.00 0.00 0.00 0.00 0.58 0.00 0.42
#> TCGA.TQ.A7RJ.01 1 0.4266 -0.5463 0.52 0.00 0.00 0.00 0.04 0.00 0.44
#> TCGA.VM.A8CB.01 2 0.0504 0.8914 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.HT.7483.01 7 0.4820 0.7158 0.38 0.00 0.00 0.00 0.10 0.00 0.52
#> TCGA.HT.7687.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.TM.A84G.01 4 0.0504 0.9246 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.E1.A7Z6.01 1 0.0504 0.7413 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.TM.A84I.01 6 0.3685 0.2704 0.00 0.00 0.32 0.00 0.00 0.66 0.02
#> TCGA.CS.5394.01 4 0.3058 0.8433 0.00 0.08 0.00 0.82 0.00 0.00 0.10
#> TCGA.DU.A76O.01 1 0.2259 0.6392 0.84 0.00 0.00 0.00 0.00 0.00 0.16
#> TCGA.DU.A5TW.01 7 0.4487 -0.0234 0.06 0.00 0.00 0.00 0.42 0.00 0.52
#> TCGA.FG.5962.01 4 0.0000 0.9265 0.00 0.00 0.00 1.00 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.HT.7693.01 5 0.2407 0.5682 0.00 0.00 0.00 0.00 0.86 0.00 0.06 0.08
#> TCGA.S9.A7J2.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.S9.A6TX.01 4 0.2025 0.8620 0.00 0.10 0.00 0.88 0.00 0.00 0.02 0.00
#> TCGA.VM.A8C8.01 1 0.0000 0.6757 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A74L.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.DU.A5TS.01 8 0.4807 0.2841 0.00 0.00 0.04 0.00 0.46 0.02 0.02 0.46
#> TCGA.06.A7TL.01 6 0.5062 0.2975 0.00 0.00 0.12 0.00 0.00 0.48 0.02 0.38
#> TCGA.E1.5311.01 2 0.0941 0.8911 0.00 0.96 0.00 0.02 0.00 0.00 0.02 0.00
#> TCGA.E1.A7YI.01 3 0.2674 0.8393 0.00 0.00 0.86 0.00 0.00 0.06 0.04 0.04
#> TCGA.E1.5305.01 8 0.4865 0.4986 0.00 0.00 0.00 0.00 0.20 0.08 0.08 0.64
#> TCGA.F6.A8O4.01 1 0.4798 0.1015 0.56 0.00 0.00 0.00 0.10 0.00 0.32 0.02
#> TCGA.DH.A66G.01 1 0.3880 0.4290 0.64 0.00 0.00 0.00 0.00 0.32 0.02 0.02
#> TCGA.P5.A731.01 1 0.1275 0.6788 0.94 0.00 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.HT.7480.01 2 0.0941 0.8911 0.00 0.96 0.00 0.02 0.00 0.00 0.02 0.00
#> TCGA.S9.A7R1.01 2 0.3618 0.3864 0.00 0.60 0.00 0.38 0.00 0.00 0.02 0.00
#> TCGA.FG.A710.01 4 0.1557 0.9074 0.00 0.06 0.00 0.92 0.00 0.00 0.00 0.02
#> TCGA.S9.A7J0.01 8 0.5682 0.4038 0.00 0.00 0.06 0.00 0.22 0.22 0.00 0.50
#> TCGA.DU.A6S6.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.FG.7634.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.DU.6407.01 5 0.0471 0.5751 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.P5.A5F1.01 1 0.3771 0.4516 0.72 0.00 0.00 0.00 0.12 0.00 0.16 0.00
#> TCGA.VM.A8CF.01 8 0.7532 0.1936 0.16 0.00 0.00 0.00 0.16 0.20 0.16 0.32
#> TCGA.DU.6542.01 1 0.3615 0.6143 0.74 0.00 0.00 0.00 0.00 0.02 0.20 0.04
#> TCGA.FG.7638.01 2 0.0808 0.9023 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.DH.5143.01 1 0.4295 0.4951 0.74 0.00 0.00 0.00 0.02 0.06 0.12 0.06
#> TCGA.DU.7299.01 6 0.4224 0.4646 0.00 0.00 0.00 0.00 0.14 0.70 0.02 0.14
#> TCGA.CS.5393.01 6 0.3303 0.5986 0.00 0.00 0.00 0.00 0.02 0.76 0.02 0.20
#> TCGA.TM.A84Q.01 7 0.4693 0.5291 0.42 0.00 0.00 0.00 0.12 0.00 0.46 0.00
#> TCGA.DB.5281.01 5 0.2224 0.5146 0.00 0.00 0.00 0.00 0.86 0.00 0.02 0.12
#> TCGA.FG.A6J1.01 2 0.0471 0.9027 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.HT.7608.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.E1.A7YU.01 6 0.1765 0.6950 0.00 0.00 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.W9.A837.01 2 0.0471 0.8977 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.TM.A7C5.01 2 0.1557 0.8670 0.00 0.92 0.00 0.06 0.00 0.00 0.02 0.00
#> TCGA.QH.A6CW.01 5 0.3385 0.4052 0.00 0.00 0.00 0.00 0.76 0.00 0.08 0.16
#> TCGA.S9.A6WO.01 1 0.1765 0.6603 0.88 0.00 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.IK.7675.01 6 0.4325 0.2553 0.00 0.00 0.38 0.00 0.00 0.56 0.04 0.02
#> TCGA.P5.A5ET.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.HT.7472.01 1 0.1408 0.6748 0.94 0.00 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.19.A6J5.01 3 0.1275 0.8774 0.00 0.00 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.P5.A77X.01 2 0.0000 0.9008 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A6IZ.01 4 0.0471 0.9218 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.HT.7873.01 6 0.0000 0.7195 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CS.4938.01 1 0.0000 0.6757 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KT.A74X.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.VM.A8CH.01 7 0.4686 0.7801 0.28 0.00 0.00 0.00 0.16 0.00 0.56 0.00
#> TCGA.HT.7476.01 5 0.3293 0.5682 0.00 0.00 0.00 0.00 0.74 0.00 0.22 0.04
#> TCGA.DB.A75L.01 5 0.2725 0.5235 0.00 0.00 0.00 0.00 0.82 0.00 0.04 0.14
#> TCGA.S9.A7IS.01 6 0.4636 0.1802 0.00 0.00 0.40 0.00 0.00 0.52 0.04 0.04
#> TCGA.TQ.A8XE.02 1 0.7402 -0.2552 0.32 0.00 0.00 0.00 0.10 0.24 0.16 0.18
#> TCGA.E1.A7YO.01 2 0.1557 0.8670 0.00 0.92 0.00 0.06 0.00 0.00 0.02 0.00
#> TCGA.TQ.A7RG.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.HW.7493.01 1 0.0000 0.6757 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RY.A847.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.DU.8166.01 1 0.3095 0.5761 0.74 0.00 0.00 0.00 0.00 0.00 0.24 0.02
#> TCGA.VM.A8CA.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.HT.7855.01 5 0.2650 0.5702 0.00 0.00 0.00 0.00 0.76 0.00 0.24 0.00
#> TCGA.S9.A89Z.01 3 0.1947 0.8315 0.00 0.00 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.DB.A4XG.01 2 0.1275 0.8805 0.00 0.94 0.00 0.04 0.00 0.00 0.02 0.00
#> TCGA.DU.7015.01 1 0.4397 0.5165 0.66 0.00 0.00 0.00 0.04 0.00 0.24 0.06
#> TCGA.HT.A616.01 1 0.6972 -0.0229 0.38 0.00 0.00 0.00 0.06 0.26 0.18 0.12
#> TCGA.HT.7611.01 5 0.4105 0.1949 0.02 0.00 0.00 0.00 0.54 0.00 0.42 0.02
#> TCGA.FG.A60K.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.S9.A6TY.01 4 0.2224 0.8388 0.00 0.12 0.00 0.86 0.00 0.00 0.02 0.00
#> TCGA.WY.A85C.01 5 0.2534 0.5746 0.00 0.00 0.00 0.00 0.78 0.00 0.22 0.00
#> TCGA.DB.A4XC.01 1 0.1091 0.6543 0.94 0.00 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.P5.A72W.01 1 0.2650 0.5816 0.76 0.00 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.S9.A6TU.01 5 0.2856 0.5597 0.00 0.00 0.00 0.00 0.78 0.00 0.20 0.02
#> TCGA.DU.5855.01 5 0.5800 0.0376 0.06 0.00 0.00 0.00 0.54 0.02 0.16 0.22
#> TCGA.HT.7884.01 1 0.3170 0.6083 0.76 0.00 0.00 0.00 0.00 0.00 0.20 0.04
#> TCGA.TQ.A7RQ.01 2 0.0000 0.9008 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IK.8125.01 4 0.1275 0.9144 0.00 0.00 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.HT.A74K.01 4 0.1804 0.9015 0.00 0.00 0.00 0.90 0.00 0.00 0.08 0.02
#> TCGA.WH.A86K.01 8 0.5147 0.4906 0.00 0.00 0.00 0.00 0.26 0.08 0.08 0.58
#> TCGA.QH.A6X8.01 4 0.1804 0.9015 0.00 0.00 0.00 0.90 0.00 0.00 0.08 0.02
#> TCGA.WY.A85E.01 1 0.4912 0.4429 0.60 0.00 0.00 0.00 0.02 0.08 0.28 0.02
#> TCGA.FG.6691.01 1 0.3272 0.1717 0.58 0.00 0.00 0.00 0.00 0.00 0.42 0.00
#> TCGA.S9.A7R3.01 1 0.3270 0.5539 0.80 0.00 0.00 0.00 0.00 0.06 0.12 0.02
#> TCGA.FG.A4MX.01 1 0.4391 -0.2363 0.50 0.00 0.00 0.00 0.08 0.00 0.42 0.00
#> TCGA.HT.7681.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.S9.A7IZ.01 6 0.2348 0.6857 0.04 0.00 0.00 0.00 0.00 0.88 0.02 0.06
#> TCGA.DU.A6S7.01 5 0.2852 0.5505 0.00 0.00 0.00 0.00 0.72 0.00 0.28 0.00
#> TCGA.06.0221.01 8 0.5070 0.3258 0.00 0.00 0.04 0.00 0.44 0.04 0.02 0.46
#> TCGA.P5.A72Z.01 4 0.1804 0.9015 0.00 0.00 0.00 0.90 0.00 0.00 0.08 0.02
#> TCGA.HT.8114.01 1 0.4302 0.0631 0.56 0.00 0.00 0.00 0.08 0.00 0.36 0.00
#> TCGA.DU.8168.01 4 0.0000 0.9232 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HW.8321.01 7 0.4799 0.7807 0.28 0.00 0.00 0.00 0.18 0.00 0.54 0.00
#> TCGA.TQ.A7RN.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.DH.5141.01 2 0.0941 0.8911 0.00 0.96 0.00 0.02 0.00 0.00 0.02 0.00
#> TCGA.EZ.7264.01 4 0.1804 0.8816 0.00 0.08 0.00 0.90 0.00 0.00 0.02 0.00
#> TCGA.P5.A5F4.01 7 0.4747 0.7795 0.30 0.00 0.00 0.00 0.16 0.00 0.54 0.00
#> TCGA.QH.A65V.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.FG.8191.01 1 0.0000 0.6757 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.5142.01 6 0.0000 0.7195 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.A6S8.01 4 0.1804 0.9015 0.00 0.00 0.00 0.90 0.00 0.00 0.08 0.02
#> TCGA.E1.A7YW.01 1 0.1091 0.6557 0.94 0.00 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.CS.6666.01 5 0.3095 0.5574 0.00 0.00 0.00 0.00 0.74 0.00 0.24 0.02
#> TCGA.DU.7298.01 5 0.4642 0.0891 0.00 0.06 0.00 0.00 0.60 0.00 0.04 0.30
#> TCGA.DB.A64R.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.CS.5390.01 4 0.0000 0.9232 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WP.01 4 0.1804 0.8816 0.00 0.08 0.00 0.90 0.00 0.00 0.02 0.00
#> TCGA.DB.5280.01 1 0.2569 0.6389 0.82 0.00 0.00 0.00 0.00 0.00 0.16 0.02
#> TCGA.TM.A84T.01 1 0.1091 0.6706 0.94 0.00 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.DH.A66D.01 1 0.1804 0.6771 0.90 0.00 0.00 0.00 0.00 0.00 0.08 0.02
#> TCGA.RY.A83Z.01 3 0.1408 0.8803 0.00 0.00 0.94 0.00 0.00 0.02 0.02 0.02
#> TCGA.TQ.A7RH.01 1 0.1091 0.6730 0.94 0.00 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.E1.A7YS.01 4 0.1804 0.9015 0.00 0.00 0.00 0.90 0.00 0.00 0.08 0.02
#> TCGA.P5.A735.01 1 0.0000 0.6757 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7294.01 2 0.1557 0.8670 0.00 0.92 0.00 0.06 0.00 0.00 0.02 0.00
#> TCGA.HT.7695.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.DB.A64X.01 3 0.3083 0.5968 0.00 0.00 0.66 0.00 0.00 0.00 0.00 0.34
#> TCGA.FG.7637.01 2 0.0471 0.9026 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.S9.A6U5.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.HT.7609.01 7 0.4403 0.4534 0.44 0.00 0.00 0.00 0.08 0.00 0.48 0.00
#> TCGA.DB.5274.01 4 0.1804 0.8816 0.00 0.08 0.00 0.90 0.00 0.00 0.02 0.00
#> TCGA.HW.7487.01 4 0.1804 0.8816 0.00 0.08 0.00 0.90 0.00 0.00 0.02 0.00
#> TCGA.HW.7491.01 2 0.1557 0.8670 0.00 0.92 0.00 0.06 0.00 0.00 0.02 0.00
#> TCGA.DB.A75M.01 1 0.2025 0.6529 0.88 0.00 0.00 0.00 0.00 0.00 0.10 0.02
#> TCGA.HW.A5KM.01 1 0.4294 0.4972 0.68 0.00 0.00 0.00 0.06 0.00 0.22 0.04
#> TCGA.HT.7477.01 6 0.4674 -0.0233 0.00 0.00 0.46 0.00 0.00 0.46 0.04 0.04
#> TCGA.HT.8012.01 2 0.0941 0.8911 0.00 0.96 0.00 0.02 0.00 0.00 0.02 0.00
#> TCGA.DU.8167.01 5 0.2938 0.3372 0.00 0.00 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.S9.A6U1.01 7 0.4747 0.7795 0.30 0.00 0.00 0.00 0.16 0.00 0.54 0.00
#> TCGA.FG.5965.01 6 0.2650 0.5301 0.24 0.00 0.00 0.00 0.00 0.76 0.00 0.00
#> TCGA.HT.A614.01 6 0.1765 0.6530 0.12 0.00 0.00 0.00 0.00 0.88 0.00 0.00
#> TCGA.S9.A7QZ.01 4 0.0000 0.9232 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6X4.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.P5.A77W.01 4 0.1804 0.8816 0.00 0.08 0.00 0.90 0.00 0.00 0.02 0.00
#> TCGA.DU.7302.01 4 0.0000 0.9232 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6399.01 5 0.2114 0.4406 0.00 0.00 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.E1.5307.01 8 0.3570 0.3781 0.00 0.00 0.02 0.00 0.36 0.00 0.00 0.62
#> TCGA.S9.A7QW.01 1 0.2267 0.6275 0.82 0.00 0.00 0.00 0.00 0.00 0.18 0.00
#> TCGA.HT.7604.01 5 0.3551 0.5708 0.00 0.00 0.00 0.00 0.72 0.00 0.22 0.06
#> TCGA.P5.A733.01 7 0.5455 0.7257 0.28 0.00 0.00 0.00 0.24 0.00 0.46 0.02
#> TCGA.HT.7684.01 1 0.1741 0.6765 0.92 0.00 0.00 0.00 0.00 0.02 0.02 0.04
#> TCGA.HW.7495.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.QH.A65R.01 4 0.1804 0.8816 0.00 0.08 0.00 0.90 0.00 0.00 0.02 0.00
#> TCGA.DH.A7UV.01 5 0.1341 0.5933 0.00 0.00 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.HT.7879.01 1 0.1947 0.6500 0.86 0.00 0.00 0.00 0.00 0.00 0.14 0.00
#> TCGA.DU.A7TC.01 1 0.4397 0.5127 0.66 0.00 0.00 0.00 0.06 0.00 0.24 0.04
#> TCGA.FG.A60J.01 1 0.2569 0.6361 0.82 0.00 0.00 0.00 0.00 0.00 0.16 0.02
#> TCGA.E1.5303.01 1 0.5045 0.3730 0.62 0.00 0.00 0.00 0.00 0.18 0.14 0.06
#> TCGA.FN.7833.01 1 0.1091 0.6706 0.94 0.00 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.E1.A7Z4.01 1 0.0000 0.6757 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7875.01 2 0.0941 0.9027 0.00 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.06.5417.01 3 0.1741 0.8776 0.00 0.00 0.92 0.00 0.00 0.04 0.02 0.02
#> TCGA.HT.7473.01 1 0.0000 0.6757 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7008.01 7 0.4141 0.3918 0.06 0.00 0.00 0.00 0.38 0.00 0.56 0.00
#> TCGA.DB.A75O.01 1 0.0000 0.6757 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7304.02 3 0.1887 0.8671 0.00 0.00 0.90 0.00 0.00 0.00 0.04 0.06
#> TCGA.DU.6394.01 4 0.0941 0.9190 0.00 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.S9.A6WD.01 4 0.0471 0.9189 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.DU.5872.01 1 0.2404 0.6693 0.84 0.00 0.00 0.00 0.00 0.02 0.14 0.00
#> TCGA.FG.8185.01 5 0.2938 0.5401 0.00 0.00 0.00 0.00 0.70 0.00 0.30 0.00
#> TCGA.TQ.A7RU.01 2 0.2981 0.6794 0.00 0.76 0.00 0.22 0.00 0.00 0.02 0.00
#> TCGA.DU.5874.01 4 0.0000 0.9232 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WE.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.FG.6690.01 5 0.6171 0.0439 0.18 0.00 0.00 0.00 0.46 0.00 0.18 0.18
#> TCGA.HW.8320.01 5 0.0471 0.5751 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.R8.A6MK.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.S9.A7J1.01 2 0.0471 0.8977 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.E1.5322.01 7 0.5433 0.7125 0.30 0.00 0.00 0.00 0.16 0.04 0.50 0.00
#> TCGA.P5.A5F0.01 2 0.1275 0.8805 0.00 0.94 0.00 0.04 0.00 0.00 0.02 0.00
#> TCGA.R8.A73M.01 2 0.1557 0.8670 0.00 0.92 0.00 0.06 0.00 0.00 0.02 0.00
#> TCGA.CS.4942.01 1 0.1275 0.6584 0.94 0.00 0.00 0.00 0.00 0.04 0.00 0.02
#> TCGA.DB.A4X9.01 1 0.0471 0.6775 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DB.A4XF.01 5 0.2756 0.5606 0.00 0.00 0.00 0.00 0.74 0.00 0.26 0.00
#> TCGA.HT.A74O.01 5 0.1275 0.5713 0.00 0.00 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.FG.8188.01 5 0.3193 0.0724 0.00 0.00 0.00 0.00 0.62 0.00 0.00 0.38
#> TCGA.DU.A6S3.01 4 0.1804 0.8816 0.00 0.08 0.00 0.90 0.00 0.00 0.02 0.00
#> TCGA.DB.A4XH.01 4 0.0000 0.9232 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7485.01 1 0.1804 0.6352 0.90 0.00 0.00 0.00 0.00 0.08 0.00 0.02
#> TCGA.VW.A7QS.01 4 0.3198 0.6238 0.00 0.26 0.00 0.72 0.00 0.00 0.02 0.00
#> TCGA.DU.8164.01 4 0.0471 0.9189 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.S9.A6TS.01 8 0.4674 0.3155 0.00 0.00 0.04 0.00 0.46 0.04 0.00 0.46
#> TCGA.DB.A64S.01 7 0.4476 0.6727 0.36 0.00 0.00 0.00 0.10 0.00 0.54 0.00
#> TCGA.VV.A86M.01 5 0.5037 0.4063 0.00 0.00 0.00 0.00 0.54 0.02 0.30 0.14
#> TCGA.TQ.A8XE.01 1 0.7041 -0.0392 0.42 0.00 0.00 0.00 0.10 0.12 0.16 0.20
#> TCGA.CS.6667.01 7 0.4897 0.7629 0.28 0.00 0.00 0.00 0.20 0.00 0.52 0.00
#> TCGA.E1.A7YV.01 3 0.1741 0.8725 0.00 0.00 0.92 0.00 0.00 0.02 0.04 0.02
#> TCGA.TQ.A7RW.01 8 0.7671 0.1300 0.22 0.00 0.00 0.00 0.16 0.22 0.16 0.24
#> TCGA.DU.A7TI.01 1 0.2569 0.6372 0.82 0.00 0.00 0.00 0.00 0.00 0.16 0.02
#> TCGA.HT.7468.01 2 0.1804 0.8505 0.00 0.90 0.00 0.08 0.00 0.00 0.02 0.00
#> TCGA.TQ.A7RI.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.DB.5279.01 4 0.1804 0.9015 0.00 0.00 0.00 0.90 0.00 0.00 0.08 0.02
#> TCGA.S9.A6U8.01 1 0.3637 0.5069 0.70 0.00 0.00 0.00 0.02 0.00 0.26 0.02
#> TCGA.R8.A6YH.01 1 0.2756 0.5611 0.74 0.00 0.00 0.00 0.00 0.00 0.26 0.00
#> TCGA.DU.7018.01 4 0.0000 0.9232 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7677.01 2 0.3658 0.3317 0.00 0.58 0.00 0.40 0.00 0.00 0.02 0.00
#> TCGA.TM.A7CA.01 1 0.3095 0.5761 0.74 0.00 0.00 0.00 0.00 0.00 0.24 0.02
#> TCGA.HT.7690.01 1 0.3570 0.3098 0.62 0.00 0.00 0.00 0.02 0.00 0.36 0.00
#> TCGA.FG.6689.01 1 0.0471 0.6714 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.DU.7007.01 6 0.2591 0.6908 0.00 0.00 0.04 0.00 0.00 0.86 0.02 0.08
#> TCGA.TQ.A7RF.01 1 0.3015 0.4653 0.68 0.00 0.00 0.00 0.00 0.00 0.32 0.00
#> TCGA.DB.5277.01 6 0.4833 0.4754 0.00 0.00 0.12 0.00 0.00 0.58 0.02 0.28
#> TCGA.TM.A84M.01 4 0.1804 0.9015 0.00 0.00 0.00 0.90 0.00 0.00 0.08 0.02
#> TCGA.F6.A8O3.01 2 0.1275 0.9030 0.00 0.94 0.00 0.00 0.00 0.00 0.02 0.04
#> TCGA.QH.A86X.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.HT.8013.01 1 0.1091 0.6557 0.94 0.00 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.HW.7490.01 1 0.3570 0.3098 0.62 0.00 0.00 0.00 0.02 0.00 0.36 0.00
#> TCGA.QH.A65S.01 6 0.2756 0.5085 0.26 0.00 0.00 0.00 0.00 0.74 0.00 0.00
#> TCGA.DU.A76R.01 2 0.0941 0.8911 0.00 0.96 0.00 0.02 0.00 0.00 0.02 0.00
#> TCGA.DH.5144.01 4 0.1804 0.8816 0.00 0.08 0.00 0.90 0.00 0.00 0.02 0.00
#> TCGA.HT.7606.01 8 0.4886 -0.3409 0.00 0.00 0.44 0.00 0.00 0.04 0.06 0.46
#> TCGA.RY.A840.01 2 0.3374 0.5514 0.00 0.68 0.00 0.30 0.00 0.00 0.02 0.00
#> TCGA.HW.A5KJ.01 4 0.0941 0.9190 0.00 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.HT.8105.01 4 0.0000 0.9232 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7471.01 2 0.2025 0.8309 0.00 0.88 0.00 0.10 0.00 0.00 0.02 0.00
#> TCGA.DU.6395.01 1 0.2756 0.5611 0.74 0.00 0.00 0.00 0.00 0.00 0.26 0.00
#> TCGA.S9.A6TV.01 6 0.1563 0.6989 0.00 0.00 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.P5.A5EW.01 1 0.1091 0.6706 0.94 0.00 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.DU.6408.01 6 0.0000 0.7195 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DB.A4XB.01 1 0.2852 0.4626 0.72 0.00 0.00 0.00 0.00 0.28 0.00 0.00
#> TCGA.FG.A4MT.01 1 0.2650 0.5846 0.76 0.00 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.FG.A4MT.02 1 0.2650 0.5846 0.76 0.00 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.HT.A619.01 4 0.1275 0.9144 0.00 0.00 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.QH.A870.01 1 0.0000 0.6757 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A5R9.01 2 0.3729 0.1290 0.00 0.52 0.00 0.46 0.00 0.00 0.02 0.00
#> TCGA.CS.5396.01 4 0.1804 0.9015 0.00 0.00 0.00 0.90 0.00 0.00 0.08 0.02
#> TCGA.DU.A7TA.01 7 0.4677 0.7546 0.32 0.00 0.00 0.00 0.14 0.00 0.54 0.00
#> TCGA.HW.8319.01 6 0.0941 0.7174 0.00 0.00 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.TM.A84H.01 1 0.5892 0.3181 0.50 0.00 0.00 0.00 0.06 0.02 0.28 0.14
#> TCGA.S9.A6TZ.01 1 0.6906 0.0464 0.38 0.00 0.00 0.00 0.14 0.04 0.20 0.24
#> TCGA.DU.6400.01 4 0.0471 0.9218 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.S9.A6WL.01 4 0.1804 0.8816 0.00 0.08 0.00 0.90 0.00 0.00 0.02 0.00
#> TCGA.DB.A75K.01 2 0.1804 0.8504 0.00 0.90 0.00 0.08 0.00 0.00 0.02 0.00
#> TCGA.DB.A4XD.01 5 0.2648 0.5637 0.00 0.00 0.00 0.00 0.84 0.00 0.08 0.08
#> TCGA.DB.A64Q.01 4 0.1804 0.9015 0.00 0.00 0.00 0.90 0.00 0.00 0.08 0.02
#> TCGA.P5.A737.01 2 0.0471 0.8977 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DB.5275.01 1 0.3374 0.5119 0.68 0.00 0.00 0.00 0.00 0.02 0.30 0.00
#> TCGA.S9.A6WH.01 4 0.0000 0.9232 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TU.01 3 0.2025 0.8567 0.00 0.00 0.88 0.00 0.00 0.02 0.00 0.10
#> TCGA.HT.A5RB.01 1 0.2852 0.5365 0.72 0.00 0.00 0.00 0.00 0.00 0.28 0.00
#> TCGA.HT.7616.01 4 0.1804 0.9015 0.00 0.00 0.00 0.90 0.00 0.00 0.08 0.02
#> TCGA.S9.A7R8.01 5 0.6306 -0.0458 0.12 0.00 0.00 0.00 0.48 0.02 0.16 0.22
#> TCGA.QH.A6XA.01 1 0.1091 0.6543 0.94 0.00 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.DU.A5TP.01 1 0.1563 0.6334 0.90 0.00 0.00 0.00 0.00 0.10 0.00 0.00
#> TCGA.RY.A83Y.01 4 0.1804 0.8816 0.00 0.08 0.00 0.90 0.00 0.00 0.02 0.00
#> TCGA.HT.7482.01 1 0.2534 0.5978 0.78 0.00 0.00 0.00 0.00 0.00 0.22 0.00
#> TCGA.TQ.A7RK.02 7 0.3690 0.2537 0.02 0.00 0.00 0.00 0.42 0.00 0.56 0.00
#> TCGA.TQ.A7RK.01 7 0.4757 0.7592 0.24 0.00 0.00 0.00 0.20 0.00 0.56 0.00
#> TCGA.HT.7475.01 1 0.3169 0.6398 0.78 0.00 0.00 0.00 0.00 0.02 0.18 0.02
#> TCGA.DB.A64U.01 2 0.0471 0.8977 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DB.A64W.01 4 0.1804 0.9015 0.00 0.00 0.00 0.90 0.00 0.00 0.08 0.02
#> TCGA.R8.A6MO.01 4 0.1804 0.8816 0.00 0.08 0.00 0.90 0.00 0.00 0.02 0.00
#> TCGA.DU.A7T8.01 1 0.2650 0.5816 0.76 0.00 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.HW.8322.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.DU.5870.02 4 0.1804 0.9015 0.00 0.00 0.00 0.90 0.00 0.00 0.08 0.02
#> TCGA.CS.6668.01 4 0.1275 0.9144 0.00 0.00 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.DU.5870.01 2 0.0471 0.8977 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.FG.7636.01 1 0.6859 -0.1380 0.36 0.00 0.00 0.00 0.04 0.30 0.16 0.14
#> TCGA.HT.7692.01 2 0.0808 0.9023 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.WY.A859.01 6 0.4467 0.3643 0.20 0.00 0.00 0.00 0.00 0.66 0.12 0.02
#> TCGA.R8.A6ML.01 4 0.0000 0.9232 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6410.01 4 0.1804 0.8816 0.00 0.08 0.00 0.90 0.00 0.00 0.02 0.00
#> TCGA.S9.A6U9.01 7 0.4747 0.7795 0.30 0.00 0.00 0.00 0.16 0.00 0.54 0.00
#> TCGA.TQ.A7RO.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.DU.7019.01 5 0.2856 0.3989 0.00 0.00 0.00 0.00 0.78 0.00 0.02 0.20
#> TCGA.TQ.A7RM.01 3 0.2719 0.8122 0.00 0.00 0.80 0.00 0.00 0.00 0.02 0.18
#> TCGA.S9.A7R4.01 1 0.2756 0.5665 0.74 0.00 0.00 0.00 0.00 0.00 0.26 0.00
#> TCGA.E1.5318.01 4 0.0000 0.9232 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7676.01 1 0.0808 0.6649 0.96 0.00 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.S9.A7J3.01 4 0.0471 0.9218 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.06.6701.01 5 0.2025 0.5381 0.00 0.00 0.00 0.00 0.88 0.00 0.02 0.10
#> TCGA.P5.A5F2.01 1 0.6038 0.2908 0.56 0.00 0.00 0.00 0.04 0.12 0.16 0.12
#> TCGA.E1.5304.01 3 0.1275 0.8809 0.00 0.00 0.94 0.00 0.00 0.04 0.00 0.02
#> TCGA.WY.A85B.01 7 0.4747 0.7795 0.30 0.00 0.00 0.00 0.16 0.00 0.54 0.00
#> TCGA.TQ.A7RS.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.S9.A7QX.01 7 0.4407 0.2107 0.08 0.00 0.00 0.00 0.46 0.00 0.46 0.00
#> TCGA.CS.4943.01 8 0.6052 0.2025 0.00 0.00 0.00 0.00 0.20 0.34 0.08 0.38
#> TCGA.QH.A65Z.01 4 0.1804 0.8816 0.00 0.08 0.00 0.90 0.00 0.00 0.02 0.00
#> TCGA.P5.A730.01 2 0.0808 0.9023 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.WY.A85D.01 8 0.4224 0.1744 0.00 0.00 0.00 0.00 0.46 0.00 0.06 0.48
#> TCGA.RY.A83X.01 2 0.0471 0.8977 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.S9.A6UB.01 4 0.0471 0.9189 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.DH.A66F.01 2 0.1275 0.8805 0.00 0.94 0.00 0.04 0.00 0.00 0.02 0.00
#> TCGA.DU.6393.01 4 0.0471 0.9189 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.HT.8108.01 1 0.2650 0.5813 0.76 0.00 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.DU.7304.01 5 0.2224 0.5087 0.00 0.00 0.00 0.00 0.86 0.00 0.02 0.12
#> TCGA.S9.A7IY.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.FG.7641.01 2 0.0471 0.8977 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.P5.A5EV.01 5 0.6535 -0.0698 0.16 0.00 0.00 0.00 0.44 0.02 0.16 0.22
#> TCGA.DU.7301.01 5 0.2404 0.5931 0.00 0.00 0.00 0.00 0.84 0.00 0.14 0.02
#> TCGA.DU.7009.01 2 0.0000 0.9008 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A4MY.01 8 0.4812 0.4832 0.00 0.00 0.00 0.00 0.28 0.06 0.06 0.60
#> TCGA.TM.A7CF.01 1 0.3036 0.6290 0.78 0.00 0.00 0.00 0.00 0.00 0.18 0.04
#> TCGA.FG.8186.01 2 0.1557 0.8977 0.00 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.S9.A6U6.01 1 0.3198 0.5488 0.72 0.00 0.00 0.00 0.00 0.00 0.26 0.02
#> TCGA.RY.A845.01 1 0.2981 0.5911 0.76 0.00 0.00 0.00 0.00 0.00 0.22 0.02
#> TCGA.DU.7010.01 3 0.2399 0.8537 0.00 0.00 0.88 0.00 0.00 0.04 0.04 0.04
#> TCGA.FG.8182.01 1 0.1557 0.6757 0.92 0.00 0.00 0.00 0.00 0.00 0.06 0.02
#> TCGA.QH.A6X3.01 7 0.5455 0.6064 0.38 0.00 0.00 0.00 0.20 0.00 0.40 0.02
#> TCGA.DU.6401.01 7 0.4677 0.7532 0.32 0.00 0.00 0.00 0.14 0.00 0.54 0.00
#> TCGA.E1.A7YH.01 1 0.3272 0.1844 0.58 0.00 0.00 0.00 0.00 0.00 0.42 0.00
#> TCGA.DU.7306.01 5 0.3444 0.5520 0.02 0.00 0.00 0.00 0.78 0.00 0.14 0.06
#> TCGA.HT.A74J.01 1 0.2807 0.5981 0.84 0.00 0.00 0.00 0.00 0.10 0.04 0.02
#> TCGA.DB.A4XE.01 1 0.2756 0.5611 0.74 0.00 0.00 0.00 0.00 0.00 0.26 0.00
#> TCGA.DB.A64L.01 4 0.1275 0.9144 0.00 0.00 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.VV.A829.01 4 0.1804 0.9015 0.00 0.00 0.00 0.90 0.00 0.00 0.08 0.02
#> TCGA.HT.A61B.01 6 0.0471 0.7195 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DH.A66B.01 5 0.2406 0.4016 0.00 0.00 0.00 0.00 0.80 0.00 0.00 0.20
#> TCGA.DU.6397.02 4 0.1804 0.9015 0.00 0.00 0.00 0.90 0.00 0.00 0.08 0.02
#> TCGA.DU.6397.01 2 0.3690 0.2702 0.00 0.56 0.00 0.42 0.00 0.00 0.02 0.00
#> TCGA.DU.5853.01 1 0.1341 0.6433 0.92 0.00 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.CS.6670.01 2 0.0471 0.8977 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DU.7014.01 5 0.4556 -0.1957 0.00 0.00 0.06 0.00 0.54 0.00 0.02 0.38
#> TCGA.QH.A65X.01 2 0.0471 0.8977 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DB.A64P.01 2 0.0941 0.8911 0.00 0.96 0.00 0.02 0.00 0.00 0.02 0.00
#> TCGA.TQ.A7RV.01 1 0.6773 0.0452 0.38 0.00 0.00 0.00 0.18 0.08 0.30 0.06
#> TCGA.06.6389.01 6 0.2591 0.6781 0.00 0.00 0.08 0.00 0.00 0.86 0.02 0.04
#> TCGA.HW.A5KL.01 5 0.2994 0.4532 0.00 0.00 0.00 0.00 0.80 0.00 0.06 0.14
#> TCGA.DH.A7UU.01 8 0.5407 0.4085 0.00 0.00 0.12 0.00 0.34 0.02 0.02 0.50
#> TCGA.QH.A6CZ.01 2 0.0941 0.8911 0.00 0.96 0.00 0.02 0.00 0.00 0.02 0.00
#> TCGA.DH.A669.02 4 0.1804 0.9015 0.00 0.00 0.00 0.90 0.00 0.00 0.08 0.02
#> TCGA.DH.A669.01 4 0.1804 0.9015 0.00 0.00 0.00 0.90 0.00 0.00 0.08 0.02
#> TCGA.QH.A6X9.01 5 0.3737 -0.1890 0.00 0.00 0.00 0.00 0.50 0.00 0.02 0.48
#> TCGA.DU.5871.01 5 0.3015 0.5217 0.00 0.00 0.00 0.00 0.68 0.00 0.32 0.00
#> TCGA.TQ.A7RJ.01 1 0.5429 -0.3835 0.46 0.00 0.00 0.00 0.14 0.00 0.36 0.04
#> TCGA.VM.A8CB.01 2 0.1091 0.9004 0.00 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.HT.7483.01 7 0.4799 0.7807 0.28 0.00 0.00 0.00 0.18 0.00 0.54 0.00
#> TCGA.HT.7687.01 4 0.0941 0.9190 0.00 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.TM.A84G.01 4 0.0000 0.9232 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7Z6.01 1 0.0000 0.6757 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84I.01 6 0.3483 0.5861 0.00 0.00 0.18 0.00 0.00 0.76 0.02 0.04
#> TCGA.CS.5394.01 4 0.1804 0.8816 0.00 0.08 0.00 0.90 0.00 0.00 0.02 0.00
#> TCGA.DU.A76O.01 1 0.3291 0.5198 0.70 0.00 0.00 0.00 0.00 0.00 0.28 0.02
#> TCGA.DU.A5TW.01 7 0.3333 -0.1326 0.00 0.00 0.00 0.00 0.50 0.00 0.50 0.00
#> TCGA.FG.5962.01 4 0.1275 0.9144 0.00 0.00 0.00 0.94 0.00 0.00 0.04 0.02
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111 , Node0112 , Node0113 , Node0121 , Node0122 , Node0123-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0141 , Node0142-leaf , Node0143 , Node0211-leaf , Node0212-leaf , Node0213-leaf , Node0214-leaf , Node0221 , Node0222 , Node0223 , Node0231 , Node0232-leaf , Node0233-leaf , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0323-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 155 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 6.
#>
#> 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 0.49067 0.510 0.510
#> 3 3 1.000 0.998 0.999 0.05735 0.972 0.945
#> 4 4 1.000 0.992 0.993 0.03363 0.985 0.970
#> 5 5 0.839 0.885 0.848 0.16849 0.829 0.636
#> 6 6 0.938 0.929 0.954 0.11524 0.953 0.852
#> 7 7 0.924 0.903 0.959 0.01412 0.995 0.982
#> 8 8 0.926 0.893 0.954 0.00711 1.000 0.999
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 6
#> 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.HT.7693.01 2 0 1 0 1
#> TCGA.VM.A8C8.01 2 0 1 0 1
#> TCGA.F6.A8O4.01 1 0 1 1 0
#> TCGA.DH.A66G.01 2 0 1 0 1
#> TCGA.P5.A731.01 2 0 1 0 1
#> TCGA.DU.6407.01 2 0 1 0 1
#> TCGA.P5.A5F1.01 1 0 1 1 0
#> TCGA.VM.A8CF.01 2 0 1 0 1
#> TCGA.DU.6542.01 1 0 1 1 0
#> TCGA.DH.5143.01 1 0 1 1 0
#> TCGA.DU.7299.01 1 0 1 1 0
#> TCGA.TM.A84Q.01 1 0 1 1 0
#> TCGA.DB.5281.01 1 0 1 1 0
#> TCGA.QH.A6CW.01 1 0 1 1 0
#> TCGA.S9.A6WO.01 1 0 1 1 0
#> TCGA.HT.7472.01 1 0 1 1 0
#> TCGA.CS.4938.01 2 0 1 0 1
#> TCGA.VM.A8CH.01 1 0 1 1 0
#> TCGA.HT.7476.01 1 0 1 1 0
#> TCGA.DB.A75L.01 2 0 1 0 1
#> TCGA.TQ.A8XE.02 2 0 1 0 1
#> TCGA.HW.7493.01 2 0 1 0 1
#> TCGA.DU.8166.01 2 0 1 0 1
#> TCGA.HT.7855.01 1 0 1 1 0
#> TCGA.DU.7015.01 2 0 1 0 1
#> TCGA.HT.A616.01 2 0 1 0 1
#> TCGA.HT.7611.01 1 0 1 1 0
#> TCGA.WY.A85C.01 1 0 1 1 0
#> TCGA.DB.A4XC.01 1 0 1 1 0
#> TCGA.P5.A72W.01 1 0 1 1 0
#> TCGA.S9.A6TU.01 1 0 1 1 0
#> TCGA.DU.5855.01 2 0 1 0 1
#> TCGA.HT.7884.01 2 0 1 0 1
#> TCGA.WY.A85E.01 2 0 1 0 1
#> TCGA.FG.6691.01 2 0 1 0 1
#> TCGA.S9.A7R3.01 2 0 1 0 1
#> TCGA.FG.A4MX.01 1 0 1 1 0
#> TCGA.S9.A7IZ.01 2 0 1 0 1
#> TCGA.DU.A6S7.01 2 0 1 0 1
#> TCGA.HT.8114.01 1 0 1 1 0
#> TCGA.HW.8321.01 1 0 1 1 0
#> TCGA.P5.A5F4.01 2 0 1 0 1
#> TCGA.FG.8191.01 1 0 1 1 0
#> TCGA.E1.A7YW.01 1 0 1 1 0
#> TCGA.CS.6666.01 1 0 1 1 0
#> TCGA.DB.5280.01 1 0 1 1 0
#> TCGA.TM.A84T.01 1 0 1 1 0
#> TCGA.DH.A66D.01 2 0 1 0 1
#> TCGA.TQ.A7RH.01 1 0 1 1 0
#> TCGA.P5.A735.01 2 0 1 0 1
#> TCGA.HT.7609.01 1 0 1 1 0
#> TCGA.DB.A75M.01 1 0 1 1 0
#> TCGA.HW.A5KM.01 1 0 1 1 0
#> TCGA.DU.8167.01 2 0 1 0 1
#> TCGA.S9.A6U1.01 2 0 1 0 1
#> TCGA.FG.5965.01 2 0 1 0 1
#> TCGA.HT.A614.01 1 0 1 1 0
#> TCGA.DU.6399.01 1 0 1 1 0
#> TCGA.S9.A7QW.01 2 0 1 0 1
#> TCGA.HT.7604.01 1 0 1 1 0
#> TCGA.P5.A733.01 2 0 1 0 1
#> TCGA.HT.7684.01 1 0 1 1 0
#> TCGA.DH.A7UV.01 1 0 1 1 0
#> TCGA.HT.7879.01 1 0 1 1 0
#> TCGA.DU.A7TC.01 1 0 1 1 0
#> TCGA.FG.A60J.01 2 0 1 0 1
#> TCGA.E1.5303.01 1 0 1 1 0
#> TCGA.FN.7833.01 1 0 1 1 0
#> TCGA.E1.A7Z4.01 1 0 1 1 0
#> TCGA.HT.7473.01 1 0 1 1 0
#> TCGA.DU.7008.01 2 0 1 0 1
#> TCGA.DB.A75O.01 1 0 1 1 0
#> TCGA.DU.5872.01 2 0 1 0 1
#> TCGA.FG.8185.01 1 0 1 1 0
#> TCGA.S9.A6WE.01 1 0 1 1 0
#> TCGA.FG.6690.01 1 0 1 1 0
#> TCGA.HW.8320.01 1 0 1 1 0
#> TCGA.E1.5322.01 2 0 1 0 1
#> TCGA.CS.4942.01 2 0 1 0 1
#> TCGA.DB.A4X9.01 2 0 1 0 1
#> TCGA.DB.A4XF.01 2 0 1 0 1
#> TCGA.HT.A74O.01 1 0 1 1 0
#> TCGA.HT.7485.01 1 0 1 1 0
#> TCGA.DB.A64S.01 1 0 1 1 0
#> TCGA.VV.A86M.01 2 0 1 0 1
#> TCGA.TQ.A8XE.01 2 0 1 0 1
#> TCGA.CS.6667.01 2 0 1 0 1
#> TCGA.TQ.A7RW.01 1 0 1 1 0
#> TCGA.DU.A7TI.01 1 0 1 1 0
#> TCGA.S9.A6U8.01 1 0 1 1 0
#> TCGA.R8.A6YH.01 1 0 1 1 0
#> TCGA.TM.A7CA.01 1 0 1 1 0
#> TCGA.HT.7690.01 1 0 1 1 0
#> TCGA.FG.6689.01 1 0 1 1 0
#> TCGA.TQ.A7RF.01 2 0 1 0 1
#> TCGA.HT.8013.01 2 0 1 0 1
#> TCGA.HW.7490.01 1 0 1 1 0
#> TCGA.QH.A65S.01 2 0 1 0 1
#> TCGA.DU.6395.01 1 0 1 1 0
#> TCGA.P5.A5EW.01 2 0 1 0 1
#> TCGA.DB.A4XB.01 1 0 1 1 0
#> TCGA.FG.A4MT.01 2 0 1 0 1
#> TCGA.FG.A4MT.02 2 0 1 0 1
#> TCGA.QH.A870.01 2 0 1 0 1
#> TCGA.DU.A7TA.01 1 0 1 1 0
#> TCGA.TM.A84H.01 2 0 1 0 1
#> TCGA.S9.A6TZ.01 2 0 1 0 1
#> TCGA.DB.A4XD.01 1 0 1 1 0
#> TCGA.DB.5275.01 1 0 1 1 0
#> TCGA.HT.A5RB.01 1 0 1 1 0
#> TCGA.S9.A7R8.01 2 0 1 0 1
#> TCGA.QH.A6XA.01 2 0 1 0 1
#> TCGA.DU.A5TP.01 1 0 1 1 0
#> TCGA.HT.7482.01 2 0 1 0 1
#> TCGA.TQ.A7RK.02 1 0 1 1 0
#> TCGA.TQ.A7RK.01 1 0 1 1 0
#> TCGA.HT.7475.01 1 0 1 1 0
#> TCGA.DU.A7T8.01 1 0 1 1 0
#> TCGA.FG.7636.01 1 0 1 1 0
#> TCGA.WY.A859.01 2 0 1 0 1
#> TCGA.S9.A6U9.01 1 0 1 1 0
#> TCGA.DU.7019.01 1 0 1 1 0
#> TCGA.S9.A7R4.01 1 0 1 1 0
#> TCGA.HT.7676.01 1 0 1 1 0
#> TCGA.06.6701.01 1 0 1 1 0
#> TCGA.P5.A5F2.01 2 0 1 0 1
#> TCGA.WY.A85B.01 1 0 1 1 0
#> TCGA.S9.A7QX.01 2 0 1 0 1
#> TCGA.CS.4943.01 1 0 1 1 0
#> TCGA.WY.A85D.01 1 0 1 1 0
#> TCGA.HT.8108.01 2 0 1 0 1
#> TCGA.DU.7304.01 1 0 1 1 0
#> TCGA.P5.A5EV.01 1 0 1 1 0
#> TCGA.DU.7301.01 1 0 1 1 0
#> TCGA.TM.A7CF.01 2 0 1 0 1
#> TCGA.S9.A6U6.01 1 0 1 1 0
#> TCGA.RY.A845.01 2 0 1 0 1
#> TCGA.FG.8182.01 1 0 1 1 0
#> TCGA.QH.A6X3.01 1 0 1 1 0
#> TCGA.DU.6401.01 2 0 1 0 1
#> TCGA.E1.A7YH.01 2 0 1 0 1
#> TCGA.DU.7306.01 1 0 1 1 0
#> TCGA.HT.A74J.01 1 0 1 1 0
#> TCGA.DB.A4XE.01 2 0 1 0 1
#> TCGA.DH.A66B.01 1 0 1 1 0
#> TCGA.DU.5853.01 1 0 1 1 0
#> TCGA.TQ.A7RV.01 1 0 1 1 0
#> TCGA.HW.A5KL.01 2 0 1 0 1
#> TCGA.QH.A6X9.01 2 0 1 0 1
#> TCGA.DU.5871.01 2 0 1 0 1
#> TCGA.TQ.A7RJ.01 2 0 1 0 1
#> TCGA.HT.7483.01 1 0 1 1 0
#> TCGA.E1.A7Z6.01 2 0 1 0 1
#> TCGA.DU.A76O.01 1 0 1 1 0
#> TCGA.DU.A5TW.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.HT.7693.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.VM.A8C8.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.F6.A8O4.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DH.A66G.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.P5.A731.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.DU.6407.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.P5.A5F1.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.VM.A8CF.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.DU.6542.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DH.5143.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DU.7299.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.TM.A84Q.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DB.5281.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.QH.A6CW.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.S9.A6WO.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.HT.7472.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CS.4938.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.VM.A8CH.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.HT.7476.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DB.A75L.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.TQ.A8XE.02 2 0.0000 0.998 0 1.00 0.00
#> TCGA.HW.7493.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.DU.8166.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.HT.7855.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DU.7015.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.HT.A616.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.HT.7611.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.WY.A85C.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DB.A4XC.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.P5.A72W.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.S9.A6TU.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DU.5855.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.HT.7884.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.WY.A85E.01 2 0.0892 0.980 0 0.98 0.02
#> TCGA.FG.6691.01 2 0.2066 0.939 0 0.94 0.06
#> TCGA.S9.A7R3.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.FG.A4MX.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.S9.A7IZ.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.DU.A6S7.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.HT.8114.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.HW.8321.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.P5.A5F4.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.FG.8191.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.E1.A7YW.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CS.6666.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DB.5280.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.TM.A84T.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DH.A66D.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.TQ.A7RH.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.P5.A735.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.HT.7609.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DB.A75M.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.HW.A5KM.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DU.8167.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.S9.A6U1.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.FG.5965.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.HT.A614.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DU.6399.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.S9.A7QW.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.HT.7604.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.P5.A733.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.HT.7684.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DH.A7UV.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.HT.7879.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DU.A7TC.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.FG.A60J.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.E1.5303.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.FN.7833.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.E1.A7Z4.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.HT.7473.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DU.7008.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.DB.A75O.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DU.5872.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.FG.8185.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.S9.A6WE.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.FG.6690.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.HW.8320.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.E1.5322.01 2 0.0892 0.980 0 0.98 0.02
#> TCGA.CS.4942.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.DB.A4X9.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.DB.A4XF.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.HT.A74O.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.HT.7485.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DB.A64S.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.VV.A86M.01 2 0.0892 0.980 0 0.98 0.02
#> TCGA.TQ.A8XE.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.CS.6667.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.TQ.A7RW.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DU.A7TI.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.S9.A6U8.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.R8.A6YH.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.TM.A7CA.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.HT.7690.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.FG.6689.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.TQ.A7RF.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.HT.8013.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.HW.7490.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.QH.A65S.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.DU.6395.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.P5.A5EW.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.DB.A4XB.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.FG.A4MT.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.FG.A4MT.02 2 0.0000 0.998 0 1.00 0.00
#> TCGA.QH.A870.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.DU.A7TA.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.TM.A84H.01 2 0.0892 0.980 0 0.98 0.02
#> TCGA.S9.A6TZ.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.DB.A4XD.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DB.5275.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.HT.A5RB.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.S9.A7R8.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.QH.A6XA.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.DU.A5TP.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.HT.7482.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.TQ.A7RK.02 1 0.0000 1.000 1 0.00 0.00
#> TCGA.TQ.A7RK.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.HT.7475.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DU.A7T8.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.FG.7636.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.WY.A859.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.S9.A6U9.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DU.7019.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.S9.A7R4.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.HT.7676.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.06.6701.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.P5.A5F2.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.WY.A85B.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.S9.A7QX.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.CS.4943.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.WY.A85D.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.HT.8108.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.DU.7304.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.P5.A5EV.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DU.7301.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.TM.A7CF.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.S9.A6U6.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.RY.A845.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.FG.8182.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.QH.A6X3.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DU.6401.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.E1.A7YH.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.DU.7306.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.HT.A74J.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DB.A4XE.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.DH.A66B.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DU.5853.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.TQ.A7RV.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.HW.A5KL.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.QH.A6X9.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.DU.5871.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.TQ.A7RJ.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.HT.7483.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.E1.A7Z6.01 2 0.0000 0.998 0 1.00 0.00
#> TCGA.DU.A76O.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DU.A5TW.01 2 0.0000 0.998 0 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.HT.7693.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.VM.A8C8.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.F6.A8O4.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.DH.A66G.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.P5.A731.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.DU.6407.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.P5.A5F1.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.VM.A8CF.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.DU.6542.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.DH.5143.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.DU.7299.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.TM.A84Q.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.DB.5281.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.QH.A6CW.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.S9.A6WO.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.HT.7472.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.CS.4938.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.VM.A8CH.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.HT.7476.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.DB.A75L.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.TQ.A8XE.02 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.HW.7493.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.DU.8166.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.HT.7855.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.DU.7015.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.HT.A616.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.HT.7611.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.WY.A85C.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.DB.A4XC.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.P5.A72W.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.S9.A6TU.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.DU.5855.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.HT.7884.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.WY.A85E.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.FG.6691.01 2 0.2921 0.833 0.00 0.86 0.14 0.00
#> TCGA.S9.A7R3.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.FG.A4MX.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.S9.A7IZ.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.DU.A6S7.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.HT.8114.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.HW.8321.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.P5.A5F4.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.FG.8191.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YW.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.CS.6666.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.DB.5280.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.TM.A84T.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.DH.A66D.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.TQ.A7RH.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.P5.A735.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.HT.7609.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.DB.A75M.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.HW.A5KM.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.DU.8167.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.S9.A6U1.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.FG.5965.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.HT.A614.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.DU.6399.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.S9.A7QW.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.HT.7604.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.P5.A733.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.HT.7684.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.DH.A7UV.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.HT.7879.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.DU.A7TC.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.FG.A60J.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.E1.5303.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.FN.7833.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.E1.A7Z4.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.HT.7473.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.DU.7008.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.DB.A75O.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.DU.5872.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.FG.8185.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.S9.A6WE.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.FG.6690.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.HW.8320.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.E1.5322.01 4 0.0707 1.000 0.00 0.02 0.00 0.98
#> TCGA.CS.4942.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.DB.A4X9.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.DB.A4XF.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.HT.A74O.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.HT.7485.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.DB.A64S.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.VV.A86M.01 4 0.0707 1.000 0.00 0.02 0.00 0.98
#> TCGA.TQ.A8XE.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.CS.6667.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.TQ.A7RW.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.DU.A7TI.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.S9.A6U8.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.R8.A6YH.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.TM.A7CA.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.HT.7690.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.FG.6689.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RF.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.HT.8013.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.HW.7490.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.QH.A65S.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.DU.6395.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.P5.A5EW.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.DB.A4XB.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.FG.A4MT.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.FG.A4MT.02 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.QH.A870.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.DU.A7TA.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.TM.A84H.01 4 0.0707 1.000 0.00 0.02 0.00 0.98
#> TCGA.S9.A6TZ.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.DB.A4XD.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.DB.5275.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.HT.A5RB.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.S9.A7R8.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.QH.A6XA.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.DU.A5TP.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.HT.7482.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.TQ.A7RK.02 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.TQ.A7RK.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.HT.7475.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.DU.A7T8.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.FG.7636.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.WY.A859.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.S9.A6U9.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.DU.7019.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.S9.A7R4.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.HT.7676.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.06.6701.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.P5.A5F2.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.WY.A85B.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.S9.A7QX.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.CS.4943.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.WY.A85D.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.HT.8108.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.DU.7304.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.P5.A5EV.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.DU.7301.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.TM.A7CF.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.S9.A6U6.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.RY.A845.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.FG.8182.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.QH.A6X3.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.DU.6401.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.E1.A7YH.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.DU.7306.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.HT.A74J.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.DB.A4XE.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.DH.A66B.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.DU.5853.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RV.01 1 0.0000 0.990 1.00 0.00 0.00 0.00
#> TCGA.HW.A5KL.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.QH.A6X9.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.DU.5871.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.TQ.A7RJ.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.HT.7483.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.E1.A7Z6.01 2 0.0000 0.997 0.00 1.00 0.00 0.00
#> TCGA.DU.A76O.01 1 0.0707 0.990 0.98 0.00 0.00 0.02
#> TCGA.DU.A5TW.01 2 0.0000 0.997 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.HT.7693.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.VM.A8C8.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.F6.A8O4.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.DH.A66G.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.P5.A731.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.DU.6407.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.P5.A5F1.01 5 0.4302 0.9592 0.48 0.00 0.00 0 0.52
#> TCGA.VM.A8CF.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.DU.6542.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.DH.5143.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.DU.7299.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.TM.A84Q.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.DB.5281.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.QH.A6CW.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.S9.A6WO.01 1 0.1043 0.8491 0.96 0.00 0.00 0 0.04
#> TCGA.HT.7472.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.CS.4938.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.VM.A8CH.01 3 0.4262 0.4033 0.00 0.00 0.56 0 0.44
#> TCGA.HT.7476.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.DB.A75L.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.TQ.A8XE.02 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.HW.7493.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.DU.8166.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.HT.7855.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.DU.7015.01 3 0.4262 0.4033 0.00 0.00 0.56 0 0.44
#> TCGA.HT.A616.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.HT.7611.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.WY.A85C.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.DB.A4XC.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.P5.A72W.01 5 0.4302 0.9592 0.48 0.00 0.00 0 0.52
#> TCGA.S9.A6TU.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.DU.5855.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.HT.7884.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.WY.A85E.01 2 0.4767 0.1214 0.00 0.56 0.42 0 0.02
#> TCGA.FG.6691.01 3 0.4818 0.0863 0.00 0.46 0.52 0 0.02
#> TCGA.S9.A7R3.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.FG.A4MX.01 1 0.4126 -0.5544 0.62 0.00 0.00 0 0.38
#> TCGA.S9.A7IZ.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.DU.A6S7.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.HT.8114.01 1 0.3895 -0.2612 0.68 0.00 0.00 0 0.32
#> TCGA.HW.8321.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.P5.A5F4.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.FG.8191.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.E1.A7YW.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.CS.6666.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.DB.5280.01 1 0.1043 0.8503 0.96 0.00 0.00 0 0.04
#> TCGA.TM.A84T.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.DH.A66D.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.TQ.A7RH.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.P5.A735.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.HT.7609.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.DB.A75M.01 1 0.0609 0.8787 0.98 0.00 0.00 0 0.02
#> TCGA.HW.A5KM.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.DU.8167.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.S9.A6U1.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.FG.5965.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.HT.A614.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.DU.6399.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.S9.A7QW.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.HT.7604.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.P5.A733.01 3 0.0609 0.5471 0.00 0.00 0.98 0 0.02
#> TCGA.HT.7684.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.DH.A7UV.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.HT.7879.01 5 0.4302 0.9592 0.48 0.00 0.00 0 0.52
#> TCGA.DU.A7TC.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.FG.A60J.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.E1.5303.01 1 0.4287 -0.8070 0.54 0.00 0.00 0 0.46
#> TCGA.FN.7833.01 1 0.4287 -0.8099 0.54 0.00 0.00 0 0.46
#> TCGA.E1.A7Z4.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.HT.7473.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.DU.7008.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.DB.A75O.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.DU.5872.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.FG.8185.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.S9.A6WE.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.FG.6690.01 1 0.3274 0.3512 0.78 0.00 0.00 0 0.22
#> TCGA.HW.8320.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.E1.5322.01 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00
#> TCGA.CS.4942.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.DB.A4X9.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.DB.A4XF.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.HT.A74O.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.HT.7485.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.DB.A64S.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.VV.A86M.01 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00
#> TCGA.TQ.A8XE.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.CS.6667.01 3 0.0000 0.5469 0.00 0.00 1.00 0 0.00
#> TCGA.TQ.A7RW.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.DU.A7TI.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.S9.A6U8.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.R8.A6YH.01 1 0.1043 0.8493 0.96 0.00 0.00 0 0.04
#> TCGA.TM.A7CA.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.HT.7690.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.FG.6689.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.TQ.A7RF.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.HT.8013.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.HW.7490.01 1 0.3895 -0.2679 0.68 0.00 0.00 0 0.32
#> TCGA.QH.A65S.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.DU.6395.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.P5.A5EW.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.DB.A4XB.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.FG.A4MT.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.FG.A4MT.02 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.QH.A870.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.DU.A7TA.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.TM.A84H.01 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00
#> TCGA.S9.A6TZ.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.DB.A4XD.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.DB.5275.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.HT.A5RB.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.S9.A7R8.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.QH.A6XA.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.DU.A5TP.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.HT.7482.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.TQ.A7RK.02 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.TQ.A7RK.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.HT.7475.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.DU.A7T8.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.FG.7636.01 5 0.4302 0.9592 0.48 0.00 0.00 0 0.52
#> TCGA.WY.A859.01 3 0.0000 0.5469 0.00 0.00 1.00 0 0.00
#> TCGA.S9.A6U9.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.DU.7019.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.S9.A7R4.01 1 0.0609 0.8784 0.98 0.00 0.00 0 0.02
#> TCGA.HT.7676.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.06.6701.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.P5.A5F2.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.WY.A85B.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.S9.A7QX.01 2 0.0609 0.9702 0.00 0.98 0.00 0 0.02
#> TCGA.CS.4943.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.WY.A85D.01 1 0.0609 0.8790 0.98 0.00 0.00 0 0.02
#> TCGA.HT.8108.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.DU.7304.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.P5.A5EV.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.DU.7301.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.TM.A7CF.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.S9.A6U6.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.RY.A845.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.FG.8182.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.QH.A6X3.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.DU.6401.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.E1.A7YH.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.DU.7306.01 1 0.1043 0.8512 0.96 0.00 0.00 0 0.04
#> TCGA.HT.A74J.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.DB.A4XE.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.DH.A66B.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.DU.5853.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.TQ.A7RV.01 5 0.4287 0.9959 0.46 0.00 0.00 0 0.54
#> TCGA.HW.A5KL.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.QH.A6X9.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.DU.5871.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.TQ.A7RJ.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.HT.7483.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.E1.A7Z6.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
#> TCGA.DU.A76O.01 1 0.0000 0.9029 1.00 0.00 0.00 0 0.00
#> TCGA.DU.A5TW.01 2 0.0000 0.9910 0.00 1.00 0.00 0 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.HT.7693.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.VM.A8C8.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.F6.A8O4.01 5 0.0547 0.922 0.02 0.00 0.00 0 0.98 0.00
#> TCGA.DH.A66G.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.P5.A731.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.DU.6407.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.P5.A5F1.01 5 0.0547 0.922 0.02 0.00 0.00 0 0.98 0.00
#> TCGA.VM.A8CF.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.DU.6542.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.DH.5143.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.DU.7299.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.TM.A84Q.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.DB.5281.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.QH.A6CW.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.S9.A6WO.01 1 0.3309 0.687 0.72 0.00 0.00 0 0.28 0.00
#> TCGA.HT.7472.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.CS.4938.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.VM.A8CH.01 6 0.0000 1.000 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.HT.7476.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.DB.A75L.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.TQ.A8XE.02 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.HW.7493.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.DU.8166.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.HT.7855.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.DU.7015.01 6 0.0000 1.000 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.HT.A616.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.HT.7611.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.WY.A85C.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.DB.A4XC.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.P5.A72W.01 5 0.0937 0.904 0.04 0.00 0.00 0 0.96 0.00
#> TCGA.S9.A6TU.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.DU.5855.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.HT.7884.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.WY.A85E.01 3 0.0547 0.714 0.02 0.00 0.98 0 0.00 0.00
#> TCGA.FG.6691.01 3 0.1865 0.719 0.00 0.04 0.92 0 0.00 0.04
#> TCGA.S9.A7R3.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.FG.A4MX.01 5 0.3647 0.422 0.36 0.00 0.00 0 0.64 0.00
#> TCGA.S9.A7IZ.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.DU.A6S7.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.HT.8114.01 5 0.3706 0.365 0.38 0.00 0.00 0 0.62 0.00
#> TCGA.HW.8321.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.P5.A5F4.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.FG.8191.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.E1.A7YW.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.CS.6666.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.DB.5280.01 1 0.3076 0.751 0.76 0.00 0.00 0 0.24 0.00
#> TCGA.TM.A84T.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.DH.A66D.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.TQ.A7RH.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.P5.A735.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.HT.7609.01 1 0.1556 0.945 0.92 0.00 0.00 0 0.08 0.00
#> TCGA.DB.A75M.01 1 0.2793 0.809 0.80 0.00 0.00 0 0.20 0.00
#> TCGA.HW.A5KM.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.DU.8167.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.S9.A6U1.01 2 0.1814 0.892 0.00 0.90 0.10 0 0.00 0.00
#> TCGA.FG.5965.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.HT.A614.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.DU.6399.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.S9.A7QW.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.HT.7604.01 1 0.1556 0.944 0.92 0.00 0.00 0 0.08 0.00
#> TCGA.P5.A733.01 3 0.3409 0.747 0.00 0.00 0.70 0 0.00 0.30
#> TCGA.HT.7684.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.DH.A7UV.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.HT.7879.01 5 0.1267 0.883 0.06 0.00 0.00 0 0.94 0.00
#> TCGA.DU.A7TC.01 1 0.1556 0.945 0.92 0.00 0.00 0 0.08 0.00
#> TCGA.FG.A60J.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.E1.5303.01 5 0.2631 0.733 0.18 0.00 0.00 0 0.82 0.00
#> TCGA.FN.7833.01 5 0.2793 0.711 0.20 0.00 0.00 0 0.80 0.00
#> TCGA.E1.A7Z4.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.HT.7473.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.DU.7008.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.DB.A75O.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.DU.5872.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.FG.8185.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.S9.A6WE.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.FG.6690.01 5 0.3797 0.180 0.42 0.00 0.00 0 0.58 0.00
#> TCGA.HW.8320.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.E1.5322.01 4 0.0000 1.000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.CS.4942.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.DB.A4X9.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.DB.A4XF.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.HT.A74O.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.HT.7485.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.DB.A64S.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.VV.A86M.01 4 0.0000 1.000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.TQ.A8XE.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.CS.6667.01 3 0.3821 0.800 0.04 0.00 0.74 0 0.00 0.22
#> TCGA.TQ.A7RW.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.DU.A7TI.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.S9.A6U8.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.R8.A6YH.01 1 0.2260 0.884 0.86 0.00 0.00 0 0.14 0.00
#> TCGA.TM.A7CA.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.HT.7690.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.FG.6689.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.TQ.A7RF.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.HT.8013.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.HW.7490.01 5 0.3647 0.401 0.36 0.00 0.00 0 0.64 0.00
#> TCGA.QH.A65S.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.DU.6395.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.P5.A5EW.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.DB.A4XB.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.FG.A4MT.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.FG.A4MT.02 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.QH.A870.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.DU.A7TA.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.TM.A84H.01 4 0.0000 1.000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.S9.A6TZ.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.DB.A4XD.01 1 0.2048 0.906 0.88 0.00 0.00 0 0.12 0.00
#> TCGA.DB.5275.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.HT.A5RB.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.S9.A7R8.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.QH.A6XA.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.DU.A5TP.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.HT.7482.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.TQ.A7RK.02 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.TQ.A7RK.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.HT.7475.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.DU.A7T8.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.FG.7636.01 5 0.2260 0.792 0.14 0.00 0.00 0 0.86 0.00
#> TCGA.WY.A859.01 3 0.3821 0.800 0.04 0.00 0.74 0 0.00 0.22
#> TCGA.S9.A6U9.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.DU.7019.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.S9.A7R4.01 1 0.2260 0.886 0.86 0.00 0.00 0 0.14 0.00
#> TCGA.HT.7676.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.06.6701.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.P5.A5F2.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.WY.A85B.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.S9.A7QX.01 2 0.3076 0.702 0.00 0.76 0.24 0 0.00 0.00
#> TCGA.CS.4943.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.WY.A85D.01 1 0.2454 0.861 0.84 0.00 0.00 0 0.16 0.00
#> TCGA.HT.8108.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.DU.7304.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.P5.A5EV.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.DU.7301.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.TM.A7CF.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.S9.A6U6.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.RY.A845.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.FG.8182.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.QH.A6X3.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.DU.6401.01 2 0.0937 0.955 0.00 0.96 0.04 0 0.00 0.00
#> TCGA.E1.A7YH.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.DU.7306.01 1 0.3309 0.693 0.72 0.00 0.00 0 0.28 0.00
#> TCGA.HT.A74J.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.DB.A4XE.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.DH.A66B.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.DU.5853.01 5 0.0547 0.922 0.02 0.00 0.00 0 0.98 0.00
#> TCGA.TQ.A7RV.01 5 0.0000 0.939 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.HW.A5KL.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.QH.A6X9.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.DU.5871.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.TQ.A7RJ.01 2 0.0547 0.975 0.00 0.98 0.02 0 0.00 0.00
#> TCGA.HT.7483.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.E1.A7Z6.01 2 0.0000 0.993 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.DU.A76O.01 1 0.1267 0.961 0.94 0.00 0.00 0 0.06 0.00
#> TCGA.DU.A5TW.01 2 0.0000 0.993 0.00 1.00 0.00 0 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.HT.7693.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.VM.A8C8.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.F6.A8O4.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.DH.A66G.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.P5.A731.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.DU.6407.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.P5.A5F1.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.VM.A8CF.01 2 0.1006 0.9529 0.02 0.96 0.02 0 0.00 0.00 0.00
#> TCGA.DU.6542.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.DH.5143.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.DU.7299.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.TM.A84Q.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.DB.5281.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.QH.A6CW.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.S9.A6WO.01 1 0.2945 0.6483 0.74 0.00 0.00 0 0.26 0.00 0.00
#> TCGA.HT.7472.01 5 0.0504 0.9190 0.02 0.00 0.00 0 0.98 0.00 0.00
#> TCGA.CS.4938.01 2 0.0504 0.9716 0.02 0.98 0.00 0 0.00 0.00 0.00
#> TCGA.VM.A8CH.01 6 0.0000 0.9755 0.00 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.HT.7476.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.DB.A75L.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.TQ.A8XE.02 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.HW.7493.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.DU.8166.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.HT.7855.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.DU.7015.01 6 0.0504 0.9752 0.00 0.00 0.00 0 0.00 0.98 0.02
#> TCGA.HT.A616.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.HT.7611.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.WY.A85C.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.DB.A4XC.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.P5.A72W.01 5 0.0863 0.9009 0.04 0.00 0.00 0 0.96 0.00 0.00
#> TCGA.S9.A6TU.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.DU.5855.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.HT.7884.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.WY.A85E.01 3 0.0000 -0.0130 0.00 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.FG.6691.01 3 0.4714 0.0284 0.00 0.12 0.60 0 0.00 0.00 0.28
#> TCGA.S9.A7R3.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.FG.A4MX.01 5 0.3358 0.4557 0.36 0.00 0.00 0 0.64 0.00 0.00
#> TCGA.S9.A7IZ.01 2 0.1006 0.9529 0.02 0.96 0.02 0 0.00 0.00 0.00
#> TCGA.DU.A6S7.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.HT.8114.01 5 0.3413 0.4097 0.38 0.00 0.00 0 0.62 0.00 0.00
#> TCGA.HW.8321.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.P5.A5F4.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.FG.8191.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.E1.A7YW.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.CS.6666.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.DB.5280.01 1 0.2832 0.6823 0.76 0.00 0.00 0 0.24 0.00 0.00
#> TCGA.TM.A84T.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.DH.A66D.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.TQ.A7RH.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.P5.A735.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.HT.7609.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.DB.A75M.01 1 0.2572 0.7467 0.80 0.00 0.00 0 0.20 0.00 0.00
#> TCGA.HW.A5KM.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.DU.8167.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.S9.A6U1.01 2 0.3755 0.3282 0.02 0.64 0.34 0 0.00 0.00 0.00
#> TCGA.FG.5965.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.HT.A614.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.DU.6399.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.S9.A7QW.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.HT.7604.01 1 0.1433 0.9020 0.92 0.00 0.00 0 0.08 0.00 0.00
#> TCGA.P5.A733.01 3 0.5546 -0.3036 0.00 0.00 0.42 0 0.00 0.26 0.32
#> TCGA.HT.7684.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.DH.A7UV.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.HT.7879.01 5 0.1433 0.8584 0.08 0.00 0.00 0 0.92 0.00 0.00
#> TCGA.DU.A7TC.01 1 0.0863 0.9406 0.96 0.00 0.00 0 0.04 0.00 0.00
#> TCGA.FG.A60J.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.E1.5303.01 5 0.2572 0.6968 0.20 0.00 0.00 0 0.80 0.00 0.00
#> TCGA.FN.7833.01 5 0.2832 0.6508 0.24 0.00 0.00 0 0.76 0.00 0.00
#> TCGA.E1.A7Z4.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.HT.7473.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.DU.7008.01 2 0.0504 0.9716 0.02 0.98 0.00 0 0.00 0.00 0.00
#> TCGA.DB.A75O.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.DU.5872.01 2 0.0504 0.9716 0.02 0.98 0.00 0 0.00 0.00 0.00
#> TCGA.FG.8185.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.S9.A6WE.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.FG.6690.01 5 0.3546 0.1098 0.46 0.00 0.00 0 0.54 0.00 0.00
#> TCGA.HW.8320.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.E1.5322.01 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.CS.4942.01 2 0.0504 0.9716 0.02 0.98 0.00 0 0.00 0.00 0.00
#> TCGA.DB.A4X9.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.DB.A4XF.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.HT.A74O.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.HT.7485.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.DB.A64S.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.VV.A86M.01 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.TQ.A8XE.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CS.6667.01 7 0.0000 1.0000 0.00 0.00 0.00 0 0.00 0.00 1.00
#> TCGA.TQ.A7RW.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.DU.A7TI.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.S9.A6U8.01 5 0.0504 0.9190 0.02 0.00 0.00 0 0.98 0.00 0.00
#> TCGA.R8.A6YH.01 1 0.1433 0.8975 0.92 0.00 0.00 0 0.08 0.00 0.00
#> TCGA.TM.A7CA.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.HT.7690.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.FG.6689.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.TQ.A7RF.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.HT.8013.01 2 0.0504 0.9716 0.02 0.98 0.00 0 0.00 0.00 0.00
#> TCGA.HW.7490.01 5 0.3358 0.4433 0.36 0.00 0.00 0 0.64 0.00 0.00
#> TCGA.QH.A65S.01 2 0.1006 0.9529 0.02 0.96 0.02 0 0.00 0.00 0.00
#> TCGA.DU.6395.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.P5.A5EW.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.DB.A4XB.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.FG.A4MT.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.FG.A4MT.02 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.QH.A870.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.DU.A7TA.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.TM.A84H.01 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.S9.A6TZ.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.DB.A4XD.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.DB.5275.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.HT.A5RB.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.S9.A7R8.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.QH.A6XA.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.DU.A5TP.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.HT.7482.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.TQ.A7RK.02 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.TQ.A7RK.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.HT.7475.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.DU.A7T8.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.FG.7636.01 5 0.1886 0.8153 0.12 0.00 0.00 0 0.88 0.00 0.00
#> TCGA.WY.A859.01 7 0.0000 1.0000 0.00 0.00 0.00 0 0.00 0.00 1.00
#> TCGA.S9.A6U9.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.DU.7019.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.S9.A7R4.01 1 0.1671 0.8798 0.90 0.00 0.00 0 0.10 0.00 0.00
#> TCGA.HT.7676.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.06.6701.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.P5.A5F2.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.WY.A85B.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.S9.A7QX.01 3 0.3525 0.1355 0.00 0.44 0.56 0 0.00 0.00 0.00
#> TCGA.CS.4943.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.WY.A85D.01 1 0.2259 0.8074 0.84 0.00 0.00 0 0.16 0.00 0.00
#> TCGA.HT.8108.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.DU.7304.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.P5.A5EV.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.DU.7301.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.TM.A7CF.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.S9.A6U6.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.RY.A845.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.FG.8182.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.QH.A6X3.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.DU.6401.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.E1.A7YH.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.DU.7306.01 1 0.2572 0.7499 0.80 0.00 0.00 0 0.20 0.00 0.00
#> TCGA.HT.A74J.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.DB.A4XE.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.DH.A66B.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.DU.5853.01 5 0.0504 0.9184 0.02 0.00 0.00 0 0.98 0.00 0.00
#> TCGA.TQ.A7RV.01 5 0.0000 0.9356 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.HW.A5KL.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.QH.A6X9.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.DU.5871.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.TQ.A7RJ.01 2 0.1006 0.9529 0.02 0.96 0.02 0 0.00 0.00 0.00
#> TCGA.HT.7483.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.E1.A7Z6.01 2 0.0000 0.9865 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.DU.A76O.01 1 0.0504 0.9593 0.98 0.00 0.00 0 0.02 0.00 0.00
#> TCGA.DU.A5TW.01 2 0.0504 0.9716 0.02 0.98 0.00 0 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.HT.7693.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8C8.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F6.A8O4.01 5 0.0808 0.897 0.04 0.00 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.DH.A66G.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A731.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6407.01 2 0.1887 0.896 0.00 0.90 0.06 0.00 0.00 0.00 0.00 0.04
#> TCGA.P5.A5F1.01 5 0.1091 0.880 0.06 0.00 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.VM.A8CF.01 2 0.1887 0.896 0.00 0.90 0.06 0.00 0.00 0.00 0.00 0.04
#> TCGA.DU.6542.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DH.5143.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7299.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.TM.A84Q.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.DB.5281.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.QH.A6CW.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.S9.A6WO.01 1 0.2267 0.769 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.HT.7472.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CS.4938.01 2 0.0471 0.956 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.VM.A8CH.01 6 0.0000 0.754 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7476.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.DB.A75L.01 2 0.0941 0.945 0.00 0.96 0.02 0.00 0.00 0.00 0.00 0.02
#> TCGA.TQ.A8XE.02 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HW.7493.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.8166.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7855.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.DU.7015.01 6 0.3169 0.720 0.02 0.00 0.00 0.00 0.00 0.78 0.02 0.18
#> TCGA.HT.A616.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7611.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.WY.A85C.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.DB.A4XC.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A72W.01 5 0.1091 0.879 0.06 0.00 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.S9.A6TU.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.DU.5855.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7884.01 2 0.0471 0.956 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.WY.A85E.01 3 0.1765 -0.450 0.00 0.00 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.FG.6691.01 8 0.1275 0.761 0.00 0.00 0.04 0.00 0.00 0.00 0.02 0.94
#> TCGA.S9.A7R3.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A4MX.01 5 0.3272 0.317 0.42 0.00 0.00 0.00 0.58 0.00 0.00 0.00
#> TCGA.S9.A7IZ.01 2 0.2674 0.847 0.00 0.86 0.06 0.04 0.00 0.00 0.00 0.04
#> TCGA.DU.A6S7.01 2 0.1275 0.932 0.00 0.94 0.04 0.00 0.00 0.00 0.00 0.02
#> TCGA.HT.8114.01 5 0.3193 0.425 0.38 0.00 0.00 0.00 0.62 0.00 0.00 0.00
#> TCGA.HW.8321.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A5F4.01 2 0.0471 0.956 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.FG.8191.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YW.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CS.6666.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.DB.5280.01 1 0.2267 0.773 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.TM.A84T.01 5 0.0471 0.913 0.02 0.00 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.DH.A66D.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RH.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A735.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7609.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.DB.A75M.01 1 0.2267 0.770 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.HW.A5KM.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.8167.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6U1.01 2 0.4786 -0.208 0.00 0.48 0.14 0.00 0.00 0.00 0.00 0.38
#> TCGA.FG.5965.01 2 0.0471 0.956 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.HT.A614.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.6399.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.S9.A7QW.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7604.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.P5.A733.01 8 0.2859 0.727 0.02 0.00 0.00 0.00 0.00 0.14 0.02 0.82
#> TCGA.HT.7684.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DH.A7UV.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.HT.7879.01 5 0.1765 0.814 0.12 0.00 0.00 0.00 0.88 0.00 0.00 0.00
#> TCGA.DU.A7TC.01 1 0.0808 0.949 0.96 0.00 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.FG.A60J.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5303.01 5 0.1765 0.807 0.12 0.00 0.00 0.00 0.88 0.00 0.00 0.00
#> TCGA.FN.7833.01 5 0.2756 0.620 0.26 0.00 0.00 0.00 0.74 0.00 0.00 0.00
#> TCGA.E1.A7Z4.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7473.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7008.01 2 0.1275 0.932 0.00 0.94 0.04 0.00 0.00 0.00 0.00 0.02
#> TCGA.DB.A75O.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.5872.01 2 0.0471 0.956 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.FG.8185.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.S9.A6WE.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.6690.01 5 0.3272 0.268 0.42 0.00 0.00 0.00 0.58 0.00 0.00 0.00
#> TCGA.HW.8320.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.E1.5322.01 4 0.0000 0.992 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.4942.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4X9.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4XF.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A74O.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.HT.7485.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.A64S.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.VV.A86M.01 4 0.0471 0.984 0.00 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.TQ.A8XE.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6667.01 7 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.TQ.A7RW.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.A7TI.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6U8.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.R8.A6YH.01 1 0.1341 0.905 0.92 0.00 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.TM.A7CA.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7690.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.6689.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RF.01 2 0.1275 0.933 0.00 0.94 0.02 0.00 0.00 0.00 0.00 0.04
#> TCGA.HT.8013.01 2 0.0941 0.946 0.00 0.96 0.02 0.00 0.00 0.00 0.00 0.02
#> TCGA.HW.7490.01 5 0.3272 0.293 0.42 0.00 0.00 0.00 0.58 0.00 0.00 0.00
#> TCGA.QH.A65S.01 2 0.1887 0.896 0.00 0.90 0.06 0.00 0.00 0.00 0.00 0.04
#> TCGA.DU.6395.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A5EW.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4XB.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.A4MT.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A4MT.02 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A870.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A7TA.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.TM.A84H.01 4 0.0000 0.992 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TZ.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4XD.01 1 0.0808 0.949 0.96 0.00 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.DB.5275.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.HT.A5RB.01 5 0.0471 0.913 0.02 0.00 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.S9.A7R8.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6XA.01 2 0.1275 0.932 0.00 0.94 0.04 0.00 0.00 0.00 0.00 0.02
#> TCGA.DU.A5TP.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7482.01 2 0.0941 0.945 0.00 0.96 0.02 0.00 0.00 0.00 0.00 0.02
#> TCGA.TQ.A7RK.02 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.TQ.A7RK.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.HT.7475.01 5 0.0471 0.913 0.02 0.00 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.DU.A7T8.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.7636.01 5 0.2267 0.740 0.18 0.00 0.00 0.00 0.82 0.00 0.00 0.00
#> TCGA.WY.A859.01 7 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A6U9.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.DU.7019.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.S9.A7R4.01 1 0.1091 0.930 0.94 0.00 0.00 0.00 0.06 0.00 0.00 0.00
#> TCGA.HT.7676.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.06.6701.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.P5.A5F2.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WY.A85B.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.S9.A7QX.01 3 0.3193 0.121 0.00 0.38 0.62 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.4943.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.WY.A85D.01 1 0.1341 0.905 0.92 0.00 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.HT.8108.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7304.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.P5.A5EV.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7301.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.TM.A7CF.01 2 0.0471 0.956 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.S9.A6U6.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.RY.A845.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8182.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.QH.A6X3.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.DU.6401.01 2 0.1275 0.932 0.00 0.94 0.04 0.00 0.00 0.00 0.00 0.02
#> TCGA.E1.A7YH.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7306.01 1 0.2756 0.630 0.74 0.00 0.00 0.00 0.26 0.00 0.00 0.00
#> TCGA.HT.A74J.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.A4XE.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A66B.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.DU.5853.01 5 0.1275 0.882 0.04 0.00 0.02 0.00 0.94 0.00 0.00 0.00
#> TCGA.TQ.A7RV.01 5 0.0000 0.927 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HW.A5KL.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6X9.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5871.01 2 0.1275 0.933 0.00 0.94 0.04 0.00 0.00 0.00 0.00 0.02
#> TCGA.TQ.A7RJ.01 2 0.1887 0.896 0.00 0.90 0.06 0.00 0.00 0.00 0.00 0.04
#> TCGA.HT.7483.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.E1.A7Z6.01 2 0.0471 0.956 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DU.A76O.01 1 0.0471 0.968 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.DU.A5TW.01 2 0.1887 0.896 0.00 0.90 0.06 0.00 0.00 0.00 0.00 0.04
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111 , Node0112 , Node0113 , Node0121 , Node0122 , Node0123-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0141 , Node0142-leaf , Node0143 , Node0211-leaf , Node0212-leaf , Node0213-leaf , Node0214-leaf , Node0221 , Node0222 , Node0223 , Node0231 , Node0232-leaf , Node0233-leaf , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0323-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 133 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 0.995 0.998 0.4802 0.520 0.520
#> 3 3 0.983 0.965 0.985 0.3705 0.699 0.482
#> 4 4 0.847 0.879 0.935 0.1149 0.891 0.692
#> 5 5 0.796 0.768 0.857 0.0704 0.914 0.693
#> 6 6 0.786 0.690 0.822 0.0438 0.892 0.560
#> 7 7 0.758 0.636 0.785 0.0311 0.971 0.835
#> 8 8 0.804 0.678 0.822 0.0206 0.947 0.702
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.S9.A7J2.01 1 0.000 0.998 1.00 0.00
#> TCGA.S9.A6TX.01 1 0.000 0.998 1.00 0.00
#> TCGA.HT.A74L.01 1 0.000 0.998 1.00 0.00
#> TCGA.E1.5311.01 1 0.000 0.998 1.00 0.00
#> TCGA.HT.7480.01 1 0.000 0.998 1.00 0.00
#> TCGA.S9.A7R1.01 1 0.000 0.998 1.00 0.00
#> TCGA.FG.A710.01 1 0.000 0.998 1.00 0.00
#> TCGA.DU.A6S6.01 1 0.000 0.998 1.00 0.00
#> TCGA.FG.7634.01 1 0.000 0.998 1.00 0.00
#> TCGA.FG.7638.01 1 0.000 0.998 1.00 0.00
#> TCGA.FG.A6J1.01 1 0.000 0.998 1.00 0.00
#> TCGA.HT.7608.01 1 0.000 0.998 1.00 0.00
#> TCGA.W9.A837.01 1 0.000 0.998 1.00 0.00
#> TCGA.TM.A7C5.01 2 0.402 0.915 0.08 0.92
#> TCGA.P5.A5ET.01 1 0.000 0.998 1.00 0.00
#> TCGA.P5.A77X.01 1 0.000 0.998 1.00 0.00
#> TCGA.FG.A6IZ.01 2 0.000 0.996 0.00 1.00
#> TCGA.KT.A74X.01 1 0.000 0.998 1.00 0.00
#> TCGA.E1.A7YO.01 1 0.000 0.998 1.00 0.00
#> TCGA.TQ.A7RG.01 1 0.000 0.998 1.00 0.00
#> TCGA.RY.A847.01 1 0.000 0.998 1.00 0.00
#> TCGA.VM.A8CA.01 1 0.000 0.998 1.00 0.00
#> TCGA.DB.A4XG.01 1 0.000 0.998 1.00 0.00
#> TCGA.FG.A60K.01 1 0.000 0.998 1.00 0.00
#> TCGA.S9.A6TY.01 2 0.000 0.996 0.00 1.00
#> TCGA.TQ.A7RQ.01 1 0.000 0.998 1.00 0.00
#> TCGA.IK.8125.01 2 0.000 0.996 0.00 1.00
#> TCGA.HT.A74K.01 2 0.000 0.996 0.00 1.00
#> TCGA.QH.A6X8.01 2 0.000 0.996 0.00 1.00
#> TCGA.HT.7681.01 1 0.000 0.998 1.00 0.00
#> TCGA.P5.A72Z.01 2 0.000 0.996 0.00 1.00
#> TCGA.DU.8168.01 2 0.000 0.996 0.00 1.00
#> TCGA.TQ.A7RN.01 1 0.000 0.998 1.00 0.00
#> TCGA.DH.5141.01 1 0.000 0.998 1.00 0.00
#> TCGA.EZ.7264.01 1 0.000 0.998 1.00 0.00
#> TCGA.QH.A65V.01 1 0.000 0.998 1.00 0.00
#> TCGA.DU.A6S8.01 1 0.000 0.998 1.00 0.00
#> TCGA.DU.7298.01 1 0.000 0.998 1.00 0.00
#> TCGA.DB.A64R.01 1 0.000 0.998 1.00 0.00
#> TCGA.CS.5390.01 2 0.000 0.996 0.00 1.00
#> TCGA.S9.A6WP.01 2 0.000 0.996 0.00 1.00
#> TCGA.E1.A7YS.01 2 0.000 0.996 0.00 1.00
#> TCGA.DU.7294.01 1 0.000 0.998 1.00 0.00
#> TCGA.HT.7695.01 1 0.000 0.998 1.00 0.00
#> TCGA.FG.7637.01 1 0.000 0.998 1.00 0.00
#> TCGA.S9.A6U5.01 1 0.000 0.998 1.00 0.00
#> TCGA.DB.5274.01 2 0.000 0.996 0.00 1.00
#> TCGA.HW.7487.01 1 0.000 0.998 1.00 0.00
#> TCGA.HW.7491.01 1 0.327 0.937 0.94 0.06
#> TCGA.HT.8012.01 1 0.000 0.998 1.00 0.00
#> TCGA.S9.A7QZ.01 2 0.000 0.996 0.00 1.00
#> TCGA.QH.A6X4.01 1 0.000 0.998 1.00 0.00
#> TCGA.P5.A77W.01 2 0.000 0.996 0.00 1.00
#> TCGA.DU.7302.01 2 0.000 0.996 0.00 1.00
#> TCGA.HW.7495.01 1 0.000 0.998 1.00 0.00
#> TCGA.QH.A65R.01 2 0.000 0.996 0.00 1.00
#> TCGA.HT.7875.01 1 0.000 0.998 1.00 0.00
#> TCGA.DU.6394.01 2 0.000 0.996 0.00 1.00
#> TCGA.S9.A6WD.01 2 0.000 0.996 0.00 1.00
#> TCGA.TQ.A7RU.01 2 0.000 0.996 0.00 1.00
#> TCGA.DU.5874.01 2 0.000 0.996 0.00 1.00
#> TCGA.R8.A6MK.01 1 0.000 0.998 1.00 0.00
#> TCGA.S9.A7J1.01 1 0.000 0.998 1.00 0.00
#> TCGA.P5.A5F0.01 1 0.000 0.998 1.00 0.00
#> TCGA.R8.A73M.01 1 0.000 0.998 1.00 0.00
#> TCGA.DU.A6S3.01 2 0.000 0.996 0.00 1.00
#> TCGA.DB.A4XH.01 2 0.000 0.996 0.00 1.00
#> TCGA.VW.A7QS.01 1 0.000 0.998 1.00 0.00
#> TCGA.DU.8164.01 2 0.000 0.996 0.00 1.00
#> TCGA.HT.7468.01 1 0.000 0.998 1.00 0.00
#> TCGA.TQ.A7RI.01 1 0.000 0.998 1.00 0.00
#> TCGA.DB.5279.01 2 0.141 0.978 0.02 0.98
#> TCGA.DU.7018.01 2 0.000 0.996 0.00 1.00
#> TCGA.HT.7677.01 2 0.402 0.915 0.08 0.92
#> TCGA.TM.A84M.01 1 0.000 0.998 1.00 0.00
#> TCGA.F6.A8O3.01 1 0.000 0.998 1.00 0.00
#> TCGA.QH.A86X.01 1 0.000 0.998 1.00 0.00
#> TCGA.DU.A76R.01 1 0.000 0.998 1.00 0.00
#> TCGA.DH.5144.01 2 0.000 0.996 0.00 1.00
#> TCGA.RY.A840.01 1 0.000 0.998 1.00 0.00
#> TCGA.HW.A5KJ.01 2 0.000 0.996 0.00 1.00
#> TCGA.HT.8105.01 2 0.000 0.996 0.00 1.00
#> TCGA.HT.7471.01 2 0.000 0.996 0.00 1.00
#> TCGA.HT.A619.01 2 0.000 0.996 0.00 1.00
#> TCGA.HT.A5R9.01 2 0.000 0.996 0.00 1.00
#> TCGA.CS.5396.01 1 0.000 0.998 1.00 0.00
#> TCGA.DU.6400.01 2 0.000 0.996 0.00 1.00
#> TCGA.S9.A6WL.01 2 0.000 0.996 0.00 1.00
#> TCGA.DB.A75K.01 1 0.000 0.998 1.00 0.00
#> TCGA.DB.A64Q.01 1 0.000 0.998 1.00 0.00
#> TCGA.P5.A737.01 1 0.000 0.998 1.00 0.00
#> TCGA.S9.A6WH.01 2 0.000 0.996 0.00 1.00
#> TCGA.HT.7616.01 2 0.000 0.996 0.00 1.00
#> TCGA.RY.A83Y.01 2 0.000 0.996 0.00 1.00
#> TCGA.DB.A64U.01 1 0.000 0.998 1.00 0.00
#> TCGA.DB.A64W.01 2 0.000 0.996 0.00 1.00
#> TCGA.R8.A6MO.01 2 0.000 0.996 0.00 1.00
#> TCGA.HW.8322.01 1 0.000 0.998 1.00 0.00
#> TCGA.DU.5870.02 1 0.327 0.937 0.94 0.06
#> TCGA.CS.6668.01 2 0.000 0.996 0.00 1.00
#> TCGA.DU.5870.01 1 0.000 0.998 1.00 0.00
#> TCGA.HT.7692.01 1 0.000 0.998 1.00 0.00
#> TCGA.R8.A6ML.01 1 0.141 0.979 0.98 0.02
#> TCGA.DU.6410.01 2 0.000 0.996 0.00 1.00
#> TCGA.TQ.A7RO.01 1 0.000 0.998 1.00 0.00
#> TCGA.E1.5318.01 2 0.000 0.996 0.00 1.00
#> TCGA.S9.A7J3.01 2 0.000 0.996 0.00 1.00
#> TCGA.TQ.A7RS.01 1 0.000 0.998 1.00 0.00
#> TCGA.QH.A65Z.01 2 0.000 0.996 0.00 1.00
#> TCGA.P5.A730.01 1 0.000 0.998 1.00 0.00
#> TCGA.RY.A83X.01 1 0.000 0.998 1.00 0.00
#> TCGA.S9.A6UB.01 2 0.000 0.996 0.00 1.00
#> TCGA.DH.A66F.01 1 0.000 0.998 1.00 0.00
#> TCGA.DU.6393.01 2 0.000 0.996 0.00 1.00
#> TCGA.S9.A7IY.01 1 0.000 0.998 1.00 0.00
#> TCGA.FG.7641.01 1 0.000 0.998 1.00 0.00
#> TCGA.DU.7009.01 1 0.000 0.998 1.00 0.00
#> TCGA.FG.8186.01 1 0.000 0.998 1.00 0.00
#> TCGA.DB.A64L.01 2 0.000 0.996 0.00 1.00
#> TCGA.VV.A829.01 1 0.000 0.998 1.00 0.00
#> TCGA.DU.6397.02 1 0.000 0.998 1.00 0.00
#> TCGA.DU.6397.01 1 0.000 0.998 1.00 0.00
#> TCGA.CS.6670.01 1 0.000 0.998 1.00 0.00
#> TCGA.QH.A65X.01 1 0.000 0.998 1.00 0.00
#> TCGA.DB.A64P.01 1 0.000 0.998 1.00 0.00
#> TCGA.QH.A6CZ.01 1 0.000 0.998 1.00 0.00
#> TCGA.DH.A669.02 2 0.000 0.996 0.00 1.00
#> TCGA.DH.A669.01 2 0.000 0.996 0.00 1.00
#> TCGA.VM.A8CB.01 1 0.000 0.998 1.00 0.00
#> TCGA.HT.7687.01 2 0.000 0.996 0.00 1.00
#> TCGA.TM.A84G.01 2 0.000 0.996 0.00 1.00
#> TCGA.CS.5394.01 2 0.000 0.996 0.00 1.00
#> TCGA.FG.5962.01 1 0.000 0.998 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.S9.A7J2.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.S9.A6TX.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.HT.A74L.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.E1.5311.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.HT.7480.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.S9.A7R1.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.FG.A710.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.DU.A6S6.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.FG.7634.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.FG.7638.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.FG.A6J1.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.HT.7608.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.W9.A837.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.TM.A7C5.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.P5.A5ET.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.P5.A77X.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.FG.A6IZ.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.KT.A74X.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.E1.A7YO.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.TQ.A7RG.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.RY.A847.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.VM.A8CA.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.DB.A4XG.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.FG.A60K.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.S9.A6TY.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.TQ.A7RQ.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.IK.8125.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.HT.A74K.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.QH.A6X8.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.HT.7681.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.P5.A72Z.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.DU.8168.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.TQ.A7RN.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.DH.5141.01 3 0.2959 0.873 0.10 0.00 0.90
#> TCGA.EZ.7264.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.QH.A65V.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.DU.A6S8.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.DU.7298.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.DB.A64R.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.CS.5390.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.S9.A6WP.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.E1.A7YS.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.DU.7294.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.HT.7695.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.FG.7637.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.S9.A6U5.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.DB.5274.01 2 0.2959 0.895 0.00 0.90 0.10
#> TCGA.HW.7487.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.HW.7491.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.HT.8012.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.S9.A7QZ.01 2 0.2959 0.895 0.00 0.90 0.10
#> TCGA.QH.A6X4.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.P5.A77W.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.DU.7302.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.HW.7495.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.QH.A65R.01 2 0.0892 0.961 0.00 0.98 0.02
#> TCGA.HT.7875.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.DU.6394.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.S9.A6WD.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.TQ.A7RU.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.DU.5874.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.R8.A6MK.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.S9.A7J1.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.P5.A5F0.01 3 0.2537 0.896 0.08 0.00 0.92
#> TCGA.R8.A73M.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.DU.A6S3.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.DB.A4XH.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.VW.A7QS.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.DU.8164.01 2 0.5560 0.611 0.00 0.70 0.30
#> TCGA.HT.7468.01 1 0.0892 0.971 0.98 0.00 0.02
#> TCGA.TQ.A7RI.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.DB.5279.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.DU.7018.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.HT.7677.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.TM.A84M.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.F6.A8O3.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.QH.A86X.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.DU.A76R.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.DH.5144.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.RY.A840.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.HW.A5KJ.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.HT.8105.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.HT.7471.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.HT.A619.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.HT.A5R9.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.CS.5396.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.DU.6400.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.S9.A6WL.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.DB.A75K.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.DB.A64Q.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.P5.A737.01 3 0.2066 0.920 0.06 0.00 0.94
#> TCGA.S9.A6WH.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.HT.7616.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.RY.A83Y.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.DB.A64U.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.DB.A64W.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.R8.A6MO.01 3 0.0892 0.963 0.00 0.02 0.98
#> TCGA.HW.8322.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.DU.5870.02 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.CS.6668.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.DU.5870.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.HT.7692.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.R8.A6ML.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.DU.6410.01 2 0.2959 0.894 0.00 0.90 0.10
#> TCGA.TQ.A7RO.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.E1.5318.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.S9.A7J3.01 2 0.0892 0.961 0.00 0.98 0.02
#> TCGA.TQ.A7RS.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.QH.A65Z.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.P5.A730.01 1 0.5948 0.421 0.64 0.00 0.36
#> TCGA.RY.A83X.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.S9.A6UB.01 2 0.5016 0.716 0.00 0.76 0.24
#> TCGA.DH.A66F.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.DU.6393.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.S9.A7IY.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.FG.7641.01 3 0.6244 0.213 0.44 0.00 0.56
#> TCGA.DU.7009.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.FG.8186.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.DB.A64L.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.VV.A829.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.DU.6397.02 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.DU.6397.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.CS.6670.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.QH.A65X.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.DB.A64P.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.QH.A6CZ.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.DH.A669.02 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.DH.A669.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.VM.A8CB.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.HT.7687.01 2 0.0000 0.972 0.00 1.00 0.00
#> TCGA.TM.A84G.01 3 0.0000 0.982 0.00 0.00 1.00
#> TCGA.CS.5394.01 2 0.0892 0.961 0.00 0.98 0.02
#> TCGA.FG.5962.01 3 0.0000 0.982 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.S9.A7J2.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.S9.A6TX.01 3 0.2345 0.898 0.00 0.00 0.90 0.10
#> TCGA.HT.A74L.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.E1.5311.01 3 0.1637 0.927 0.00 0.00 0.94 0.06
#> TCGA.HT.7480.01 3 0.1637 0.927 0.00 0.00 0.94 0.06
#> TCGA.S9.A7R1.01 3 0.1637 0.927 0.00 0.00 0.94 0.06
#> TCGA.FG.A710.01 4 0.4277 0.665 0.28 0.00 0.00 0.72
#> TCGA.DU.A6S6.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.FG.7634.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.FG.7638.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.FG.A6J1.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.HT.7608.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.W9.A837.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.TM.A7C5.01 3 0.0000 0.922 0.00 0.00 1.00 0.00
#> TCGA.P5.A5ET.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.P5.A77X.01 1 0.0707 0.964 0.98 0.00 0.00 0.02
#> TCGA.FG.A6IZ.01 2 0.0000 0.896 0.00 1.00 0.00 0.00
#> TCGA.KT.A74X.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YO.01 3 0.1637 0.927 0.00 0.00 0.94 0.06
#> TCGA.TQ.A7RG.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.RY.A847.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.VM.A8CA.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.DB.A4XG.01 3 0.1637 0.927 0.00 0.00 0.94 0.06
#> TCGA.FG.A60K.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.S9.A6TY.01 3 0.0000 0.922 0.00 0.00 1.00 0.00
#> TCGA.TQ.A7RQ.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.IK.8125.01 4 0.3610 0.721 0.00 0.00 0.20 0.80
#> TCGA.HT.A74K.01 4 0.3172 0.761 0.00 0.00 0.16 0.84
#> TCGA.QH.A6X8.01 2 0.0000 0.896 0.00 1.00 0.00 0.00
#> TCGA.HT.7681.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.P5.A72Z.01 2 0.2921 0.817 0.00 0.86 0.00 0.14
#> TCGA.DU.8168.01 2 0.0000 0.896 0.00 1.00 0.00 0.00
#> TCGA.TQ.A7RN.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.DH.5141.01 3 0.4227 0.805 0.12 0.00 0.82 0.06
#> TCGA.EZ.7264.01 4 0.0000 0.848 0.00 0.00 0.00 1.00
#> TCGA.QH.A65V.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.DU.A6S8.01 4 0.0000 0.848 0.00 0.00 0.00 1.00
#> TCGA.DU.7298.01 3 0.1637 0.927 0.00 0.00 0.94 0.06
#> TCGA.DB.A64R.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.CS.5390.01 2 0.0000 0.896 0.00 1.00 0.00 0.00
#> TCGA.S9.A6WP.01 3 0.0000 0.922 0.00 0.00 1.00 0.00
#> TCGA.E1.A7YS.01 2 0.0000 0.896 0.00 1.00 0.00 0.00
#> TCGA.DU.7294.01 3 0.1637 0.927 0.00 0.00 0.94 0.06
#> TCGA.HT.7695.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.FG.7637.01 1 0.1637 0.912 0.94 0.00 0.06 0.00
#> TCGA.S9.A6U5.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.DB.5274.01 2 0.4855 0.488 0.00 0.60 0.40 0.00
#> TCGA.HW.7487.01 3 0.1637 0.927 0.00 0.00 0.94 0.06
#> TCGA.HW.7491.01 3 0.1211 0.927 0.00 0.00 0.96 0.04
#> TCGA.HT.8012.01 3 0.1637 0.927 0.00 0.00 0.94 0.06
#> TCGA.S9.A7QZ.01 2 0.6617 0.612 0.00 0.60 0.28 0.12
#> TCGA.QH.A6X4.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.P5.A77W.01 3 0.0000 0.922 0.00 0.00 1.00 0.00
#> TCGA.DU.7302.01 2 0.3821 0.816 0.00 0.84 0.04 0.12
#> TCGA.HW.7495.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.QH.A65R.01 2 0.4406 0.663 0.00 0.70 0.30 0.00
#> TCGA.HT.7875.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.DU.6394.01 2 0.0000 0.896 0.00 1.00 0.00 0.00
#> TCGA.S9.A6WD.01 4 0.3975 0.669 0.00 0.00 0.24 0.76
#> TCGA.TQ.A7RU.01 3 0.0000 0.922 0.00 0.00 1.00 0.00
#> TCGA.DU.5874.01 2 0.0000 0.896 0.00 1.00 0.00 0.00
#> TCGA.R8.A6MK.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.S9.A7J1.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.P5.A5F0.01 3 0.4731 0.752 0.16 0.00 0.78 0.06
#> TCGA.R8.A73M.01 3 0.1637 0.927 0.00 0.00 0.94 0.06
#> TCGA.DU.A6S3.01 3 0.0000 0.922 0.00 0.00 1.00 0.00
#> TCGA.DB.A4XH.01 2 0.0000 0.896 0.00 1.00 0.00 0.00
#> TCGA.VW.A7QS.01 4 0.3037 0.792 0.02 0.00 0.10 0.88
#> TCGA.DU.8164.01 2 0.6808 0.557 0.00 0.56 0.32 0.12
#> TCGA.HT.7468.01 4 0.2921 0.806 0.14 0.00 0.00 0.86
#> TCGA.TQ.A7RI.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.DB.5279.01 4 0.0000 0.848 0.00 0.00 0.00 1.00
#> TCGA.DU.7018.01 2 0.0000 0.896 0.00 1.00 0.00 0.00
#> TCGA.HT.7677.01 3 0.0000 0.922 0.00 0.00 1.00 0.00
#> TCGA.TM.A84M.01 4 0.0000 0.848 0.00 0.00 0.00 1.00
#> TCGA.F6.A8O3.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.QH.A86X.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.DU.A76R.01 1 0.4907 0.150 0.58 0.00 0.00 0.42
#> TCGA.DH.5144.01 3 0.0000 0.922 0.00 0.00 1.00 0.00
#> TCGA.RY.A840.01 4 0.4713 0.521 0.36 0.00 0.00 0.64
#> TCGA.HW.A5KJ.01 2 0.0000 0.896 0.00 1.00 0.00 0.00
#> TCGA.HT.8105.01 2 0.0000 0.896 0.00 1.00 0.00 0.00
#> TCGA.HT.7471.01 3 0.0000 0.922 0.00 0.00 1.00 0.00
#> TCGA.HT.A619.01 2 0.0000 0.896 0.00 1.00 0.00 0.00
#> TCGA.HT.A5R9.01 3 0.0000 0.922 0.00 0.00 1.00 0.00
#> TCGA.CS.5396.01 4 0.0707 0.847 0.02 0.00 0.00 0.98
#> TCGA.DU.6400.01 2 0.0000 0.896 0.00 1.00 0.00 0.00
#> TCGA.S9.A6WL.01 2 0.1637 0.870 0.00 0.94 0.06 0.00
#> TCGA.DB.A75K.01 3 0.1637 0.927 0.00 0.00 0.94 0.06
#> TCGA.DB.A64Q.01 4 0.3610 0.762 0.20 0.00 0.00 0.80
#> TCGA.P5.A737.01 4 0.4332 0.782 0.16 0.00 0.04 0.80
#> TCGA.S9.A6WH.01 2 0.0000 0.896 0.00 1.00 0.00 0.00
#> TCGA.HT.7616.01 2 0.1637 0.868 0.00 0.94 0.00 0.06
#> TCGA.RY.A83Y.01 3 0.0707 0.925 0.00 0.00 0.98 0.02
#> TCGA.DB.A64U.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.DB.A64W.01 2 0.0000 0.896 0.00 1.00 0.00 0.00
#> TCGA.R8.A6MO.01 3 0.0000 0.922 0.00 0.00 1.00 0.00
#> TCGA.HW.8322.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.DU.5870.02 4 0.0000 0.848 0.00 0.00 0.00 1.00
#> TCGA.CS.6668.01 4 0.0000 0.848 0.00 0.00 0.00 1.00
#> TCGA.DU.5870.01 4 0.4977 0.271 0.46 0.00 0.00 0.54
#> TCGA.HT.7692.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.R8.A6ML.01 4 0.1637 0.822 0.00 0.00 0.06 0.94
#> TCGA.DU.6410.01 2 0.5863 0.714 0.00 0.70 0.18 0.12
#> TCGA.TQ.A7RO.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.E1.5318.01 2 0.0000 0.896 0.00 1.00 0.00 0.00
#> TCGA.S9.A7J3.01 2 0.4227 0.806 0.00 0.82 0.06 0.12
#> TCGA.TQ.A7RS.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.QH.A65Z.01 3 0.0000 0.922 0.00 0.00 1.00 0.00
#> TCGA.P5.A730.01 3 0.4277 0.601 0.28 0.00 0.72 0.00
#> TCGA.RY.A83X.01 3 0.1637 0.927 0.00 0.00 0.94 0.06
#> TCGA.S9.A6UB.01 2 0.6617 0.613 0.00 0.60 0.28 0.12
#> TCGA.DH.A66F.01 3 0.3198 0.884 0.04 0.00 0.88 0.08
#> TCGA.DU.6393.01 2 0.0000 0.896 0.00 1.00 0.00 0.00
#> TCGA.S9.A7IY.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.FG.7641.01 3 0.5489 0.630 0.24 0.00 0.70 0.06
#> TCGA.DU.7009.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.FG.8186.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.DB.A64L.01 2 0.2647 0.830 0.00 0.88 0.00 0.12
#> TCGA.VV.A829.01 4 0.0000 0.848 0.00 0.00 0.00 1.00
#> TCGA.DU.6397.02 4 0.2647 0.815 0.12 0.00 0.00 0.88
#> TCGA.DU.6397.01 1 0.2011 0.889 0.92 0.00 0.00 0.08
#> TCGA.CS.6670.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.QH.A65X.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.DB.A64P.01 3 0.1637 0.927 0.00 0.00 0.94 0.06
#> TCGA.QH.A6CZ.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.DH.A669.02 2 0.0000 0.896 0.00 1.00 0.00 0.00
#> TCGA.DH.A669.01 2 0.0000 0.896 0.00 1.00 0.00 0.00
#> TCGA.VM.A8CB.01 1 0.0000 0.985 1.00 0.00 0.00 0.00
#> TCGA.HT.7687.01 2 0.0000 0.896 0.00 1.00 0.00 0.00
#> TCGA.TM.A84G.01 3 0.3172 0.763 0.00 0.00 0.84 0.16
#> TCGA.CS.5394.01 2 0.4406 0.663 0.00 0.70 0.30 0.00
#> TCGA.FG.5962.01 4 0.0000 0.848 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.S9.A7J2.01 1 0.0000 0.867 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TX.01 3 0.0000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.A74L.01 1 0.0000 0.867 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5311.01 3 0.0000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7480.01 3 0.0000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A7R1.01 3 0.0000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.FG.A710.01 4 0.1410 0.708 0.06 0.00 0.00 0.94 0.00
#> TCGA.DU.A6S6.01 1 0.0000 0.867 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7634.01 1 0.0000 0.867 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7638.01 1 0.2331 0.847 0.90 0.00 0.02 0.08 0.00
#> TCGA.FG.A6J1.01 1 0.2012 0.853 0.92 0.00 0.02 0.06 0.00
#> TCGA.HT.7608.01 1 0.3895 0.730 0.68 0.00 0.00 0.32 0.00
#> TCGA.W9.A837.01 1 0.3895 0.730 0.68 0.00 0.00 0.32 0.00
#> TCGA.TM.A7C5.01 3 0.0609 0.896 0.00 0.00 0.98 0.00 0.02
#> TCGA.P5.A5ET.01 1 0.0000 0.867 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A77X.01 1 0.3895 0.730 0.68 0.00 0.00 0.32 0.00
#> TCGA.FG.A6IZ.01 2 0.0000 0.932 0.00 1.00 0.00 0.00 0.00
#> TCGA.KT.A74X.01 1 0.3561 0.764 0.74 0.00 0.00 0.26 0.00
#> TCGA.E1.A7YO.01 3 0.0000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.TQ.A7RG.01 1 0.0609 0.867 0.98 0.00 0.00 0.02 0.00
#> TCGA.RY.A847.01 1 0.1732 0.855 0.92 0.00 0.00 0.08 0.00
#> TCGA.VM.A8CA.01 1 0.3895 0.730 0.68 0.00 0.00 0.32 0.00
#> TCGA.DB.A4XG.01 3 0.0000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.FG.A60K.01 1 0.0609 0.867 0.98 0.00 0.00 0.02 0.00
#> TCGA.S9.A6TY.01 5 0.4302 0.360 0.00 0.00 0.48 0.00 0.52
#> TCGA.TQ.A7RQ.01 1 0.4252 0.742 0.70 0.00 0.02 0.28 0.00
#> TCGA.IK.8125.01 5 0.1648 0.515 0.00 0.00 0.02 0.04 0.94
#> TCGA.HT.A74K.01 5 0.1043 0.487 0.00 0.00 0.00 0.04 0.96
#> TCGA.QH.A6X8.01 2 0.0000 0.932 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7681.01 1 0.0000 0.867 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A72Z.01 2 0.4360 0.595 0.00 0.68 0.00 0.02 0.30
#> TCGA.DU.8168.01 2 0.0000 0.932 0.00 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RN.01 1 0.0000 0.867 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.5141.01 3 0.1410 0.861 0.06 0.00 0.94 0.00 0.00
#> TCGA.EZ.7264.01 4 0.4360 0.765 0.00 0.00 0.02 0.68 0.30
#> TCGA.QH.A65V.01 1 0.0609 0.867 0.98 0.00 0.00 0.02 0.00
#> TCGA.DU.A6S8.01 4 0.3796 0.776 0.00 0.00 0.00 0.70 0.30
#> TCGA.DU.7298.01 3 0.0000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.DB.A64R.01 1 0.0000 0.867 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.5390.01 2 0.3895 0.420 0.00 0.68 0.00 0.00 0.32
#> TCGA.S9.A6WP.01 5 0.4227 0.500 0.00 0.00 0.42 0.00 0.58
#> TCGA.E1.A7YS.01 2 0.0000 0.932 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7294.01 3 0.0000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7695.01 1 0.0609 0.866 0.98 0.00 0.00 0.02 0.00
#> TCGA.FG.7637.01 3 0.4726 0.319 0.40 0.00 0.58 0.02 0.00
#> TCGA.S9.A6U5.01 1 0.1410 0.862 0.94 0.00 0.00 0.06 0.00
#> TCGA.DB.5274.01 5 0.5733 0.685 0.00 0.22 0.16 0.00 0.62
#> TCGA.HW.7487.01 3 0.0000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.HW.7491.01 3 0.0609 0.896 0.00 0.00 0.98 0.00 0.02
#> TCGA.HT.8012.01 3 0.0000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A7QZ.01 5 0.4728 0.659 0.00 0.24 0.06 0.00 0.70
#> TCGA.QH.A6X4.01 1 0.3895 0.730 0.68 0.00 0.00 0.32 0.00
#> TCGA.P5.A77W.01 5 0.4262 0.461 0.00 0.00 0.44 0.00 0.56
#> TCGA.DU.7302.01 5 0.3796 0.572 0.00 0.30 0.00 0.00 0.70
#> TCGA.HW.7495.01 1 0.0000 0.867 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A65R.01 5 0.5700 0.652 0.00 0.28 0.12 0.00 0.60
#> TCGA.HT.7875.01 1 0.3895 0.730 0.68 0.00 0.00 0.32 0.00
#> TCGA.DU.6394.01 2 0.0000 0.932 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6WD.01 5 0.1216 0.538 0.00 0.00 0.02 0.02 0.96
#> TCGA.TQ.A7RU.01 3 0.1732 0.836 0.00 0.00 0.92 0.00 0.08
#> TCGA.DU.5874.01 2 0.0000 0.932 0.00 1.00 0.00 0.00 0.00
#> TCGA.R8.A6MK.01 1 0.1732 0.855 0.92 0.00 0.00 0.08 0.00
#> TCGA.S9.A7J1.01 1 0.3895 0.730 0.68 0.00 0.00 0.32 0.00
#> TCGA.P5.A5F0.01 3 0.2012 0.844 0.06 0.00 0.92 0.02 0.00
#> TCGA.R8.A73M.01 3 0.0000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.A6S3.01 5 0.4262 0.461 0.00 0.00 0.44 0.00 0.56
#> TCGA.DB.A4XH.01 2 0.0000 0.932 0.00 1.00 0.00 0.00 0.00
#> TCGA.VW.A7QS.01 4 0.4170 0.698 0.00 0.00 0.14 0.78 0.08
#> TCGA.DU.8164.01 5 0.4876 0.678 0.00 0.22 0.08 0.00 0.70
#> TCGA.HT.7468.01 4 0.0609 0.743 0.00 0.00 0.00 0.98 0.02
#> TCGA.TQ.A7RI.01 1 0.0000 0.867 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5279.01 4 0.4060 0.744 0.00 0.00 0.00 0.64 0.36
#> TCGA.DU.7018.01 2 0.0000 0.932 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7677.01 3 0.0609 0.896 0.00 0.00 0.98 0.00 0.02
#> TCGA.TM.A84M.01 4 0.3796 0.776 0.00 0.00 0.00 0.70 0.30
#> TCGA.F6.A8O3.01 1 0.4840 0.457 0.64 0.00 0.32 0.04 0.00
#> TCGA.QH.A86X.01 1 0.0000 0.867 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A76R.01 4 0.4360 0.213 0.30 0.00 0.02 0.68 0.00
#> TCGA.DH.5144.01 5 0.4182 0.532 0.00 0.00 0.40 0.00 0.60
#> TCGA.RY.A840.01 4 0.1732 0.695 0.08 0.00 0.00 0.92 0.00
#> TCGA.HW.A5KJ.01 2 0.0000 0.932 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.8105.01 2 0.0000 0.932 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7471.01 3 0.3424 0.561 0.00 0.00 0.76 0.00 0.24
#> TCGA.HT.A619.01 2 0.1732 0.868 0.00 0.92 0.00 0.00 0.08
#> TCGA.HT.A5R9.01 3 0.3895 0.342 0.00 0.00 0.68 0.00 0.32
#> TCGA.CS.5396.01 4 0.3274 0.780 0.00 0.00 0.00 0.78 0.22
#> TCGA.DU.6400.01 2 0.0000 0.932 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6WL.01 5 0.4182 0.457 0.00 0.40 0.00 0.00 0.60
#> TCGA.DB.A75K.01 3 0.0000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.DB.A64Q.01 4 0.1216 0.736 0.02 0.00 0.00 0.96 0.02
#> TCGA.P5.A737.01 4 0.3424 0.558 0.00 0.00 0.24 0.76 0.00
#> TCGA.S9.A6WH.01 2 0.0000 0.932 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7616.01 2 0.2516 0.807 0.00 0.86 0.00 0.00 0.14
#> TCGA.RY.A83Y.01 3 0.2929 0.681 0.00 0.00 0.82 0.00 0.18
#> TCGA.DB.A64U.01 1 0.1410 0.862 0.94 0.00 0.00 0.06 0.00
#> TCGA.DB.A64W.01 2 0.0000 0.932 0.00 1.00 0.00 0.00 0.00
#> TCGA.R8.A6MO.01 5 0.4675 0.557 0.00 0.02 0.38 0.00 0.60
#> TCGA.HW.8322.01 1 0.1410 0.862 0.94 0.00 0.00 0.06 0.00
#> TCGA.DU.5870.02 4 0.3895 0.767 0.00 0.00 0.00 0.68 0.32
#> TCGA.CS.6668.01 4 0.4126 0.728 0.00 0.00 0.00 0.62 0.38
#> TCGA.DU.5870.01 4 0.2280 0.644 0.12 0.00 0.00 0.88 0.00
#> TCGA.HT.7692.01 1 0.3895 0.730 0.68 0.00 0.00 0.32 0.00
#> TCGA.R8.A6ML.01 4 0.4360 0.761 0.00 0.00 0.02 0.68 0.30
#> TCGA.DU.6410.01 5 0.4588 0.669 0.00 0.22 0.06 0.00 0.72
#> TCGA.TQ.A7RO.01 1 0.2438 0.829 0.90 0.00 0.06 0.04 0.00
#> TCGA.E1.5318.01 2 0.0000 0.932 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A7J3.01 5 0.3796 0.572 0.00 0.30 0.00 0.00 0.70
#> TCGA.TQ.A7RS.01 1 0.0000 0.867 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A65Z.01 5 0.4182 0.532 0.00 0.00 0.40 0.00 0.60
#> TCGA.P5.A730.01 3 0.1410 0.861 0.06 0.00 0.94 0.00 0.00
#> TCGA.RY.A83X.01 3 0.0000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6UB.01 5 0.4876 0.678 0.00 0.22 0.08 0.00 0.70
#> TCGA.DH.A66F.01 3 0.1410 0.857 0.00 0.00 0.94 0.06 0.00
#> TCGA.DU.6393.01 2 0.0609 0.914 0.00 0.98 0.00 0.00 0.02
#> TCGA.S9.A7IY.01 1 0.0609 0.867 0.98 0.00 0.00 0.02 0.00
#> TCGA.FG.7641.01 3 0.2012 0.844 0.06 0.00 0.92 0.02 0.00
#> TCGA.DU.7009.01 1 0.1410 0.860 0.94 0.00 0.00 0.06 0.00
#> TCGA.FG.8186.01 1 0.0000 0.867 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64L.01 2 0.4227 0.224 0.00 0.58 0.00 0.00 0.42
#> TCGA.VV.A829.01 4 0.3796 0.776 0.00 0.00 0.00 0.70 0.30
#> TCGA.DU.6397.02 4 0.2280 0.767 0.00 0.00 0.00 0.88 0.12
#> TCGA.DU.6397.01 1 0.4798 0.517 0.54 0.00 0.02 0.44 0.00
#> TCGA.CS.6670.01 1 0.3895 0.730 0.68 0.00 0.00 0.32 0.00
#> TCGA.QH.A65X.01 1 0.1043 0.864 0.96 0.00 0.00 0.04 0.00
#> TCGA.DB.A64P.01 3 0.0000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.QH.A6CZ.01 1 0.3895 0.730 0.68 0.00 0.00 0.32 0.00
#> TCGA.DH.A669.02 2 0.0000 0.932 0.00 1.00 0.00 0.00 0.00
#> TCGA.DH.A669.01 2 0.0000 0.932 0.00 1.00 0.00 0.00 0.00
#> TCGA.VM.A8CB.01 1 0.0000 0.867 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7687.01 2 0.0000 0.932 0.00 1.00 0.00 0.00 0.00
#> TCGA.TM.A84G.01 5 0.2280 0.645 0.00 0.00 0.12 0.00 0.88
#> TCGA.CS.5394.01 5 0.5579 0.632 0.00 0.30 0.10 0.00 0.60
#> TCGA.FG.5962.01 4 0.3895 0.767 0.00 0.00 0.00 0.68 0.32
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.S9.A7J2.01 1 0.0000 0.9114 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TX.01 3 0.2403 0.8409 0.00 0.00 0.90 0.04 0.04 0.02
#> TCGA.HT.A74L.01 1 0.0000 0.9114 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5311.01 3 0.0547 0.8692 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.HT.7480.01 3 0.0937 0.8669 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.S9.A7R1.01 3 0.1092 0.8617 0.00 0.00 0.96 0.02 0.00 0.02
#> TCGA.FG.A710.01 6 0.2794 0.5022 0.08 0.00 0.00 0.06 0.00 0.86
#> TCGA.DU.A6S6.01 1 0.0000 0.9114 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7634.01 1 0.0000 0.9114 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7638.01 1 0.5569 -0.0417 0.52 0.00 0.16 0.00 0.00 0.32
#> TCGA.FG.A6J1.01 1 0.4265 0.3285 0.66 0.00 0.04 0.00 0.00 0.30
#> TCGA.HT.7608.01 6 0.3851 0.5349 0.46 0.00 0.00 0.00 0.00 0.54
#> TCGA.W9.A837.01 6 0.3706 0.6159 0.38 0.00 0.00 0.00 0.00 0.62
#> TCGA.TM.A7C5.01 3 0.3834 0.6277 0.00 0.00 0.76 0.02 0.20 0.02
#> TCGA.P5.A5ET.01 1 0.0000 0.9114 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A77X.01 6 0.3647 0.6254 0.36 0.00 0.00 0.00 0.00 0.64
#> TCGA.FG.A6IZ.01 2 0.0000 0.8950 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.KT.A74X.01 6 0.4576 0.5578 0.40 0.00 0.04 0.00 0.00 0.56
#> TCGA.E1.A7YO.01 3 0.1092 0.8617 0.00 0.00 0.96 0.02 0.00 0.02
#> TCGA.TQ.A7RG.01 1 0.0000 0.9114 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RY.A847.01 1 0.0547 0.8994 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.VM.A8CA.01 6 0.3851 0.5349 0.46 0.00 0.00 0.00 0.00 0.54
#> TCGA.DB.A4XG.01 3 0.1480 0.8539 0.00 0.00 0.94 0.02 0.00 0.04
#> TCGA.FG.A60K.01 1 0.0000 0.9114 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TY.01 5 0.3506 0.7361 0.00 0.00 0.16 0.02 0.80 0.02
#> TCGA.TQ.A7RQ.01 6 0.5083 0.5735 0.32 0.00 0.10 0.00 0.00 0.58
#> TCGA.IK.8125.01 4 0.4246 0.1558 0.00 0.00 0.00 0.58 0.40 0.02
#> TCGA.HT.A74K.01 4 0.3797 0.1555 0.00 0.00 0.00 0.58 0.42 0.00
#> TCGA.QH.A6X8.01 2 0.0000 0.8950 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7681.01 1 0.0000 0.9114 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A72Z.01 4 0.5265 -0.0465 0.00 0.40 0.00 0.50 0.10 0.00
#> TCGA.DU.8168.01 2 0.1480 0.8887 0.00 0.94 0.00 0.04 0.00 0.02
#> TCGA.TQ.A7RN.01 1 0.0000 0.9114 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.5141.01 3 0.1267 0.8602 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.EZ.7264.01 4 0.5302 0.6404 0.00 0.00 0.04 0.56 0.04 0.36
#> TCGA.QH.A65V.01 1 0.0547 0.9013 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DU.A6S8.01 4 0.3756 0.6266 0.00 0.00 0.00 0.60 0.00 0.40
#> TCGA.DU.7298.01 3 0.1092 0.8576 0.00 0.00 0.96 0.02 0.02 0.00
#> TCGA.DB.A64R.01 1 0.0547 0.8970 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CS.5390.01 2 0.5189 0.4204 0.00 0.58 0.00 0.06 0.34 0.02
#> TCGA.S9.A6WP.01 5 0.3111 0.7597 0.00 0.00 0.12 0.02 0.84 0.02
#> TCGA.E1.A7YS.01 2 0.0000 0.8950 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7294.01 3 0.1865 0.8516 0.00 0.00 0.92 0.04 0.00 0.04
#> TCGA.HT.7695.01 1 0.1556 0.8456 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.FG.7637.01 3 0.2794 0.7982 0.06 0.00 0.86 0.00 0.00 0.08
#> TCGA.S9.A6U5.01 1 0.0547 0.8994 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DB.5274.01 5 0.1807 0.7708 0.00 0.02 0.06 0.00 0.92 0.00
#> TCGA.HW.7487.01 3 0.1092 0.8617 0.00 0.00 0.96 0.02 0.00 0.02
#> TCGA.HW.7491.01 3 0.2020 0.8291 0.00 0.00 0.92 0.02 0.04 0.02
#> TCGA.HT.8012.01 3 0.0000 0.8668 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A7QZ.01 5 0.3351 0.6647 0.00 0.04 0.00 0.16 0.80 0.00
#> TCGA.QH.A6X4.01 6 0.3851 0.5349 0.46 0.00 0.00 0.00 0.00 0.54
#> TCGA.P5.A77W.01 5 0.3318 0.7501 0.00 0.00 0.14 0.02 0.82 0.02
#> TCGA.DU.7302.01 5 0.4552 0.4688 0.00 0.06 0.00 0.30 0.64 0.00
#> TCGA.HW.7495.01 1 0.0000 0.9114 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A65R.01 5 0.1865 0.7655 0.00 0.04 0.04 0.00 0.92 0.00
#> TCGA.HT.7875.01 6 0.3828 0.5635 0.44 0.00 0.00 0.00 0.00 0.56
#> TCGA.DU.6394.01 2 0.0000 0.8950 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WD.01 4 0.4282 0.1027 0.00 0.00 0.00 0.56 0.42 0.02
#> TCGA.TQ.A7RU.01 3 0.4787 -0.0068 0.00 0.00 0.52 0.02 0.44 0.02
#> TCGA.DU.5874.01 2 0.1480 0.8887 0.00 0.94 0.00 0.04 0.00 0.02
#> TCGA.R8.A6MK.01 1 0.0937 0.8806 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.S9.A7J1.01 6 0.3828 0.5554 0.44 0.00 0.00 0.00 0.00 0.56
#> TCGA.P5.A5F0.01 3 0.1267 0.8602 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.R8.A73M.01 3 0.0937 0.8689 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.DU.A6S3.01 5 0.3318 0.7501 0.00 0.00 0.14 0.02 0.82 0.02
#> TCGA.DB.A4XH.01 2 0.1480 0.8887 0.00 0.94 0.00 0.04 0.00 0.02
#> TCGA.VW.A7QS.01 6 0.4042 0.3506 0.00 0.00 0.18 0.04 0.02 0.76
#> TCGA.DU.8164.01 5 0.1480 0.7424 0.00 0.04 0.00 0.02 0.94 0.00
#> TCGA.HT.7468.01 6 0.1814 0.3353 0.00 0.00 0.00 0.10 0.00 0.90
#> TCGA.TQ.A7RI.01 1 0.0000 0.9114 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5279.01 4 0.2793 0.6912 0.00 0.00 0.00 0.80 0.00 0.20
#> TCGA.DU.7018.01 2 0.0000 0.8950 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7677.01 3 0.4334 0.5852 0.00 0.00 0.72 0.02 0.22 0.04
#> TCGA.TM.A84M.01 4 0.3797 0.6054 0.00 0.00 0.00 0.58 0.00 0.42
#> TCGA.F6.A8O3.01 3 0.3746 0.7055 0.14 0.00 0.78 0.00 0.00 0.08
#> TCGA.QH.A86X.01 1 0.0000 0.9114 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A76R.01 6 0.3678 0.6266 0.18 0.00 0.02 0.02 0.00 0.78
#> TCGA.DH.5144.01 5 0.2882 0.7658 0.00 0.00 0.10 0.02 0.86 0.02
#> TCGA.RY.A840.01 6 0.2474 0.5154 0.08 0.00 0.00 0.04 0.00 0.88
#> TCGA.HW.A5KJ.01 2 0.0000 0.8950 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8105.01 2 0.1480 0.8887 0.00 0.94 0.00 0.04 0.00 0.02
#> TCGA.HT.7471.01 5 0.4689 0.3970 0.00 0.00 0.38 0.02 0.58 0.02
#> TCGA.HT.A619.01 2 0.3321 0.7489 0.00 0.82 0.00 0.10 0.08 0.00
#> TCGA.HT.A5R9.01 5 0.4222 0.6327 0.00 0.00 0.26 0.02 0.70 0.02
#> TCGA.CS.5396.01 4 0.3828 0.5810 0.00 0.00 0.00 0.56 0.00 0.44
#> TCGA.DU.6400.01 2 0.1480 0.8887 0.00 0.94 0.00 0.04 0.00 0.02
#> TCGA.S9.A6WL.01 5 0.3318 0.6758 0.00 0.14 0.00 0.02 0.82 0.02
#> TCGA.DB.A75K.01 3 0.0937 0.8687 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.DB.A64Q.01 6 0.2956 0.3678 0.04 0.00 0.00 0.12 0.00 0.84
#> TCGA.P5.A737.01 6 0.3351 0.4030 0.00 0.00 0.16 0.04 0.00 0.80
#> TCGA.S9.A6WH.01 2 0.1480 0.8887 0.00 0.94 0.00 0.04 0.00 0.02
#> TCGA.HT.7616.01 2 0.4929 0.4711 0.00 0.62 0.00 0.28 0.10 0.00
#> TCGA.RY.A83Y.01 5 0.5381 0.2958 0.00 0.00 0.40 0.04 0.52 0.04
#> TCGA.DB.A64U.01 1 0.1267 0.8655 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.DB.A64W.01 2 0.0547 0.8936 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.R8.A6MO.01 5 0.1556 0.7716 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.HW.8322.01 1 0.0937 0.8864 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.DU.5870.02 4 0.3309 0.6806 0.00 0.00 0.00 0.72 0.00 0.28
#> TCGA.CS.6668.01 4 0.3660 0.6874 0.00 0.00 0.00 0.78 0.06 0.16
#> TCGA.DU.5870.01 6 0.2728 0.5306 0.10 0.00 0.00 0.04 0.00 0.86
#> TCGA.HT.7692.01 6 0.3864 0.4915 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.R8.A6ML.01 4 0.4631 0.6821 0.00 0.00 0.02 0.70 0.06 0.22
#> TCGA.DU.6410.01 5 0.2956 0.6963 0.00 0.04 0.00 0.12 0.84 0.00
#> TCGA.TQ.A7RO.01 3 0.5295 0.0099 0.44 0.00 0.46 0.00 0.00 0.10
#> TCGA.E1.5318.01 2 0.1480 0.8887 0.00 0.94 0.00 0.04 0.00 0.02
#> TCGA.S9.A7J3.01 5 0.4265 0.4940 0.00 0.04 0.00 0.30 0.66 0.00
#> TCGA.TQ.A7RS.01 1 0.0000 0.9114 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A65Z.01 5 0.2350 0.7695 0.00 0.00 0.10 0.00 0.88 0.02
#> TCGA.P5.A730.01 3 0.1267 0.8602 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.RY.A83X.01 3 0.0937 0.8669 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.S9.A6UB.01 5 0.3163 0.6818 0.00 0.04 0.00 0.14 0.82 0.00
#> TCGA.DH.A66F.01 3 0.1814 0.8461 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.DU.6393.01 2 0.3258 0.8117 0.00 0.84 0.00 0.04 0.10 0.02
#> TCGA.S9.A7IY.01 1 0.0000 0.9114 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7641.01 3 0.1556 0.8464 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.DU.7009.01 1 0.3309 0.4623 0.72 0.00 0.00 0.00 0.00 0.28
#> TCGA.FG.8186.01 1 0.0547 0.8970 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DB.A64L.01 2 0.5987 0.1618 0.00 0.44 0.00 0.30 0.26 0.00
#> TCGA.VV.A829.01 4 0.3647 0.6388 0.00 0.00 0.00 0.64 0.00 0.36
#> TCGA.DU.6397.02 6 0.3864 -0.5059 0.00 0.00 0.00 0.48 0.00 0.52
#> TCGA.DU.6397.01 6 0.3950 0.6520 0.24 0.00 0.04 0.00 0.00 0.72
#> TCGA.CS.6670.01 6 0.3706 0.6070 0.38 0.00 0.00 0.00 0.00 0.62
#> TCGA.QH.A65X.01 1 0.3198 0.5168 0.74 0.00 0.00 0.00 0.00 0.26
#> TCGA.DB.A64P.01 3 0.0000 0.8668 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.QH.A6CZ.01 6 0.3864 0.4915 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.DH.A669.02 2 0.0000 0.8950 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A669.01 2 0.0000 0.8950 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8CB.01 1 0.0547 0.8995 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.HT.7687.01 2 0.0000 0.8950 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84G.01 5 0.3309 0.4953 0.00 0.00 0.00 0.28 0.72 0.00
#> TCGA.CS.5394.01 5 0.1865 0.7655 0.00 0.04 0.04 0.00 0.92 0.00
#> TCGA.FG.5962.01 4 0.4247 0.6906 0.00 0.00 0.00 0.70 0.06 0.24
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.S9.A7J2.01 1 0.0000 0.8818 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TX.01 3 0.4440 0.6531 0.00 0.00 0.74 0.12 0.02 0.02 0.10
#> TCGA.HT.A74L.01 1 0.1006 0.8678 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.E1.5311.01 3 0.1671 0.7239 0.00 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.HT.7480.01 3 0.2512 0.7136 0.00 0.00 0.86 0.00 0.00 0.04 0.10
#> TCGA.S9.A7R1.01 3 0.2355 0.7267 0.00 0.00 0.90 0.04 0.02 0.02 0.02
#> TCGA.FG.A710.01 6 0.2259 0.5551 0.00 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.DU.A6S6.01 1 0.1006 0.8678 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.FG.7634.01 1 0.0000 0.8818 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7638.01 6 0.6816 0.3252 0.24 0.00 0.18 0.00 0.00 0.40 0.18
#> TCGA.FG.A6J1.01 1 0.6371 -0.1399 0.40 0.00 0.10 0.00 0.00 0.36 0.14
#> TCGA.HT.7608.01 6 0.3755 0.6316 0.34 0.00 0.00 0.00 0.00 0.64 0.02
#> TCGA.W9.A837.01 6 0.2708 0.7285 0.22 0.00 0.00 0.00 0.00 0.78 0.00
#> TCGA.TM.A7C5.01 3 0.4535 0.4716 0.00 0.00 0.64 0.00 0.24 0.00 0.12
#> TCGA.P5.A5ET.01 1 0.0000 0.8818 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A77X.01 6 0.3396 0.6998 0.14 0.00 0.00 0.04 0.00 0.80 0.02
#> TCGA.FG.A6IZ.01 2 0.0000 0.8712 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KT.A74X.01 6 0.5204 0.6112 0.22 0.00 0.04 0.00 0.00 0.62 0.12
#> TCGA.E1.A7YO.01 3 0.2355 0.7285 0.00 0.00 0.90 0.04 0.02 0.02 0.02
#> TCGA.TQ.A7RG.01 1 0.0000 0.8818 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RY.A847.01 1 0.1664 0.8347 0.92 0.00 0.00 0.00 0.00 0.06 0.02
#> TCGA.VM.A8CA.01 6 0.3685 0.6598 0.32 0.00 0.00 0.00 0.00 0.66 0.02
#> TCGA.DB.A4XG.01 3 0.3876 0.6860 0.00 0.00 0.78 0.04 0.02 0.02 0.14
#> TCGA.FG.A60K.01 1 0.0000 0.8818 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TY.01 5 0.4629 0.4878 0.00 0.00 0.20 0.00 0.64 0.00 0.16
#> TCGA.TQ.A7RQ.01 6 0.4536 0.6738 0.14 0.00 0.08 0.00 0.00 0.72 0.06
#> TCGA.IK.8125.01 7 0.5546 0.4654 0.00 0.00 0.00 0.26 0.32 0.00 0.42
#> TCGA.HT.A74K.01 7 0.5546 0.4654 0.00 0.00 0.00 0.26 0.32 0.00 0.42
#> TCGA.QH.A6X8.01 2 0.1671 0.8302 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.HT.7681.01 1 0.0000 0.8818 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A72Z.01 7 0.5915 0.3804 0.00 0.30 0.00 0.18 0.04 0.00 0.48
#> TCGA.DU.8168.01 2 0.1860 0.8650 0.00 0.92 0.00 0.00 0.02 0.02 0.04
#> TCGA.TQ.A7RN.01 1 0.0504 0.8764 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DH.5141.01 3 0.3263 0.6915 0.00 0.00 0.80 0.00 0.00 0.08 0.12
#> TCGA.EZ.7264.01 4 0.5091 0.6039 0.00 0.00 0.06 0.66 0.00 0.12 0.16
#> TCGA.QH.A65V.01 1 0.1006 0.8625 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.DU.A6S8.01 4 0.2572 0.7696 0.00 0.00 0.00 0.80 0.00 0.20 0.00
#> TCGA.DU.7298.01 3 0.2769 0.7088 0.00 0.00 0.86 0.02 0.04 0.00 0.08
#> TCGA.DB.A64R.01 1 0.1363 0.8533 0.94 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.CS.5390.01 2 0.4692 0.0352 0.00 0.50 0.00 0.00 0.42 0.00 0.08
#> TCGA.S9.A6WP.01 5 0.2512 0.6258 0.00 0.00 0.04 0.00 0.86 0.00 0.10
#> TCGA.E1.A7YS.01 2 0.1671 0.8302 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.DU.7294.01 3 0.4892 0.6441 0.00 0.00 0.70 0.08 0.02 0.04 0.16
#> TCGA.HT.7695.01 1 0.2829 0.7559 0.84 0.00 0.00 0.00 0.00 0.08 0.08
#> TCGA.FG.7637.01 3 0.4696 0.6182 0.06 0.00 0.70 0.00 0.00 0.08 0.16
#> TCGA.S9.A6U5.01 1 0.1363 0.8475 0.94 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.DB.5274.01 5 0.0863 0.6203 0.00 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.HW.7487.01 3 0.3000 0.7162 0.00 0.00 0.86 0.06 0.02 0.02 0.04
#> TCGA.HW.7491.01 3 0.3744 0.6566 0.00 0.00 0.78 0.02 0.08 0.00 0.12
#> TCGA.HT.8012.01 3 0.0863 0.7372 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.S9.A7QZ.01 5 0.4107 0.3190 0.00 0.04 0.00 0.02 0.70 0.00 0.24
#> TCGA.QH.A6X4.01 6 0.3685 0.6598 0.32 0.00 0.00 0.00 0.00 0.66 0.02
#> TCGA.P5.A77W.01 5 0.3487 0.5940 0.00 0.00 0.10 0.00 0.78 0.00 0.12
#> TCGA.DU.7302.01 5 0.4070 0.1405 0.00 0.04 0.00 0.00 0.62 0.00 0.34
#> TCGA.HW.7495.01 1 0.0000 0.8818 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A65R.01 5 0.1363 0.6171 0.00 0.04 0.00 0.00 0.94 0.00 0.02
#> TCGA.HT.7875.01 6 0.3517 0.6921 0.28 0.00 0.00 0.00 0.00 0.70 0.02
#> TCGA.DU.6394.01 2 0.0000 0.8712 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WD.01 7 0.5546 0.4654 0.00 0.00 0.00 0.26 0.32 0.00 0.42
#> TCGA.TQ.A7RU.01 3 0.5002 0.1279 0.00 0.00 0.48 0.00 0.40 0.00 0.12
#> TCGA.DU.5874.01 2 0.1860 0.8650 0.00 0.92 0.00 0.00 0.02 0.02 0.04
#> TCGA.R8.A6MK.01 1 0.2376 0.7701 0.86 0.00 0.00 0.00 0.00 0.12 0.02
#> TCGA.S9.A7J1.01 6 0.3685 0.6598 0.32 0.00 0.00 0.00 0.00 0.66 0.02
#> TCGA.P5.A5F0.01 3 0.3449 0.6811 0.00 0.00 0.78 0.00 0.00 0.08 0.14
#> TCGA.R8.A73M.01 3 0.2159 0.7286 0.00 0.00 0.90 0.02 0.00 0.02 0.06
#> TCGA.DU.A6S3.01 5 0.3617 0.5901 0.00 0.00 0.08 0.00 0.76 0.00 0.16
#> TCGA.DB.A4XH.01 2 0.1860 0.8650 0.00 0.92 0.00 0.00 0.02 0.02 0.04
#> TCGA.VW.A7QS.01 6 0.6111 0.2703 0.00 0.00 0.16 0.18 0.00 0.54 0.12
#> TCGA.DU.8164.01 5 0.1006 0.6293 0.00 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.HT.7468.01 6 0.3526 0.4834 0.00 0.00 0.00 0.18 0.00 0.76 0.06
#> TCGA.TQ.A7RI.01 1 0.0000 0.8818 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5279.01 4 0.3566 0.6820 0.00 0.00 0.00 0.78 0.02 0.04 0.16
#> TCGA.DU.7018.01 2 0.0000 0.8712 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7677.01 3 0.5511 0.4738 0.00 0.00 0.60 0.06 0.20 0.00 0.14
#> TCGA.TM.A84M.01 4 0.2572 0.7696 0.00 0.00 0.00 0.80 0.00 0.20 0.00
#> TCGA.F6.A8O3.01 3 0.5652 0.5125 0.12 0.00 0.60 0.00 0.00 0.10 0.18
#> TCGA.QH.A86X.01 1 0.0000 0.8818 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A76R.01 6 0.2512 0.7035 0.10 0.00 0.00 0.04 0.00 0.86 0.00
#> TCGA.DH.5144.01 5 0.3835 0.5766 0.00 0.00 0.10 0.00 0.74 0.00 0.16
#> TCGA.RY.A840.01 6 0.2163 0.6009 0.02 0.00 0.00 0.10 0.00 0.88 0.00
#> TCGA.HW.A5KJ.01 2 0.0000 0.8712 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8105.01 2 0.1860 0.8650 0.00 0.92 0.00 0.00 0.02 0.02 0.04
#> TCGA.HT.7471.01 3 0.5143 0.0261 0.00 0.00 0.44 0.00 0.42 0.00 0.14
#> TCGA.HT.A619.01 2 0.3388 0.5949 0.00 0.76 0.00 0.00 0.04 0.00 0.20
#> TCGA.HT.A5R9.01 5 0.5086 0.1433 0.00 0.00 0.36 0.00 0.50 0.00 0.14
#> TCGA.CS.5396.01 4 0.2572 0.7696 0.00 0.00 0.00 0.80 0.00 0.20 0.00
#> TCGA.DU.6400.01 2 0.1363 0.8678 0.00 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.S9.A6WL.01 5 0.2745 0.5006 0.00 0.16 0.00 0.00 0.82 0.00 0.02
#> TCGA.DB.A75K.01 3 0.1006 0.7365 0.00 0.00 0.96 0.02 0.00 0.02 0.00
#> TCGA.DB.A64Q.01 6 0.3052 0.5074 0.00 0.00 0.00 0.20 0.00 0.78 0.02
#> TCGA.P5.A737.01 6 0.4574 0.5021 0.00 0.00 0.06 0.10 0.00 0.72 0.12
#> TCGA.S9.A6WH.01 2 0.1860 0.8650 0.00 0.92 0.00 0.00 0.02 0.02 0.04
#> TCGA.HT.7616.01 7 0.4710 0.1112 0.00 0.46 0.00 0.04 0.02 0.00 0.48
#> TCGA.RY.A83Y.01 3 0.6184 0.1688 0.00 0.00 0.44 0.06 0.32 0.00 0.18
#> TCGA.DB.A64U.01 1 0.2376 0.7692 0.86 0.00 0.00 0.00 0.00 0.12 0.02
#> TCGA.DB.A64W.01 2 0.2163 0.8344 0.00 0.88 0.00 0.00 0.00 0.02 0.10
#> TCGA.R8.A6MO.01 5 0.0863 0.6358 0.00 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.HW.8322.01 1 0.2163 0.7940 0.88 0.00 0.00 0.00 0.00 0.10 0.02
#> TCGA.DU.5870.02 4 0.3541 0.7350 0.00 0.00 0.00 0.80 0.02 0.10 0.08
#> TCGA.CS.6668.01 4 0.3052 0.5839 0.00 0.00 0.00 0.78 0.02 0.00 0.20
#> TCGA.DU.5870.01 6 0.2081 0.5744 0.00 0.00 0.00 0.14 0.00 0.86 0.00
#> TCGA.HT.7692.01 6 0.3685 0.6598 0.32 0.00 0.00 0.00 0.00 0.66 0.02
#> TCGA.R8.A6ML.01 4 0.4431 0.5399 0.00 0.00 0.04 0.68 0.00 0.04 0.24
#> TCGA.DU.6410.01 5 0.3637 0.3671 0.00 0.04 0.00 0.00 0.72 0.00 0.24
#> TCGA.TQ.A7RO.01 3 0.6416 0.3410 0.22 0.00 0.48 0.00 0.00 0.12 0.18
#> TCGA.E1.5318.01 2 0.1860 0.8650 0.00 0.92 0.00 0.00 0.02 0.02 0.04
#> TCGA.S9.A7J3.01 5 0.5166 -0.1042 0.00 0.04 0.00 0.06 0.52 0.00 0.38
#> TCGA.TQ.A7RS.01 1 0.0000 0.8818 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A65Z.01 5 0.3011 0.6170 0.00 0.00 0.06 0.00 0.82 0.00 0.12
#> TCGA.P5.A730.01 3 0.3449 0.6823 0.00 0.00 0.78 0.00 0.00 0.08 0.14
#> TCGA.RY.A83X.01 3 0.3263 0.6915 0.00 0.00 0.80 0.00 0.00 0.08 0.12
#> TCGA.S9.A6UB.01 5 0.4107 0.3506 0.00 0.04 0.00 0.02 0.70 0.00 0.24
#> TCGA.DH.A66F.01 3 0.3404 0.7205 0.00 0.00 0.82 0.04 0.00 0.06 0.08
#> TCGA.DU.6393.01 2 0.3722 0.6814 0.00 0.76 0.00 0.00 0.18 0.02 0.04
#> TCGA.S9.A7IY.01 1 0.0000 0.8818 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7641.01 3 0.3449 0.6811 0.00 0.00 0.78 0.00 0.00 0.08 0.14
#> TCGA.DU.7009.01 1 0.4505 -0.0754 0.50 0.00 0.00 0.00 0.00 0.44 0.06
#> TCGA.FG.8186.01 1 0.1363 0.8533 0.94 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.DB.A64L.01 7 0.6445 0.4177 0.00 0.30 0.00 0.06 0.28 0.00 0.36
#> TCGA.VV.A829.01 4 0.3086 0.7590 0.00 0.00 0.00 0.80 0.00 0.16 0.04
#> TCGA.DU.6397.02 4 0.3139 0.6857 0.00 0.00 0.00 0.70 0.00 0.30 0.00
#> TCGA.DU.6397.01 6 0.2654 0.7045 0.10 0.00 0.00 0.02 0.00 0.86 0.02
#> TCGA.CS.6670.01 6 0.2906 0.7268 0.18 0.00 0.00 0.00 0.00 0.80 0.02
#> TCGA.QH.A65X.01 1 0.5438 0.1562 0.52 0.00 0.02 0.00 0.00 0.32 0.14
#> TCGA.DB.A64P.01 3 0.1166 0.7315 0.00 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.QH.A6CZ.01 6 0.3755 0.6316 0.34 0.00 0.00 0.00 0.00 0.64 0.02
#> TCGA.DH.A669.02 2 0.1671 0.8302 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.DH.A669.01 2 0.1671 0.8302 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.VM.A8CB.01 1 0.0863 0.8703 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.HT.7687.01 2 0.0000 0.8712 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84G.01 5 0.4783 0.0457 0.00 0.00 0.00 0.10 0.54 0.00 0.36
#> TCGA.CS.5394.01 5 0.1363 0.6171 0.00 0.04 0.00 0.00 0.94 0.00 0.02
#> TCGA.FG.5962.01 4 0.3086 0.6332 0.00 0.00 0.00 0.80 0.00 0.04 0.16
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.S9.A7J2.01 1 0.0000 0.930686 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TX.01 3 0.5659 -0.100178 0.00 0.00 0.44 0.00 0.08 0.02 0.06 0.40
#> TCGA.HT.A74L.01 1 0.1091 0.917429 0.94 0.00 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.E1.5311.01 3 0.0808 0.737985 0.00 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.HT.7480.01 3 0.0471 0.739394 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.S9.A7R1.01 3 0.2407 0.714522 0.00 0.00 0.86 0.00 0.06 0.00 0.00 0.08
#> TCGA.FG.A710.01 6 0.1408 0.771338 0.02 0.00 0.00 0.02 0.00 0.94 0.00 0.02
#> TCGA.DU.A6S6.01 1 0.1091 0.917429 0.94 0.00 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.FG.7634.01 1 0.0000 0.930686 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7638.01 6 0.6211 0.439763 0.14 0.00 0.20 0.00 0.00 0.44 0.00 0.22
#> TCGA.FG.A6J1.01 6 0.6040 0.427155 0.28 0.00 0.08 0.00 0.00 0.42 0.00 0.22
#> TCGA.HT.7608.01 6 0.2025 0.786361 0.10 0.00 0.00 0.00 0.00 0.88 0.00 0.02
#> TCGA.W9.A837.01 6 0.1887 0.789620 0.06 0.00 0.00 0.00 0.00 0.90 0.00 0.04
#> TCGA.TM.A7C5.01 3 0.4480 0.388852 0.00 0.00 0.58 0.00 0.30 0.00 0.00 0.12
#> TCGA.P5.A5ET.01 1 0.0000 0.930686 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A77X.01 6 0.1741 0.775485 0.04 0.00 0.00 0.02 0.00 0.92 0.00 0.02
#> TCGA.FG.A6IZ.01 2 0.0471 0.889361 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.KT.A74X.01 6 0.4079 0.733683 0.08 0.00 0.06 0.00 0.00 0.74 0.00 0.12
#> TCGA.E1.A7YO.01 3 0.3314 0.681106 0.00 0.00 0.80 0.00 0.08 0.00 0.02 0.10
#> TCGA.TQ.A7RG.01 1 0.0000 0.930686 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RY.A847.01 1 0.2025 0.852388 0.88 0.00 0.00 0.00 0.00 0.10 0.00 0.02
#> TCGA.VM.A8CA.01 6 0.2025 0.786361 0.10 0.00 0.00 0.00 0.00 0.88 0.00 0.02
#> TCGA.DB.A4XG.01 3 0.4953 0.425932 0.00 0.00 0.58 0.00 0.16 0.00 0.02 0.24
#> TCGA.FG.A60K.01 1 0.0471 0.928085 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.S9.A6TY.01 5 0.3503 0.657294 0.00 0.00 0.08 0.00 0.78 0.00 0.02 0.12
#> TCGA.TQ.A7RQ.01 6 0.4544 0.680935 0.06 0.00 0.06 0.00 0.00 0.66 0.00 0.22
#> TCGA.IK.8125.01 7 0.3078 0.608468 0.00 0.00 0.00 0.06 0.02 0.00 0.82 0.10
#> TCGA.HT.A74K.01 7 0.2348 0.682951 0.00 0.00 0.00 0.06 0.04 0.00 0.88 0.02
#> TCGA.QH.A6X8.01 2 0.1804 0.868591 0.00 0.90 0.00 0.00 0.00 0.00 0.02 0.08
#> TCGA.HT.7681.01 1 0.0000 0.930686 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A72Z.01 7 0.3913 0.620642 0.00 0.04 0.00 0.06 0.00 0.00 0.74 0.16
#> TCGA.DU.8168.01 2 0.0808 0.889674 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.TQ.A7RN.01 1 0.0471 0.927768 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DH.5141.01 3 0.1091 0.732152 0.00 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.EZ.7264.01 8 0.6187 0.276738 0.00 0.00 0.02 0.28 0.00 0.06 0.20 0.44
#> TCGA.QH.A65V.01 1 0.1607 0.897181 0.92 0.00 0.00 0.00 0.00 0.04 0.00 0.04
#> TCGA.DU.A6S8.01 4 0.1091 0.773125 0.00 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.DU.7298.01 3 0.3263 0.661683 0.00 0.00 0.78 0.00 0.10 0.00 0.00 0.12
#> TCGA.DB.A64R.01 1 0.1091 0.917429 0.94 0.00 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.CS.5390.01 2 0.5930 -0.000846 0.00 0.40 0.00 0.00 0.32 0.00 0.22 0.06
#> TCGA.S9.A6WP.01 5 0.0471 0.694521 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.E1.A7YS.01 2 0.1804 0.868591 0.00 0.90 0.00 0.00 0.00 0.00 0.02 0.08
#> TCGA.DU.7294.01 8 0.5456 -0.242051 0.00 0.00 0.42 0.00 0.08 0.02 0.04 0.44
#> TCGA.HT.7695.01 1 0.3586 0.780864 0.78 0.00 0.04 0.00 0.00 0.06 0.00 0.12
#> TCGA.FG.7637.01 3 0.2807 0.655574 0.04 0.00 0.84 0.00 0.00 0.02 0.00 0.10
#> TCGA.S9.A6U5.01 1 0.1557 0.887253 0.92 0.00 0.00 0.00 0.00 0.06 0.00 0.02
#> TCGA.DB.5274.01 5 0.2591 0.634060 0.00 0.02 0.00 0.00 0.86 0.00 0.08 0.04
#> TCGA.HW.7487.01 3 0.3102 0.695048 0.00 0.00 0.82 0.00 0.08 0.00 0.02 0.08
#> TCGA.HW.7491.01 3 0.4371 0.553535 0.00 0.00 0.68 0.02 0.16 0.00 0.00 0.14
#> TCGA.HT.8012.01 3 0.2407 0.702908 0.00 0.00 0.86 0.00 0.08 0.00 0.00 0.06
#> TCGA.S9.A7QZ.01 7 0.3291 0.623494 0.00 0.00 0.00 0.00 0.28 0.00 0.70 0.02
#> TCGA.QH.A6X4.01 6 0.2025 0.786361 0.10 0.00 0.00 0.00 0.00 0.88 0.00 0.02
#> TCGA.P5.A77W.01 5 0.2132 0.706674 0.00 0.00 0.04 0.00 0.88 0.00 0.00 0.08
#> TCGA.DU.7302.01 7 0.3551 0.662589 0.00 0.00 0.00 0.00 0.22 0.00 0.72 0.06
#> TCGA.HW.7495.01 1 0.0471 0.928085 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.QH.A65R.01 5 0.2624 0.634051 0.00 0.02 0.00 0.00 0.86 0.00 0.06 0.06
#> TCGA.HT.7875.01 6 0.1557 0.786759 0.06 0.00 0.00 0.00 0.00 0.92 0.00 0.02
#> TCGA.DU.6394.01 2 0.1091 0.877312 0.00 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.S9.A6WD.01 7 0.3586 0.610967 0.00 0.00 0.00 0.06 0.04 0.00 0.78 0.12
#> TCGA.TQ.A7RU.01 5 0.4211 0.582955 0.00 0.00 0.16 0.00 0.70 0.00 0.02 0.12
#> TCGA.DU.5874.01 2 0.0808 0.889674 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.R8.A6MK.01 1 0.2981 0.697179 0.76 0.00 0.00 0.00 0.00 0.22 0.00 0.02
#> TCGA.S9.A7J1.01 6 0.2025 0.786361 0.10 0.00 0.00 0.00 0.00 0.88 0.00 0.02
#> TCGA.P5.A5F0.01 3 0.1091 0.732152 0.00 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.R8.A73M.01 3 0.3922 0.483650 0.00 0.00 0.64 0.00 0.06 0.00 0.00 0.30
#> TCGA.DU.A6S3.01 5 0.2591 0.700214 0.00 0.00 0.04 0.00 0.86 0.00 0.02 0.08
#> TCGA.DB.A4XH.01 2 0.0808 0.889674 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.VW.A7QS.01 6 0.5839 0.074634 0.00 0.00 0.14 0.02 0.00 0.42 0.04 0.38
#> TCGA.DU.8164.01 5 0.2224 0.617525 0.00 0.00 0.00 0.00 0.86 0.00 0.12 0.02
#> TCGA.HT.7468.01 6 0.3523 0.654111 0.00 0.00 0.00 0.10 0.00 0.78 0.02 0.10
#> TCGA.TQ.A7RI.01 1 0.0000 0.930686 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5279.01 4 0.2569 0.731334 0.00 0.00 0.00 0.82 0.00 0.00 0.02 0.16
#> TCGA.DU.7018.01 2 0.1563 0.846701 0.00 0.90 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.HT.7677.01 5 0.5445 0.041750 0.00 0.00 0.36 0.00 0.42 0.00 0.02 0.20
#> TCGA.TM.A84M.01 4 0.1091 0.773125 0.00 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.F6.A8O3.01 3 0.3002 0.635442 0.04 0.00 0.82 0.00 0.00 0.02 0.00 0.12
#> TCGA.QH.A86X.01 1 0.0000 0.930686 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A76R.01 6 0.1607 0.783790 0.04 0.00 0.00 0.00 0.00 0.92 0.00 0.04
#> TCGA.DH.5144.01 5 0.2265 0.706532 0.00 0.00 0.02 0.00 0.88 0.00 0.02 0.08
#> TCGA.RY.A840.01 6 0.0471 0.775324 0.02 0.00 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.HW.A5KJ.01 2 0.0471 0.889361 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.HT.8105.01 2 0.0808 0.889674 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.HT.7471.01 5 0.4211 0.582955 0.00 0.00 0.16 0.00 0.70 0.00 0.02 0.12
#> TCGA.HT.A619.01 7 0.3618 0.357780 0.00 0.38 0.00 0.00 0.02 0.00 0.60 0.00
#> TCGA.HT.A5R9.01 5 0.3314 0.666774 0.00 0.00 0.10 0.00 0.80 0.00 0.02 0.08
#> TCGA.CS.5396.01 4 0.1091 0.773125 0.00 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.DU.6400.01 2 0.0471 0.891200 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.S9.A6WL.01 5 0.4433 0.425785 0.00 0.20 0.00 0.00 0.68 0.00 0.06 0.06
#> TCGA.DB.A75K.01 3 0.2407 0.717776 0.00 0.00 0.86 0.00 0.06 0.00 0.00 0.08
#> TCGA.DB.A64Q.01 6 0.3198 0.523145 0.00 0.00 0.00 0.26 0.00 0.72 0.00 0.02
#> TCGA.P5.A737.01 6 0.3880 0.511968 0.00 0.00 0.02 0.00 0.00 0.64 0.02 0.32
#> TCGA.S9.A6WH.01 2 0.0808 0.889674 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.HT.7616.01 7 0.3404 0.574517 0.00 0.24 0.00 0.00 0.00 0.00 0.72 0.04
#> TCGA.RY.A83Y.01 5 0.5458 0.326046 0.00 0.00 0.22 0.00 0.52 0.00 0.04 0.22
#> TCGA.DB.A64U.01 1 0.3299 0.703623 0.76 0.00 0.00 0.00 0.00 0.18 0.00 0.06
#> TCGA.DB.A64W.01 2 0.1341 0.870796 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.R8.A6MO.01 5 0.1804 0.658161 0.00 0.00 0.00 0.00 0.90 0.00 0.08 0.02
#> TCGA.HW.8322.01 1 0.2719 0.767206 0.80 0.00 0.00 0.00 0.00 0.18 0.00 0.02
#> TCGA.DU.5870.02 4 0.2224 0.745196 0.00 0.00 0.00 0.86 0.00 0.00 0.02 0.12
#> TCGA.CS.6668.01 4 0.4244 0.377817 0.00 0.00 0.00 0.64 0.00 0.00 0.24 0.12
#> TCGA.DU.5870.01 6 0.1741 0.769912 0.02 0.00 0.00 0.02 0.00 0.92 0.00 0.04
#> TCGA.HT.7692.01 6 0.2025 0.786361 0.10 0.00 0.00 0.00 0.00 0.88 0.00 0.02
#> TCGA.R8.A6ML.01 8 0.5855 0.205258 0.00 0.00 0.00 0.32 0.00 0.04 0.28 0.36
#> TCGA.DU.6410.01 5 0.4224 -0.250352 0.00 0.00 0.00 0.00 0.48 0.00 0.46 0.06
#> TCGA.TQ.A7RO.01 3 0.4211 0.480337 0.12 0.00 0.70 0.00 0.00 0.02 0.00 0.16
#> TCGA.E1.5318.01 2 0.0808 0.889674 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.S9.A7J3.01 7 0.1563 0.713895 0.00 0.00 0.00 0.00 0.10 0.00 0.90 0.00
#> TCGA.TQ.A7RS.01 1 0.0000 0.930686 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A65Z.01 5 0.2071 0.711750 0.00 0.00 0.02 0.00 0.90 0.00 0.04 0.04
#> TCGA.P5.A730.01 3 0.1341 0.722147 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.RY.A83X.01 3 0.1091 0.732152 0.00 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.S9.A6UB.01 7 0.3449 0.570338 0.00 0.00 0.00 0.00 0.32 0.00 0.66 0.02
#> TCGA.DH.A66F.01 3 0.2981 0.634549 0.00 0.00 0.76 0.00 0.00 0.00 0.02 0.22
#> TCGA.DU.6393.01 2 0.4294 0.562847 0.00 0.68 0.00 0.00 0.22 0.00 0.04 0.06
#> TCGA.S9.A7IY.01 1 0.0000 0.930686 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7641.01 3 0.1091 0.732152 0.00 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.DU.7009.01 6 0.5062 0.334572 0.38 0.00 0.02 0.00 0.00 0.48 0.00 0.12
#> TCGA.FG.8186.01 1 0.1091 0.917429 0.94 0.00 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.DB.A64L.01 7 0.1607 0.714997 0.00 0.04 0.00 0.00 0.04 0.00 0.92 0.00
#> TCGA.VV.A829.01 4 0.2224 0.750239 0.00 0.00 0.00 0.86 0.00 0.02 0.00 0.12
#> TCGA.DU.6397.02 4 0.1887 0.769153 0.00 0.00 0.00 0.90 0.00 0.06 0.00 0.04
#> TCGA.DU.6397.01 6 0.1887 0.779668 0.04 0.00 0.00 0.00 0.00 0.90 0.00 0.06
#> TCGA.CS.6670.01 6 0.1887 0.789620 0.06 0.00 0.00 0.00 0.00 0.90 0.00 0.04
#> TCGA.QH.A65X.01 6 0.5918 0.230676 0.38 0.00 0.08 0.00 0.00 0.38 0.00 0.16
#> TCGA.DB.A64P.01 3 0.1091 0.732122 0.00 0.00 0.94 0.00 0.06 0.00 0.00 0.00
#> TCGA.QH.A6CZ.01 6 0.2025 0.786361 0.10 0.00 0.00 0.00 0.00 0.88 0.00 0.02
#> TCGA.DH.A669.02 2 0.1804 0.868591 0.00 0.90 0.00 0.00 0.00 0.00 0.02 0.08
#> TCGA.DH.A669.01 2 0.1804 0.868591 0.00 0.90 0.00 0.00 0.00 0.00 0.02 0.08
#> TCGA.VM.A8CB.01 1 0.1091 0.912326 0.94 0.00 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.HT.7687.01 2 0.1091 0.877312 0.00 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.TM.A84G.01 7 0.3270 0.627789 0.00 0.00 0.00 0.00 0.06 0.02 0.80 0.12
#> TCGA.CS.5394.01 5 0.2624 0.634051 0.00 0.02 0.00 0.00 0.86 0.00 0.06 0.06
#> TCGA.FG.5962.01 4 0.5770 -0.220056 0.00 0.00 0.00 0.42 0.00 0.04 0.28 0.26
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: Node01111-leaf , Node01112-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01211-leaf , Node01212-leaf , Node01213 , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node01224-leaf , Node01225-leaf , Node01311-leaf , Node01312-leaf , Node01313-leaf , Node01411-leaf , Node01412-leaf , Node01431-leaf , Node01432-leaf , Node02211-leaf , Node02212 , Node02221 , Node02222-leaf , Node02223-leaf , Node02231 , Node02232-leaf , Node02233-leaf , Node02234-leaf , Node02311-leaf , Node02312-leaf , Node02313-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 53 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 0.4954 0.505 0.505
#> 3 3 0.651 0.645 0.854 0.2179 0.958 0.917
#> 4 4 0.613 0.502 0.755 0.1010 0.888 0.760
#> 5 5 0.598 0.509 0.710 0.0718 0.875 0.657
#> 6 6 0.597 0.451 0.763 0.0501 0.817 0.477
#> 7 7 0.635 0.637 0.768 0.0635 0.828 0.448
#> 8 8 0.686 0.646 0.783 0.0208 0.953 0.760
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.S9.A7J2.01 1 0 1 1 0
#> TCGA.HT.A74L.01 2 0 1 0 1
#> TCGA.FG.A710.01 2 0 1 0 1
#> TCGA.DU.A6S6.01 2 0 1 0 1
#> TCGA.FG.7634.01 1 0 1 1 0
#> TCGA.FG.7638.01 2 0 1 0 1
#> TCGA.FG.A6J1.01 2 0 1 0 1
#> TCGA.HT.7608.01 1 0 1 1 0
#> TCGA.W9.A837.01 1 0 1 1 0
#> TCGA.P5.A5ET.01 1 0 1 1 0
#> TCGA.P5.A77X.01 2 0 1 0 1
#> TCGA.KT.A74X.01 1 0 1 1 0
#> TCGA.TQ.A7RG.01 1 0 1 1 0
#> TCGA.RY.A847.01 1 0 1 1 0
#> TCGA.VM.A8CA.01 1 0 1 1 0
#> TCGA.FG.A60K.01 2 0 1 0 1
#> TCGA.TQ.A7RQ.01 2 0 1 0 1
#> TCGA.HT.7681.01 2 0 1 0 1
#> TCGA.TQ.A7RN.01 1 0 1 1 0
#> TCGA.QH.A65V.01 2 0 1 0 1
#> TCGA.DB.A64R.01 2 0 1 0 1
#> TCGA.HT.7695.01 2 0 1 0 1
#> TCGA.FG.7637.01 1 0 1 1 0
#> TCGA.S9.A6U5.01 1 0 1 1 0
#> TCGA.QH.A6X4.01 1 0 1 1 0
#> TCGA.HW.7495.01 2 0 1 0 1
#> TCGA.HT.7875.01 1 0 1 1 0
#> TCGA.R8.A6MK.01 1 0 1 1 0
#> TCGA.S9.A7J1.01 1 0 1 1 0
#> TCGA.HT.7468.01 1 0 1 1 0
#> TCGA.TQ.A7RI.01 2 0 1 0 1
#> TCGA.F6.A8O3.01 1 0 1 1 0
#> TCGA.QH.A86X.01 1 0 1 1 0
#> TCGA.DU.A76R.01 1 0 1 1 0
#> TCGA.RY.A840.01 1 0 1 1 0
#> TCGA.CS.5396.01 2 0 1 0 1
#> TCGA.DB.A64Q.01 2 0 1 0 1
#> TCGA.DB.A64U.01 2 0 1 0 1
#> TCGA.HW.8322.01 1 0 1 1 0
#> TCGA.DU.5870.01 2 0 1 0 1
#> TCGA.HT.7692.01 1 0 1 1 0
#> TCGA.TQ.A7RO.01 1 0 1 1 0
#> TCGA.TQ.A7RS.01 2 0 1 0 1
#> TCGA.P5.A730.01 1 0 1 1 0
#> TCGA.S9.A7IY.01 1 0 1 1 0
#> TCGA.DU.7009.01 2 0 1 0 1
#> TCGA.FG.8186.01 2 0 1 0 1
#> TCGA.DU.6397.02 1 0 1 1 0
#> TCGA.DU.6397.01 1 0 1 1 0
#> TCGA.CS.6670.01 1 0 1 1 0
#> TCGA.QH.A65X.01 2 0 1 0 1
#> TCGA.QH.A6CZ.01 1 0 1 1 0
#> TCGA.VM.A8CB.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.S9.A7J2.01 1 0.0000 0.7196 1.00 0.00 0.00
#> TCGA.HT.A74L.01 2 0.0892 0.8896 0.00 0.98 0.02
#> TCGA.FG.A710.01 2 0.5706 0.8228 0.00 0.68 0.32
#> TCGA.DU.A6S6.01 2 0.5706 0.8228 0.00 0.68 0.32
#> TCGA.FG.7634.01 1 0.5216 0.4918 0.74 0.00 0.26
#> TCGA.FG.7638.01 2 0.3340 0.8886 0.00 0.88 0.12
#> TCGA.FG.A6J1.01 2 0.2959 0.8912 0.00 0.90 0.10
#> TCGA.HT.7608.01 1 0.4291 0.6012 0.82 0.00 0.18
#> TCGA.W9.A837.01 1 0.5835 0.0821 0.66 0.00 0.34
#> TCGA.P5.A5ET.01 1 0.0000 0.7196 1.00 0.00 0.00
#> TCGA.P5.A77X.01 2 0.4291 0.8758 0.00 0.82 0.18
#> TCGA.KT.A74X.01 1 0.0000 0.7196 1.00 0.00 0.00
#> TCGA.TQ.A7RG.01 1 0.6045 -0.2726 0.62 0.00 0.38
#> TCGA.RY.A847.01 1 0.4291 0.6012 0.82 0.00 0.18
#> TCGA.VM.A8CA.01 1 0.4291 0.6012 0.82 0.00 0.18
#> TCGA.FG.A60K.01 2 0.0000 0.8973 0.00 1.00 0.00
#> TCGA.TQ.A7RQ.01 2 0.5706 0.8228 0.00 0.68 0.32
#> TCGA.HT.7681.01 2 0.0000 0.8973 0.00 1.00 0.00
#> TCGA.TQ.A7RN.01 1 0.2537 0.6412 0.92 0.00 0.08
#> TCGA.QH.A65V.01 2 0.0000 0.8973 0.00 1.00 0.00
#> TCGA.DB.A64R.01 2 0.0892 0.8896 0.00 0.98 0.02
#> TCGA.HT.7695.01 2 0.0000 0.8973 0.00 1.00 0.00
#> TCGA.FG.7637.01 1 0.3686 0.5803 0.86 0.00 0.14
#> TCGA.S9.A6U5.01 1 0.6126 -0.3585 0.60 0.00 0.40
#> TCGA.QH.A6X4.01 1 0.0000 0.7196 1.00 0.00 0.00
#> TCGA.HW.7495.01 2 0.0000 0.8973 0.00 1.00 0.00
#> TCGA.HT.7875.01 1 0.0000 0.7196 1.00 0.00 0.00
#> TCGA.R8.A6MK.01 3 0.6280 0.7713 0.46 0.00 0.54
#> TCGA.S9.A7J1.01 1 0.4002 0.6043 0.84 0.00 0.16
#> TCGA.HT.7468.01 1 0.0000 0.7196 1.00 0.00 0.00
#> TCGA.TQ.A7RI.01 2 0.5706 0.8228 0.00 0.68 0.32
#> TCGA.F6.A8O3.01 1 0.0892 0.7064 0.98 0.00 0.02
#> TCGA.QH.A86X.01 1 0.5835 0.0353 0.66 0.00 0.34
#> TCGA.DU.A76R.01 1 0.6280 -0.6187 0.54 0.00 0.46
#> TCGA.RY.A840.01 1 0.0000 0.7196 1.00 0.00 0.00
#> TCGA.CS.5396.01 2 0.5706 0.8228 0.00 0.68 0.32
#> TCGA.DB.A64Q.01 2 0.0000 0.8973 0.00 1.00 0.00
#> TCGA.DB.A64U.01 2 0.0000 0.8973 0.00 1.00 0.00
#> TCGA.HW.8322.01 1 0.0000 0.7196 1.00 0.00 0.00
#> TCGA.DU.5870.01 2 0.5706 0.8228 0.00 0.68 0.32
#> TCGA.HT.7692.01 1 0.0892 0.7125 0.98 0.00 0.02
#> TCGA.TQ.A7RO.01 3 0.6045 0.7991 0.38 0.00 0.62
#> TCGA.TQ.A7RS.01 2 0.4555 0.8698 0.00 0.80 0.20
#> TCGA.P5.A730.01 1 0.5016 0.3231 0.76 0.00 0.24
#> TCGA.S9.A7IY.01 1 0.4291 0.6012 0.82 0.00 0.18
#> TCGA.DU.7009.01 2 0.0000 0.8973 0.00 1.00 0.00
#> TCGA.FG.8186.01 2 0.0000 0.8973 0.00 1.00 0.00
#> TCGA.DU.6397.02 1 0.4291 0.6012 0.82 0.00 0.18
#> TCGA.DU.6397.01 1 0.2537 0.6891 0.92 0.00 0.08
#> TCGA.CS.6670.01 1 0.6045 -0.4050 0.62 0.00 0.38
#> TCGA.QH.A65X.01 2 0.3340 0.8886 0.00 0.88 0.12
#> TCGA.QH.A6CZ.01 1 0.0000 0.7196 1.00 0.00 0.00
#> TCGA.VM.A8CB.01 1 0.0892 0.7125 0.98 0.00 0.02
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.S9.A7J2.01 1 0.0000 0.6128 1.00 0.00 0.00 0.00
#> TCGA.HT.A74L.01 2 0.2011 0.7217 0.00 0.92 0.08 0.00
#> TCGA.FG.A710.01 4 0.6299 0.9390 0.00 0.42 0.06 0.52
#> TCGA.DU.A6S6.01 4 0.5957 0.8863 0.00 0.42 0.04 0.54
#> TCGA.FG.7634.01 1 0.7583 -0.1033 0.48 0.00 0.28 0.24
#> TCGA.FG.7638.01 2 0.3975 0.4129 0.00 0.76 0.00 0.24
#> TCGA.FG.A6J1.01 2 0.5512 0.1106 0.00 0.66 0.04 0.30
#> TCGA.HT.7608.01 1 0.5956 0.3398 0.68 0.00 0.22 0.10
#> TCGA.W9.A837.01 1 0.6370 0.1614 0.62 0.00 0.28 0.10
#> TCGA.P5.A5ET.01 1 0.0707 0.6069 0.98 0.00 0.00 0.02
#> TCGA.P5.A77X.01 2 0.5256 0.2308 0.00 0.70 0.04 0.26
#> TCGA.KT.A74X.01 1 0.1411 0.5964 0.96 0.00 0.02 0.02
#> TCGA.TQ.A7RG.01 1 0.5355 -0.2258 0.62 0.00 0.36 0.02
#> TCGA.RY.A847.01 1 0.5956 0.3398 0.68 0.00 0.22 0.10
#> TCGA.VM.A8CA.01 1 0.5956 0.3398 0.68 0.00 0.22 0.10
#> TCGA.FG.A60K.01 2 0.0000 0.7923 0.00 1.00 0.00 0.00
#> TCGA.TQ.A7RQ.01 4 0.6586 0.9211 0.00 0.42 0.08 0.50
#> TCGA.HT.7681.01 2 0.0000 0.7923 0.00 1.00 0.00 0.00
#> TCGA.TQ.A7RN.01 1 0.3606 0.4213 0.84 0.00 0.14 0.02
#> TCGA.QH.A65V.01 2 0.0000 0.7923 0.00 1.00 0.00 0.00
#> TCGA.DB.A64R.01 2 0.2345 0.7072 0.00 0.90 0.10 0.00
#> TCGA.HT.7695.01 2 0.0000 0.7923 0.00 1.00 0.00 0.00
#> TCGA.FG.7637.01 1 0.7095 0.0286 0.56 0.00 0.26 0.18
#> TCGA.S9.A6U5.01 3 0.6005 0.5162 0.46 0.00 0.50 0.04
#> TCGA.QH.A6X4.01 1 0.1411 0.5964 0.96 0.00 0.02 0.02
#> TCGA.HW.7495.01 2 0.0000 0.7923 0.00 1.00 0.00 0.00
#> TCGA.HT.7875.01 1 0.0707 0.6069 0.98 0.00 0.00 0.02
#> TCGA.R8.A6MK.01 3 0.6586 0.6612 0.42 0.00 0.50 0.08
#> TCGA.S9.A7J1.01 1 0.4553 0.4279 0.78 0.00 0.18 0.04
#> TCGA.HT.7468.01 1 0.0000 0.6128 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RI.01 4 0.6299 0.9390 0.00 0.42 0.06 0.52
#> TCGA.F6.A8O3.01 1 0.0000 0.6128 1.00 0.00 0.00 0.00
#> TCGA.QH.A86X.01 1 0.7382 -0.1395 0.52 0.00 0.26 0.22
#> TCGA.DU.A76R.01 3 0.4994 0.6079 0.48 0.00 0.52 0.00
#> TCGA.RY.A840.01 1 0.0000 0.6128 1.00 0.00 0.00 0.00
#> TCGA.CS.5396.01 4 0.5957 0.8863 0.00 0.42 0.04 0.54
#> TCGA.DB.A64Q.01 2 0.0000 0.7923 0.00 1.00 0.00 0.00
#> TCGA.DB.A64U.01 2 0.0000 0.7923 0.00 1.00 0.00 0.00
#> TCGA.HW.8322.01 1 0.0000 0.6128 1.00 0.00 0.00 0.00
#> TCGA.DU.5870.01 4 0.6299 0.9390 0.00 0.42 0.06 0.52
#> TCGA.HT.7692.01 1 0.1211 0.5978 0.96 0.00 0.04 0.00
#> TCGA.TQ.A7RO.01 3 0.6836 0.5443 0.28 0.00 0.58 0.14
#> TCGA.TQ.A7RS.01 2 0.4948 -0.5362 0.00 0.56 0.00 0.44
#> TCGA.P5.A730.01 1 0.6617 -0.0561 0.60 0.00 0.28 0.12
#> TCGA.S9.A7IY.01 1 0.5956 0.3398 0.68 0.00 0.22 0.10
#> TCGA.DU.7009.01 2 0.0000 0.7923 0.00 1.00 0.00 0.00
#> TCGA.FG.8186.01 2 0.0000 0.7923 0.00 1.00 0.00 0.00
#> TCGA.DU.6397.02 1 0.5956 0.3398 0.68 0.00 0.22 0.10
#> TCGA.DU.6397.01 1 0.5151 0.4384 0.76 0.00 0.14 0.10
#> TCGA.CS.6670.01 1 0.5487 -0.2919 0.58 0.00 0.40 0.02
#> TCGA.QH.A65X.01 2 0.4134 0.3657 0.00 0.74 0.00 0.26
#> TCGA.QH.A6CZ.01 1 0.1411 0.5964 0.96 0.00 0.02 0.02
#> TCGA.VM.A8CB.01 1 0.0000 0.6128 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.S9.A7J2.01 1 0.0000 0.6923 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A74L.01 2 0.2331 0.7078 0.00 0.90 0.00 0.02 0.08
#> TCGA.FG.A710.01 4 0.5925 0.8820 0.00 0.40 0.06 0.52 0.02
#> TCGA.DU.A6S6.01 4 0.6172 0.7880 0.00 0.40 0.02 0.50 0.08
#> TCGA.FG.7634.01 1 0.8139 -0.1855 0.34 0.00 0.10 0.28 0.28
#> TCGA.FG.7638.01 2 0.4132 0.3567 0.00 0.72 0.00 0.26 0.02
#> TCGA.FG.A6J1.01 2 0.4854 0.2773 0.00 0.68 0.00 0.26 0.06
#> TCGA.HT.7608.01 5 0.4287 0.7477 0.46 0.00 0.00 0.00 0.54
#> TCGA.W9.A837.01 5 0.6139 0.6637 0.38 0.00 0.08 0.02 0.52
#> TCGA.P5.A5ET.01 1 0.0000 0.6923 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A77X.01 2 0.4060 0.0155 0.00 0.64 0.00 0.36 0.00
#> TCGA.KT.A74X.01 1 0.0000 0.6923 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RG.01 1 0.5689 -0.4746 0.48 0.00 0.44 0.00 0.08
#> TCGA.RY.A847.01 5 0.4287 0.7477 0.46 0.00 0.00 0.00 0.54
#> TCGA.VM.A8CA.01 5 0.4287 0.7477 0.46 0.00 0.00 0.00 0.54
#> TCGA.FG.A60K.01 2 0.0000 0.7738 0.00 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RQ.01 4 0.7171 0.8305 0.00 0.40 0.12 0.42 0.06
#> TCGA.HT.7681.01 2 0.0000 0.7738 0.00 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RN.01 1 0.2929 0.4807 0.82 0.00 0.18 0.00 0.00
#> TCGA.QH.A65V.01 2 0.0000 0.7738 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.A64R.01 2 0.2873 0.6737 0.00 0.86 0.00 0.02 0.12
#> TCGA.HT.7695.01 2 0.0000 0.7738 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.7637.01 1 0.8029 -0.1385 0.38 0.00 0.10 0.30 0.22
#> TCGA.S9.A6U5.01 5 0.6610 0.2254 0.26 0.00 0.28 0.00 0.46
#> TCGA.QH.A6X4.01 1 0.0000 0.6923 1.00 0.00 0.00 0.00 0.00
#> TCGA.HW.7495.01 2 0.0000 0.7738 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7875.01 1 0.0000 0.6923 1.00 0.00 0.00 0.00 0.00
#> TCGA.R8.A6MK.01 3 0.6148 0.6480 0.26 0.00 0.60 0.02 0.12
#> TCGA.S9.A7J1.01 1 0.4227 -0.5293 0.58 0.00 0.00 0.00 0.42
#> TCGA.HT.7468.01 1 0.0000 0.6923 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RI.01 4 0.5925 0.8820 0.00 0.40 0.06 0.52 0.02
#> TCGA.F6.A8O3.01 1 0.0609 0.6784 0.98 0.00 0.00 0.00 0.02
#> TCGA.QH.A86X.01 5 0.8560 -0.2428 0.26 0.00 0.22 0.22 0.30
#> TCGA.DU.A76R.01 3 0.6503 0.5075 0.30 0.00 0.48 0.00 0.22
#> TCGA.RY.A840.01 1 0.0000 0.6923 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.5396.01 4 0.4182 0.8273 0.00 0.40 0.00 0.60 0.00
#> TCGA.DB.A64Q.01 2 0.0000 0.7738 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.A64U.01 2 0.0000 0.7738 0.00 1.00 0.00 0.00 0.00
#> TCGA.HW.8322.01 1 0.0000 0.6923 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5870.01 4 0.6903 0.8497 0.00 0.40 0.12 0.44 0.04
#> TCGA.HT.7692.01 1 0.1043 0.6438 0.96 0.00 0.00 0.00 0.04
#> TCGA.TQ.A7RO.01 3 0.3106 0.5824 0.14 0.00 0.84 0.02 0.00
#> TCGA.TQ.A7RS.01 2 0.4302 -0.5445 0.00 0.52 0.00 0.48 0.00
#> TCGA.P5.A730.01 1 0.6912 -0.1308 0.54 0.00 0.28 0.12 0.06
#> TCGA.S9.A7IY.01 5 0.4287 0.7477 0.46 0.00 0.00 0.00 0.54
#> TCGA.DU.7009.01 2 0.0000 0.7738 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.8186.01 2 0.0000 0.7738 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.6397.02 5 0.4287 0.7477 0.46 0.00 0.00 0.00 0.54
#> TCGA.DU.6397.01 1 0.4307 -0.7031 0.50 0.00 0.00 0.00 0.50
#> TCGA.CS.6670.01 3 0.5304 0.5071 0.42 0.00 0.54 0.02 0.02
#> TCGA.QH.A65X.01 2 0.4360 0.2500 0.00 0.68 0.00 0.30 0.02
#> TCGA.QH.A6CZ.01 1 0.0000 0.6923 1.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8CB.01 1 0.0000 0.6923 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.S9.A7J2.01 1 0.0000 0.6071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A74L.01 2 0.6171 0.5910 0.00 0.66 0.06 0.08 0.10 0.10
#> TCGA.FG.A710.01 4 0.4887 0.7573 0.00 0.12 0.00 0.70 0.16 0.02
#> TCGA.DU.A6S6.01 4 0.5778 0.7101 0.00 0.12 0.00 0.64 0.08 0.16
#> TCGA.FG.7634.01 6 0.5569 0.6434 0.32 0.00 0.02 0.00 0.10 0.56
#> TCGA.FG.7638.01 4 0.3578 0.6945 0.00 0.34 0.00 0.66 0.00 0.00
#> TCGA.FG.A6J1.01 4 0.4675 0.7205 0.00 0.28 0.00 0.66 0.04 0.02
#> TCGA.HT.7608.01 1 0.5992 -0.5784 0.48 0.00 0.14 0.02 0.36 0.00
#> TCGA.W9.A837.01 5 0.6047 0.0000 0.34 0.00 0.26 0.00 0.40 0.00
#> TCGA.P5.A5ET.01 1 0.0547 0.5998 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.P5.A77X.01 4 0.3309 0.7455 0.00 0.28 0.00 0.72 0.00 0.00
#> TCGA.KT.A74X.01 1 0.0000 0.6071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RG.01 1 0.4337 -0.2283 0.50 0.00 0.48 0.00 0.02 0.00
#> TCGA.RY.A847.01 1 0.5555 -0.5824 0.48 0.00 0.14 0.00 0.38 0.00
#> TCGA.VM.A8CA.01 1 0.5555 -0.5824 0.48 0.00 0.14 0.00 0.38 0.00
#> TCGA.FG.A60K.01 2 0.0000 0.9316 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RQ.01 4 0.6158 0.6366 0.00 0.12 0.00 0.48 0.36 0.04
#> TCGA.HT.7681.01 2 0.0000 0.9316 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RN.01 1 0.2048 0.4736 0.88 0.00 0.12 0.00 0.00 0.00
#> TCGA.QH.A65V.01 2 0.0000 0.9316 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64R.01 2 0.5733 0.6319 0.00 0.68 0.08 0.02 0.12 0.10
#> TCGA.HT.7695.01 2 0.0000 0.9316 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7637.01 6 0.5058 0.6109 0.40 0.00 0.02 0.00 0.04 0.54
#> TCGA.S9.A6U5.01 3 0.5721 -0.0228 0.24 0.00 0.52 0.00 0.24 0.00
#> TCGA.QH.A6X4.01 1 0.0000 0.6071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HW.7495.01 2 0.0000 0.9316 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7875.01 1 0.0000 0.6071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.R8.A6MK.01 3 0.2048 0.6145 0.12 0.00 0.88 0.00 0.00 0.00
#> TCGA.S9.A7J1.01 1 0.5364 -0.4240 0.56 0.00 0.14 0.00 0.30 0.00
#> TCGA.HT.7468.01 1 0.0000 0.6071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RI.01 4 0.4887 0.7573 0.00 0.12 0.00 0.70 0.16 0.02
#> TCGA.F6.A8O3.01 1 0.1556 0.5199 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.QH.A86X.01 6 0.8365 0.1765 0.24 0.00 0.16 0.08 0.16 0.36
#> TCGA.DU.A76R.01 3 0.4613 0.4727 0.26 0.00 0.66 0.00 0.08 0.00
#> TCGA.RY.A840.01 1 0.0000 0.6071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.5396.01 4 0.2581 0.7743 0.00 0.12 0.00 0.86 0.00 0.02
#> TCGA.DB.A64Q.01 2 0.0000 0.9316 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64U.01 2 0.0000 0.9316 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HW.8322.01 1 0.0000 0.6071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5870.01 4 0.5609 0.7049 0.00 0.12 0.00 0.58 0.28 0.02
#> TCGA.HT.7692.01 1 0.0547 0.5964 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.TQ.A7RO.01 3 0.3851 0.5298 0.08 0.00 0.82 0.02 0.02 0.06
#> TCGA.TQ.A7RS.01 4 0.3711 0.7630 0.00 0.26 0.00 0.72 0.02 0.00
#> TCGA.P5.A730.01 1 0.5235 -0.4333 0.52 0.00 0.10 0.00 0.00 0.38
#> TCGA.S9.A7IY.01 1 0.5555 -0.5824 0.48 0.00 0.14 0.00 0.38 0.00
#> TCGA.DU.7009.01 2 0.0000 0.9316 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8186.01 2 0.0000 0.9316 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6397.02 1 0.5555 -0.5824 0.48 0.00 0.14 0.00 0.38 0.00
#> TCGA.DU.6397.01 1 0.4144 -0.1323 0.62 0.00 0.00 0.02 0.36 0.00
#> TCGA.CS.6670.01 1 0.5106 -0.2397 0.50 0.00 0.44 0.00 0.02 0.04
#> TCGA.QH.A65X.01 4 0.3499 0.7195 0.00 0.32 0.00 0.68 0.00 0.00
#> TCGA.QH.A6CZ.01 1 0.0000 0.6071 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8CB.01 1 0.0547 0.5964 0.98 0.00 0.00 0.00 0.02 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.S9.A7J2.01 1 0.0000 0.9230 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A74L.01 7 0.3047 0.5919 0.00 0.28 0.00 0.00 0.00 0.00 0.72
#> TCGA.FG.A710.01 4 0.1886 0.7824 0.00 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.DU.A6S6.01 4 0.6869 0.6721 0.00 0.22 0.02 0.52 0.08 0.04 0.12
#> TCGA.FG.7634.01 6 0.4092 0.5437 0.08 0.02 0.00 0.00 0.16 0.74 0.00
#> TCGA.FG.7638.01 7 0.5401 -0.2544 0.00 0.20 0.00 0.36 0.00 0.00 0.44
#> TCGA.FG.A6J1.01 7 0.5474 -0.2817 0.00 0.22 0.00 0.36 0.00 0.00 0.42
#> TCGA.HT.7608.01 5 0.3417 0.8389 0.26 0.00 0.00 0.02 0.72 0.00 0.00
#> TCGA.W9.A837.01 5 0.3667 0.7738 0.20 0.00 0.06 0.00 0.74 0.00 0.00
#> TCGA.P5.A5ET.01 1 0.2654 0.7995 0.86 0.00 0.00 0.02 0.10 0.02 0.00
#> TCGA.P5.A77X.01 7 0.5755 -0.3895 0.00 0.18 0.00 0.40 0.00 0.02 0.40
#> TCGA.KT.A74X.01 1 0.0504 0.9160 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RG.01 3 0.5504 0.4337 0.22 0.00 0.58 0.00 0.16 0.04 0.00
#> TCGA.RY.A847.01 5 0.2945 0.8394 0.26 0.00 0.00 0.00 0.74 0.00 0.00
#> TCGA.VM.A8CA.01 5 0.3417 0.8366 0.26 0.02 0.00 0.00 0.72 0.00 0.00
#> TCGA.FG.A60K.01 7 0.0000 0.7811 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.TQ.A7RQ.01 4 0.3494 0.7491 0.00 0.02 0.00 0.80 0.00 0.06 0.12
#> TCGA.HT.7681.01 7 0.0000 0.7811 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.TQ.A7RN.01 1 0.3388 0.6277 0.76 0.00 0.20 0.00 0.00 0.04 0.00
#> TCGA.QH.A65V.01 7 0.0000 0.7811 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DB.A64R.01 7 0.3606 0.5555 0.00 0.30 0.00 0.00 0.02 0.00 0.68
#> TCGA.HT.7695.01 7 0.0000 0.7811 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.FG.7637.01 6 0.4492 0.5534 0.12 0.00 0.04 0.00 0.12 0.72 0.00
#> TCGA.S9.A6U5.01 5 0.4869 -0.0316 0.06 0.02 0.38 0.00 0.54 0.00 0.00
#> TCGA.QH.A6X4.01 1 0.0504 0.9160 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.HW.7495.01 7 0.0000 0.7811 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.7875.01 1 0.0504 0.9082 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.R8.A6MK.01 3 0.4492 0.4657 0.04 0.12 0.72 0.00 0.12 0.00 0.00
#> TCGA.S9.A7J1.01 5 0.3413 0.7296 0.38 0.00 0.00 0.00 0.62 0.00 0.00
#> TCGA.HT.7468.01 1 0.0000 0.9230 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RI.01 4 0.1886 0.7824 0.00 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.F6.A8O3.01 1 0.3772 0.7294 0.80 0.06 0.02 0.10 0.02 0.00 0.00
#> TCGA.QH.A86X.01 6 0.7728 0.2815 0.10 0.20 0.14 0.00 0.18 0.38 0.00
#> TCGA.DU.A76R.01 3 0.5051 0.4949 0.10 0.02 0.66 0.00 0.20 0.02 0.00
#> TCGA.RY.A840.01 1 0.0000 0.9230 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.5396.01 4 0.4162 0.7578 0.00 0.12 0.00 0.74 0.00 0.02 0.12
#> TCGA.DB.A64Q.01 7 0.0000 0.7811 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DB.A64U.01 7 0.0000 0.7811 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.HW.8322.01 1 0.0000 0.9230 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5870.01 4 0.3208 0.7621 0.00 0.02 0.00 0.82 0.00 0.04 0.12
#> TCGA.HT.7692.01 1 0.0863 0.8862 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.TQ.A7RO.01 3 0.4969 0.3039 0.00 0.20 0.66 0.00 0.08 0.06 0.00
#> TCGA.TQ.A7RS.01 4 0.5233 0.5244 0.00 0.20 0.00 0.52 0.00 0.00 0.28
#> TCGA.P5.A730.01 6 0.6110 0.1213 0.24 0.00 0.28 0.00 0.04 0.44 0.00
#> TCGA.S9.A7IY.01 5 0.3047 0.8367 0.28 0.00 0.00 0.00 0.72 0.00 0.00
#> TCGA.DU.7009.01 7 0.0000 0.7811 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.FG.8186.01 7 0.0000 0.7811 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.6397.02 5 0.3685 0.7924 0.32 0.02 0.00 0.00 0.66 0.00 0.00
#> TCGA.DU.6397.01 5 0.4107 0.7934 0.24 0.00 0.00 0.02 0.70 0.04 0.00
#> TCGA.CS.6670.01 3 0.4461 0.3307 0.32 0.00 0.62 0.00 0.04 0.02 0.00
#> TCGA.QH.A65X.01 4 0.5421 0.2279 0.00 0.20 0.00 0.40 0.00 0.00 0.40
#> TCGA.QH.A6CZ.01 1 0.1006 0.9028 0.96 0.00 0.02 0.00 0.02 0.00 0.00
#> TCGA.VM.A8CB.01 1 0.0000 0.9230 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.S9.A7J2.01 1 0.0000 0.9274 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A74L.01 7 0.6382 0.5092 0.00 0.04 0.14 0.10 0.04 0.04 0.60 0.04
#> TCGA.FG.A710.01 4 0.3808 0.2512 0.00 0.00 0.00 0.62 0.00 0.00 0.04 0.34
#> TCGA.DU.A6S6.01 4 0.5587 0.2425 0.00 0.00 0.32 0.54 0.04 0.02 0.04 0.04
#> TCGA.FG.7634.01 6 0.4585 0.4877 0.04 0.02 0.02 0.04 0.08 0.76 0.00 0.04
#> TCGA.FG.7638.01 4 0.2852 0.5649 0.00 0.00 0.00 0.72 0.00 0.00 0.28 0.00
#> TCGA.FG.A6J1.01 4 0.4779 0.4977 0.00 0.00 0.08 0.60 0.00 0.00 0.28 0.04
#> TCGA.HT.7608.01 5 0.2406 0.8888 0.20 0.00 0.00 0.00 0.80 0.00 0.00 0.00
#> TCGA.W9.A837.01 5 0.3337 0.8323 0.16 0.02 0.00 0.00 0.78 0.00 0.00 0.04
#> TCGA.P5.A5ET.01 1 0.1408 0.8926 0.94 0.02 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.P5.A77X.01 4 0.4174 0.5722 0.00 0.00 0.04 0.70 0.00 0.02 0.22 0.02
#> TCGA.KT.A74X.01 1 0.0471 0.9215 0.98 0.02 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RG.01 2 0.5366 0.4536 0.34 0.52 0.02 0.00 0.08 0.04 0.00 0.00
#> TCGA.RY.A847.01 5 0.2406 0.8888 0.20 0.00 0.00 0.00 0.80 0.00 0.00 0.00
#> TCGA.VM.A8CA.01 5 0.2406 0.8888 0.20 0.00 0.00 0.00 0.80 0.00 0.00 0.00
#> TCGA.FG.A60K.01 7 0.0000 0.9149 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.TQ.A7RQ.01 8 0.4791 -0.4236 0.00 0.00 0.02 0.42 0.02 0.00 0.04 0.50
#> TCGA.HT.7681.01 7 0.0000 0.9149 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.TQ.A7RN.01 1 0.3843 0.4404 0.70 0.24 0.02 0.00 0.00 0.04 0.00 0.00
#> TCGA.QH.A65V.01 7 0.0000 0.9149 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DB.A64R.01 7 0.6854 0.4618 0.00 0.06 0.14 0.06 0.10 0.04 0.56 0.04
#> TCGA.HT.7695.01 7 0.0000 0.9149 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FG.7637.01 6 0.2680 0.5842 0.12 0.02 0.00 0.00 0.02 0.84 0.00 0.00
#> TCGA.S9.A6U5.01 5 0.4537 0.2192 0.10 0.40 0.00 0.00 0.50 0.00 0.00 0.00
#> TCGA.QH.A6X4.01 1 0.0471 0.9215 0.98 0.02 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HW.7495.01 7 0.0000 0.9149 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7875.01 1 0.0000 0.9274 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.R8.A6MK.01 2 0.3402 0.4586 0.06 0.82 0.06 0.00 0.04 0.02 0.00 0.00
#> TCGA.S9.A7J1.01 5 0.3374 0.7738 0.30 0.02 0.00 0.00 0.68 0.00 0.00 0.00
#> TCGA.HT.7468.01 1 0.0000 0.9274 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RI.01 4 0.4284 0.2415 0.00 0.00 0.02 0.58 0.00 0.00 0.04 0.36
#> TCGA.F6.A8O3.01 1 0.3131 0.7685 0.84 0.02 0.04 0.00 0.00 0.06 0.00 0.04
#> TCGA.QH.A86X.01 8 0.7964 -0.4326 0.12 0.08 0.10 0.00 0.12 0.26 0.00 0.32
#> TCGA.DU.A76R.01 2 0.4500 0.5098 0.14 0.70 0.00 0.00 0.12 0.02 0.00 0.02
#> TCGA.RY.A840.01 1 0.0000 0.9274 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.5396.01 4 0.2858 0.4950 0.00 0.00 0.04 0.86 0.00 0.02 0.04 0.04
#> TCGA.DB.A64Q.01 7 0.0000 0.9149 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DB.A64U.01 7 0.0000 0.9149 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HW.8322.01 1 0.0000 0.9274 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5870.01 4 0.4004 0.0604 0.00 0.00 0.00 0.50 0.00 0.00 0.04 0.46
#> TCGA.HT.7692.01 1 0.0808 0.8986 0.96 0.00 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.TQ.A7RO.01 2 0.4655 0.3038 0.04 0.58 0.34 0.00 0.02 0.02 0.00 0.00
#> TCGA.TQ.A7RS.01 4 0.2888 0.5756 0.00 0.00 0.00 0.80 0.00 0.00 0.16 0.04
#> TCGA.P5.A730.01 6 0.5518 0.2050 0.26 0.20 0.04 0.00 0.00 0.50 0.00 0.00
#> TCGA.S9.A7IY.01 5 0.2406 0.8888 0.20 0.00 0.00 0.00 0.80 0.00 0.00 0.00
#> TCGA.DU.7009.01 7 0.0000 0.9149 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FG.8186.01 7 0.0000 0.9149 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.6397.02 5 0.2756 0.8434 0.26 0.00 0.00 0.00 0.74 0.00 0.00 0.00
#> TCGA.DU.6397.01 5 0.2856 0.8766 0.20 0.00 0.00 0.00 0.78 0.02 0.00 0.00
#> TCGA.CS.6670.01 2 0.5889 0.3938 0.36 0.48 0.04 0.00 0.04 0.02 0.00 0.06
#> TCGA.QH.A65X.01 4 0.2756 0.5738 0.00 0.00 0.00 0.74 0.00 0.00 0.26 0.00
#> TCGA.QH.A6CZ.01 1 0.0471 0.9215 0.98 0.02 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8CB.01 1 0.0808 0.8986 0.96 0.00 0.00 0.00 0.04 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: Node0221. Child nodes: Node012131-leaf , Node012132-leaf , Node012133-leaf , Node012134-leaf , Node022121-leaf , Node022122-leaf , Node022123-leaf , Node022211-leaf , Node022212-leaf , Node022311-leaf , Node022312-leaf , Node022313-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["02212"]
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 22 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 1.000 1.000 0.4551 0.545 0.545
#> 3 3 1.000 1.000 1.000 0.1140 0.948 0.905
#> 4 4 0.937 0.966 0.955 0.4367 0.758 0.509
#> 5 5 0.786 0.773 0.859 0.0709 0.801 0.410
#> 6 6 0.753 0.576 0.807 0.0489 0.922 0.679
#> 7 7 0.732 0.782 0.787 0.0273 0.909 0.543
#> 8 8 0.795 0.782 0.875 0.0350 0.987 0.897
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.HT.A74L.01 1 0 1 1 0
#> TCGA.FG.A710.01 2 0 1 0 1
#> TCGA.DU.A6S6.01 1 0 1 1 0
#> TCGA.FG.7638.01 1 0 1 1 0
#> TCGA.FG.A6J1.01 1 0 1 1 0
#> TCGA.P5.A77X.01 2 0 1 0 1
#> TCGA.FG.A60K.01 1 0 1 1 0
#> TCGA.TQ.A7RQ.01 2 0 1 0 1
#> TCGA.HT.7681.01 1 0 1 1 0
#> TCGA.QH.A65V.01 1 0 1 1 0
#> TCGA.DB.A64R.01 1 0 1 1 0
#> TCGA.HT.7695.01 1 0 1 1 0
#> TCGA.HW.7495.01 1 0 1 1 0
#> TCGA.TQ.A7RI.01 1 0 1 1 0
#> TCGA.CS.5396.01 2 0 1 0 1
#> TCGA.DB.A64Q.01 2 0 1 0 1
#> TCGA.DB.A64U.01 1 0 1 1 0
#> TCGA.DU.5870.01 2 0 1 0 1
#> TCGA.TQ.A7RS.01 1 0 1 1 0
#> TCGA.DU.7009.01 1 0 1 1 0
#> TCGA.FG.8186.01 1 0 1 1 0
#> TCGA.QH.A65X.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.HT.A74L.01 1 0 1 1 0 0
#> TCGA.FG.A710.01 2 0 1 0 1 0
#> TCGA.DU.A6S6.01 1 0 1 1 0 0
#> TCGA.FG.7638.01 1 0 1 1 0 0
#> TCGA.FG.A6J1.01 1 0 1 1 0 0
#> TCGA.P5.A77X.01 3 0 1 0 0 1
#> TCGA.FG.A60K.01 1 0 1 1 0 0
#> TCGA.TQ.A7RQ.01 2 0 1 0 1 0
#> TCGA.HT.7681.01 1 0 1 1 0 0
#> TCGA.QH.A65V.01 1 0 1 1 0 0
#> TCGA.DB.A64R.01 1 0 1 1 0 0
#> TCGA.HT.7695.01 1 0 1 1 0 0
#> TCGA.HW.7495.01 1 0 1 1 0 0
#> TCGA.TQ.A7RI.01 1 0 1 1 0 0
#> TCGA.CS.5396.01 3 0 1 0 0 1
#> TCGA.DB.A64Q.01 3 0 1 0 0 1
#> TCGA.DB.A64U.01 1 0 1 1 0 0
#> TCGA.DU.5870.01 2 0 1 0 1 0
#> TCGA.TQ.A7RS.01 1 0 1 1 0 0
#> TCGA.DU.7009.01 1 0 1 1 0 0
#> TCGA.FG.8186.01 1 0 1 1 0 0
#> TCGA.QH.A65X.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.HT.A74L.01 1 0.2011 0.946 0.92 0.00 0 0.08
#> TCGA.FG.A710.01 2 0.0000 0.976 0.00 1.00 0 0.00
#> TCGA.DU.A6S6.01 1 0.2011 0.946 0.92 0.00 0 0.08
#> TCGA.FG.7638.01 1 0.3610 0.888 0.80 0.00 0 0.20
#> TCGA.FG.A6J1.01 1 0.3610 0.888 0.80 0.00 0 0.20
#> TCGA.P5.A77X.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.FG.A60K.01 4 0.0000 0.996 0.00 0.00 0 1.00
#> TCGA.TQ.A7RQ.01 2 0.0707 0.974 0.02 0.98 0 0.00
#> TCGA.HT.7681.01 1 0.2011 0.946 0.92 0.00 0 0.08
#> TCGA.QH.A65V.01 4 0.0000 0.996 0.00 0.00 0 1.00
#> TCGA.DB.A64R.01 1 0.2011 0.946 0.92 0.00 0 0.08
#> TCGA.HT.7695.01 1 0.3172 0.917 0.84 0.00 0 0.16
#> TCGA.HW.7495.01 4 0.0000 0.996 0.00 0.00 0 1.00
#> TCGA.TQ.A7RI.01 4 0.0000 0.996 0.00 0.00 0 1.00
#> TCGA.CS.5396.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.DB.A64Q.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.DB.A64U.01 4 0.0000 0.996 0.00 0.00 0 1.00
#> TCGA.DU.5870.01 2 0.0000 0.976 0.00 1.00 0 0.00
#> TCGA.TQ.A7RS.01 4 0.0707 0.975 0.02 0.00 0 0.98
#> TCGA.DU.7009.01 4 0.0000 0.996 0.00 0.00 0 1.00
#> TCGA.FG.8186.01 1 0.2011 0.946 0.92 0.00 0 0.08
#> TCGA.QH.A65X.01 2 0.2011 0.947 0.08 0.92 0 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.HT.A74L.01 1 0.0609 0.969 0.98 0.00 0 0.02 0.00
#> TCGA.FG.A710.01 2 0.0000 0.928 0.00 1.00 0 0.00 0.00
#> TCGA.DU.A6S6.01 1 0.2331 0.905 0.90 0.00 0 0.02 0.08
#> TCGA.FG.7638.01 4 0.3561 0.609 0.26 0.00 0 0.74 0.00
#> TCGA.FG.A6J1.01 4 0.3561 0.609 0.26 0.00 0 0.74 0.00
#> TCGA.P5.A77X.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.FG.A60K.01 4 0.2929 0.464 0.00 0.00 0 0.82 0.18
#> TCGA.TQ.A7RQ.01 2 0.1648 0.921 0.02 0.94 0 0.00 0.04
#> TCGA.HT.7681.01 4 0.4182 0.377 0.40 0.00 0 0.60 0.00
#> TCGA.QH.A65V.01 4 0.2929 0.464 0.00 0.00 0 0.82 0.18
#> TCGA.DB.A64R.01 1 0.0609 0.969 0.98 0.00 0 0.02 0.00
#> TCGA.HT.7695.01 4 0.3684 0.585 0.28 0.00 0 0.72 0.00
#> TCGA.HW.7495.01 4 0.2929 0.464 0.00 0.00 0 0.82 0.18
#> TCGA.TQ.A7RI.01 5 0.3895 1.000 0.00 0.00 0 0.32 0.68
#> TCGA.CS.5396.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.DB.A64Q.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.DB.A64U.01 4 0.2929 0.464 0.00 0.00 0 0.82 0.18
#> TCGA.DU.5870.01 2 0.0000 0.928 0.00 1.00 0 0.00 0.00
#> TCGA.TQ.A7RS.01 4 0.1732 0.548 0.00 0.00 0 0.92 0.08
#> TCGA.DU.7009.01 5 0.3895 1.000 0.00 0.00 0 0.32 0.68
#> TCGA.FG.8186.01 1 0.0609 0.969 0.98 0.00 0 0.02 0.00
#> TCGA.QH.A65X.01 2 0.3424 0.826 0.00 0.76 0 0.00 0.24
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.HT.A74L.01 1 0.0000 0.897 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A710.01 2 0.0000 0.848 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A6S6.01 1 0.4420 0.653 0.62 0.00 0.00 0.04 0.00 0.34
#> TCGA.FG.7638.01 4 0.1814 0.630 0.10 0.00 0.00 0.90 0.00 0.00
#> TCGA.FG.A6J1.01 4 0.1814 0.630 0.10 0.00 0.00 0.90 0.00 0.00
#> TCGA.P5.A77X.01 3 0.1556 0.940 0.00 0.00 0.92 0.08 0.00 0.00
#> TCGA.FG.A60K.01 5 0.5703 0.179 0.00 0.00 0.00 0.42 0.42 0.16
#> TCGA.TQ.A7RQ.01 2 0.2629 0.832 0.00 0.88 0.00 0.02 0.02 0.08
#> TCGA.HT.7681.01 4 0.3578 0.339 0.34 0.00 0.00 0.66 0.00 0.00
#> TCGA.QH.A65V.01 4 0.5703 -0.473 0.00 0.00 0.00 0.42 0.42 0.16
#> TCGA.DB.A64R.01 1 0.0000 0.897 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7695.01 4 0.2048 0.622 0.12 0.00 0.00 0.88 0.00 0.00
#> TCGA.HW.7495.01 4 0.5285 -0.355 0.00 0.00 0.00 0.48 0.42 0.10
#> TCGA.TQ.A7RI.01 5 0.0547 0.507 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.CS.5396.01 3 0.0000 0.971 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.A64Q.01 3 0.0000 0.971 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.A64U.01 5 0.5703 0.179 0.00 0.00 0.00 0.42 0.42 0.16
#> TCGA.DU.5870.01 2 0.0000 0.848 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RS.01 4 0.1814 0.544 0.00 0.00 0.00 0.90 0.10 0.00
#> TCGA.DU.7009.01 5 0.1092 0.500 0.00 0.00 0.00 0.02 0.96 0.02
#> TCGA.FG.8186.01 1 0.0000 0.897 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A65X.01 2 0.3864 0.613 0.00 0.52 0.00 0.00 0.00 0.48
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.HT.A74L.01 1 0.2422 0.765 0.82 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.FG.A710.01 2 0.0000 0.807 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A6S6.01 1 0.7188 0.191 0.36 0.00 0.00 0.08 0.16 0.34 0.06
#> TCGA.FG.7638.01 4 0.0000 0.864 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.A6J1.01 4 0.0000 0.864 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A77X.01 3 0.2509 0.901 0.06 0.00 0.88 0.00 0.04 0.00 0.02
#> TCGA.FG.A60K.01 5 0.3221 0.979 0.00 0.00 0.00 0.32 0.68 0.00 0.00
#> TCGA.TQ.A7RQ.01 2 0.4260 0.541 0.00 0.74 0.00 0.00 0.04 0.08 0.14
#> TCGA.HT.7681.01 4 0.2912 0.648 0.14 0.00 0.00 0.82 0.04 0.00 0.00
#> TCGA.QH.A65V.01 5 0.3221 0.979 0.00 0.00 0.00 0.32 0.68 0.00 0.00
#> TCGA.DB.A64R.01 1 0.3244 0.757 0.78 0.00 0.00 0.18 0.04 0.00 0.00
#> TCGA.HT.7695.01 4 0.0000 0.864 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HW.7495.01 5 0.3358 0.936 0.00 0.00 0.00 0.36 0.64 0.00 0.00
#> TCGA.TQ.A7RI.01 7 0.2945 1.000 0.00 0.00 0.00 0.00 0.26 0.00 0.74
#> TCGA.CS.5396.01 3 0.0000 0.945 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64Q.01 3 0.0504 0.945 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.DB.A64U.01 5 0.3221 0.979 0.00 0.00 0.00 0.32 0.68 0.00 0.00
#> TCGA.DU.5870.01 2 0.0000 0.807 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RS.01 4 0.3011 0.675 0.12 0.00 0.00 0.82 0.06 0.00 0.00
#> TCGA.DU.7009.01 7 0.2945 1.000 0.00 0.00 0.00 0.00 0.26 0.00 0.74
#> TCGA.FG.8186.01 1 0.3386 0.760 0.78 0.00 0.00 0.18 0.02 0.00 0.02
#> TCGA.QH.A65X.01 6 0.3294 0.000 0.00 0.34 0.00 0.00 0.00 0.66 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.HT.A74L.01 1 0.0000 0.953 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A710.01 2 0.0000 0.802 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A6S6.01 8 0.2569 0.000 0.16 0.00 0.00 0.02 0.00 0.00 0.00 0.82
#> TCGA.FG.7638.01 4 0.3404 0.861 0.04 0.00 0.00 0.72 0.24 0.00 0.00 0.00
#> TCGA.FG.A6J1.01 4 0.3404 0.861 0.04 0.00 0.00 0.72 0.24 0.00 0.00 0.00
#> TCGA.P5.A77X.01 3 0.4110 0.775 0.00 0.00 0.76 0.06 0.00 0.02 0.10 0.06
#> TCGA.FG.A60K.01 5 0.0000 0.972 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RQ.01 2 0.4615 0.507 0.00 0.68 0.00 0.08 0.00 0.16 0.00 0.08
#> TCGA.HT.7681.01 4 0.3154 0.706 0.16 0.00 0.00 0.78 0.06 0.00 0.00 0.00
#> TCGA.QH.A65V.01 5 0.0000 0.972 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.A64R.01 1 0.1091 0.922 0.94 0.00 0.00 0.06 0.00 0.00 0.00 0.00
#> TCGA.HT.7695.01 4 0.3404 0.861 0.04 0.00 0.00 0.72 0.24 0.00 0.00 0.00
#> TCGA.HW.7495.01 5 0.1091 0.914 0.00 0.00 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.TQ.A7RI.01 7 0.2725 0.968 0.00 0.00 0.00 0.00 0.14 0.00 0.82 0.04
#> TCGA.CS.5396.01 3 0.0000 0.886 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64Q.01 3 0.0471 0.886 0.00 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.DB.A64U.01 5 0.0000 0.972 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.5870.01 2 0.0000 0.802 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RS.01 4 0.5241 0.673 0.00 0.00 0.00 0.62 0.16 0.16 0.02 0.04
#> TCGA.DU.7009.01 7 0.1947 0.968 0.00 0.00 0.00 0.00 0.14 0.00 0.86 0.00
#> TCGA.FG.8186.01 1 0.0471 0.949 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.QH.A65X.01 6 0.2267 0.000 0.00 0.18 0.00 0.00 0.00 0.82 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node022. Child nodes: Node01111-leaf , Node01112-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01211-leaf , Node01212-leaf , Node01213 , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node01224-leaf , Node01225-leaf , Node01311-leaf , Node01312-leaf , Node01313-leaf , Node01411-leaf , Node01412-leaf , Node01431-leaf , Node01432-leaf , Node02211-leaf , Node02212 , Node02221 , Node02222-leaf , Node02223-leaf , Node02231 , Node02232-leaf , Node02233-leaf , Node02234-leaf , Node02311-leaf , Node02312-leaf , Node02313-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 33 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 0.873 0.863 0.953 0.3686 0.621 0.621
#> 3 3 1.000 0.995 0.998 0.5760 0.708 0.562
#> 4 4 0.746 0.920 0.938 0.2168 0.748 0.472
#> 5 5 0.884 0.845 0.906 0.0658 0.972 0.900
#> 6 6 0.819 0.771 0.862 0.0533 0.905 0.658
#> 7 7 0.776 0.734 0.848 0.0213 0.983 0.917
#> 8 8 0.784 0.605 0.828 0.0294 0.966 0.830
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.FG.A6IZ.01 1 0.000 0.9669 1.00 0.00
#> TCGA.QH.A6X8.01 1 0.680 0.7281 0.82 0.18
#> TCGA.P5.A72Z.01 2 0.000 0.8675 0.00 1.00
#> TCGA.DU.8168.01 1 0.000 0.9669 1.00 0.00
#> TCGA.CS.5390.01 1 0.000 0.9669 1.00 0.00
#> TCGA.E1.A7YS.01 2 0.000 0.8675 0.00 1.00
#> TCGA.DB.5274.01 1 0.000 0.9669 1.00 0.00
#> TCGA.S9.A7QZ.01 1 0.000 0.9669 1.00 0.00
#> TCGA.DU.7302.01 1 0.000 0.9669 1.00 0.00
#> TCGA.QH.A65R.01 1 0.000 0.9669 1.00 0.00
#> TCGA.DU.6394.01 2 0.943 0.4455 0.36 0.64
#> TCGA.DU.5874.01 1 0.000 0.9669 1.00 0.00
#> TCGA.DB.A4XH.01 1 0.000 0.9669 1.00 0.00
#> TCGA.DU.8164.01 1 0.000 0.9669 1.00 0.00
#> TCGA.DU.7018.01 1 0.000 0.9669 1.00 0.00
#> TCGA.HW.A5KJ.01 1 1.000 -0.2015 0.50 0.50
#> TCGA.HT.8105.01 1 0.000 0.9669 1.00 0.00
#> TCGA.HT.A619.01 2 1.000 0.0494 0.50 0.50
#> TCGA.DU.6400.01 1 0.000 0.9669 1.00 0.00
#> TCGA.S9.A6WL.01 1 0.000 0.9669 1.00 0.00
#> TCGA.S9.A6WH.01 1 0.000 0.9669 1.00 0.00
#> TCGA.HT.7616.01 2 0.000 0.8675 0.00 1.00
#> TCGA.DB.A64W.01 1 0.000 0.9669 1.00 0.00
#> TCGA.DU.6410.01 2 0.000 0.8675 0.00 1.00
#> TCGA.E1.5318.01 1 0.000 0.9669 1.00 0.00
#> TCGA.S9.A7J3.01 1 0.000 0.9669 1.00 0.00
#> TCGA.S9.A6UB.01 1 0.000 0.9669 1.00 0.00
#> TCGA.DU.6393.01 1 0.000 0.9669 1.00 0.00
#> TCGA.DB.A64L.01 1 0.000 0.9669 1.00 0.00
#> TCGA.DH.A669.02 2 0.000 0.8675 0.00 1.00
#> TCGA.DH.A669.01 2 0.000 0.8675 0.00 1.00
#> TCGA.HT.7687.01 1 0.000 0.9669 1.00 0.00
#> TCGA.CS.5394.01 1 0.000 0.9669 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.FG.A6IZ.01 2 0.000 1.000 0.00 1.00 0
#> TCGA.QH.A6X8.01 2 0.000 1.000 0.00 1.00 0
#> TCGA.P5.A72Z.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.DU.8168.01 1 0.000 0.995 1.00 0.00 0
#> TCGA.CS.5390.01 2 0.000 1.000 0.00 1.00 0
#> TCGA.E1.A7YS.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.DB.5274.01 1 0.000 0.995 1.00 0.00 0
#> TCGA.S9.A7QZ.01 1 0.000 0.995 1.00 0.00 0
#> TCGA.DU.7302.01 1 0.000 0.995 1.00 0.00 0
#> TCGA.QH.A65R.01 1 0.000 0.995 1.00 0.00 0
#> TCGA.DU.6394.01 2 0.000 1.000 0.00 1.00 0
#> TCGA.DU.5874.01 1 0.000 0.995 1.00 0.00 0
#> TCGA.DB.A4XH.01 1 0.000 0.995 1.00 0.00 0
#> TCGA.DU.8164.01 1 0.000 0.995 1.00 0.00 0
#> TCGA.DU.7018.01 1 0.153 0.956 0.96 0.04 0
#> TCGA.HW.A5KJ.01 2 0.000 1.000 0.00 1.00 0
#> TCGA.HT.8105.01 1 0.000 0.995 1.00 0.00 0
#> TCGA.HT.A619.01 2 0.000 1.000 0.00 1.00 0
#> TCGA.DU.6400.01 1 0.000 0.995 1.00 0.00 0
#> TCGA.S9.A6WL.01 1 0.153 0.956 0.96 0.04 0
#> TCGA.S9.A6WH.01 1 0.000 0.995 1.00 0.00 0
#> TCGA.HT.7616.01 2 0.000 1.000 0.00 1.00 0
#> TCGA.DB.A64W.01 1 0.000 0.995 1.00 0.00 0
#> TCGA.DU.6410.01 2 0.000 1.000 0.00 1.00 0
#> TCGA.E1.5318.01 1 0.000 0.995 1.00 0.00 0
#> TCGA.S9.A7J3.01 1 0.000 0.995 1.00 0.00 0
#> TCGA.S9.A6UB.01 1 0.000 0.995 1.00 0.00 0
#> TCGA.DU.6393.01 1 0.000 0.995 1.00 0.00 0
#> TCGA.DB.A64L.01 2 0.000 1.000 0.00 1.00 0
#> TCGA.DH.A669.02 3 0.000 1.000 0.00 0.00 1
#> TCGA.DH.A669.01 3 0.000 1.000 0.00 0.00 1
#> TCGA.HT.7687.01 2 0.000 1.000 0.00 1.00 0
#> TCGA.CS.5394.01 1 0.000 0.995 1.00 0.00 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.FG.A6IZ.01 4 0.164 0.794 0.00 0.06 0.0 0.94
#> TCGA.QH.A6X8.01 4 0.471 0.244 0.00 0.36 0.0 0.64
#> TCGA.P5.A72Z.01 3 0.234 0.955 0.00 0.10 0.9 0.00
#> TCGA.DU.8168.01 1 0.000 0.994 1.00 0.00 0.0 0.00
#> TCGA.CS.5390.01 4 0.000 0.829 0.00 0.00 0.0 1.00
#> TCGA.E1.A7YS.01 3 0.234 0.955 0.00 0.10 0.9 0.00
#> TCGA.DB.5274.01 1 0.000 0.994 1.00 0.00 0.0 0.00
#> TCGA.S9.A7QZ.01 4 0.265 0.870 0.12 0.00 0.0 0.88
#> TCGA.DU.7302.01 4 0.265 0.870 0.12 0.00 0.0 0.88
#> TCGA.QH.A65R.01 1 0.000 0.994 1.00 0.00 0.0 0.00
#> TCGA.DU.6394.01 2 0.265 0.995 0.00 0.88 0.0 0.12
#> TCGA.DU.5874.01 1 0.000 0.994 1.00 0.00 0.0 0.00
#> TCGA.DB.A4XH.01 1 0.000 0.994 1.00 0.00 0.0 0.00
#> TCGA.DU.8164.01 1 0.000 0.994 1.00 0.00 0.0 0.00
#> TCGA.DU.7018.01 4 0.265 0.870 0.12 0.00 0.0 0.88
#> TCGA.HW.A5KJ.01 2 0.265 0.995 0.00 0.88 0.0 0.12
#> TCGA.HT.8105.01 1 0.000 0.994 1.00 0.00 0.0 0.00
#> TCGA.HT.A619.01 2 0.265 0.995 0.00 0.88 0.0 0.12
#> TCGA.DU.6400.01 1 0.000 0.994 1.00 0.00 0.0 0.00
#> TCGA.S9.A6WL.01 4 0.265 0.870 0.12 0.00 0.0 0.88
#> TCGA.S9.A6WH.01 1 0.000 0.994 1.00 0.00 0.0 0.00
#> TCGA.HT.7616.01 2 0.265 0.995 0.00 0.88 0.0 0.12
#> TCGA.DB.A64W.01 1 0.164 0.930 0.94 0.00 0.0 0.06
#> TCGA.DU.6410.01 2 0.234 0.979 0.00 0.90 0.0 0.10
#> TCGA.E1.5318.01 1 0.000 0.994 1.00 0.00 0.0 0.00
#> TCGA.S9.A7J3.01 4 0.265 0.870 0.12 0.00 0.0 0.88
#> TCGA.S9.A6UB.01 4 0.265 0.870 0.12 0.00 0.0 0.88
#> TCGA.DU.6393.01 1 0.000 0.994 1.00 0.00 0.0 0.00
#> TCGA.DB.A64L.01 4 0.164 0.794 0.00 0.06 0.0 0.94
#> TCGA.DH.A669.02 3 0.000 0.955 0.00 0.00 1.0 0.00
#> TCGA.DH.A669.01 3 0.000 0.955 0.00 0.00 1.0 0.00
#> TCGA.HT.7687.01 4 0.000 0.829 0.00 0.00 0.0 1.00
#> TCGA.CS.5394.01 1 0.000 0.994 1.00 0.00 0.0 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.FG.A6IZ.01 4 0.5892 0.513 0.00 0.18 0.00 0.60 0.22
#> TCGA.QH.A6X8.01 5 0.4263 0.824 0.00 0.18 0.00 0.06 0.76
#> TCGA.P5.A72Z.01 3 0.0000 0.957 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.8168.01 1 0.0000 0.957 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.5390.01 4 0.2873 0.815 0.00 0.12 0.00 0.86 0.02
#> TCGA.E1.A7YS.01 3 0.0000 0.957 0.00 0.00 1.00 0.00 0.00
#> TCGA.DB.5274.01 1 0.0609 0.950 0.98 0.00 0.00 0.00 0.02
#> TCGA.S9.A7QZ.01 4 0.0609 0.845 0.02 0.00 0.00 0.98 0.00
#> TCGA.DU.7302.01 4 0.1216 0.837 0.02 0.00 0.00 0.96 0.02
#> TCGA.QH.A65R.01 1 0.0609 0.950 0.98 0.00 0.00 0.00 0.02
#> TCGA.DU.6394.01 2 0.2732 0.797 0.00 0.84 0.00 0.00 0.16
#> TCGA.DU.5874.01 1 0.0000 0.957 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4XH.01 1 0.0000 0.957 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.8164.01 1 0.0000 0.957 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7018.01 4 0.0609 0.845 0.02 0.00 0.00 0.98 0.00
#> TCGA.HW.A5KJ.01 2 0.0000 0.712 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.8105.01 1 0.0000 0.957 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A619.01 5 0.3424 0.808 0.00 0.24 0.00 0.00 0.76
#> TCGA.DU.6400.01 1 0.2012 0.901 0.92 0.00 0.00 0.06 0.02
#> TCGA.S9.A6WL.01 4 0.2616 0.829 0.02 0.10 0.00 0.88 0.00
#> TCGA.S9.A6WH.01 1 0.0000 0.957 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7616.01 2 0.2732 0.797 0.00 0.84 0.00 0.00 0.16
#> TCGA.DB.A64W.01 1 0.4840 0.518 0.64 0.00 0.00 0.32 0.04
#> TCGA.DU.6410.01 2 0.3561 0.689 0.00 0.74 0.00 0.00 0.26
#> TCGA.E1.5318.01 1 0.0000 0.957 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7J3.01 4 0.1216 0.837 0.02 0.00 0.00 0.96 0.02
#> TCGA.S9.A6UB.01 4 0.0609 0.845 0.02 0.00 0.00 0.98 0.00
#> TCGA.DU.6393.01 1 0.0609 0.950 0.98 0.00 0.00 0.00 0.02
#> TCGA.DB.A64L.01 4 0.6359 0.342 0.00 0.26 0.00 0.52 0.22
#> TCGA.DH.A669.02 3 0.2012 0.957 0.00 0.00 0.92 0.02 0.06
#> TCGA.DH.A669.01 3 0.2012 0.957 0.00 0.00 0.92 0.02 0.06
#> TCGA.HT.7687.01 4 0.2873 0.815 0.00 0.12 0.00 0.86 0.02
#> TCGA.CS.5394.01 1 0.0000 0.957 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.FG.A6IZ.01 4 0.4247 0.685 0.00 0.00 0.00 0.70 0.06 0.24
#> TCGA.QH.A6X8.01 5 0.0547 0.891 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.P5.A72Z.01 3 0.1092 0.975 0.00 0.02 0.96 0.02 0.00 0.00
#> TCGA.DU.8168.01 1 0.0000 0.936 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.5390.01 4 0.3198 0.679 0.00 0.00 0.00 0.74 0.00 0.26
#> TCGA.E1.A7YS.01 3 0.0547 0.984 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.DB.5274.01 1 0.2020 0.922 0.92 0.04 0.00 0.02 0.02 0.00
#> TCGA.S9.A7QZ.01 6 0.1267 0.789 0.00 0.00 0.00 0.06 0.00 0.94
#> TCGA.DU.7302.01 6 0.0000 0.796 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.QH.A65R.01 1 0.2020 0.922 0.92 0.04 0.00 0.02 0.02 0.00
#> TCGA.DU.6394.01 2 0.5618 0.688 0.00 0.50 0.00 0.16 0.34 0.00
#> TCGA.DU.5874.01 1 0.0000 0.936 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4XH.01 1 0.0000 0.936 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.8164.01 1 0.1092 0.932 0.96 0.00 0.00 0.02 0.02 0.00
#> TCGA.DU.7018.01 6 0.2793 0.595 0.00 0.00 0.00 0.20 0.00 0.80
#> TCGA.HW.A5KJ.01 4 0.4348 -0.179 0.00 0.32 0.00 0.64 0.04 0.00
#> TCGA.HT.8105.01 1 0.1635 0.928 0.94 0.02 0.00 0.02 0.02 0.00
#> TCGA.HT.A619.01 5 0.2094 0.890 0.00 0.02 0.00 0.08 0.90 0.00
#> TCGA.DU.6400.01 1 0.5337 0.473 0.60 0.04 0.00 0.02 0.02 0.32
#> TCGA.S9.A6WL.01 4 0.3756 0.581 0.00 0.00 0.00 0.60 0.00 0.40
#> TCGA.S9.A6WH.01 1 0.0000 0.936 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7616.01 2 0.5618 0.688 0.00 0.50 0.00 0.16 0.34 0.00
#> TCGA.DB.A64W.01 6 0.3460 0.505 0.22 0.00 0.00 0.02 0.00 0.76
#> TCGA.DU.6410.01 2 0.1267 0.445 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.E1.5318.01 1 0.0000 0.936 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7J3.01 6 0.0000 0.796 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.S9.A6UB.01 6 0.1814 0.762 0.00 0.00 0.00 0.10 0.00 0.90
#> TCGA.DU.6393.01 1 0.2020 0.922 0.92 0.04 0.00 0.02 0.02 0.00
#> TCGA.DB.A64L.01 4 0.3787 0.617 0.00 0.00 0.00 0.78 0.10 0.12
#> TCGA.DH.A669.02 3 0.0000 0.985 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DH.A669.01 3 0.0000 0.985 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7687.01 4 0.3756 0.581 0.00 0.00 0.00 0.60 0.00 0.40
#> TCGA.CS.5394.01 1 0.0000 0.936 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.FG.A6IZ.01 4 0.2906 0.8650 0.00 0.00 0.00 0.80 0.02 0.18 0.00
#> TCGA.QH.A6X8.01 5 0.3656 0.8090 0.00 0.08 0.00 0.04 0.80 0.00 0.08
#> TCGA.P5.A72Z.01 3 0.5001 0.7872 0.00 0.08 0.68 0.12 0.00 0.00 0.12
#> TCGA.DU.8168.01 1 0.0000 0.9043 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.5390.01 4 0.2259 0.8557 0.00 0.00 0.00 0.84 0.00 0.16 0.00
#> TCGA.E1.A7YS.01 3 0.4812 0.7961 0.00 0.08 0.70 0.10 0.00 0.00 0.12
#> TCGA.DB.5274.01 1 0.2422 0.8246 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.S9.A7QZ.01 6 0.0863 0.8157 0.00 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.DU.7302.01 6 0.0000 0.8224 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.QH.A65R.01 1 0.2422 0.8246 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.DU.6394.01 2 0.2081 0.4253 0.00 0.86 0.00 0.00 0.14 0.00 0.00
#> TCGA.DU.5874.01 1 0.0000 0.9043 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4XH.01 1 0.0000 0.9043 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.8164.01 1 0.0000 0.9043 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7018.01 6 0.2832 0.5515 0.00 0.00 0.00 0.24 0.00 0.76 0.00
#> TCGA.HW.A5KJ.01 2 0.3562 0.0997 0.00 0.50 0.00 0.50 0.00 0.00 0.00
#> TCGA.HT.8105.01 1 0.0504 0.8983 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.HT.A619.01 5 0.0000 0.8099 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.6400.01 1 0.5241 0.3332 0.50 0.00 0.00 0.00 0.00 0.32 0.18
#> TCGA.S9.A6WL.01 4 0.3745 0.8178 0.00 0.00 0.00 0.70 0.00 0.26 0.04
#> TCGA.S9.A6WH.01 1 0.0000 0.9043 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7616.01 2 0.2081 0.4253 0.00 0.86 0.00 0.00 0.14 0.00 0.00
#> TCGA.DB.A64W.01 6 0.2422 0.5939 0.18 0.00 0.00 0.00 0.00 0.82 0.00
#> TCGA.DU.6410.01 7 0.4214 0.0000 0.00 0.40 0.00 0.00 0.04 0.00 0.56
#> TCGA.E1.5318.01 1 0.0000 0.9043 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7J3.01 6 0.0000 0.8224 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A6UB.01 6 0.2803 0.7426 0.00 0.00 0.00 0.10 0.00 0.84 0.06
#> TCGA.DU.6393.01 1 0.2422 0.8246 0.82 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.DB.A64L.01 4 0.3680 0.6853 0.00 0.14 0.00 0.78 0.02 0.06 0.00
#> TCGA.DH.A669.02 3 0.0000 0.8090 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A669.01 3 0.0000 0.8090 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7687.01 4 0.2945 0.8412 0.00 0.00 0.00 0.74 0.00 0.26 0.00
#> TCGA.CS.5394.01 1 0.0000 0.9043 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.FG.A6IZ.01 4 0.1091 0.7307 0.00 0.00 0.0 0.94 0.00 0.06 0.00 0.00
#> TCGA.QH.A6X8.01 5 0.6362 0.5872 0.00 0.18 0.0 0.10 0.50 0.00 0.04 0.18
#> TCGA.P5.A72Z.01 3 0.4041 0.7990 0.00 0.00 0.7 0.00 0.04 0.00 0.04 0.22
#> TCGA.DU.8168.01 1 0.0471 0.7353 0.98 0.00 0.0 0.00 0.00 0.00 0.02 0.00
#> TCGA.CS.5390.01 4 0.2407 0.7277 0.00 0.00 0.0 0.86 0.00 0.08 0.06 0.00
#> TCGA.E1.A7YS.01 3 0.3843 0.7990 0.00 0.00 0.7 0.00 0.02 0.00 0.04 0.24
#> TCGA.DB.5274.01 1 0.3193 0.1283 0.62 0.00 0.0 0.00 0.00 0.00 0.00 0.38
#> TCGA.S9.A7QZ.01 6 0.1563 0.7898 0.00 0.00 0.0 0.10 0.00 0.90 0.00 0.00
#> TCGA.DU.7302.01 6 0.0000 0.8065 0.00 0.00 0.0 0.00 0.00 1.00 0.00 0.00
#> TCGA.QH.A65R.01 1 0.3193 0.1283 0.62 0.00 0.0 0.00 0.00 0.00 0.00 0.38
#> TCGA.DU.6394.01 2 0.0000 1.0000 0.00 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5874.01 1 0.0000 0.7403 1.00 0.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4XH.01 1 0.0000 0.7403 1.00 0.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.8164.01 1 0.2404 0.6427 0.84 0.00 0.0 0.00 0.00 0.00 0.02 0.14
#> TCGA.DU.7018.01 6 0.3504 0.5691 0.00 0.00 0.0 0.26 0.00 0.70 0.04 0.00
#> TCGA.HW.A5KJ.01 4 0.5936 -0.1777 0.00 0.38 0.0 0.40 0.04 0.00 0.02 0.16
#> TCGA.HT.8105.01 1 0.2114 0.6234 0.84 0.00 0.0 0.00 0.00 0.00 0.00 0.16
#> TCGA.HT.A619.01 5 0.1341 0.5860 0.00 0.08 0.0 0.00 0.92 0.00 0.00 0.00
#> TCGA.DU.6400.01 8 0.5178 0.0000 0.36 0.00 0.0 0.00 0.00 0.24 0.00 0.40
#> TCGA.S9.A6WL.01 4 0.3299 0.6558 0.00 0.00 0.0 0.76 0.00 0.18 0.06 0.00
#> TCGA.S9.A6WH.01 1 0.0000 0.7403 1.00 0.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7616.01 2 0.0000 1.0000 0.00 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64W.01 6 0.1607 0.7380 0.04 0.00 0.0 0.00 0.00 0.92 0.00 0.04
#> TCGA.DU.6410.01 7 0.2267 0.0000 0.00 0.18 0.0 0.00 0.00 0.00 0.82 0.00
#> TCGA.E1.5318.01 1 0.0000 0.7403 1.00 0.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7J3.01 6 0.0000 0.8065 0.00 0.00 0.0 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6UB.01 6 0.3728 0.5842 0.00 0.00 0.0 0.28 0.00 0.68 0.02 0.02
#> TCGA.DU.6393.01 1 0.3237 0.0496 0.60 0.00 0.0 0.00 0.00 0.00 0.00 0.40
#> TCGA.DB.A64L.01 4 0.2547 0.6610 0.00 0.12 0.0 0.84 0.00 0.04 0.00 0.00
#> TCGA.DH.A669.02 3 0.0000 0.8047 0.00 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A669.01 3 0.0000 0.8047 0.00 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7687.01 4 0.2267 0.6951 0.00 0.00 0.0 0.82 0.00 0.18 0.00 0.00
#> TCGA.CS.5394.01 1 0.0471 0.7353 0.98 0.00 0.0 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: Node0222. Child nodes: Node012131-leaf , Node012132-leaf , Node012133-leaf , Node012134-leaf , Node022121-leaf , Node022122-leaf , Node022123-leaf , Node022211-leaf , Node022212-leaf , Node022311-leaf , Node022312-leaf , Node022313-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["02221"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 19 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4917 0.509 0.509
#> 3 3 0.760 0.955 0.934 0.2565 0.842 0.690
#> 4 4 0.643 0.843 0.889 0.0858 1.000 1.000
#> 5 5 0.673 0.732 0.860 0.0616 0.965 0.900
#> 6 6 0.684 0.533 0.804 0.0699 0.988 0.963
#> 7 7 0.678 0.465 0.753 0.0396 0.912 0.712
#> 8 8 0.702 0.493 0.812 0.0359 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] 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.DU.8168.01 2 0 1 0 1
#> TCGA.DB.5274.01 2 0 1 0 1
#> TCGA.S9.A7QZ.01 1 0 1 1 0
#> TCGA.DU.7302.01 2 0 1 0 1
#> TCGA.QH.A65R.01 2 0 1 0 1
#> TCGA.DU.5874.01 2 0 1 0 1
#> TCGA.DB.A4XH.01 2 0 1 0 1
#> TCGA.DU.8164.01 1 0 1 1 0
#> TCGA.DU.7018.01 2 0 1 0 1
#> TCGA.HT.8105.01 1 0 1 1 0
#> TCGA.DU.6400.01 2 0 1 0 1
#> TCGA.S9.A6WL.01 1 0 1 1 0
#> TCGA.S9.A6WH.01 2 0 1 0 1
#> TCGA.DB.A64W.01 2 0 1 0 1
#> TCGA.E1.5318.01 2 0 1 0 1
#> TCGA.S9.A7J3.01 2 0 1 0 1
#> TCGA.S9.A6UB.01 1 0 1 1 0
#> TCGA.DU.6393.01 1 0 1 1 0
#> TCGA.CS.5394.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.DU.8168.01 2 0.0000 0.983 0.00 1.00 0.00
#> TCGA.DB.5274.01 2 0.0000 0.983 0.00 1.00 0.00
#> TCGA.S9.A7QZ.01 1 0.0892 0.953 0.98 0.00 0.02
#> TCGA.DU.7302.01 2 0.0000 0.983 0.00 1.00 0.00
#> TCGA.QH.A65R.01 3 0.5560 0.971 0.00 0.30 0.70
#> TCGA.DU.5874.01 3 0.5397 0.986 0.00 0.28 0.72
#> TCGA.DB.A4XH.01 2 0.0000 0.983 0.00 1.00 0.00
#> TCGA.DU.8164.01 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.DU.7018.01 2 0.0000 0.983 0.00 1.00 0.00
#> TCGA.HT.8105.01 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.DU.6400.01 2 0.2959 0.842 0.00 0.90 0.10
#> TCGA.S9.A6WL.01 1 0.5216 0.757 0.74 0.00 0.26
#> TCGA.S9.A6WH.01 3 0.5397 0.986 0.00 0.28 0.72
#> TCGA.DB.A64W.01 2 0.0000 0.983 0.00 1.00 0.00
#> TCGA.E1.5318.01 2 0.0000 0.983 0.00 1.00 0.00
#> TCGA.S9.A7J3.01 2 0.0000 0.983 0.00 1.00 0.00
#> TCGA.S9.A6UB.01 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.DU.6393.01 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.CS.5394.01 1 0.0892 0.953 0.98 0.00 0.02
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.DU.8168.01 2 0.0000 0.914 0.00 1.00 0.00 0.00
#> TCGA.DB.5274.01 2 0.2706 0.866 0.00 0.90 0.08 0.02
#> TCGA.S9.A7QZ.01 1 0.1411 0.907 0.96 0.00 0.02 0.02
#> TCGA.DU.7302.01 2 0.0000 0.914 0.00 1.00 0.00 0.00
#> TCGA.QH.A65R.01 3 0.6808 0.731 0.00 0.12 0.56 0.32
#> TCGA.DU.5874.01 3 0.6049 0.759 0.00 0.12 0.68 0.20
#> TCGA.DB.A4XH.01 2 0.1637 0.886 0.00 0.94 0.00 0.06
#> TCGA.DU.8164.01 1 0.0000 0.916 1.00 0.00 0.00 0.00
#> TCGA.DU.7018.01 2 0.0000 0.914 0.00 1.00 0.00 0.00
#> TCGA.HT.8105.01 1 0.2345 0.873 0.90 0.00 0.10 0.00
#> TCGA.DU.6400.01 2 0.4134 0.640 0.00 0.74 0.26 0.00
#> TCGA.S9.A6WL.01 1 0.4907 0.533 0.58 0.00 0.00 0.42
#> TCGA.S9.A6WH.01 3 0.3610 0.746 0.00 0.20 0.80 0.00
#> TCGA.DB.A64W.01 2 0.1637 0.886 0.00 0.94 0.00 0.06
#> TCGA.E1.5318.01 2 0.2706 0.866 0.00 0.90 0.08 0.02
#> TCGA.S9.A7J3.01 2 0.0000 0.914 0.00 1.00 0.00 0.00
#> TCGA.S9.A6UB.01 1 0.0000 0.916 1.00 0.00 0.00 0.00
#> TCGA.DU.6393.01 1 0.0000 0.916 1.00 0.00 0.00 0.00
#> TCGA.CS.5394.01 1 0.0707 0.912 0.98 0.00 0.00 0.02
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.DU.8168.01 4 0.0000 0.872 0.00 0.00 0.00 1.00 0.00
#> TCGA.DB.5274.01 4 0.3319 0.790 0.00 0.00 0.16 0.82 0.02
#> TCGA.S9.A7QZ.01 1 0.3390 0.779 0.84 0.10 0.06 0.00 0.00
#> TCGA.DU.7302.01 4 0.0000 0.872 0.00 0.00 0.00 1.00 0.00
#> TCGA.QH.A65R.01 3 0.6958 0.481 0.00 0.22 0.56 0.06 0.16
#> TCGA.DU.5874.01 3 0.5457 0.497 0.00 0.46 0.48 0.06 0.00
#> TCGA.DB.A4XH.01 4 0.3037 0.797 0.00 0.04 0.00 0.86 0.10
#> TCGA.DU.8164.01 1 0.0000 0.898 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7018.01 4 0.0000 0.872 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.8105.01 1 0.3274 0.674 0.78 0.22 0.00 0.00 0.00
#> TCGA.DU.6400.01 4 0.3684 0.666 0.00 0.00 0.28 0.72 0.00
#> TCGA.S9.A6WL.01 5 0.3684 0.000 0.28 0.00 0.00 0.00 0.72
#> TCGA.S9.A6WH.01 3 0.2516 0.554 0.00 0.00 0.86 0.14 0.00
#> TCGA.DB.A64W.01 4 0.3037 0.797 0.00 0.04 0.00 0.86 0.10
#> TCGA.E1.5318.01 4 0.2732 0.802 0.00 0.00 0.16 0.84 0.00
#> TCGA.S9.A7J3.01 4 0.0000 0.872 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A6UB.01 1 0.0000 0.898 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6393.01 1 0.0000 0.898 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.5394.01 1 0.0609 0.890 0.98 0.02 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.DU.8168.01 4 0.0000 0.72004 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DB.5274.01 4 0.5248 0.40539 0.04 0.00 0.34 0.58 0.04 0.00
#> TCGA.S9.A7QZ.01 2 0.3846 0.70972 0.10 0.80 0.08 0.00 0.02 0.00
#> TCGA.DU.7302.01 4 0.0000 0.72004 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.QH.A65R.01 6 0.0547 0.00000 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.DU.5874.01 3 0.5682 -0.00661 0.38 0.00 0.46 0.00 0.00 0.16
#> TCGA.DB.A4XH.01 4 0.3647 0.49158 0.36 0.00 0.00 0.64 0.00 0.00
#> TCGA.DU.8164.01 2 0.0000 0.88834 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7018.01 4 0.0000 0.72004 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.8105.01 2 0.3270 0.72355 0.12 0.82 0.06 0.00 0.00 0.00
#> TCGA.DU.6400.01 4 0.4328 0.23595 0.00 0.00 0.46 0.52 0.00 0.02
#> TCGA.S9.A6WL.01 5 0.3499 0.00000 0.00 0.32 0.00 0.00 0.68 0.00
#> TCGA.S9.A6WH.01 3 0.6907 0.09703 0.00 0.00 0.48 0.10 0.22 0.20
#> TCGA.DB.A64W.01 4 0.3647 0.49158 0.36 0.00 0.00 0.64 0.00 0.00
#> TCGA.E1.5318.01 4 0.3592 0.57472 0.00 0.00 0.24 0.74 0.02 0.00
#> TCGA.S9.A7J3.01 4 0.0547 0.71432 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.S9.A6UB.01 2 0.0000 0.88834 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6393.01 2 0.0000 0.88834 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.5394.01 2 0.0937 0.87315 0.00 0.96 0.00 0.00 0.04 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.DU.8168.01 4 0.2832 0.42972 0.00 0.00 0.00 0.76 0.00 0.00 0.24
#> TCGA.DB.5274.01 4 0.4536 0.18400 0.14 0.00 0.00 0.72 0.06 0.00 0.08
#> TCGA.S9.A7QZ.01 2 0.3307 0.64777 0.24 0.74 0.00 0.00 0.00 0.00 0.02
#> TCGA.DU.7302.01 4 0.2708 0.46214 0.00 0.00 0.00 0.78 0.00 0.00 0.22
#> TCGA.QH.A65R.01 6 0.1664 0.00000 0.00 0.00 0.06 0.02 0.00 0.92 0.00
#> TCGA.DU.5874.01 3 0.0000 0.00000 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4XH.01 7 0.3294 1.00000 0.00 0.00 0.00 0.34 0.00 0.00 0.66
#> TCGA.DU.8164.01 2 0.0000 0.84708 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7018.01 4 0.2708 0.46214 0.00 0.00 0.00 0.78 0.00 0.00 0.22
#> TCGA.HT.8105.01 2 0.5731 0.39899 0.20 0.58 0.00 0.00 0.00 0.08 0.14
#> TCGA.DU.6400.01 4 0.3908 0.00943 0.20 0.00 0.08 0.72 0.00 0.00 0.00
#> TCGA.S9.A6WL.01 5 0.1886 0.00000 0.00 0.12 0.00 0.00 0.88 0.00 0.00
#> TCGA.S9.A6WH.01 1 0.5564 0.00000 0.50 0.00 0.16 0.32 0.00 0.02 0.00
#> TCGA.DB.A64W.01 7 0.3294 1.00000 0.00 0.00 0.00 0.34 0.00 0.00 0.66
#> TCGA.E1.5318.01 4 0.1166 0.49931 0.06 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.S9.A7J3.01 4 0.4569 0.35378 0.02 0.00 0.00 0.64 0.06 0.00 0.28
#> TCGA.S9.A6UB.01 2 0.0000 0.84708 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6393.01 2 0.0000 0.84708 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.5394.01 2 0.0504 0.83973 0.00 0.98 0.00 0.00 0.00 0.00 0.02
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.DU.8168.01 4 0.0471 0.641 0.00 0.00 0.0 0.98 0.00 0.00 0.02 0.00
#> TCGA.DB.5274.01 4 0.5644 0.311 0.16 0.00 0.0 0.46 0.02 0.34 0.02 0.00
#> TCGA.S9.A7QZ.01 2 0.3272 0.439 0.00 0.58 0.0 0.00 0.00 0.42 0.00 0.00
#> TCGA.DU.7302.01 4 0.0000 0.636 0.00 0.00 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A65R.01 8 0.0471 0.000 0.02 0.00 0.0 0.00 0.00 0.00 0.00 0.98
#> TCGA.DU.5874.01 3 0.0000 0.000 0.00 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4XH.01 7 0.3237 1.000 0.00 0.00 0.0 0.40 0.00 0.00 0.60 0.00
#> TCGA.DU.8164.01 2 0.0000 0.763 0.00 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7018.01 4 0.0000 0.636 0.00 0.00 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8105.01 2 0.6140 0.196 0.16 0.46 0.0 0.00 0.00 0.16 0.22 0.00
#> TCGA.DU.6400.01 4 0.5398 0.392 0.20 0.00 0.1 0.58 0.00 0.12 0.00 0.00
#> TCGA.S9.A6WL.01 5 0.1765 0.000 0.00 0.12 0.0 0.00 0.88 0.00 0.00 0.00
#> TCGA.S9.A6WH.01 1 0.2862 0.000 0.82 0.00 0.1 0.08 0.00 0.00 0.00 0.00
#> TCGA.DB.A64W.01 7 0.3237 1.000 0.00 0.00 0.0 0.40 0.00 0.00 0.60 0.00
#> TCGA.E1.5318.01 4 0.3619 0.615 0.12 0.00 0.0 0.74 0.00 0.14 0.00 0.00
#> TCGA.S9.A7J3.01 4 0.3894 0.505 0.00 0.00 0.0 0.76 0.10 0.08 0.06 0.00
#> TCGA.S9.A6UB.01 2 0.0000 0.763 0.00 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6393.01 2 0.0000 0.763 0.00 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.5394.01 2 0.2591 0.713 0.00 0.86 0.0 0.00 0.00 0.04 0.08 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: Node01111-leaf , Node01112-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01211-leaf , Node01212-leaf , Node01213 , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node01224-leaf , Node01225-leaf , Node01311-leaf , Node01312-leaf , Node01313-leaf , Node01411-leaf , Node01412-leaf , Node01431-leaf , Node01432-leaf , Node02211-leaf , Node02212 , Node02221 , Node02222-leaf , Node02223-leaf , Node02231 , Node02232-leaf , Node02233-leaf , Node02234-leaf , Node02311-leaf , Node02312-leaf , Node02313-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 47 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 0.962 0.983 0.3755 0.611 0.611
#> 3 3 1.000 0.985 0.992 0.3210 0.859 0.777
#> 4 4 1.000 0.988 0.991 0.3999 0.751 0.531
#> 5 5 0.828 0.854 0.882 0.0628 1.000 1.000
#> 6 6 0.760 0.587 0.706 0.0431 0.952 0.840
#> 7 7 0.736 0.669 0.809 0.0418 0.855 0.508
#> 8 8 0.754 0.656 0.832 0.0332 0.930 0.667
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.S9.A6TX.01 1 0.000 0.997 1.00 0.00
#> TCGA.E1.5311.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7480.01 1 0.000 0.997 1.00 0.00
#> TCGA.S9.A7R1.01 1 0.000 0.997 1.00 0.00
#> TCGA.TM.A7C5.01 1 0.000 0.997 1.00 0.00
#> TCGA.E1.A7YO.01 1 0.000 0.997 1.00 0.00
#> TCGA.DB.A4XG.01 1 0.000 0.997 1.00 0.00
#> TCGA.S9.A6TY.01 1 0.000 0.997 1.00 0.00
#> TCGA.IK.8125.01 2 0.000 0.937 0.00 1.00
#> TCGA.HT.A74K.01 2 0.000 0.937 0.00 1.00
#> TCGA.DH.5141.01 1 0.000 0.997 1.00 0.00
#> TCGA.EZ.7264.01 2 0.925 0.527 0.34 0.66
#> TCGA.DU.A6S8.01 2 0.000 0.937 0.00 1.00
#> TCGA.DU.7298.01 1 0.000 0.997 1.00 0.00
#> TCGA.S9.A6WP.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.7294.01 1 0.000 0.997 1.00 0.00
#> TCGA.HW.7487.01 1 0.000 0.997 1.00 0.00
#> TCGA.HW.7491.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.8012.01 1 0.000 0.997 1.00 0.00
#> TCGA.P5.A77W.01 1 0.000 0.997 1.00 0.00
#> TCGA.S9.A6WD.01 2 0.925 0.527 0.34 0.66
#> TCGA.TQ.A7RU.01 1 0.000 0.997 1.00 0.00
#> TCGA.P5.A5F0.01 1 0.000 0.997 1.00 0.00
#> TCGA.R8.A73M.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.A6S3.01 1 0.000 0.997 1.00 0.00
#> TCGA.VW.A7QS.01 2 0.000 0.937 0.00 1.00
#> TCGA.DB.5279.01 2 0.000 0.937 0.00 1.00
#> TCGA.HT.7677.01 1 0.000 0.997 1.00 0.00
#> TCGA.TM.A84M.01 2 0.000 0.937 0.00 1.00
#> TCGA.DH.5144.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7471.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.A5R9.01 1 0.000 0.997 1.00 0.00
#> TCGA.DB.A75K.01 1 0.000 0.997 1.00 0.00
#> TCGA.P5.A737.01 1 0.000 0.997 1.00 0.00
#> TCGA.RY.A83Y.01 1 0.000 0.997 1.00 0.00
#> TCGA.R8.A6MO.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.5870.02 2 0.000 0.937 0.00 1.00
#> TCGA.CS.6668.01 2 0.000 0.937 0.00 1.00
#> TCGA.R8.A6ML.01 1 0.000 0.997 1.00 0.00
#> TCGA.QH.A65Z.01 1 0.000 0.997 1.00 0.00
#> TCGA.RY.A83X.01 1 0.000 0.997 1.00 0.00
#> TCGA.DH.A66F.01 1 0.000 0.997 1.00 0.00
#> TCGA.FG.7641.01 1 0.000 0.997 1.00 0.00
#> TCGA.VV.A829.01 2 0.000 0.937 0.00 1.00
#> TCGA.DB.A64P.01 1 0.000 0.997 1.00 0.00
#> TCGA.TM.A84G.01 1 0.469 0.879 0.90 0.10
#> TCGA.FG.5962.01 2 0.000 0.937 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.S9.A6TX.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.E1.5311.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.HT.7480.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.S9.A7R1.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.TM.A7C5.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.E1.A7YO.01 1 0.153 0.960 0.96 0.04 0.00
#> TCGA.DB.A4XG.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.S9.A6TY.01 1 0.153 0.960 0.96 0.04 0.00
#> TCGA.IK.8125.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.HT.A74K.01 2 0.153 0.957 0.00 0.96 0.04
#> TCGA.DH.5141.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.EZ.7264.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.DU.A6S8.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.DU.7298.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.S9.A6WP.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.DU.7294.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.HW.7487.01 1 0.334 0.872 0.88 0.12 0.00
#> TCGA.HW.7491.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.HT.8012.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.P5.A77W.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.S9.A6WD.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.TQ.A7RU.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.P5.A5F0.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.R8.A73M.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.DU.A6S3.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.VW.A7QS.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.DB.5279.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.HT.7677.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.TM.A84M.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.DH.5144.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.HT.7471.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.HT.A5R9.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.DB.A75K.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.P5.A737.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.RY.A83Y.01 1 0.153 0.960 0.96 0.04 0.00
#> TCGA.R8.A6MO.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.DU.5870.02 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.CS.6668.01 2 0.153 0.957 0.00 0.96 0.04
#> TCGA.R8.A6ML.01 1 0.153 0.960 0.96 0.04 0.00
#> TCGA.QH.A65Z.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.RY.A83X.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.DH.A66F.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.FG.7641.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.VV.A829.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.DB.A64P.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.TM.A84G.01 2 0.000 0.990 0.00 1.00 0.00
#> TCGA.FG.5962.01 2 0.000 0.990 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.S9.A6TX.01 4 0.0707 0.963 0.00 0.02 0.00 0.98
#> TCGA.E1.5311.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HT.7480.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.S9.A7R1.01 4 0.2011 0.917 0.08 0.00 0.00 0.92
#> TCGA.TM.A7C5.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YO.01 4 0.0707 0.979 0.02 0.00 0.00 0.98
#> TCGA.DB.A4XG.01 4 0.0707 0.979 0.02 0.00 0.00 0.98
#> TCGA.S9.A6TY.01 4 0.0707 0.979 0.02 0.00 0.00 0.98
#> TCGA.IK.8125.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.HT.A74K.01 2 0.0707 0.983 0.00 0.98 0.00 0.02
#> TCGA.DH.5141.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EZ.7264.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.DU.A6S8.01 3 0.0000 0.996 0.00 0.00 1.00 0.00
#> TCGA.DU.7298.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.S9.A6WP.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DU.7294.01 4 0.0707 0.979 0.02 0.00 0.00 0.98
#> TCGA.HW.7487.01 4 0.0707 0.963 0.00 0.02 0.00 0.98
#> TCGA.HW.7491.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HT.8012.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.P5.A77W.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.S9.A6WD.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.TQ.A7RU.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.P5.A5F0.01 4 0.0707 0.979 0.02 0.00 0.00 0.98
#> TCGA.R8.A73M.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DU.A6S3.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.VW.A7QS.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.DB.5279.01 3 0.0000 0.996 0.00 0.00 1.00 0.00
#> TCGA.HT.7677.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.TM.A84M.01 3 0.0707 0.985 0.00 0.00 0.98 0.02
#> TCGA.DH.5144.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HT.7471.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HT.A5R9.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DB.A75K.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.P5.A737.01 4 0.0707 0.963 0.00 0.02 0.00 0.98
#> TCGA.RY.A83Y.01 4 0.0707 0.979 0.02 0.00 0.00 0.98
#> TCGA.R8.A6MO.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DU.5870.02 3 0.0000 0.996 0.00 0.00 1.00 0.00
#> TCGA.CS.6668.01 2 0.0707 0.983 0.00 0.98 0.00 0.02
#> TCGA.R8.A6ML.01 4 0.0707 0.979 0.02 0.00 0.00 0.98
#> TCGA.QH.A65Z.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.RY.A83X.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DH.A66F.01 4 0.0707 0.979 0.02 0.00 0.00 0.98
#> TCGA.FG.7641.01 4 0.2011 0.917 0.08 0.00 0.00 0.92
#> TCGA.VV.A829.01 3 0.0000 0.996 0.00 0.00 1.00 0.00
#> TCGA.DB.A64P.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.TM.A84G.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.FG.5962.01 2 0.0000 0.994 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.S9.A6TX.01 5 0.0000 0.864 0.00 0.00 0.00 0.00 1.00
#> TCGA.E1.5311.01 1 0.0000 0.898 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7480.01 1 0.3424 0.806 0.76 0.00 0.00 0.24 0.00
#> TCGA.S9.A7R1.01 5 0.4840 0.754 0.04 0.00 0.00 0.32 0.64
#> TCGA.TM.A7C5.01 1 0.0000 0.898 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YO.01 5 0.2873 0.874 0.02 0.00 0.00 0.12 0.86
#> TCGA.DB.A4XG.01 5 0.3999 0.832 0.02 0.00 0.00 0.24 0.74
#> TCGA.S9.A6TY.01 5 0.2616 0.875 0.02 0.00 0.00 0.10 0.88
#> TCGA.IK.8125.01 2 0.0000 0.828 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.A74K.01 2 0.1732 0.800 0.00 0.92 0.00 0.08 0.00
#> TCGA.DH.5141.01 1 0.0000 0.898 1.00 0.00 0.00 0.00 0.00
#> TCGA.EZ.7264.01 2 0.4132 0.828 0.00 0.72 0.00 0.26 0.02
#> TCGA.DU.A6S8.01 3 0.0000 0.977 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.7298.01 1 0.4126 0.707 0.62 0.00 0.00 0.38 0.00
#> TCGA.S9.A6WP.01 1 0.3274 0.810 0.78 0.00 0.00 0.22 0.00
#> TCGA.DU.7294.01 5 0.3513 0.776 0.02 0.00 0.00 0.18 0.80
#> TCGA.HW.7487.01 5 0.0000 0.864 0.00 0.00 0.00 0.00 1.00
#> TCGA.HW.7491.01 1 0.1410 0.885 0.94 0.00 0.00 0.06 0.00
#> TCGA.HT.8012.01 1 0.0000 0.898 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A77W.01 1 0.1043 0.895 0.96 0.00 0.00 0.04 0.00
#> TCGA.S9.A6WD.01 2 0.4132 0.828 0.00 0.72 0.00 0.26 0.02
#> TCGA.TQ.A7RU.01 1 0.0000 0.898 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A5F0.01 5 0.1648 0.871 0.02 0.00 0.00 0.04 0.94
#> TCGA.R8.A73M.01 1 0.3274 0.809 0.78 0.00 0.00 0.22 0.00
#> TCGA.DU.A6S3.01 1 0.0000 0.898 1.00 0.00 0.00 0.00 0.00
#> TCGA.VW.A7QS.01 2 0.4132 0.828 0.00 0.72 0.00 0.26 0.02
#> TCGA.DB.5279.01 3 0.0000 0.977 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7677.01 1 0.3424 0.806 0.76 0.00 0.00 0.24 0.00
#> TCGA.TM.A84M.01 3 0.2280 0.904 0.00 0.00 0.88 0.12 0.00
#> TCGA.DH.5144.01 1 0.1043 0.895 0.96 0.00 0.00 0.04 0.00
#> TCGA.HT.7471.01 1 0.0609 0.896 0.98 0.00 0.00 0.02 0.00
#> TCGA.HT.A5R9.01 1 0.0000 0.898 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A75K.01 1 0.4126 0.707 0.62 0.00 0.00 0.38 0.00
#> TCGA.P5.A737.01 5 0.2020 0.869 0.00 0.00 0.00 0.10 0.90
#> TCGA.RY.A83Y.01 5 0.0609 0.872 0.02 0.00 0.00 0.00 0.98
#> TCGA.R8.A6MO.01 1 0.4126 0.707 0.62 0.00 0.00 0.38 0.00
#> TCGA.DU.5870.02 3 0.0000 0.977 0.00 0.00 1.00 0.00 0.00
#> TCGA.CS.6668.01 2 0.1732 0.800 0.00 0.92 0.00 0.08 0.00
#> TCGA.R8.A6ML.01 5 0.0609 0.872 0.02 0.00 0.00 0.00 0.98
#> TCGA.QH.A65Z.01 1 0.0000 0.898 1.00 0.00 0.00 0.00 0.00
#> TCGA.RY.A83X.01 1 0.1043 0.895 0.96 0.00 0.00 0.04 0.00
#> TCGA.DH.A66F.01 5 0.3513 0.857 0.02 0.00 0.00 0.18 0.80
#> TCGA.FG.7641.01 5 0.4840 0.754 0.04 0.00 0.00 0.32 0.64
#> TCGA.VV.A829.01 3 0.0000 0.977 0.00 0.00 1.00 0.00 0.00
#> TCGA.DB.A64P.01 1 0.0000 0.898 1.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84G.01 2 0.4726 0.750 0.00 0.58 0.00 0.40 0.02
#> TCGA.FG.5962.01 2 0.0000 0.828 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.S9.A6TX.01 4 0.3797 0.6442 0.00 0.00 0.00 0.58 0.42 0.00
#> TCGA.E1.5311.01 1 0.0937 0.8311 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.HT.7480.01 1 0.3647 0.6800 0.64 0.00 0.00 0.00 0.36 0.00
#> TCGA.S9.A7R1.01 5 0.0000 0.4042 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.TM.A7C5.01 1 0.0000 0.8340 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YO.01 5 0.3916 0.2993 0.00 0.00 0.00 0.30 0.68 0.02
#> TCGA.DB.A4XG.01 5 0.2581 0.4496 0.00 0.00 0.00 0.12 0.86 0.02
#> TCGA.S9.A6TY.01 5 0.4144 0.1307 0.00 0.00 0.00 0.36 0.62 0.02
#> TCGA.IK.8125.01 2 0.3756 -0.4733 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.HT.A74K.01 6 0.3797 0.9559 0.00 0.42 0.00 0.00 0.00 0.58
#> TCGA.DH.5141.01 1 0.0937 0.8311 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.EZ.7264.01 2 0.0000 0.5083 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A6S8.01 3 0.0000 0.9478 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7298.01 1 0.6646 0.4854 0.42 0.00 0.00 0.22 0.32 0.04
#> TCGA.S9.A6WP.01 1 0.4078 0.6816 0.64 0.00 0.00 0.02 0.34 0.00
#> TCGA.DU.7294.01 4 0.4576 0.0207 0.00 0.00 0.00 0.56 0.40 0.04
#> TCGA.HW.7487.01 4 0.3797 0.6442 0.00 0.00 0.00 0.58 0.42 0.00
#> TCGA.HW.7491.01 1 0.2454 0.7927 0.84 0.00 0.00 0.00 0.16 0.00
#> TCGA.HT.8012.01 1 0.0000 0.8340 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A77W.01 1 0.0000 0.8340 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WD.01 2 0.0547 0.5014 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.TQ.A7RU.01 1 0.0000 0.8340 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A5F0.01 5 0.3647 -0.1648 0.00 0.00 0.00 0.36 0.64 0.00
#> TCGA.R8.A73M.01 1 0.5529 0.6424 0.64 0.00 0.00 0.20 0.12 0.04
#> TCGA.DU.A6S3.01 1 0.0937 0.8311 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.VW.A7QS.01 2 0.0000 0.5083 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5279.01 3 0.0000 0.9478 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7677.01 1 0.3578 0.6964 0.66 0.00 0.00 0.00 0.34 0.00
#> TCGA.TM.A84M.01 3 0.3829 0.7595 0.00 0.00 0.76 0.06 0.00 0.18
#> TCGA.DH.5144.01 1 0.0937 0.8299 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.HT.7471.01 1 0.0000 0.8340 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A5R9.01 1 0.0000 0.8340 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A75K.01 1 0.6610 0.4966 0.44 0.00 0.00 0.22 0.30 0.04
#> TCGA.P5.A737.01 5 0.3647 0.1487 0.00 0.00 0.00 0.36 0.64 0.00
#> TCGA.RY.A83Y.01 4 0.3797 0.6442 0.00 0.00 0.00 0.58 0.42 0.00
#> TCGA.R8.A6MO.01 1 0.6610 0.4966 0.44 0.00 0.00 0.22 0.30 0.04
#> TCGA.DU.5870.02 3 0.0000 0.9478 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CS.6668.01 6 0.3756 0.9566 0.00 0.40 0.00 0.00 0.00 0.60
#> TCGA.R8.A6ML.01 4 0.3864 0.4995 0.00 0.00 0.00 0.52 0.48 0.00
#> TCGA.QH.A65Z.01 1 0.0000 0.8340 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RY.A83X.01 1 0.1267 0.8291 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.DH.A66F.01 5 0.3198 0.3841 0.00 0.00 0.00 0.26 0.74 0.00
#> TCGA.FG.7641.01 5 0.0000 0.4042 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.VV.A829.01 3 0.0000 0.9478 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.A64P.01 1 0.0000 0.8340 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84G.01 2 0.5481 0.2284 0.00 0.52 0.00 0.14 0.00 0.34
#> TCGA.FG.5962.01 2 0.3756 -0.4733 0.00 0.60 0.00 0.00 0.00 0.40
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.S9.A6TX.01 5 0.5189 0.5626 0.00 0.00 0.00 0.08 0.62 0.24 0.06
#> TCGA.E1.5311.01 1 0.0504 0.8824 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.HT.7480.01 4 0.3994 0.3664 0.48 0.00 0.00 0.50 0.00 0.02 0.00
#> TCGA.S9.A7R1.01 5 0.3968 0.1890 0.00 0.00 0.00 0.44 0.54 0.02 0.00
#> TCGA.TM.A7C5.01 1 0.0000 0.8903 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YO.01 5 0.2159 0.6117 0.00 0.00 0.00 0.06 0.90 0.02 0.02
#> TCGA.DB.A4XG.01 5 0.4269 0.3236 0.00 0.00 0.00 0.36 0.60 0.02 0.02
#> TCGA.S9.A6TY.01 5 0.3548 0.6013 0.00 0.00 0.00 0.04 0.80 0.12 0.04
#> TCGA.IK.8125.01 6 0.3496 0.9392 0.00 0.42 0.00 0.00 0.00 0.58 0.00
#> TCGA.HT.A74K.01 6 0.3413 0.9338 0.00 0.38 0.00 0.00 0.00 0.62 0.00
#> TCGA.DH.5141.01 1 0.0504 0.8824 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.EZ.7264.01 2 0.0000 0.9243 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A6S8.01 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7298.01 4 0.2906 0.5713 0.18 0.00 0.00 0.80 0.00 0.02 0.00
#> TCGA.S9.A6WP.01 4 0.4386 0.4722 0.42 0.00 0.00 0.54 0.02 0.02 0.00
#> TCGA.DU.7294.01 4 0.4418 -0.1513 0.00 0.00 0.00 0.62 0.30 0.08 0.00
#> TCGA.HW.7487.01 5 0.5189 0.5626 0.00 0.00 0.00 0.08 0.62 0.24 0.06
#> TCGA.HW.7491.01 1 0.1671 0.8018 0.90 0.00 0.00 0.10 0.00 0.00 0.00
#> TCGA.HT.8012.01 1 0.0504 0.8871 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.P5.A77W.01 1 0.2376 0.8139 0.86 0.00 0.00 0.12 0.00 0.02 0.00
#> TCGA.S9.A6WD.01 2 0.1433 0.8578 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.TQ.A7RU.01 1 0.0000 0.8903 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A5F0.01 5 0.5279 0.4084 0.00 0.00 0.00 0.40 0.48 0.10 0.02
#> TCGA.R8.A73M.01 1 0.3994 0.0345 0.50 0.00 0.00 0.48 0.00 0.02 0.00
#> TCGA.DU.A6S3.01 1 0.0504 0.8824 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.VW.A7QS.01 2 0.0000 0.9243 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5279.01 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7677.01 4 0.3985 0.4121 0.46 0.00 0.00 0.52 0.00 0.02 0.00
#> TCGA.TM.A84M.01 3 0.2278 0.8790 0.00 0.00 0.88 0.04 0.00 0.08 0.00
#> TCGA.DH.5144.01 1 0.2569 0.7936 0.84 0.00 0.00 0.14 0.00 0.02 0.00
#> TCGA.HT.7471.01 1 0.1006 0.8802 0.96 0.00 0.00 0.02 0.00 0.02 0.00
#> TCGA.HT.A5R9.01 1 0.1006 0.8802 0.96 0.00 0.00 0.02 0.00 0.02 0.00
#> TCGA.DB.A75K.01 4 0.2259 0.5770 0.16 0.00 0.00 0.84 0.00 0.00 0.00
#> TCGA.P5.A737.01 5 0.2569 0.5515 0.00 0.14 0.00 0.00 0.84 0.02 0.00
#> TCGA.RY.A83Y.01 5 0.5086 0.5702 0.00 0.00 0.00 0.08 0.64 0.22 0.06
#> TCGA.R8.A6MO.01 4 0.2259 0.5770 0.16 0.00 0.00 0.84 0.00 0.00 0.00
#> TCGA.DU.5870.02 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6668.01 6 0.4317 0.9137 0.00 0.38 0.00 0.02 0.00 0.58 0.02
#> TCGA.R8.A6ML.01 5 0.3765 0.6155 0.00 0.00 0.00 0.10 0.78 0.10 0.02
#> TCGA.QH.A65Z.01 1 0.0000 0.8903 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RY.A83X.01 1 0.2569 0.7936 0.84 0.00 0.00 0.14 0.00 0.02 0.00
#> TCGA.DH.A66F.01 5 0.2745 0.5787 0.00 0.00 0.00 0.16 0.82 0.02 0.00
#> TCGA.FG.7641.01 4 0.3994 -0.2316 0.00 0.00 0.00 0.50 0.48 0.02 0.00
#> TCGA.VV.A829.01 3 0.0000 0.9716 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64P.01 1 0.0000 0.8903 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84G.01 7 0.1671 0.0000 0.00 0.10 0.00 0.00 0.00 0.00 0.90
#> TCGA.FG.5962.01 6 0.3496 0.9392 0.00 0.42 0.00 0.00 0.00 0.58 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.S9.A6TX.01 8 0.0000 0.8430 0.00 0.00 0.0 0.00 0.00 0.00 0.00 1.00
#> TCGA.E1.5311.01 1 0.0000 0.9220 1.00 0.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7480.01 4 0.5381 0.3456 0.38 0.00 0.0 0.42 0.18 0.00 0.02 0.00
#> TCGA.S9.A7R1.01 5 0.4028 0.4984 0.00 0.00 0.0 0.28 0.66 0.00 0.02 0.04
#> TCGA.TM.A7C5.01 1 0.0000 0.9220 1.00 0.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YO.01 5 0.3735 0.5065 0.00 0.00 0.0 0.04 0.72 0.00 0.02 0.22
#> TCGA.DB.A4XG.01 5 0.3170 0.5655 0.00 0.00 0.0 0.20 0.76 0.00 0.00 0.04
#> TCGA.S9.A6TY.01 5 0.3272 0.0946 0.00 0.00 0.0 0.00 0.58 0.00 0.00 0.42
#> TCGA.IK.8125.01 6 0.2888 0.8161 0.00 0.16 0.0 0.00 0.00 0.80 0.04 0.00
#> TCGA.HT.A74K.01 6 0.0000 0.8166 0.00 0.00 0.0 0.00 0.00 1.00 0.00 0.00
#> TCGA.DH.5141.01 1 0.0000 0.9220 1.00 0.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.EZ.7264.01 2 0.2348 0.8780 0.00 0.88 0.0 0.00 0.06 0.02 0.04 0.00
#> TCGA.DU.A6S8.01 3 0.0000 0.9246 0.00 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7298.01 4 0.1741 0.4272 0.02 0.02 0.0 0.92 0.00 0.00 0.04 0.00
#> TCGA.S9.A6WP.01 4 0.5190 0.3329 0.32 0.00 0.0 0.42 0.26 0.00 0.00 0.00
#> TCGA.DU.7294.01 4 0.4578 0.2341 0.00 0.02 0.0 0.70 0.08 0.00 0.04 0.16
#> TCGA.HW.7487.01 8 0.0000 0.8430 0.00 0.00 0.0 0.00 0.00 0.00 0.00 1.00
#> TCGA.HW.7491.01 1 0.3630 0.6643 0.78 0.00 0.0 0.08 0.10 0.00 0.04 0.00
#> TCGA.HT.8012.01 1 0.0000 0.9220 1.00 0.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A77W.01 1 0.2267 0.7709 0.82 0.00 0.0 0.18 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WD.01 2 0.0471 0.9412 0.00 0.98 0.0 0.00 0.00 0.02 0.00 0.00
#> TCGA.TQ.A7RU.01 1 0.0000 0.9220 1.00 0.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A5F0.01 4 0.6355 -0.1378 0.00 0.02 0.0 0.38 0.26 0.00 0.06 0.28
#> TCGA.R8.A73M.01 4 0.3015 0.2929 0.32 0.00 0.0 0.68 0.00 0.00 0.00 0.00
#> TCGA.DU.A6S3.01 1 0.0000 0.9220 1.00 0.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.VW.A7QS.01 2 0.0471 0.9412 0.00 0.98 0.0 0.00 0.00 0.02 0.00 0.00
#> TCGA.DB.5279.01 3 0.0000 0.9246 0.00 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7677.01 4 0.4990 0.3494 0.38 0.00 0.0 0.44 0.18 0.00 0.00 0.00
#> TCGA.TM.A84M.01 3 0.4409 0.6484 0.00 0.00 0.7 0.02 0.08 0.18 0.02 0.00
#> TCGA.DH.5144.01 1 0.2267 0.7709 0.82 0.00 0.0 0.18 0.00 0.00 0.00 0.00
#> TCGA.HT.7471.01 1 0.0471 0.9105 0.98 0.00 0.0 0.02 0.00 0.00 0.00 0.00
#> TCGA.HT.A5R9.01 1 0.0000 0.9220 1.00 0.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A75K.01 4 0.1804 0.4455 0.02 0.00 0.0 0.90 0.08 0.00 0.00 0.00
#> TCGA.P5.A737.01 5 0.5032 0.1688 0.00 0.16 0.0 0.00 0.56 0.00 0.02 0.26
#> TCGA.RY.A83Y.01 8 0.0000 0.8430 0.00 0.00 0.0 0.00 0.00 0.00 0.00 1.00
#> TCGA.R8.A6MO.01 4 0.1804 0.4455 0.02 0.00 0.0 0.90 0.08 0.00 0.00 0.00
#> TCGA.DU.5870.02 3 0.0000 0.9246 0.00 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6668.01 6 0.0471 0.8186 0.00 0.00 0.0 0.00 0.00 0.98 0.02 0.00
#> TCGA.R8.A6ML.01 8 0.3808 0.3062 0.00 0.00 0.0 0.02 0.30 0.00 0.02 0.66
#> TCGA.QH.A65Z.01 1 0.0000 0.9220 1.00 0.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.RY.A83X.01 1 0.2406 0.7419 0.80 0.00 0.0 0.20 0.00 0.00 0.00 0.00
#> TCGA.DH.A66F.01 5 0.4727 0.5563 0.00 0.00 0.0 0.14 0.62 0.00 0.02 0.22
#> TCGA.FG.7641.01 5 0.4284 0.3627 0.00 0.00 0.0 0.36 0.58 0.00 0.02 0.04
#> TCGA.VV.A829.01 3 0.0000 0.9246 0.00 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64P.01 1 0.0000 0.9220 1.00 0.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84G.01 7 0.1947 0.0000 0.00 0.14 0.0 0.00 0.00 0.00 0.86 0.00
#> TCGA.FG.5962.01 6 0.2888 0.8161 0.00 0.16 0.0 0.00 0.00 0.80 0.04 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0223. Child nodes: Node012131-leaf , Node012132-leaf , Node012133-leaf , Node012134-leaf , Node022121-leaf , Node022122-leaf , Node022123-leaf , Node022211-leaf , Node022212-leaf , Node022311-leaf , Node022312-leaf , Node022313-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["02231"]
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 '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 0.5243 0.476 0.476
#> 3 3 0.963 0.969 0.983 0.1383 0.924 0.840
#> 4 4 0.957 0.831 0.933 0.0408 0.995 0.988
#> 5 5 1.000 0.857 1.000 0.0279 0.967 0.916
#> 6 6 1.000 0.804 0.996 0.0459 0.971 0.921
#> 7 7 0.948 0.689 0.953 0.0376 0.976 0.929
#> 8 8 0.967 0.676 0.973 0.0272 0.981 0.938
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.E1.5311.01 1 0 1 1 0
#> TCGA.HT.7480.01 1 0 1 1 0
#> TCGA.TM.A7C5.01 1 0 1 1 0
#> TCGA.DH.5141.01 1 0 1 1 0
#> TCGA.DU.7298.01 2 0 1 0 1
#> TCGA.S9.A6WP.01 1 0 1 1 0
#> TCGA.HW.7491.01 1 0 1 1 0
#> TCGA.HT.8012.01 2 0 1 0 1
#> TCGA.P5.A77W.01 2 0 1 0 1
#> TCGA.TQ.A7RU.01 1 0 1 1 0
#> TCGA.R8.A73M.01 2 0 1 0 1
#> TCGA.DU.A6S3.01 1 0 1 1 0
#> TCGA.HT.7677.01 1 0 1 1 0
#> TCGA.DH.5144.01 2 0 1 0 1
#> TCGA.HT.7471.01 2 0 1 0 1
#> TCGA.HT.A5R9.01 2 0 1 0 1
#> TCGA.DB.A75K.01 2 0 1 0 1
#> TCGA.R8.A6MO.01 2 0 1 0 1
#> TCGA.QH.A65Z.01 1 0 1 1 0
#> TCGA.RY.A83X.01 2 0 1 0 1
#> TCGA.DB.A64P.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.E1.5311.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.HT.7480.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.TM.A7C5.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DH.5141.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DU.7298.01 2 0.0000 0.978 0 1.00 0.00
#> TCGA.S9.A6WP.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.HW.7491.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.HT.8012.01 2 0.0000 0.978 0 1.00 0.00
#> TCGA.P5.A77W.01 2 0.3340 0.860 0 0.88 0.12
#> TCGA.TQ.A7RU.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.R8.A73M.01 2 0.0000 0.978 0 1.00 0.00
#> TCGA.DU.A6S3.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.HT.7677.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DH.5144.01 2 0.0892 0.963 0 0.98 0.02
#> TCGA.HT.7471.01 2 0.0000 0.978 0 1.00 0.00
#> TCGA.HT.A5R9.01 3 0.4002 0.815 0 0.16 0.84
#> TCGA.DB.A75K.01 2 0.0000 0.978 0 1.00 0.00
#> TCGA.R8.A6MO.01 2 0.0000 0.978 0 1.00 0.00
#> TCGA.QH.A65Z.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.RY.A83X.01 3 0.2066 0.834 0 0.06 0.94
#> TCGA.DB.A64P.01 1 0.0000 1.000 1 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.E1.5311.01 1 0.000 1.00000 1 0.00 0.00 0.00
#> TCGA.HT.7480.01 1 0.000 1.00000 1 0.00 0.00 0.00
#> TCGA.TM.A7C5.01 1 0.000 1.00000 1 0.00 0.00 0.00
#> TCGA.DH.5141.01 1 0.000 1.00000 1 0.00 0.00 0.00
#> TCGA.DU.7298.01 2 0.000 0.91980 0 1.00 0.00 0.00
#> TCGA.S9.A6WP.01 1 0.000 1.00000 1 0.00 0.00 0.00
#> TCGA.HW.7491.01 1 0.000 1.00000 1 0.00 0.00 0.00
#> TCGA.HT.8012.01 2 0.000 0.91980 0 1.00 0.00 0.00
#> TCGA.P5.A77W.01 2 0.771 0.00892 0 0.44 0.24 0.32
#> TCGA.TQ.A7RU.01 1 0.000 1.00000 1 0.00 0.00 0.00
#> TCGA.R8.A73M.01 2 0.000 0.91980 0 1.00 0.00 0.00
#> TCGA.DU.A6S3.01 1 0.000 1.00000 1 0.00 0.00 0.00
#> TCGA.HT.7677.01 1 0.000 1.00000 1 0.00 0.00 0.00
#> TCGA.DH.5144.01 2 0.000 0.91980 0 1.00 0.00 0.00
#> TCGA.HT.7471.01 2 0.000 0.91980 0 1.00 0.00 0.00
#> TCGA.HT.A5R9.01 3 0.000 0.00000 0 0.00 1.00 0.00
#> TCGA.DB.A75K.01 2 0.000 0.91980 0 1.00 0.00 0.00
#> TCGA.R8.A6MO.01 2 0.000 0.91980 0 1.00 0.00 0.00
#> TCGA.QH.A65Z.01 1 0.000 1.00000 1 0.00 0.00 0.00
#> TCGA.RY.A83X.01 4 0.452 0.00000 0 0.00 0.32 0.68
#> TCGA.DB.A64P.01 1 0.000 1.00000 1 0.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.E1.5311.01 1 0 1 1 0 0 0 0
#> TCGA.HT.7480.01 1 0 1 1 0 0 0 0
#> TCGA.TM.A7C5.01 1 0 1 1 0 0 0 0
#> TCGA.DH.5141.01 1 0 1 1 0 0 0 0
#> TCGA.DU.7298.01 2 0 1 0 1 0 0 0
#> TCGA.S9.A6WP.01 1 0 1 1 0 0 0 0
#> TCGA.HW.7491.01 1 0 1 1 0 0 0 0
#> TCGA.HT.8012.01 2 0 1 0 1 0 0 0
#> TCGA.P5.A77W.01 5 0 0 0 0 0 0 1
#> TCGA.TQ.A7RU.01 1 0 1 1 0 0 0 0
#> TCGA.R8.A73M.01 2 0 1 0 1 0 0 0
#> TCGA.DU.A6S3.01 1 0 1 1 0 0 0 0
#> TCGA.HT.7677.01 1 0 1 1 0 0 0 0
#> TCGA.DH.5144.01 2 0 1 0 1 0 0 0
#> TCGA.HT.7471.01 2 0 1 0 1 0 0 0
#> TCGA.HT.A5R9.01 3 0 0 0 0 1 0 0
#> TCGA.DB.A75K.01 2 0 1 0 1 0 0 0
#> TCGA.R8.A6MO.01 2 0 1 0 1 0 0 0
#> TCGA.QH.A65Z.01 1 0 1 1 0 0 0 0
#> TCGA.RY.A83X.01 4 0 0 0 0 0 1 0
#> TCGA.DB.A64P.01 1 0 1 1 0 0 0 0
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.E1.5311.01 1 0.0000 1.000 1 0.00 0 0 0 0.00
#> TCGA.HT.7480.01 1 0.0000 1.000 1 0.00 0 0 0 0.00
#> TCGA.TM.A7C5.01 1 0.0000 1.000 1 0.00 0 0 0 0.00
#> TCGA.DH.5141.01 1 0.0000 1.000 1 0.00 0 0 0 0.00
#> TCGA.DU.7298.01 2 0.0000 0.988 0 1.00 0 0 0 0.00
#> TCGA.S9.A6WP.01 1 0.0000 1.000 1 0.00 0 0 0 0.00
#> TCGA.HW.7491.01 1 0.0000 1.000 1 0.00 0 0 0 0.00
#> TCGA.HT.8012.01 2 0.0000 0.988 0 1.00 0 0 0 0.00
#> TCGA.P5.A77W.01 5 0.0000 0.000 0 0.00 0 0 1 0.00
#> TCGA.TQ.A7RU.01 1 0.0000 1.000 1 0.00 0 0 0 0.00
#> TCGA.R8.A73M.01 2 0.0547 0.975 0 0.98 0 0 0 0.02
#> TCGA.DU.A6S3.01 1 0.0000 1.000 1 0.00 0 0 0 0.00
#> TCGA.HT.7677.01 1 0.0000 1.000 1 0.00 0 0 0 0.00
#> TCGA.DH.5144.01 6 0.0547 0.000 0 0.02 0 0 0 0.98
#> TCGA.HT.7471.01 2 0.0937 0.957 0 0.96 0 0 0 0.04
#> TCGA.HT.A5R9.01 3 0.0000 0.000 0 0.00 1 0 0 0.00
#> TCGA.DB.A75K.01 2 0.0000 0.988 0 1.00 0 0 0 0.00
#> TCGA.R8.A6MO.01 2 0.0000 0.988 0 1.00 0 0 0 0.00
#> TCGA.QH.A65Z.01 1 0.0000 1.000 1 0.00 0 0 0 0.00
#> TCGA.RY.A83X.01 4 0.0000 0.000 0 0.00 0 1 0 0.00
#> TCGA.DB.A64P.01 1 0.0000 1.000 1 0.00 0 0 0 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.E1.5311.01 1 0.0000 1.000 1 0.00 0 0 0 0.00 0.00
#> TCGA.HT.7480.01 1 0.0000 1.000 1 0.00 0 0 0 0.00 0.00
#> TCGA.TM.A7C5.01 1 0.0000 1.000 1 0.00 0 0 0 0.00 0.00
#> TCGA.DH.5141.01 1 0.0000 1.000 1 0.00 0 0 0 0.00 0.00
#> TCGA.DU.7298.01 2 0.3496 0.750 0 0.58 0 0 0 0.00 0.42
#> TCGA.S9.A6WP.01 1 0.0000 1.000 1 0.00 0 0 0 0.00 0.00
#> TCGA.HW.7491.01 1 0.0000 1.000 1 0.00 0 0 0 0.00 0.00
#> TCGA.HT.8012.01 2 0.3047 0.743 0 0.72 0 0 0 0.00 0.28
#> TCGA.P5.A77W.01 5 0.0000 0.000 0 0.00 0 0 1 0.00 0.00
#> TCGA.TQ.A7RU.01 1 0.0000 1.000 1 0.00 0 0 0 0.00 0.00
#> TCGA.R8.A73M.01 7 0.0000 0.000 0 0.00 0 0 0 0.00 1.00
#> TCGA.DU.A6S3.01 1 0.0000 1.000 1 0.00 0 0 0 0.00 0.00
#> TCGA.HT.7677.01 1 0.0000 1.000 1 0.00 0 0 0 0.00 0.00
#> TCGA.DH.5144.01 6 0.1006 0.000 0 0.02 0 0 0 0.96 0.02
#> TCGA.HT.7471.01 2 0.0863 0.405 0 0.96 0 0 0 0.04 0.00
#> TCGA.HT.A5R9.01 3 0.0000 0.000 0 0.00 1 0 0 0.00 0.00
#> TCGA.DB.A75K.01 2 0.3413 0.783 0 0.62 0 0 0 0.00 0.38
#> TCGA.R8.A6MO.01 2 0.3413 0.783 0 0.62 0 0 0 0.00 0.38
#> TCGA.QH.A65Z.01 1 0.0000 1.000 1 0.00 0 0 0 0.00 0.00
#> TCGA.RY.A83X.01 4 0.0000 0.000 0 0.00 0 1 0 0.00 0.00
#> TCGA.DB.A64P.01 1 0.0000 1.000 1 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.E1.5311.01 1 0.0000 1.000 1 0.00 0 0 0 0 0.00 0.00
#> TCGA.HT.7480.01 1 0.0000 1.000 1 0.00 0 0 0 0 0.00 0.00
#> TCGA.TM.A7C5.01 1 0.0000 1.000 1 0.00 0 0 0 0 0.00 0.00
#> TCGA.DH.5141.01 1 0.0000 1.000 1 0.00 0 0 0 0 0.00 0.00
#> TCGA.DU.7298.01 2 0.1341 0.827 0 0.92 0 0 0 0 0.08 0.00
#> TCGA.S9.A6WP.01 1 0.0000 1.000 1 0.00 0 0 0 0 0.00 0.00
#> TCGA.HW.7491.01 1 0.0000 1.000 1 0.00 0 0 0 0 0.00 0.00
#> TCGA.HT.8012.01 2 0.3856 0.653 0 0.70 0 0 0 0 0.10 0.20
#> TCGA.P5.A77W.01 5 0.0000 0.000 0 0.00 0 0 1 0 0.00 0.00
#> TCGA.TQ.A7RU.01 1 0.0000 1.000 1 0.00 0 0 0 0 0.00 0.00
#> TCGA.R8.A73M.01 7 0.1563 0.000 0 0.10 0 0 0 0 0.90 0.00
#> TCGA.DU.A6S3.01 1 0.0000 1.000 1 0.00 0 0 0 0 0.00 0.00
#> TCGA.HT.7677.01 1 0.0000 1.000 1 0.00 0 0 0 0 0.00 0.00
#> TCGA.DH.5144.01 6 0.0000 0.000 0 0.00 0 0 0 1 0.00 0.00
#> TCGA.HT.7471.01 8 0.0808 0.000 0 0.04 0 0 0 0 0.00 0.96
#> TCGA.HT.A5R9.01 3 0.0000 0.000 0 0.00 1 0 0 0 0.00 0.00
#> TCGA.DB.A75K.01 2 0.0808 0.859 0 0.96 0 0 0 0 0.00 0.04
#> TCGA.R8.A6MO.01 2 0.0000 0.856 0 1.00 0 0 0 0 0.00 0.00
#> TCGA.QH.A65Z.01 1 0.0000 1.000 1 0.00 0 0 0 0 0.00 0.00
#> TCGA.RY.A83X.01 4 0.0000 0.000 0 0.00 0 1 0 0 0.00 0.00
#> TCGA.DB.A64P.01 1 0.0000 1.000 1 0.00 0 0 0 0 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 , Node0112 , Node0113 , Node0121 , Node0122 , Node0123-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0141 , Node0142-leaf , Node0143 , Node0211-leaf , Node0212-leaf , Node0213-leaf , Node0214-leaf , Node0221 , Node0222 , Node0223 , Node0231 , Node0232-leaf , Node0233-leaf , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0323-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 40 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 0.4672 0.533 0.533
#> 3 3 1.000 0.996 0.998 0.3960 0.742 0.547
#> 4 4 0.898 0.907 0.939 0.0868 0.931 0.805
#> 5 5 0.836 0.834 0.886 0.0495 1.000 1.000
#> 6 6 0.815 0.745 0.858 0.0430 0.921 0.729
#> 7 7 0.771 0.665 0.785 0.0414 0.965 0.843
#> 8 8 0.791 0.758 0.827 0.0263 0.968 0.838
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.DU.A5TS.01 1 0 1 1 0
#> TCGA.06.A7TL.01 1 0 1 1 0
#> TCGA.E1.A7YI.01 2 0 1 0 1
#> TCGA.E1.5305.01 1 0 1 1 0
#> TCGA.S9.A7J0.01 1 0 1 1 0
#> TCGA.CS.5393.01 1 0 1 1 0
#> TCGA.E1.A7YU.01 1 0 1 1 0
#> TCGA.IK.7675.01 1 0 1 1 0
#> TCGA.19.A6J5.01 2 0 1 0 1
#> TCGA.HT.7873.01 1 0 1 1 0
#> TCGA.S9.A7IS.01 2 0 1 0 1
#> TCGA.S9.A89Z.01 1 0 1 1 0
#> TCGA.WH.A86K.01 1 0 1 1 0
#> TCGA.06.0221.01 2 0 1 0 1
#> TCGA.DH.5142.01 1 0 1 1 0
#> TCGA.RY.A83Z.01 2 0 1 0 1
#> TCGA.DB.A64X.01 1 0 1 1 0
#> TCGA.HT.7477.01 2 0 1 0 1
#> TCGA.E1.5307.01 1 0 1 1 0
#> TCGA.06.5417.01 2 0 1 0 1
#> TCGA.DU.7304.02 2 0 1 0 1
#> TCGA.FG.8188.01 1 0 1 1 0
#> TCGA.S9.A6TS.01 1 0 1 1 0
#> TCGA.E1.A7YV.01 2 0 1 0 1
#> TCGA.DU.7007.01 1 0 1 1 0
#> TCGA.DB.5277.01 2 0 1 0 1
#> TCGA.HT.7606.01 2 0 1 0 1
#> TCGA.S9.A6TV.01 1 0 1 1 0
#> TCGA.DU.6408.01 1 0 1 1 0
#> TCGA.HW.8319.01 1 0 1 1 0
#> TCGA.DU.A5TU.01 1 0 1 1 0
#> TCGA.TQ.A7RM.01 2 0 1 0 1
#> TCGA.E1.5304.01 1 0 1 1 0
#> TCGA.FG.A4MY.01 1 0 1 1 0
#> TCGA.DU.7010.01 2 0 1 0 1
#> TCGA.HT.A61B.01 1 0 1 1 0
#> TCGA.DU.7014.01 1 0 1 1 0
#> TCGA.06.6389.01 1 0 1 1 0
#> TCGA.DH.A7UU.01 1 0 1 1 0
#> TCGA.TM.A84I.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.DU.A5TS.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.06.A7TL.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.E1.A7YI.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.E1.5305.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.S9.A7J0.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.CS.5393.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.E1.A7YU.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.IK.7675.01 3 0.000 0.993 0.00 0 1.00
#> TCGA.19.A6J5.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.HT.7873.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.S9.A7IS.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.S9.A89Z.01 3 0.000 0.993 0.00 0 1.00
#> TCGA.WH.A86K.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.06.0221.01 3 0.000 0.993 0.00 0 1.00
#> TCGA.DH.5142.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.RY.A83Z.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DB.A64X.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.HT.7477.01 3 0.000 0.993 0.00 0 1.00
#> TCGA.E1.5307.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.06.5417.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DU.7304.02 2 0.000 1.000 0.00 1 0.00
#> TCGA.FG.8188.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.S9.A6TS.01 3 0.000 0.993 0.00 0 1.00
#> TCGA.E1.A7YV.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DU.7007.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.DB.5277.01 3 0.000 0.993 0.00 0 1.00
#> TCGA.HT.7606.01 3 0.000 0.993 0.00 0 1.00
#> TCGA.S9.A6TV.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.DU.6408.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.HW.8319.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.DU.A5TU.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.TQ.A7RM.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.E1.5304.01 3 0.000 0.993 0.00 0 1.00
#> TCGA.FG.A4MY.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.DU.7010.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.HT.A61B.01 3 0.000 0.993 0.00 0 1.00
#> TCGA.DU.7014.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.06.6389.01 3 0.207 0.926 0.06 0 0.94
#> TCGA.DH.A7UU.01 3 0.000 0.993 0.00 0 1.00
#> TCGA.TM.A84I.01 2 0.000 1.000 0.00 1 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.DU.A5TS.01 1 0.0000 0.970 1.00 0.00 0.00 0.00
#> TCGA.06.A7TL.01 1 0.0707 0.952 0.98 0.00 0.02 0.00
#> TCGA.E1.A7YI.01 2 0.2345 0.940 0.00 0.90 0.10 0.00
#> TCGA.E1.5305.01 1 0.0000 0.970 1.00 0.00 0.00 0.00
#> TCGA.S9.A7J0.01 1 0.0000 0.970 1.00 0.00 0.00 0.00
#> TCGA.CS.5393.01 1 0.0000 0.970 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YU.01 1 0.0000 0.970 1.00 0.00 0.00 0.00
#> TCGA.IK.7675.01 4 0.1211 0.986 0.00 0.00 0.04 0.96
#> TCGA.19.A6J5.01 2 0.2345 0.940 0.00 0.90 0.10 0.00
#> TCGA.HT.7873.01 1 0.0000 0.970 1.00 0.00 0.00 0.00
#> TCGA.S9.A7IS.01 2 0.1211 0.932 0.00 0.96 0.00 0.04
#> TCGA.S9.A89Z.01 3 0.2921 0.870 0.00 0.00 0.86 0.14
#> TCGA.WH.A86K.01 1 0.0000 0.970 1.00 0.00 0.00 0.00
#> TCGA.06.0221.01 4 0.0000 0.943 0.00 0.00 0.00 1.00
#> TCGA.DH.5142.01 1 0.0000 0.970 1.00 0.00 0.00 0.00
#> TCGA.RY.A83Z.01 2 0.2345 0.940 0.00 0.90 0.10 0.00
#> TCGA.DB.A64X.01 1 0.0000 0.970 1.00 0.00 0.00 0.00
#> TCGA.HT.7477.01 4 0.1211 0.986 0.00 0.00 0.04 0.96
#> TCGA.E1.5307.01 1 0.0000 0.970 1.00 0.00 0.00 0.00
#> TCGA.06.5417.01 2 0.2345 0.940 0.00 0.90 0.10 0.00
#> TCGA.DU.7304.02 2 0.1211 0.932 0.00 0.96 0.00 0.04
#> TCGA.FG.8188.01 1 0.0000 0.970 1.00 0.00 0.00 0.00
#> TCGA.S9.A6TS.01 3 0.2921 0.870 0.00 0.00 0.86 0.14
#> TCGA.E1.A7YV.01 2 0.2345 0.940 0.00 0.90 0.10 0.00
#> TCGA.DU.7007.01 1 0.0000 0.970 1.00 0.00 0.00 0.00
#> TCGA.DB.5277.01 4 0.1211 0.986 0.00 0.00 0.04 0.96
#> TCGA.HT.7606.01 4 0.1211 0.986 0.00 0.00 0.04 0.96
#> TCGA.S9.A6TV.01 1 0.0000 0.970 1.00 0.00 0.00 0.00
#> TCGA.DU.6408.01 1 0.0000 0.970 1.00 0.00 0.00 0.00
#> TCGA.HW.8319.01 1 0.4977 0.111 0.54 0.00 0.46 0.00
#> TCGA.DU.A5TU.01 1 0.0000 0.970 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RM.01 2 0.1211 0.932 0.00 0.96 0.00 0.04
#> TCGA.E1.5304.01 3 0.2647 0.850 0.00 0.00 0.88 0.12
#> TCGA.FG.A4MY.01 3 0.3400 0.659 0.18 0.00 0.82 0.00
#> TCGA.DU.7010.01 2 0.0000 0.937 0.00 1.00 0.00 0.00
#> TCGA.HT.A61B.01 3 0.2921 0.870 0.00 0.00 0.86 0.14
#> TCGA.DU.7014.01 1 0.0000 0.970 1.00 0.00 0.00 0.00
#> TCGA.06.6389.01 3 0.3335 0.862 0.02 0.00 0.86 0.12
#> TCGA.DH.A7UU.01 3 0.4855 0.470 0.00 0.00 0.60 0.40
#> TCGA.TM.A84I.01 2 0.1211 0.932 0.00 0.96 0.00 0.04
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.DU.A5TS.01 1 0.0000 0.907 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.A7TL.01 1 0.5487 0.594 0.62 0.00 0.10 0.28 0.00
#> TCGA.E1.A7YI.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.5305.01 1 0.0000 0.907 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7J0.01 1 0.3109 0.790 0.80 0.00 0.00 0.20 0.00
#> TCGA.CS.5393.01 1 0.0000 0.907 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YU.01 1 0.0000 0.907 1.00 0.00 0.00 0.00 0.00
#> TCGA.IK.7675.01 5 0.4437 0.772 0.00 0.00 0.14 0.10 0.76
#> TCGA.19.A6J5.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7873.01 1 0.0000 0.907 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IS.01 2 0.3274 0.884 0.00 0.78 0.00 0.22 0.00
#> TCGA.S9.A89Z.01 3 0.0000 0.809 0.00 0.00 1.00 0.00 0.00
#> TCGA.WH.A86K.01 1 0.0000 0.907 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.0221.01 5 0.1648 0.908 0.00 0.00 0.02 0.04 0.94
#> TCGA.DH.5142.01 1 0.0000 0.907 1.00 0.00 0.00 0.00 0.00
#> TCGA.RY.A83Z.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.A64X.01 1 0.3561 0.743 0.74 0.00 0.00 0.26 0.00
#> TCGA.HT.7477.01 5 0.0609 0.909 0.00 0.00 0.02 0.00 0.98
#> TCGA.E1.5307.01 1 0.0000 0.907 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.5417.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7304.02 2 0.3274 0.884 0.00 0.78 0.00 0.22 0.00
#> TCGA.FG.8188.01 1 0.0000 0.907 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TS.01 3 0.0609 0.808 0.00 0.00 0.98 0.02 0.00
#> TCGA.E1.A7YV.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7007.01 1 0.0000 0.907 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5277.01 5 0.1732 0.886 0.00 0.00 0.00 0.08 0.92
#> TCGA.HT.7606.01 5 0.1648 0.908 0.00 0.00 0.02 0.04 0.94
#> TCGA.S9.A6TV.01 1 0.0000 0.907 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6408.01 1 0.0609 0.899 0.98 0.00 0.00 0.02 0.00
#> TCGA.HW.8319.01 1 0.6532 0.309 0.48 0.00 0.24 0.28 0.00
#> TCGA.DU.A5TU.01 1 0.3561 0.743 0.74 0.00 0.00 0.26 0.00
#> TCGA.TQ.A7RM.01 2 0.3109 0.893 0.00 0.80 0.00 0.20 0.00
#> TCGA.E1.5304.01 3 0.5095 0.478 0.00 0.00 0.56 0.40 0.04
#> TCGA.FG.A4MY.01 3 0.4132 0.681 0.02 0.00 0.72 0.26 0.00
#> TCGA.DU.7010.01 2 0.2929 0.898 0.00 0.82 0.00 0.18 0.00
#> TCGA.HT.A61B.01 3 0.0000 0.809 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.7014.01 1 0.0000 0.907 1.00 0.00 0.00 0.00 0.00
#> TCGA.06.6389.01 3 0.3109 0.740 0.00 0.00 0.80 0.20 0.00
#> TCGA.DH.A7UU.01 3 0.3421 0.700 0.00 0.00 0.84 0.08 0.08
#> TCGA.TM.A84I.01 2 0.2929 0.898 0.00 0.82 0.00 0.18 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.DU.A5TS.01 1 0.0000 0.900 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.A7TL.01 6 0.4873 0.785 0.32 0.00 0.08 0.00 0.00 0.60
#> TCGA.E1.A7YI.01 2 0.3821 0.843 0.00 0.74 0.00 0.04 0.00 0.22
#> TCGA.E1.5305.01 1 0.0547 0.895 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.S9.A7J0.01 1 0.4310 -0.648 0.54 0.00 0.00 0.02 0.00 0.44
#> TCGA.CS.5393.01 1 0.0547 0.890 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.E1.A7YU.01 1 0.0937 0.887 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.IK.7675.01 5 0.5769 0.533 0.00 0.00 0.22 0.08 0.62 0.08
#> TCGA.19.A6J5.01 2 0.3821 0.843 0.00 0.74 0.00 0.04 0.00 0.22
#> TCGA.HT.7873.01 1 0.0547 0.895 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.S9.A7IS.01 2 0.1480 0.796 0.00 0.94 0.00 0.04 0.00 0.02
#> TCGA.S9.A89Z.01 3 0.0000 0.732 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.WH.A86K.01 1 0.0000 0.900 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.0221.01 5 0.0547 0.875 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.DH.5142.01 1 0.0547 0.890 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.RY.A83Z.01 2 0.3821 0.843 0.00 0.74 0.00 0.04 0.00 0.22
#> TCGA.DB.A64X.01 6 0.3864 0.732 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.HT.7477.01 5 0.0547 0.875 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.E1.5307.01 1 0.0547 0.895 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.06.5417.01 2 0.3821 0.843 0.00 0.74 0.00 0.04 0.00 0.22
#> TCGA.DU.7304.02 2 0.3111 0.790 0.00 0.84 0.00 0.12 0.02 0.02
#> TCGA.FG.8188.01 1 0.0000 0.900 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TS.01 3 0.0937 0.730 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.E1.A7YV.01 2 0.3821 0.843 0.00 0.74 0.00 0.04 0.00 0.22
#> TCGA.DU.7007.01 1 0.0547 0.895 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DB.5277.01 5 0.3111 0.814 0.00 0.00 0.02 0.02 0.84 0.12
#> TCGA.HT.7606.01 5 0.0547 0.875 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.S9.A6TV.01 1 0.0000 0.900 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6408.01 1 0.2981 0.589 0.82 0.00 0.00 0.02 0.00 0.16
#> TCGA.HW.8319.01 6 0.5120 0.736 0.28 0.00 0.12 0.00 0.00 0.60
#> TCGA.DU.A5TU.01 6 0.3864 0.732 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.TQ.A7RM.01 2 0.2882 0.792 0.00 0.86 0.00 0.10 0.02 0.02
#> TCGA.E1.5304.01 4 0.3409 0.000 0.00 0.00 0.30 0.70 0.00 0.00
#> TCGA.FG.A4MY.01 3 0.4078 0.483 0.02 0.00 0.64 0.00 0.00 0.34
#> TCGA.DU.7010.01 2 0.0000 0.820 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A61B.01 3 0.0000 0.732 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7014.01 1 0.0000 0.900 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.6389.01 3 0.3309 0.578 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.DH.A7UU.01 3 0.1480 0.668 0.00 0.00 0.94 0.02 0.00 0.04
#> TCGA.TM.A84I.01 2 0.0000 0.820 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.DU.A5TS.01 1 0.0504 0.905 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.06.A7TL.01 6 0.2278 0.685 0.08 0.00 0.04 0.00 0.00 0.88 0.00
#> TCGA.E1.A7YI.01 2 0.0000 0.660 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5305.01 1 0.1433 0.899 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.S9.A7J0.01 6 0.5223 0.632 0.36 0.00 0.00 0.10 0.00 0.52 0.02
#> TCGA.CS.5393.01 1 0.0504 0.905 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.E1.A7YU.01 1 0.1433 0.899 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.IK.7675.01 5 0.5915 0.464 0.00 0.00 0.24 0.22 0.50 0.04 0.00
#> TCGA.19.A6J5.01 2 0.0000 0.660 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7873.01 1 0.1433 0.899 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.S9.A7IS.01 7 0.3558 -0.644 0.00 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.S9.A89Z.01 3 0.0000 0.802 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.WH.A86K.01 1 0.0504 0.905 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.06.0221.01 5 0.0000 0.843 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DH.5142.01 1 0.1166 0.902 0.94 0.00 0.00 0.06 0.00 0.00 0.00
#> TCGA.RY.A83Z.01 2 0.0000 0.660 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64X.01 6 0.3139 0.790 0.30 0.00 0.00 0.00 0.00 0.70 0.00
#> TCGA.HT.7477.01 5 0.0000 0.843 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E1.5307.01 1 0.1433 0.899 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.06.5417.01 2 0.0000 0.660 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7304.02 2 0.5212 0.254 0.00 0.48 0.00 0.06 0.00 0.04 0.42
#> TCGA.FG.8188.01 1 0.0504 0.905 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.S9.A6TS.01 3 0.2081 0.790 0.00 0.00 0.86 0.00 0.00 0.14 0.00
#> TCGA.E1.A7YV.01 2 0.0000 0.660 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7007.01 1 0.1433 0.899 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.DB.5277.01 5 0.3709 0.739 0.00 0.00 0.02 0.16 0.78 0.02 0.02
#> TCGA.HT.7606.01 5 0.0000 0.843 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6TV.01 1 0.0504 0.905 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DU.6408.01 1 0.3047 0.411 0.72 0.00 0.00 0.00 0.00 0.28 0.00
#> TCGA.HW.8319.01 6 0.2278 0.685 0.08 0.00 0.04 0.00 0.00 0.88 0.00
#> TCGA.DU.A5TU.01 6 0.3139 0.790 0.30 0.00 0.00 0.00 0.00 0.70 0.00
#> TCGA.TQ.A7RM.01 2 0.4936 0.246 0.00 0.48 0.00 0.06 0.00 0.02 0.44
#> TCGA.E1.5304.01 7 0.5798 -0.241 0.00 0.00 0.20 0.34 0.02 0.00 0.44
#> TCGA.FG.A4MY.01 3 0.3459 0.599 0.00 0.00 0.60 0.00 0.00 0.40 0.00
#> TCGA.DU.7010.01 2 0.3546 0.327 0.00 0.54 0.00 0.00 0.00 0.00 0.46
#> TCGA.HT.A61B.01 3 0.0000 0.802 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7014.01 1 0.0504 0.905 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.06.6389.01 3 0.3294 0.676 0.00 0.00 0.66 0.00 0.00 0.34 0.00
#> TCGA.DH.A7UU.01 3 0.0000 0.802 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84I.01 2 0.3546 0.327 0.00 0.54 0.00 0.00 0.00 0.00 0.46
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.DU.A5TS.01 1 0.000 0.8186 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.A7TL.01 6 0.156 0.7393 0.10 0.00 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.E1.A7YI.01 2 0.319 1.0000 0.00 0.62 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.E1.5305.01 1 0.265 0.7995 0.76 0.00 0.00 0.00 0.24 0.00 0.00 0.00
#> TCGA.S9.A7J0.01 6 0.571 0.6163 0.28 0.10 0.00 0.00 0.12 0.50 0.00 0.00
#> TCGA.CS.5393.01 1 0.000 0.8186 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YU.01 1 0.265 0.7995 0.76 0.00 0.00 0.00 0.24 0.00 0.00 0.00
#> TCGA.IK.7675.01 4 0.609 0.2310 0.00 0.08 0.12 0.42 0.36 0.00 0.02 0.00
#> TCGA.19.A6J5.01 2 0.319 1.0000 0.00 0.62 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.HT.7873.01 1 0.265 0.7995 0.76 0.00 0.00 0.00 0.24 0.00 0.00 0.00
#> TCGA.S9.A7IS.01 8 0.000 0.8343 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.S9.A89Z.01 3 0.000 0.8609 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WH.A86K.01 1 0.000 0.8186 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.0221.01 4 0.000 0.7768 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.5142.01 1 0.195 0.8147 0.86 0.00 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.RY.A83Z.01 2 0.319 1.0000 0.00 0.62 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.DB.A64X.01 6 0.276 0.7884 0.26 0.00 0.00 0.00 0.00 0.74 0.00 0.00
#> TCGA.HT.7477.01 4 0.000 0.7768 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5307.01 1 0.265 0.7995 0.76 0.00 0.00 0.00 0.24 0.00 0.00 0.00
#> TCGA.06.5417.01 2 0.319 1.0000 0.00 0.62 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.DU.7304.02 8 0.286 0.7324 0.00 0.00 0.00 0.00 0.08 0.06 0.02 0.84
#> TCGA.FG.8188.01 1 0.000 0.8186 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TS.01 3 0.156 0.8500 0.00 0.00 0.90 0.00 0.00 0.10 0.00 0.00
#> TCGA.E1.A7YV.01 2 0.319 1.0000 0.00 0.62 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.DU.7007.01 1 0.265 0.7995 0.76 0.00 0.00 0.00 0.24 0.00 0.00 0.00
#> TCGA.DB.5277.01 4 0.435 0.5725 0.00 0.12 0.02 0.68 0.18 0.00 0.00 0.00
#> TCGA.HT.7606.01 4 0.000 0.7768 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TV.01 1 0.000 0.8186 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6408.01 1 0.324 -0.0832 0.60 0.00 0.00 0.00 0.00 0.40 0.00 0.00
#> TCGA.HW.8319.01 6 0.241 0.6614 0.06 0.08 0.00 0.00 0.00 0.86 0.00 0.00
#> TCGA.DU.A5TU.01 6 0.276 0.7884 0.26 0.00 0.00 0.00 0.00 0.74 0.00 0.00
#> TCGA.TQ.A7RM.01 8 0.128 0.8304 0.00 0.00 0.00 0.00 0.02 0.00 0.04 0.94
#> TCGA.E1.5304.01 7 0.109 0.0000 0.00 0.00 0.06 0.00 0.00 0.00 0.94 0.00
#> TCGA.FG.A4MY.01 3 0.276 0.7552 0.00 0.00 0.74 0.00 0.00 0.26 0.00 0.00
#> TCGA.DU.7010.01 8 0.176 0.7868 0.00 0.12 0.00 0.00 0.00 0.00 0.00 0.88
#> TCGA.HT.A61B.01 3 0.000 0.8609 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7014.01 1 0.000 0.8186 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.06.6389.01 3 0.253 0.7941 0.00 0.00 0.78 0.00 0.00 0.22 0.00 0.00
#> TCGA.DH.A7UU.01 3 0.000 0.8609 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84I.01 8 0.176 0.7868 0.00 0.12 0.00 0.00 0.00 0.00 0.00 0.88
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: Node01111-leaf , Node01112-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01211-leaf , Node01212-leaf , Node01213 , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node01224-leaf , Node01225-leaf , Node01311-leaf , Node01312-leaf , Node01313-leaf , Node01411-leaf , Node01412-leaf , Node01431-leaf , Node01432-leaf , Node02211-leaf , Node02212 , Node02221 , Node02222-leaf , Node02223-leaf , Node02231 , Node02232-leaf , Node02233-leaf , Node02234-leaf , Node02311-leaf , Node02312-leaf , Node02313-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0231"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 19 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.895 0.984 0.993 0.5119 0.485 0.485
#> 3 3 0.725 0.958 0.968 0.1558 0.930 0.855
#> 4 4 1.000 0.995 0.997 0.2243 0.860 0.662
#> 5 5 0.918 0.891 0.928 0.0325 1.000 1.000
#> 6 6 0.860 0.699 0.865 0.0367 0.982 0.936
#> 7 7 0.807 0.744 0.900 0.0317 0.953 0.818
#> 8 8 0.772 0.621 0.816 0.0594 1.000 1.000
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
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.DU.A5TS.01 1 0.000 1.000 1.00 0.00
#> TCGA.06.A7TL.01 2 0.000 0.980 0.00 1.00
#> TCGA.E1.5305.01 1 0.000 1.000 1.00 0.00
#> TCGA.S9.A7J0.01 2 0.000 0.980 0.00 1.00
#> TCGA.CS.5393.01 1 0.000 1.000 1.00 0.00
#> TCGA.E1.A7YU.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7873.01 1 0.000 1.000 1.00 0.00
#> TCGA.WH.A86K.01 1 0.000 1.000 1.00 0.00
#> TCGA.DH.5142.01 1 0.000 1.000 1.00 0.00
#> TCGA.DB.A64X.01 2 0.000 0.980 0.00 1.00
#> TCGA.E1.5307.01 2 0.584 0.837 0.14 0.86
#> TCGA.FG.8188.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.7007.01 1 0.000 1.000 1.00 0.00
#> TCGA.S9.A6TV.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.6408.01 2 0.000 0.980 0.00 1.00
#> TCGA.HW.8319.01 2 0.000 0.980 0.00 1.00
#> TCGA.DU.A5TU.01 2 0.000 0.980 0.00 1.00
#> TCGA.FG.A4MY.01 2 0.000 0.980 0.00 1.00
#> TCGA.DU.7014.01 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.DU.A5TS.01 1 0.000 0.971 1.0 0.0 0.0
#> TCGA.06.A7TL.01 2 0.000 0.969 0.0 1.0 0.0
#> TCGA.E1.5305.01 1 0.000 0.971 1.0 0.0 0.0
#> TCGA.S9.A7J0.01 2 0.000 0.969 0.0 1.0 0.0
#> TCGA.CS.5393.01 1 0.000 0.971 1.0 0.0 0.0
#> TCGA.E1.A7YU.01 1 0.296 0.918 0.9 0.0 0.1
#> TCGA.HT.7873.01 1 0.296 0.918 0.9 0.0 0.1
#> TCGA.WH.A86K.01 1 0.000 0.971 1.0 0.0 0.0
#> TCGA.DH.5142.01 1 0.296 0.918 0.9 0.0 0.1
#> TCGA.DB.A64X.01 2 0.000 0.969 0.0 1.0 0.0
#> TCGA.E1.5307.01 2 0.296 0.840 0.1 0.9 0.0
#> TCGA.FG.8188.01 1 0.000 0.971 1.0 0.0 0.0
#> TCGA.DU.7007.01 1 0.000 0.971 1.0 0.0 0.0
#> TCGA.S9.A6TV.01 1 0.000 0.971 1.0 0.0 0.0
#> TCGA.DU.6408.01 3 0.296 1.000 0.0 0.1 0.9
#> TCGA.HW.8319.01 3 0.296 1.000 0.0 0.1 0.9
#> TCGA.DU.A5TU.01 2 0.000 0.969 0.0 1.0 0.0
#> TCGA.FG.A4MY.01 2 0.000 0.969 0.0 1.0 0.0
#> TCGA.DU.7014.01 1 0.000 0.971 1.0 0.0 0.0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.DU.A5TS.01 1 0.0707 0.979 0.98 0 0 0.02
#> TCGA.06.A7TL.01 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.E1.5305.01 1 0.0000 0.997 1.00 0 0 0.00
#> TCGA.S9.A7J0.01 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.CS.5393.01 1 0.0000 0.997 1.00 0 0 0.00
#> TCGA.E1.A7YU.01 4 0.0000 0.970 0.00 0 0 1.00
#> TCGA.HT.7873.01 4 0.0707 0.985 0.02 0 0 0.98
#> TCGA.WH.A86K.01 1 0.0000 0.997 1.00 0 0 0.00
#> TCGA.DH.5142.01 4 0.0707 0.985 0.02 0 0 0.98
#> TCGA.DB.A64X.01 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.E1.5307.01 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.FG.8188.01 1 0.0000 0.997 1.00 0 0 0.00
#> TCGA.DU.7007.01 1 0.0000 0.997 1.00 0 0 0.00
#> TCGA.S9.A6TV.01 1 0.0000 0.997 1.00 0 0 0.00
#> TCGA.DU.6408.01 3 0.0000 1.000 0.00 0 1 0.00
#> TCGA.HW.8319.01 3 0.0000 1.000 0.00 0 1 0.00
#> TCGA.DU.A5TU.01 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.FG.A4MY.01 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.DU.7014.01 1 0.0000 0.997 1.00 0 0 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.DU.A5TS.01 1 0.1410 0.957 0.94 0.00 0.06 0.00 0.0
#> TCGA.06.A7TL.01 2 0.0000 0.937 0.00 1.00 0.00 0.00 0.0
#> TCGA.E1.5305.01 1 0.0000 0.967 1.00 0.00 0.00 0.00 0.0
#> TCGA.S9.A7J0.01 2 0.0000 0.937 0.00 1.00 0.00 0.00 0.0
#> TCGA.CS.5393.01 1 0.1410 0.957 0.94 0.00 0.06 0.00 0.0
#> TCGA.E1.A7YU.01 4 0.0000 0.689 0.00 0.00 0.00 1.00 0.0
#> TCGA.HT.7873.01 4 0.3895 0.846 0.00 0.00 0.32 0.68 0.0
#> TCGA.WH.A86K.01 1 0.0609 0.964 0.98 0.00 0.02 0.00 0.0
#> TCGA.DH.5142.01 4 0.3983 0.842 0.00 0.00 0.34 0.66 0.0
#> TCGA.DB.A64X.01 2 0.0000 0.937 0.00 1.00 0.00 0.00 0.0
#> TCGA.E1.5307.01 2 0.2732 0.870 0.00 0.84 0.16 0.00 0.0
#> TCGA.FG.8188.01 1 0.0000 0.967 1.00 0.00 0.00 0.00 0.0
#> TCGA.DU.7007.01 1 0.1732 0.938 0.92 0.00 0.08 0.00 0.0
#> TCGA.S9.A6TV.01 1 0.1410 0.951 0.94 0.00 0.06 0.00 0.0
#> TCGA.DU.6408.01 5 0.0000 0.702 0.00 0.00 0.00 0.00 1.0
#> TCGA.HW.8319.01 5 0.4182 0.702 0.00 0.00 0.40 0.00 0.6
#> TCGA.DU.A5TU.01 2 0.0000 0.937 0.00 1.00 0.00 0.00 0.0
#> TCGA.FG.A4MY.01 2 0.2929 0.857 0.00 0.82 0.18 0.00 0.0
#> TCGA.DU.7014.01 1 0.0000 0.967 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.DU.A5TS.01 1 0.2581 0.898 0.86 0.00 0.00 0.12 0.02 0.0
#> TCGA.06.A7TL.01 2 0.0000 0.790 0.00 1.00 0.00 0.00 0.00 0.0
#> TCGA.E1.5305.01 1 0.0547 0.936 0.98 0.00 0.00 0.02 0.00 0.0
#> TCGA.S9.A7J0.01 2 0.0547 0.786 0.00 0.98 0.00 0.00 0.02 0.0
#> TCGA.CS.5393.01 1 0.2350 0.906 0.88 0.00 0.00 0.10 0.02 0.0
#> TCGA.E1.A7YU.01 3 0.0000 0.000 0.00 0.00 1.00 0.00 0.00 0.0
#> TCGA.HT.7873.01 4 0.3864 0.885 0.00 0.00 0.48 0.52 0.00 0.0
#> TCGA.WH.A86K.01 1 0.1807 0.923 0.92 0.00 0.00 0.06 0.02 0.0
#> TCGA.DH.5142.01 4 0.3797 0.890 0.00 0.00 0.42 0.58 0.00 0.0
#> TCGA.DB.A64X.01 2 0.0000 0.790 0.00 1.00 0.00 0.00 0.00 0.0
#> TCGA.E1.5307.01 2 0.5938 0.473 0.00 0.46 0.00 0.28 0.26 0.0
#> TCGA.FG.8188.01 1 0.0000 0.936 1.00 0.00 0.00 0.00 0.00 0.0
#> TCGA.DU.7007.01 1 0.1480 0.916 0.94 0.00 0.00 0.04 0.02 0.0
#> TCGA.S9.A6TV.01 1 0.1807 0.904 0.92 0.00 0.00 0.06 0.02 0.0
#> TCGA.DU.6408.01 5 0.3409 0.000 0.00 0.00 0.00 0.00 0.70 0.3
#> TCGA.HW.8319.01 6 0.0000 0.000 0.00 0.00 0.00 0.00 0.00 1.0
#> TCGA.DU.A5TU.01 2 0.0000 0.790 0.00 1.00 0.00 0.00 0.00 0.0
#> TCGA.FG.A4MY.01 2 0.5712 0.529 0.00 0.52 0.00 0.26 0.22 0.0
#> TCGA.DU.7014.01 1 0.0000 0.936 1.00 0.00 0.00 0.00 0.00 0.0
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.DU.A5TS.01 1 0.3914 0.829 0.78 0.00 0.06 0.00 0.0 0.06 0.10
#> TCGA.06.A7TL.01 2 0.0000 0.990 0.00 1.00 0.00 0.00 0.0 0.00 0.00
#> TCGA.E1.5305.01 1 0.0504 0.893 0.98 0.00 0.00 0.00 0.0 0.02 0.00
#> TCGA.S9.A7J0.01 2 0.0504 0.970 0.00 0.98 0.00 0.00 0.0 0.00 0.02
#> TCGA.CS.5393.01 1 0.4920 0.779 0.72 0.00 0.06 0.04 0.0 0.06 0.12
#> TCGA.E1.A7YU.01 3 0.1433 0.000 0.00 0.00 0.92 0.08 0.0 0.00 0.00
#> TCGA.HT.7873.01 4 0.0863 0.750 0.00 0.00 0.04 0.96 0.0 0.00 0.00
#> TCGA.WH.A86K.01 1 0.3289 0.851 0.82 0.00 0.02 0.00 0.0 0.06 0.10
#> TCGA.DH.5142.01 4 0.3887 0.747 0.02 0.00 0.06 0.80 0.0 0.04 0.08
#> TCGA.DB.A64X.01 2 0.0000 0.990 0.00 1.00 0.00 0.00 0.0 0.00 0.00
#> TCGA.E1.5307.01 7 0.3047 0.913 0.00 0.28 0.00 0.00 0.0 0.00 0.72
#> TCGA.FG.8188.01 1 0.0000 0.892 1.00 0.00 0.00 0.00 0.0 0.00 0.00
#> TCGA.DU.7007.01 1 0.2159 0.859 0.90 0.00 0.02 0.00 0.0 0.02 0.06
#> TCGA.S9.A6TV.01 1 0.0863 0.880 0.96 0.00 0.00 0.00 0.0 0.00 0.04
#> TCGA.DU.6408.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1.0 0.00 0.00
#> TCGA.HW.8319.01 6 0.1671 0.000 0.00 0.00 0.00 0.00 0.1 0.90 0.00
#> TCGA.DU.A5TU.01 2 0.0000 0.990 0.00 1.00 0.00 0.00 0.0 0.00 0.00
#> TCGA.FG.A4MY.01 7 0.3294 0.908 0.00 0.34 0.00 0.00 0.0 0.00 0.66
#> TCGA.DU.7014.01 1 0.0000 0.892 1.00 0.00 0.00 0.00 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.DU.A5TS.01 1 0.3808 0.626 0.66 0.00 0.00 0.00 0.02 0.0 0.02 0.30
#> TCGA.06.A7TL.01 2 0.0000 0.983 0.00 1.00 0.00 0.00 0.00 0.0 0.00 0.00
#> TCGA.E1.5305.01 1 0.0000 0.715 1.00 0.00 0.00 0.00 0.00 0.0 0.00 0.00
#> TCGA.S9.A7J0.01 2 0.0808 0.947 0.00 0.96 0.00 0.00 0.00 0.0 0.04 0.00
#> TCGA.CS.5393.01 1 0.4239 0.609 0.64 0.00 0.00 0.02 0.02 0.0 0.02 0.30
#> TCGA.E1.A7YU.01 3 0.0000 0.000 0.00 0.00 1.00 0.00 0.00 0.0 0.00 0.00
#> TCGA.HT.7873.01 4 0.0808 0.719 0.00 0.00 0.04 0.96 0.00 0.0 0.00 0.00
#> TCGA.WH.A86K.01 1 0.3036 0.673 0.78 0.00 0.00 0.00 0.04 0.0 0.00 0.18
#> TCGA.DH.5142.01 4 0.4046 0.723 0.00 0.00 0.02 0.74 0.02 0.0 0.06 0.16
#> TCGA.DB.A64X.01 2 0.0000 0.983 0.00 1.00 0.00 0.00 0.00 0.0 0.00 0.00
#> TCGA.E1.5307.01 7 0.2224 0.742 0.00 0.12 0.00 0.00 0.00 0.0 0.86 0.02
#> TCGA.FG.8188.01 1 0.0808 0.712 0.96 0.00 0.00 0.00 0.00 0.0 0.00 0.04
#> TCGA.DU.7007.01 1 0.3808 0.554 0.62 0.00 0.00 0.00 0.00 0.0 0.04 0.34
#> TCGA.S9.A6TV.01 1 0.3329 0.445 0.52 0.00 0.00 0.00 0.00 0.0 0.00 0.48
#> TCGA.DU.6408.01 5 0.1563 0.000 0.00 0.00 0.00 0.00 0.90 0.1 0.00 0.00
#> TCGA.HW.8319.01 6 0.0000 0.000 0.00 0.00 0.00 0.00 0.00 1.0 0.00 0.00
#> TCGA.DU.A5TU.01 2 0.0000 0.983 0.00 1.00 0.00 0.00 0.00 0.0 0.00 0.00
#> TCGA.FG.A4MY.01 7 0.4147 0.749 0.00 0.24 0.00 0.00 0.04 0.0 0.68 0.04
#> TCGA.DU.7014.01 1 0.3227 0.645 0.78 0.00 0.00 0.00 0.00 0.0 0.14 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: Node0. Child nodes: Node011 , Node012 , Node013 , Node014 , Node021 , Node022 , Node023 , Node031 , Node032 , Node033-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 114 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 0.988 0.995 0.3600 0.635 0.635
#> 3 3 1.000 0.973 0.990 0.3277 0.841 0.759
#> 4 4 0.676 0.805 0.878 0.2448 0.907 0.827
#> 5 5 0.706 0.827 0.875 0.2230 0.785 0.531
#> 6 6 0.836 0.683 0.853 0.1018 0.871 0.547
#> 7 7 0.834 0.791 0.876 0.0264 0.923 0.647
#> 8 8 0.826 0.762 0.853 0.0292 0.969 0.829
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.E1.5319.01 1 0.000 1.000 1.00 0.00
#> TCGA.CS.6665.01 2 0.000 0.978 0.00 1.00
#> TCGA.FG.A6J3.01 2 0.000 0.978 0.00 1.00
#> TCGA.DB.A4XA.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.A4DV.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.8113.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7620.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7689.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.8109.01 1 0.000 1.000 1.00 0.00
#> TCGA.E1.A7YE.01 2 0.000 0.978 0.00 1.00
#> TCGA.HT.7877.01 1 0.000 1.000 1.00 0.00
#> TCGA.QH.A6CU.01 1 0.000 1.000 1.00 0.00
#> TCGA.HW.7486.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.8163.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.6407.02 2 0.000 0.978 0.00 1.00
#> TCGA.HT.8010.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.7011.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7605.01 1 0.000 1.000 1.00 0.00
#> TCGA.DB.5270.01 1 0.000 1.000 1.00 0.00
#> TCGA.S9.A6WQ.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.8106.01 2 0.000 0.978 0.00 1.00
#> TCGA.26.5133.01 2 0.000 0.978 0.00 1.00
#> TCGA.S9.A7QY.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7601.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7880.01 1 0.000 1.000 1.00 0.00
#> TCGA.26.1442.01 2 0.000 0.978 0.00 1.00
#> TCGA.E1.A7Z3.01 1 0.000 1.000 1.00 0.00
#> TCGA.P5.A5EX.01 2 0.000 0.978 0.00 1.00
#> TCGA.HT.8563.01 2 0.000 0.978 0.00 1.00
#> TCGA.RY.A843.01 1 0.000 1.000 1.00 0.00
#> TCGA.QH.A6X5.01 1 0.000 1.000 1.00 0.00
#> TCGA.DH.A7UT.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.8018.01 2 0.722 0.751 0.20 0.80
#> TCGA.HT.7856.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.5851.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.A7T6.01 2 0.000 0.978 0.00 1.00
#> TCGA.TM.A84O.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.A61A.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.A5R5.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.A618.01 2 0.000 0.978 0.00 1.00
#> TCGA.HT.7467.01 1 0.000 1.000 1.00 0.00
#> TCGA.FG.A60L.01 1 0.000 1.000 1.00 0.00
#> TCGA.DB.5278.01 1 0.000 1.000 1.00 0.00
#> TCGA.TQ.A7RR.01 2 0.000 0.978 0.00 1.00
#> TCGA.15.1444.01 2 0.000 0.978 0.00 1.00
#> TCGA.HT.7881.01 1 0.000 1.000 1.00 0.00
#> TCGA.P5.A5EU.01 2 0.000 0.978 0.00 1.00
#> TCGA.VM.A8CE.01 1 0.000 1.000 1.00 0.00
#> TCGA.CS.4944.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.A6S2.01 1 0.000 1.000 1.00 0.00
#> TCGA.S9.A7R7.01 2 0.943 0.452 0.36 0.64
#> TCGA.TM.A84R.01 1 0.000 1.000 1.00 0.00
#> TCGA.06.0221.02 2 0.000 0.978 0.00 1.00
#> TCGA.FG.8187.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.A7TG.01 1 0.000 1.000 1.00 0.00
#> TCGA.TM.A84F.01 2 0.000 0.978 0.00 1.00
#> TCGA.HT.7610.01 1 0.000 1.000 1.00 0.00
#> TCGA.S9.A6TW.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7481.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.A5TR.01 1 0.000 1.000 1.00 0.00
#> TCGA.S9.A7IQ.01 1 0.000 1.000 1.00 0.00
#> TCGA.S9.A6WG.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7688.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7902.01 2 0.000 0.978 0.00 1.00
#> TCGA.QH.A6CY.01 1 0.000 1.000 1.00 0.00
#> TCGA.P5.A72X.01 1 0.000 1.000 1.00 0.00
#> TCGA.S9.A6WI.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.5849.01 1 0.000 1.000 1.00 0.00
#> TCGA.HW.7489.01 1 0.000 1.000 1.00 0.00
#> TCGA.FG.A713.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.7300.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7694.01 1 0.000 1.000 1.00 0.00
#> TCGA.P5.A780.01 1 0.000 1.000 1.00 0.00
#> TCGA.DB.A64V.01 1 0.000 1.000 1.00 0.00
#> TCGA.E1.5302.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.A615.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.7309.01 1 0.000 1.000 1.00 0.00
#> TCGA.E1.A7YK.01 2 0.000 0.978 0.00 1.00
#> TCGA.HT.7874.01 1 0.000 1.000 1.00 0.00
#> TCGA.E1.A7YY.01 1 0.000 1.000 1.00 0.00
#> TCGA.FG.5964.01 1 0.000 1.000 1.00 0.00
#> TCGA.DH.A7UR.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7479.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7602.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.8111.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7858.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7686.01 2 0.000 0.978 0.00 1.00
#> TCGA.CS.6290.01 1 0.000 1.000 1.00 0.00
#> TCGA.FG.A711.01 1 0.000 1.000 1.00 0.00
#> TCGA.TM.A84S.01 1 0.000 1.000 1.00 0.00
#> TCGA.DB.5276.01 1 0.000 1.000 1.00 0.00
#> TCGA.TM.A84L.01 1 0.000 1.000 1.00 0.00
#> TCGA.DB.5273.01 1 0.000 1.000 1.00 0.00
#> TCGA.TM.A7C4.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7607.01 1 0.000 1.000 1.00 0.00
#> TCGA.P5.A736.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7470.01 2 0.000 0.978 0.00 1.00
#> TCGA.P5.A781.01 1 0.000 1.000 1.00 0.00
#> TCGA.TM.A7CF.02 1 0.000 1.000 1.00 0.00
#> TCGA.S9.A6U2.01 1 0.000 1.000 1.00 0.00
#> TCGA.S9.A6WN.01 2 0.000 0.978 0.00 1.00
#> TCGA.DU.6396.01 2 0.000 0.978 0.00 1.00
#> TCGA.DH.A7US.01 1 0.000 1.000 1.00 0.00
#> TCGA.FG.A87N.01 2 0.000 0.978 0.00 1.00
#> TCGA.HT.7478.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7603.01 1 0.000 1.000 1.00 0.00
#> TCGA.FG.5965.02 2 0.000 0.978 0.00 1.00
#> TCGA.FG.A70Y.01 1 0.000 1.000 1.00 0.00
#> TCGA.TQ.A7RV.02 1 0.000 1.000 1.00 0.00
#> TCGA.HT.A5R7.01 2 0.000 0.978 0.00 1.00
#> TCGA.HT.7474.01 1 0.000 1.000 1.00 0.00
#> TCGA.P5.A5EZ.01 1 0.000 1.000 1.00 0.00
#> TCGA.WY.A858.01 1 0.000 1.000 1.00 0.00
#> TCGA.WY.A85A.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.E1.5319.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.CS.6665.01 3 0.0000 0.9636 0.00 0.00 1.00
#> TCGA.FG.A6J3.01 3 0.0000 0.9636 0.00 0.00 1.00
#> TCGA.DB.A4XA.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HT.A4DV.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HT.8113.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HT.7620.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HT.7689.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.HT.8109.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.E1.A7YE.01 3 0.0000 0.9636 0.00 0.00 1.00
#> TCGA.HT.7877.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.QH.A6CU.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HW.7486.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.DU.8163.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.DU.6407.02 3 0.0000 0.9636 0.00 0.00 1.00
#> TCGA.HT.8010.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.DU.7011.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HT.7605.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.DB.5270.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.S9.A6WQ.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HT.8106.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.26.5133.01 3 0.0000 0.9636 0.00 0.00 1.00
#> TCGA.S9.A7QY.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HT.7601.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.HT.7880.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.26.1442.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.E1.A7Z3.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.P5.A5EX.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.HT.8563.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.RY.A843.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.QH.A6X5.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.DH.A7UT.01 1 0.6302 0.0783 0.52 0.48 0.00
#> TCGA.HT.8018.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.HT.7856.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.DU.5851.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.DU.A7T6.01 2 0.4291 0.7743 0.00 0.82 0.18
#> TCGA.TM.A84O.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HT.A61A.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HT.A5R5.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HT.A618.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.HT.7467.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.FG.A60L.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.DB.5278.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.TQ.A7RR.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.15.1444.01 2 0.4555 0.7444 0.00 0.80 0.20
#> TCGA.HT.7881.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.P5.A5EU.01 3 0.0000 0.9636 0.00 0.00 1.00
#> TCGA.VM.A8CE.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.CS.4944.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.DU.A6S2.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.S9.A7R7.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.TM.A84R.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.06.0221.02 3 0.0000 0.9636 0.00 0.00 1.00
#> TCGA.FG.8187.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.DU.A7TG.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.TM.A84F.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.HT.7610.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.S9.A6TW.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HT.7481.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.DU.A5TR.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.S9.A7IQ.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.S9.A6WG.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HT.7688.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.HT.7902.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.QH.A6CY.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.P5.A72X.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.S9.A6WI.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.DU.5849.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HW.7489.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.FG.A713.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.DU.7300.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HT.7694.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.P5.A780.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.DB.A64V.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.E1.5302.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HT.A615.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.DU.7309.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.E1.A7YK.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.HT.7874.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.E1.A7YY.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.FG.5964.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.DH.A7UR.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HT.7479.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HT.7602.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HT.8111.01 2 0.0892 0.9508 0.02 0.98 0.00
#> TCGA.HT.7858.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HT.7686.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.CS.6290.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.FG.A711.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.TM.A84S.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.DB.5276.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.TM.A84L.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.DB.5273.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.TM.A7C4.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HT.7607.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.P5.A736.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HT.7470.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.P5.A781.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.TM.A7CF.02 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.S9.A6U2.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.S9.A6WN.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.DU.6396.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.DH.A7US.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.FG.A87N.01 3 0.0000 0.9636 0.00 0.00 1.00
#> TCGA.HT.7478.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HT.7603.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.FG.5965.02 3 0.5397 0.5981 0.00 0.28 0.72
#> TCGA.FG.A70Y.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.TQ.A7RV.02 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.HT.A5R7.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.HT.7474.01 1 0.0000 0.9931 1.00 0.00 0.00
#> TCGA.P5.A5EZ.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.WY.A858.01 2 0.0000 0.9830 0.00 1.00 0.00
#> TCGA.WY.A85A.01 1 0.0000 0.9931 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.E1.5319.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.CS.6665.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.FG.A6J3.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.DB.A4XA.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.HT.A4DV.01 1 0.0000 0.801 1.00 0.00 0.00 0.00
#> TCGA.HT.8113.01 1 0.0000 0.801 1.00 0.00 0.00 0.00
#> TCGA.HT.7620.01 1 0.0000 0.801 1.00 0.00 0.00 0.00
#> TCGA.HT.7689.01 4 0.4277 0.602 0.00 0.28 0.00 0.72
#> TCGA.HT.8109.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.E1.A7YE.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.HT.7877.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.QH.A6CU.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.HW.7486.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.DU.8163.01 1 0.1211 0.802 0.96 0.00 0.00 0.04
#> TCGA.DU.6407.02 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.HT.8010.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.DU.7011.01 1 0.4277 0.834 0.72 0.00 0.00 0.28
#> TCGA.HT.7605.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.DB.5270.01 1 0.0707 0.791 0.98 0.00 0.00 0.02
#> TCGA.S9.A6WQ.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.HT.8106.01 2 0.0707 0.939 0.00 0.98 0.00 0.02
#> TCGA.26.5133.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.S9.A7QY.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.HT.7601.01 4 0.4277 0.602 0.00 0.28 0.00 0.72
#> TCGA.HT.7880.01 1 0.0000 0.801 1.00 0.00 0.00 0.00
#> TCGA.26.1442.01 2 0.0000 0.940 0.00 1.00 0.00 0.00
#> TCGA.E1.A7Z3.01 1 0.1637 0.808 0.94 0.00 0.00 0.06
#> TCGA.P5.A5EX.01 2 0.1637 0.930 0.00 0.94 0.00 0.06
#> TCGA.HT.8563.01 2 0.1637 0.930 0.00 0.94 0.00 0.06
#> TCGA.RY.A843.01 1 0.4277 0.834 0.72 0.00 0.00 0.28
#> TCGA.QH.A6X5.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.DH.A7UT.01 4 0.4797 0.664 0.26 0.02 0.00 0.72
#> TCGA.HT.8018.01 2 0.2647 0.897 0.00 0.88 0.00 0.12
#> TCGA.HT.7856.01 1 0.0000 0.801 1.00 0.00 0.00 0.00
#> TCGA.DU.5851.01 4 0.5327 0.676 0.06 0.22 0.00 0.72
#> TCGA.DU.A7T6.01 2 0.0707 0.927 0.00 0.98 0.02 0.00
#> TCGA.TM.A84O.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.HT.A61A.01 1 0.0000 0.801 1.00 0.00 0.00 0.00
#> TCGA.HT.A5R5.01 1 0.4277 0.834 0.72 0.00 0.00 0.28
#> TCGA.HT.A618.01 2 0.0000 0.940 0.00 1.00 0.00 0.00
#> TCGA.HT.7467.01 1 0.0000 0.801 1.00 0.00 0.00 0.00
#> TCGA.FG.A60L.01 4 0.4790 0.594 0.38 0.00 0.00 0.62
#> TCGA.DB.5278.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.TQ.A7RR.01 2 0.2647 0.897 0.00 0.88 0.00 0.12
#> TCGA.15.1444.01 2 0.1211 0.911 0.00 0.96 0.04 0.00
#> TCGA.HT.7881.01 1 0.0000 0.801 1.00 0.00 0.00 0.00
#> TCGA.P5.A5EU.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.VM.A8CE.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.CS.4944.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.DU.A6S2.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.S9.A7R7.01 2 0.2647 0.897 0.00 0.88 0.00 0.12
#> TCGA.TM.A84R.01 1 0.0000 0.801 1.00 0.00 0.00 0.00
#> TCGA.06.0221.02 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.FG.8187.01 1 0.0000 0.801 1.00 0.00 0.00 0.00
#> TCGA.DU.A7TG.01 1 0.0000 0.801 1.00 0.00 0.00 0.00
#> TCGA.TM.A84F.01 2 0.2647 0.897 0.00 0.88 0.00 0.12
#> TCGA.HT.7610.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.S9.A6TW.01 1 0.3610 0.835 0.80 0.00 0.00 0.20
#> TCGA.HT.7481.01 1 0.0000 0.801 1.00 0.00 0.00 0.00
#> TCGA.DU.A5TR.01 1 0.3975 0.432 0.76 0.00 0.00 0.24
#> TCGA.S9.A7IQ.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.S9.A6WG.01 1 0.4277 0.834 0.72 0.00 0.00 0.28
#> TCGA.HT.7688.01 4 0.5327 0.676 0.06 0.22 0.00 0.72
#> TCGA.HT.7902.01 2 0.0000 0.940 0.00 1.00 0.00 0.00
#> TCGA.QH.A6CY.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.P5.A72X.01 1 0.0707 0.791 0.98 0.00 0.00 0.02
#> TCGA.S9.A6WI.01 1 0.1211 0.764 0.96 0.00 0.00 0.04
#> TCGA.DU.5849.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.HW.7489.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.FG.A713.01 1 0.1211 0.813 0.96 0.00 0.00 0.04
#> TCGA.DU.7300.01 1 0.3610 0.840 0.80 0.00 0.00 0.20
#> TCGA.HT.7694.01 1 0.0000 0.801 1.00 0.00 0.00 0.00
#> TCGA.P5.A780.01 4 0.5327 0.676 0.06 0.22 0.00 0.72
#> TCGA.DB.A64V.01 1 0.0000 0.801 1.00 0.00 0.00 0.00
#> TCGA.E1.5302.01 1 0.0707 0.791 0.98 0.00 0.00 0.02
#> TCGA.HT.A615.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.DU.7309.01 1 0.4277 0.834 0.72 0.00 0.00 0.28
#> TCGA.E1.A7YK.01 2 0.2647 0.897 0.00 0.88 0.00 0.12
#> TCGA.HT.7874.01 1 0.0000 0.801 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YY.01 1 0.0000 0.801 1.00 0.00 0.00 0.00
#> TCGA.FG.5964.01 1 0.0000 0.801 1.00 0.00 0.00 0.00
#> TCGA.DH.A7UR.01 4 0.4790 0.594 0.38 0.00 0.00 0.62
#> TCGA.HT.7479.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.HT.7602.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.HT.8111.01 4 0.4797 0.664 0.26 0.02 0.00 0.72
#> TCGA.HT.7858.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.HT.7686.01 2 0.0000 0.940 0.00 1.00 0.00 0.00
#> TCGA.CS.6290.01 1 0.0707 0.791 0.98 0.00 0.00 0.02
#> TCGA.FG.A711.01 4 0.4277 0.602 0.00 0.28 0.00 0.72
#> TCGA.TM.A84S.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.DB.5276.01 4 0.4994 0.460 0.48 0.00 0.00 0.52
#> TCGA.TM.A84L.01 1 0.3610 0.835 0.80 0.00 0.00 0.20
#> TCGA.DB.5273.01 1 0.0707 0.791 0.98 0.00 0.00 0.02
#> TCGA.TM.A7C4.01 1 0.4277 0.834 0.72 0.00 0.00 0.28
#> TCGA.HT.7607.01 1 0.4522 0.153 0.68 0.00 0.00 0.32
#> TCGA.P5.A736.01 1 0.3172 0.829 0.84 0.00 0.00 0.16
#> TCGA.HT.7470.01 2 0.0000 0.940 0.00 1.00 0.00 0.00
#> TCGA.P5.A781.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.TM.A7CF.02 1 0.0000 0.801 1.00 0.00 0.00 0.00
#> TCGA.S9.A6U2.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.S9.A6WN.01 2 0.1637 0.930 0.00 0.94 0.00 0.06
#> TCGA.DU.6396.01 2 0.0000 0.940 0.00 1.00 0.00 0.00
#> TCGA.DH.A7US.01 1 0.4134 0.841 0.74 0.00 0.00 0.26
#> TCGA.FG.A87N.01 3 0.0000 1.000 0.00 0.00 1.00 0.00
#> TCGA.HT.7478.01 1 0.3610 0.835 0.80 0.00 0.00 0.20
#> TCGA.HT.7603.01 1 0.0000 0.801 1.00 0.00 0.00 0.00
#> TCGA.FG.5965.02 2 0.2345 0.848 0.00 0.90 0.10 0.00
#> TCGA.FG.A70Y.01 4 0.4790 0.594 0.38 0.00 0.00 0.62
#> TCGA.TQ.A7RV.02 1 0.2345 0.702 0.90 0.00 0.00 0.10
#> TCGA.HT.A5R7.01 2 0.0000 0.940 0.00 1.00 0.00 0.00
#> TCGA.HT.7474.01 1 0.0000 0.801 1.00 0.00 0.00 0.00
#> TCGA.P5.A5EZ.01 4 0.5657 0.692 0.12 0.16 0.00 0.72
#> TCGA.WY.A858.01 4 0.4277 0.602 0.00 0.28 0.00 0.72
#> TCGA.WY.A85A.01 1 0.5000 -0.455 0.50 0.00 0.00 0.50
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.E1.5319.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.CS.6665.01 3 0.0609 0.9873 0.02 0.00 0.98 0.00 0.00
#> TCGA.FG.A6J3.01 3 0.0000 0.9958 0.00 0.00 1.00 0.00 0.00
#> TCGA.DB.A4XA.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.HT.A4DV.01 5 0.0000 0.9320 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.8113.01 5 0.0000 0.9320 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.7620.01 5 0.0000 0.9320 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.7689.01 4 0.2516 0.7919 0.00 0.14 0.00 0.86 0.00
#> TCGA.HT.8109.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.E1.A7YE.01 3 0.0000 0.9958 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7877.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.QH.A6CU.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.HW.7486.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.DU.8163.01 5 0.6184 -0.1504 0.38 0.00 0.00 0.14 0.48
#> TCGA.DU.6407.02 3 0.0000 0.9958 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.8010.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.DU.7011.01 1 0.3106 0.6436 0.84 0.00 0.00 0.14 0.02
#> TCGA.HT.7605.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.DB.5270.01 5 0.1648 0.8855 0.02 0.00 0.00 0.04 0.94
#> TCGA.S9.A6WQ.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.HT.8106.01 2 0.0000 0.9229 0.00 1.00 0.00 0.00 0.00
#> TCGA.26.5133.01 3 0.0000 0.9958 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A7QY.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.HT.7601.01 4 0.2516 0.7919 0.00 0.14 0.00 0.86 0.00
#> TCGA.HT.7880.01 5 0.0000 0.9320 0.00 0.00 0.00 0.00 1.00
#> TCGA.26.1442.01 2 0.0000 0.9229 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.A7Z3.01 5 0.6184 -0.1504 0.38 0.00 0.00 0.14 0.48
#> TCGA.P5.A5EX.01 2 0.0000 0.9229 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.8563.01 2 0.0000 0.9229 0.00 1.00 0.00 0.00 0.00
#> TCGA.RY.A843.01 1 0.3521 0.6726 0.82 0.00 0.00 0.14 0.04
#> TCGA.QH.A6X5.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.DH.A7UT.01 4 0.2516 0.7065 0.00 0.00 0.00 0.86 0.14
#> TCGA.HT.8018.01 2 0.3274 0.7679 0.00 0.78 0.00 0.22 0.00
#> TCGA.HT.7856.01 5 0.0000 0.9320 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.5851.01 4 0.2516 0.7919 0.00 0.14 0.00 0.86 0.00
#> TCGA.DU.A7T6.01 2 0.0609 0.9156 0.02 0.98 0.00 0.00 0.00
#> TCGA.TM.A84O.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.HT.A61A.01 5 0.0000 0.9320 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.A5R5.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.HT.A618.01 2 0.0000 0.9229 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7467.01 5 0.0000 0.9320 0.00 0.00 0.00 0.00 1.00
#> TCGA.FG.A60L.01 4 0.3922 0.6131 0.18 0.00 0.00 0.78 0.04
#> TCGA.DB.5278.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.TQ.A7RR.01 2 0.3274 0.7679 0.00 0.78 0.00 0.22 0.00
#> TCGA.15.1444.01 2 0.0609 0.9084 0.00 0.98 0.02 0.00 0.00
#> TCGA.HT.7881.01 5 0.0000 0.9320 0.00 0.00 0.00 0.00 1.00
#> TCGA.P5.A5EU.01 3 0.0000 0.9958 0.00 0.00 1.00 0.00 0.00
#> TCGA.VM.A8CE.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.CS.4944.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.DU.A6S2.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.S9.A7R7.01 2 0.3274 0.7679 0.00 0.78 0.00 0.22 0.00
#> TCGA.TM.A84R.01 5 0.0000 0.9320 0.00 0.00 0.00 0.00 1.00
#> TCGA.06.0221.02 3 0.0000 0.9958 0.00 0.00 1.00 0.00 0.00
#> TCGA.FG.8187.01 5 0.0000 0.9320 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.A7TG.01 5 0.0000 0.9320 0.00 0.00 0.00 0.00 1.00
#> TCGA.TM.A84F.01 2 0.3274 0.7679 0.00 0.78 0.00 0.22 0.00
#> TCGA.HT.7610.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.S9.A6TW.01 1 0.5414 0.7579 0.66 0.00 0.00 0.14 0.20
#> TCGA.HT.7481.01 5 0.0000 0.9320 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.A5TR.01 5 0.5555 0.5232 0.22 0.00 0.00 0.14 0.64
#> TCGA.S9.A7IQ.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.S9.A6WG.01 1 0.5083 0.7932 0.70 0.00 0.00 0.14 0.16
#> TCGA.HT.7688.01 4 0.3106 0.7902 0.02 0.14 0.00 0.84 0.00
#> TCGA.HT.7902.01 2 0.0000 0.9229 0.00 1.00 0.00 0.00 0.00
#> TCGA.QH.A6CY.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.P5.A72X.01 1 0.6102 0.0808 0.52 0.00 0.00 0.14 0.34
#> TCGA.S9.A6WI.01 5 0.0000 0.9320 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.5849.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.HW.7489.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.FG.A713.01 5 0.0000 0.9320 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.7300.01 1 0.3109 0.8844 0.80 0.00 0.00 0.00 0.20
#> TCGA.HT.7694.01 5 0.0000 0.9320 0.00 0.00 0.00 0.00 1.00
#> TCGA.P5.A780.01 4 0.3106 0.7902 0.02 0.14 0.00 0.84 0.00
#> TCGA.DB.A64V.01 5 0.0000 0.9320 0.00 0.00 0.00 0.00 1.00
#> TCGA.E1.5302.01 1 0.6102 0.0808 0.52 0.00 0.00 0.14 0.34
#> TCGA.HT.A615.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.DU.7309.01 1 0.3106 0.6436 0.84 0.00 0.00 0.14 0.02
#> TCGA.E1.A7YK.01 2 0.3274 0.7679 0.00 0.78 0.00 0.22 0.00
#> TCGA.HT.7874.01 5 0.0000 0.9320 0.00 0.00 0.00 0.00 1.00
#> TCGA.E1.A7YY.01 5 0.0000 0.9320 0.00 0.00 0.00 0.00 1.00
#> TCGA.FG.5964.01 5 0.0000 0.9320 0.00 0.00 0.00 0.00 1.00
#> TCGA.DH.A7UR.01 4 0.3922 0.6131 0.18 0.00 0.00 0.78 0.04
#> TCGA.HT.7479.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.HT.7602.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.HT.8111.01 4 0.2516 0.7065 0.00 0.00 0.00 0.86 0.14
#> TCGA.HT.7858.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.HT.7686.01 2 0.0000 0.9229 0.00 1.00 0.00 0.00 0.00
#> TCGA.CS.6290.01 5 0.0609 0.9141 0.02 0.00 0.00 0.00 0.98
#> TCGA.FG.A711.01 4 0.2516 0.7919 0.00 0.14 0.00 0.86 0.00
#> TCGA.TM.A84S.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.DB.5276.01 5 0.1410 0.8678 0.06 0.00 0.00 0.00 0.94
#> TCGA.TM.A84L.01 1 0.5258 0.7777 0.68 0.00 0.00 0.14 0.18
#> TCGA.DB.5273.01 5 0.2331 0.8509 0.08 0.00 0.00 0.02 0.90
#> TCGA.TM.A7C4.01 1 0.4437 0.7472 0.76 0.00 0.00 0.14 0.10
#> TCGA.HT.7607.01 5 0.0000 0.9320 0.00 0.00 0.00 0.00 1.00
#> TCGA.P5.A736.01 1 0.5895 0.3067 0.46 0.00 0.00 0.10 0.44
#> TCGA.HT.7470.01 2 0.0000 0.9229 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A781.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.TM.A7CF.02 5 0.0000 0.9320 0.00 0.00 0.00 0.00 1.00
#> TCGA.S9.A6U2.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.S9.A6WN.01 2 0.0000 0.9229 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.6396.01 2 0.0000 0.9229 0.00 1.00 0.00 0.00 0.00
#> TCGA.DH.A7US.01 1 0.2929 0.9028 0.82 0.00 0.00 0.00 0.18
#> TCGA.FG.A87N.01 3 0.0609 0.9873 0.02 0.00 0.98 0.00 0.00
#> TCGA.HT.7478.01 1 0.6219 0.3128 0.44 0.00 0.00 0.14 0.42
#> TCGA.HT.7603.01 5 0.1410 0.8700 0.06 0.00 0.00 0.00 0.94
#> TCGA.FG.5965.02 2 0.2012 0.8634 0.02 0.92 0.06 0.00 0.00
#> TCGA.FG.A70Y.01 4 0.3922 0.6131 0.18 0.00 0.00 0.78 0.04
#> TCGA.TQ.A7RV.02 5 0.0609 0.9141 0.02 0.00 0.00 0.00 0.98
#> TCGA.HT.A5R7.01 2 0.0000 0.9229 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7474.01 5 0.0000 0.9320 0.00 0.00 0.00 0.00 1.00
#> TCGA.P5.A5EZ.01 4 0.2516 0.7919 0.00 0.14 0.00 0.86 0.00
#> TCGA.WY.A858.01 4 0.2516 0.7919 0.00 0.14 0.00 0.86 0.00
#> TCGA.WY.A85A.01 4 0.6610 0.2569 0.26 0.00 0.00 0.46 0.28
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.E1.5319.01 1 0.0000 0.9270 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6665.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.A6J3.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.A4XA.01 1 0.0547 0.9253 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.HT.A4DV.01 5 0.0547 0.9422 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.HT.8113.01 5 0.0547 0.9422 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.HT.7620.01 5 0.0547 0.9422 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.HT.7689.01 4 0.4282 0.5039 0.00 0.42 0.00 0.56 0.00 0.02
#> TCGA.HT.8109.01 1 0.0547 0.9253 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YE.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7877.01 1 0.0000 0.9270 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CU.01 1 0.0000 0.9270 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HW.7486.01 1 0.0547 0.9253 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.DU.8163.01 6 0.3679 0.7412 0.20 0.00 0.00 0.00 0.04 0.76
#> TCGA.DU.6407.02 3 0.0000 1.0000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.8010.01 1 0.0000 0.9270 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7011.01 6 0.2631 0.7475 0.18 0.00 0.00 0.00 0.00 0.82
#> TCGA.HT.7605.01 1 0.0547 0.9253 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.DB.5270.01 6 0.4337 -0.0281 0.02 0.00 0.00 0.00 0.48 0.50
#> TCGA.S9.A6WQ.01 1 0.3578 0.3950 0.66 0.00 0.00 0.00 0.00 0.34
#> TCGA.HT.8106.01 4 0.3851 -0.6513 0.00 0.46 0.00 0.54 0.00 0.00
#> TCGA.26.5133.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A7QY.01 1 0.0000 0.9270 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7601.01 4 0.3797 0.5018 0.00 0.42 0.00 0.58 0.00 0.00
#> TCGA.HT.7880.01 5 0.0547 0.9422 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.26.1442.01 2 0.3851 0.7148 0.00 0.54 0.00 0.46 0.00 0.00
#> TCGA.E1.A7Z3.01 6 0.3315 0.7458 0.20 0.00 0.00 0.00 0.02 0.78
#> TCGA.P5.A5EX.01 4 0.4282 -0.5696 0.00 0.42 0.00 0.56 0.02 0.00
#> TCGA.HT.8563.01 4 0.4246 -0.5698 0.00 0.40 0.00 0.58 0.02 0.00
#> TCGA.RY.A843.01 6 0.2941 0.7381 0.22 0.00 0.00 0.00 0.00 0.78
#> TCGA.QH.A6X5.01 1 0.0000 0.9270 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A7UT.01 4 0.5564 0.4849 0.00 0.42 0.00 0.48 0.02 0.08
#> TCGA.HT.8018.01 4 0.0000 0.3102 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7856.01 5 0.0547 0.9422 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.DU.5851.01 4 0.4873 0.4986 0.00 0.42 0.00 0.52 0.00 0.06
#> TCGA.DU.A7T6.01 2 0.4310 0.6930 0.00 0.54 0.00 0.44 0.02 0.00
#> TCGA.TM.A84O.01 1 0.0000 0.9270 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A61A.01 5 0.0547 0.9422 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.HT.A5R5.01 1 0.0547 0.9146 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.HT.A618.01 2 0.3851 0.7148 0.00 0.54 0.00 0.46 0.00 0.00
#> TCGA.HT.7467.01 5 0.0547 0.9422 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.FG.A60L.01 6 0.3578 0.2774 0.00 0.34 0.00 0.00 0.00 0.66
#> TCGA.DB.5278.01 1 0.0547 0.9253 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RR.01 4 0.0000 0.3102 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.15.1444.01 2 0.3828 0.7046 0.00 0.56 0.00 0.44 0.00 0.00
#> TCGA.HT.7881.01 5 0.0547 0.9422 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.P5.A5EU.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VM.A8CE.01 1 0.0547 0.9253 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.CS.4944.01 1 0.3916 0.4873 0.68 0.02 0.00 0.00 0.00 0.30
#> TCGA.DU.A6S2.01 1 0.0000 0.9270 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7R7.01 4 0.0000 0.3102 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.TM.A84R.01 5 0.0547 0.9422 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.06.0221.02 3 0.0000 1.0000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.8187.01 5 0.0547 0.9422 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.DU.A7TG.01 5 0.0547 0.9422 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.TM.A84F.01 4 0.0000 0.3102 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7610.01 1 0.0000 0.9270 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TW.01 6 0.2941 0.7381 0.22 0.00 0.00 0.00 0.00 0.78
#> TCGA.HT.7481.01 5 0.0547 0.9422 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.DU.A5TR.01 6 0.0937 0.6647 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.S9.A7IQ.01 1 0.0000 0.9270 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WG.01 6 0.3309 0.6787 0.28 0.00 0.00 0.00 0.00 0.72
#> TCGA.HT.7688.01 2 0.5802 -0.5049 0.00 0.42 0.00 0.40 0.00 0.18
#> TCGA.HT.7902.01 2 0.3851 0.7148 0.00 0.54 0.00 0.46 0.00 0.00
#> TCGA.QH.A6CY.01 1 0.0547 0.9253 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.P5.A72X.01 6 0.0937 0.6647 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.S9.A6WI.01 5 0.0547 0.9422 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.DU.5849.01 1 0.0547 0.9253 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.HW.7489.01 1 0.4078 0.3928 0.64 0.02 0.00 0.00 0.00 0.34
#> TCGA.FG.A713.01 5 0.0547 0.9422 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.DU.7300.01 1 0.1267 0.8685 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.HT.7694.01 5 0.0547 0.9422 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.P5.A780.01 2 0.5802 -0.5049 0.00 0.42 0.00 0.40 0.00 0.18
#> TCGA.DB.A64V.01 5 0.0547 0.9422 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.E1.5302.01 6 0.2190 0.7034 0.06 0.00 0.00 0.00 0.04 0.90
#> TCGA.HT.A615.01 1 0.0000 0.9270 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7309.01 6 0.3198 0.6733 0.26 0.00 0.00 0.00 0.00 0.74
#> TCGA.E1.A7YK.01 4 0.0000 0.3102 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7874.01 5 0.0547 0.9422 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.E1.A7YY.01 5 0.0547 0.9422 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.FG.5964.01 5 0.1480 0.9053 0.02 0.00 0.00 0.00 0.94 0.04
#> TCGA.DH.A7UR.01 6 0.3578 0.2774 0.00 0.34 0.00 0.00 0.00 0.66
#> TCGA.HT.7479.01 1 0.2094 0.8519 0.90 0.02 0.00 0.00 0.00 0.08
#> TCGA.HT.7602.01 1 0.1092 0.9128 0.96 0.02 0.00 0.00 0.00 0.02
#> TCGA.HT.8111.01 4 0.5749 0.4763 0.00 0.42 0.00 0.46 0.02 0.10
#> TCGA.HT.7858.01 1 0.4078 0.3928 0.64 0.02 0.00 0.00 0.00 0.34
#> TCGA.HT.7686.01 2 0.3851 0.7148 0.00 0.54 0.00 0.46 0.00 0.00
#> TCGA.CS.6290.01 5 0.4337 0.0187 0.02 0.00 0.00 0.00 0.50 0.48
#> TCGA.FG.A711.01 4 0.4282 0.5039 0.00 0.42 0.00 0.56 0.00 0.02
#> TCGA.TM.A84S.01 1 0.0547 0.9253 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.DB.5276.01 5 0.0547 0.9422 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.TM.A84L.01 6 0.3076 0.7221 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.DB.5273.01 6 0.4199 0.2907 0.02 0.00 0.00 0.00 0.38 0.60
#> TCGA.TM.A7C4.01 6 0.2941 0.7381 0.22 0.00 0.00 0.00 0.00 0.78
#> TCGA.HT.7607.01 5 0.0547 0.9422 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.P5.A736.01 6 0.4348 0.6117 0.32 0.00 0.00 0.00 0.04 0.64
#> TCGA.HT.7470.01 2 0.3864 0.6942 0.00 0.52 0.00 0.48 0.00 0.00
#> TCGA.P5.A781.01 1 0.0000 0.9270 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A7CF.02 5 0.0547 0.9422 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.S9.A6U2.01 1 0.0000 0.9270 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WN.01 4 0.4282 -0.5696 0.00 0.42 0.00 0.56 0.02 0.00
#> TCGA.DU.6396.01 2 0.3851 0.7148 0.00 0.54 0.00 0.46 0.00 0.00
#> TCGA.DH.A7US.01 1 0.0547 0.9253 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.FG.A87N.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7478.01 6 0.3309 0.6787 0.28 0.00 0.00 0.00 0.00 0.72
#> TCGA.HT.7603.01 5 0.4078 0.4358 0.02 0.00 0.00 0.00 0.64 0.34
#> TCGA.FG.5965.02 2 0.4282 0.6866 0.00 0.56 0.02 0.42 0.00 0.00
#> TCGA.FG.A70Y.01 6 0.3578 0.2774 0.00 0.34 0.00 0.00 0.00 0.66
#> TCGA.TQ.A7RV.02 5 0.1092 0.9246 0.02 0.00 0.00 0.00 0.96 0.02
#> TCGA.HT.A5R7.01 2 0.3851 0.7148 0.00 0.54 0.00 0.46 0.00 0.00
#> TCGA.HT.7474.01 5 0.4078 0.4358 0.02 0.00 0.00 0.00 0.64 0.34
#> TCGA.P5.A5EZ.01 4 0.5285 0.4841 0.00 0.42 0.00 0.48 0.00 0.10
#> TCGA.WY.A858.01 4 0.5095 0.4923 0.00 0.42 0.00 0.50 0.00 0.08
#> TCGA.WY.A85A.01 6 0.0547 0.6603 0.00 0.00 0.00 0.00 0.02 0.98
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.E1.5319.01 1 0.0000 0.940 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6665.01 3 0.1006 0.974 0.00 0.00 0.96 0.00 0.02 0.02 0.00
#> TCGA.FG.A6J3.01 3 0.0000 0.991 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4XA.01 1 0.0504 0.939 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.HT.A4DV.01 5 0.1363 0.969 0.04 0.00 0.00 0.00 0.94 0.00 0.02
#> TCGA.HT.8113.01 5 0.0863 0.974 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.HT.7620.01 5 0.1363 0.969 0.04 0.00 0.00 0.00 0.94 0.00 0.02
#> TCGA.HT.7689.01 4 0.1166 0.729 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.HT.8109.01 1 0.1166 0.925 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.E1.A7YE.01 3 0.0000 0.991 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7877.01 1 0.0000 0.940 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CU.01 1 0.0000 0.940 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HW.7486.01 1 0.1166 0.925 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.DU.8163.01 6 0.2163 0.699 0.10 0.00 0.00 0.00 0.02 0.88 0.00
#> TCGA.DU.6407.02 3 0.0000 0.991 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8010.01 1 0.0863 0.927 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.DU.7011.01 6 0.2912 0.521 0.04 0.00 0.00 0.00 0.00 0.82 0.14
#> TCGA.HT.7605.01 1 0.0504 0.939 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DB.5270.01 6 0.3307 0.560 0.02 0.00 0.00 0.00 0.24 0.74 0.00
#> TCGA.S9.A6WQ.01 6 0.3358 0.541 0.36 0.00 0.00 0.00 0.00 0.64 0.00
#> TCGA.HT.8106.01 2 0.3517 0.736 0.00 0.70 0.00 0.02 0.00 0.00 0.28
#> TCGA.26.5133.01 3 0.0000 0.991 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7QY.01 1 0.0000 0.940 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7601.01 4 0.2512 0.716 0.00 0.04 0.00 0.86 0.00 0.00 0.10
#> TCGA.HT.7880.01 5 0.0863 0.974 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.26.1442.01 2 0.0000 0.895 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7Z3.01 6 0.2163 0.699 0.10 0.00 0.00 0.00 0.02 0.88 0.00
#> TCGA.P5.A5EX.01 2 0.3606 0.736 0.00 0.68 0.00 0.02 0.00 0.00 0.30
#> TCGA.HT.8563.01 2 0.3517 0.736 0.00 0.70 0.00 0.02 0.00 0.00 0.28
#> TCGA.RY.A843.01 6 0.3263 0.668 0.12 0.00 0.00 0.00 0.00 0.80 0.08
#> TCGA.QH.A6X5.01 1 0.0863 0.927 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.DH.A7UT.01 4 0.1363 0.705 0.00 0.00 0.00 0.94 0.04 0.00 0.02
#> TCGA.HT.8018.01 4 0.5055 0.594 0.00 0.18 0.00 0.56 0.00 0.00 0.26
#> TCGA.HT.7856.01 5 0.0863 0.974 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.DU.5851.01 4 0.0000 0.720 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.A7T6.01 2 0.1006 0.882 0.00 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.TM.A84O.01 1 0.0863 0.927 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.HT.A61A.01 5 0.0863 0.974 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.HT.A5R5.01 1 0.1886 0.811 0.88 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.HT.A618.01 2 0.0000 0.895 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7467.01 5 0.0863 0.974 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.FG.A60L.01 7 0.5513 0.930 0.00 0.00 0.00 0.16 0.02 0.30 0.52
#> TCGA.DB.5278.01 1 0.0504 0.939 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.TQ.A7RR.01 4 0.5259 0.542 0.00 0.22 0.00 0.52 0.00 0.00 0.26
#> TCGA.15.1444.01 2 0.1006 0.882 0.00 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.HT.7881.01 5 0.0863 0.974 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.P5.A5EU.01 3 0.0504 0.986 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.VM.A8CE.01 1 0.0504 0.939 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.CS.4944.01 6 0.4070 0.525 0.34 0.00 0.00 0.00 0.00 0.62 0.04
#> TCGA.DU.A6S2.01 1 0.0000 0.940 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7R7.01 4 0.5055 0.594 0.00 0.18 0.00 0.56 0.00 0.00 0.26
#> TCGA.TM.A84R.01 5 0.0863 0.974 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.06.0221.02 3 0.0000 0.991 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8187.01 5 0.1718 0.959 0.04 0.00 0.00 0.00 0.92 0.00 0.04
#> TCGA.DU.A7TG.01 5 0.0863 0.974 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.TM.A84F.01 4 0.5325 0.528 0.00 0.22 0.00 0.50 0.00 0.00 0.28
#> TCGA.HT.7610.01 1 0.0000 0.940 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TW.01 6 0.3263 0.668 0.12 0.00 0.00 0.00 0.00 0.80 0.08
#> TCGA.HT.7481.01 5 0.1718 0.959 0.04 0.00 0.00 0.00 0.92 0.00 0.04
#> TCGA.DU.A5TR.01 6 0.3186 0.316 0.00 0.00 0.00 0.00 0.02 0.76 0.22
#> TCGA.S9.A7IQ.01 1 0.0000 0.940 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WG.01 6 0.2259 0.692 0.16 0.00 0.00 0.00 0.00 0.84 0.00
#> TCGA.HT.7688.01 4 0.3228 0.537 0.00 0.00 0.00 0.80 0.02 0.02 0.16
#> TCGA.HT.7902.01 2 0.0000 0.895 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CY.01 1 0.0504 0.939 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.P5.A72X.01 6 0.3186 0.316 0.00 0.00 0.00 0.00 0.02 0.76 0.22
#> TCGA.S9.A6WI.01 5 0.0863 0.974 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.DU.5849.01 1 0.0504 0.939 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.HW.7489.01 6 0.3755 0.545 0.34 0.00 0.00 0.00 0.00 0.64 0.02
#> TCGA.FG.A713.01 5 0.1363 0.969 0.04 0.00 0.00 0.00 0.94 0.00 0.02
#> TCGA.DU.7300.01 1 0.2016 0.869 0.90 0.00 0.00 0.00 0.06 0.00 0.04
#> TCGA.HT.7694.01 5 0.1718 0.959 0.04 0.00 0.00 0.00 0.92 0.00 0.04
#> TCGA.P5.A780.01 4 0.3228 0.537 0.00 0.00 0.00 0.80 0.02 0.02 0.16
#> TCGA.DB.A64V.01 5 0.1718 0.959 0.04 0.00 0.00 0.00 0.92 0.00 0.04
#> TCGA.E1.5302.01 6 0.0504 0.609 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.HT.A615.01 1 0.0000 0.940 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7309.01 6 0.5207 -0.280 0.16 0.00 0.00 0.00 0.00 0.48 0.36
#> TCGA.E1.A7YK.01 4 0.5259 0.542 0.00 0.22 0.00 0.52 0.00 0.00 0.26
#> TCGA.HT.7874.01 5 0.0863 0.974 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.E1.A7YY.01 5 0.0863 0.974 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.FG.5964.01 5 0.3734 0.786 0.04 0.00 0.00 0.00 0.78 0.14 0.04
#> TCGA.DH.A7UR.01 7 0.5196 0.872 0.00 0.00 0.00 0.16 0.02 0.22 0.60
#> TCGA.HT.7479.01 1 0.3909 0.168 0.58 0.00 0.00 0.00 0.00 0.40 0.02
#> TCGA.HT.7602.01 1 0.4108 0.494 0.66 0.00 0.00 0.00 0.00 0.28 0.06
#> TCGA.HT.8111.01 4 0.0504 0.711 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.HT.7858.01 6 0.3755 0.545 0.34 0.00 0.00 0.00 0.00 0.64 0.02
#> TCGA.HT.7686.01 2 0.0000 0.895 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6290.01 6 0.2745 0.626 0.02 0.00 0.00 0.00 0.16 0.82 0.00
#> TCGA.FG.A711.01 4 0.0863 0.729 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.TM.A84S.01 1 0.0504 0.939 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DB.5276.01 5 0.0863 0.934 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.TM.A84L.01 6 0.2081 0.697 0.14 0.00 0.00 0.00 0.00 0.86 0.00
#> TCGA.DB.5273.01 6 0.2569 0.636 0.02 0.00 0.00 0.00 0.14 0.84 0.00
#> TCGA.TM.A7C4.01 6 0.2722 0.688 0.12 0.00 0.00 0.00 0.00 0.84 0.04
#> TCGA.HT.7607.01 5 0.1006 0.957 0.02 0.00 0.00 0.02 0.96 0.00 0.00
#> TCGA.P5.A736.01 6 0.2569 0.701 0.14 0.00 0.00 0.00 0.02 0.84 0.00
#> TCGA.HT.7470.01 2 0.1166 0.873 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.P5.A781.01 1 0.0000 0.940 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A7CF.02 5 0.1363 0.969 0.04 0.00 0.00 0.00 0.94 0.00 0.02
#> TCGA.S9.A6U2.01 1 0.0000 0.940 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WN.01 2 0.3606 0.736 0.00 0.68 0.00 0.02 0.00 0.00 0.30
#> TCGA.DU.6396.01 2 0.0000 0.895 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A7US.01 1 0.1166 0.925 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.FG.A87N.01 3 0.0504 0.986 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.HT.7478.01 6 0.2569 0.701 0.14 0.00 0.00 0.00 0.02 0.84 0.00
#> TCGA.HT.7603.01 6 0.3417 0.545 0.02 0.00 0.00 0.00 0.26 0.72 0.00
#> TCGA.FG.5965.02 2 0.1006 0.882 0.00 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.FG.A70Y.01 7 0.5564 0.917 0.00 0.00 0.00 0.16 0.02 0.32 0.50
#> TCGA.TQ.A7RV.02 5 0.1363 0.936 0.02 0.00 0.00 0.00 0.94 0.04 0.00
#> TCGA.HT.A5R7.01 2 0.0000 0.895 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7474.01 6 0.3417 0.545 0.02 0.00 0.00 0.00 0.26 0.72 0.00
#> TCGA.P5.A5EZ.01 4 0.1006 0.699 0.00 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.WY.A858.01 4 0.0000 0.720 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.WY.A85A.01 6 0.3985 -0.515 0.00 0.00 0.00 0.02 0.00 0.52 0.46
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.E1.5319.01 1 0.0000 0.9245 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6665.01 3 0.2071 0.9347 0.00 0.00 0.90 0.00 0.00 0.04 0.02 0.04
#> TCGA.FG.A6J3.01 3 0.0000 0.9789 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4XA.01 1 0.1563 0.9127 0.90 0.00 0.00 0.00 0.00 0.10 0.00 0.00
#> TCGA.HT.A4DV.01 5 0.2025 0.9055 0.00 0.00 0.00 0.00 0.88 0.10 0.00 0.02
#> TCGA.HT.8113.01 5 0.0000 0.9218 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7620.01 5 0.2025 0.9055 0.00 0.00 0.00 0.00 0.88 0.10 0.00 0.02
#> TCGA.HT.7689.01 4 0.0471 0.8059 0.00 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.HT.8109.01 1 0.1947 0.8955 0.86 0.00 0.00 0.00 0.00 0.14 0.00 0.00
#> TCGA.E1.A7YE.01 3 0.0000 0.9789 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7877.01 1 0.0000 0.9245 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CU.01 1 0.0000 0.9245 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HW.7486.01 1 0.2534 0.8359 0.78 0.00 0.00 0.00 0.00 0.22 0.00 0.00
#> TCGA.DU.8163.01 8 0.1275 0.5934 0.04 0.00 0.00 0.00 0.00 0.00 0.02 0.94
#> TCGA.DU.6407.02 3 0.0000 0.9789 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8010.01 1 0.2071 0.8763 0.90 0.00 0.00 0.00 0.00 0.04 0.02 0.04
#> TCGA.DU.7011.01 7 0.3333 0.4114 0.00 0.00 0.00 0.00 0.00 0.00 0.50 0.50
#> TCGA.HT.7605.01 1 0.1563 0.9127 0.90 0.00 0.00 0.00 0.00 0.10 0.00 0.00
#> TCGA.DB.5270.01 8 0.3291 0.3864 0.00 0.00 0.00 0.00 0.28 0.00 0.02 0.70
#> TCGA.S9.A6WQ.01 8 0.3637 0.5529 0.26 0.00 0.00 0.00 0.00 0.02 0.02 0.70
#> TCGA.HT.8106.01 2 0.2534 0.7894 0.00 0.78 0.00 0.00 0.00 0.22 0.00 0.00
#> TCGA.26.5133.01 3 0.0000 0.9789 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7QY.01 1 0.0471 0.9238 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.HT.7601.01 4 0.1091 0.8020 0.00 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.HT.7880.01 5 0.0000 0.9218 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.26.1442.01 2 0.0000 0.8789 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7Z3.01 8 0.3002 0.5165 0.04 0.00 0.00 0.00 0.02 0.00 0.12 0.82
#> TCGA.P5.A5EX.01 2 0.3570 0.7309 0.00 0.62 0.00 0.00 0.00 0.36 0.02 0.00
#> TCGA.HT.8563.01 2 0.3083 0.7358 0.00 0.66 0.00 0.00 0.00 0.34 0.00 0.00
#> TCGA.RY.A843.01 8 0.4100 -0.0681 0.06 0.00 0.00 0.00 0.00 0.00 0.36 0.58
#> TCGA.QH.A6X5.01 1 0.2348 0.8618 0.88 0.00 0.00 0.00 0.00 0.06 0.02 0.04
#> TCGA.DH.A7UT.01 4 0.1607 0.7908 0.00 0.00 0.00 0.92 0.00 0.04 0.04 0.00
#> TCGA.HT.8018.01 4 0.3970 0.7010 0.00 0.10 0.00 0.68 0.00 0.22 0.00 0.00
#> TCGA.HT.7856.01 5 0.0000 0.9218 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.5851.01 4 0.0471 0.8050 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.DU.A7T6.01 2 0.3303 0.8070 0.00 0.76 0.00 0.00 0.00 0.20 0.02 0.02
#> TCGA.TM.A84O.01 1 0.2265 0.8700 0.88 0.00 0.00 0.00 0.00 0.08 0.02 0.02
#> TCGA.HT.A61A.01 5 0.0000 0.9218 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.A5R5.01 1 0.1275 0.8930 0.94 0.00 0.00 0.00 0.00 0.00 0.02 0.04
#> TCGA.HT.A618.01 2 0.0000 0.8789 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7467.01 5 0.1557 0.9160 0.00 0.00 0.00 0.00 0.92 0.06 0.00 0.02
#> TCGA.FG.A60L.01 7 0.3314 0.6349 0.00 0.00 0.00 0.02 0.00 0.08 0.80 0.10
#> TCGA.DB.5278.01 1 0.1341 0.9150 0.92 0.00 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.TQ.A7RR.01 4 0.4458 0.6403 0.00 0.18 0.00 0.62 0.00 0.20 0.00 0.00
#> TCGA.15.1444.01 2 0.2020 0.8495 0.00 0.90 0.00 0.00 0.00 0.06 0.02 0.02
#> TCGA.HT.7881.01 5 0.1557 0.9160 0.00 0.00 0.00 0.00 0.92 0.06 0.00 0.02
#> TCGA.P5.A5EU.01 3 0.1408 0.9605 0.00 0.00 0.94 0.00 0.00 0.02 0.02 0.02
#> TCGA.VM.A8CE.01 1 0.1563 0.9127 0.90 0.00 0.00 0.00 0.00 0.10 0.00 0.00
#> TCGA.CS.4944.01 8 0.4211 0.5530 0.22 0.00 0.00 0.00 0.00 0.08 0.02 0.68
#> TCGA.DU.A6S2.01 1 0.0000 0.9245 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7R7.01 4 0.3970 0.7010 0.00 0.10 0.00 0.68 0.00 0.22 0.00 0.00
#> TCGA.TM.A84R.01 5 0.0000 0.9218 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.06.0221.02 3 0.0000 0.9789 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8187.01 5 0.3227 0.8467 0.00 0.00 0.00 0.00 0.78 0.14 0.00 0.08
#> TCGA.DU.A7TG.01 5 0.0000 0.9218 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.TM.A84F.01 4 0.5257 0.5965 0.00 0.14 0.00 0.54 0.00 0.28 0.04 0.00
#> TCGA.HT.7610.01 1 0.0000 0.9245 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TW.01 8 0.4655 -0.0461 0.04 0.00 0.00 0.00 0.02 0.02 0.34 0.58
#> TCGA.HT.7481.01 5 0.2994 0.8637 0.00 0.00 0.00 0.00 0.80 0.14 0.00 0.06
#> TCGA.DU.A5TR.01 7 0.3329 0.4622 0.00 0.00 0.00 0.00 0.00 0.00 0.52 0.48
#> TCGA.S9.A7IQ.01 1 0.0000 0.9245 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WG.01 8 0.2648 0.5812 0.08 0.00 0.00 0.00 0.00 0.00 0.08 0.84
#> TCGA.HT.7688.01 4 0.3729 0.6548 0.00 0.00 0.00 0.72 0.00 0.10 0.18 0.00
#> TCGA.HT.7902.01 2 0.0000 0.8789 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CY.01 1 0.1563 0.9127 0.90 0.00 0.00 0.00 0.00 0.10 0.00 0.00
#> TCGA.P5.A72X.01 7 0.3318 0.4962 0.00 0.00 0.00 0.00 0.00 0.00 0.54 0.46
#> TCGA.S9.A6WI.01 5 0.0000 0.9218 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.5849.01 1 0.1563 0.9127 0.90 0.00 0.00 0.00 0.00 0.10 0.00 0.00
#> TCGA.HW.7489.01 8 0.3657 0.5723 0.20 0.00 0.00 0.00 0.00 0.08 0.00 0.72
#> TCGA.FG.A713.01 5 0.1091 0.9165 0.00 0.00 0.00 0.00 0.94 0.06 0.00 0.00
#> TCGA.DU.7300.01 1 0.3710 0.7198 0.76 0.00 0.00 0.00 0.10 0.12 0.00 0.02
#> TCGA.HT.7694.01 5 0.2725 0.8764 0.00 0.00 0.00 0.00 0.82 0.14 0.00 0.04
#> TCGA.P5.A780.01 4 0.3729 0.6548 0.00 0.00 0.00 0.72 0.00 0.10 0.18 0.00
#> TCGA.DB.A64V.01 5 0.2994 0.8637 0.00 0.00 0.00 0.00 0.80 0.14 0.00 0.06
#> TCGA.E1.5302.01 8 0.2650 0.2872 0.00 0.00 0.00 0.00 0.00 0.00 0.24 0.76
#> TCGA.HT.A615.01 1 0.0000 0.9245 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7309.01 7 0.3856 0.6185 0.10 0.00 0.00 0.00 0.00 0.00 0.70 0.20
#> TCGA.E1.A7YK.01 4 0.4458 0.6403 0.00 0.18 0.00 0.62 0.00 0.20 0.00 0.00
#> TCGA.HT.7874.01 5 0.0000 0.9218 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YY.01 5 0.0000 0.9218 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.5964.01 5 0.4190 0.6877 0.00 0.00 0.00 0.00 0.66 0.14 0.00 0.20
#> TCGA.DH.A7UR.01 7 0.4314 0.5232 0.00 0.00 0.00 0.02 0.00 0.24 0.66 0.08
#> TCGA.HT.7479.01 8 0.4628 0.3511 0.36 0.00 0.00 0.00 0.00 0.12 0.00 0.52
#> TCGA.HT.7602.01 8 0.5054 0.2138 0.36 0.00 0.00 0.00 0.00 0.20 0.00 0.44
#> TCGA.HT.8111.01 4 0.0808 0.8022 0.00 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.HT.7858.01 8 0.3880 0.5431 0.24 0.00 0.00 0.00 0.00 0.08 0.00 0.68
#> TCGA.HT.7686.01 2 0.0000 0.8789 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6290.01 8 0.1563 0.5704 0.00 0.00 0.00 0.00 0.10 0.00 0.00 0.90
#> TCGA.FG.A711.01 4 0.0471 0.8059 0.00 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.TM.A84S.01 1 0.1563 0.9127 0.90 0.00 0.00 0.00 0.00 0.10 0.00 0.00
#> TCGA.DB.5276.01 5 0.0941 0.9199 0.00 0.00 0.00 0.00 0.96 0.02 0.00 0.02
#> TCGA.TM.A84L.01 8 0.1887 0.5877 0.06 0.00 0.00 0.00 0.00 0.00 0.04 0.90
#> TCGA.DB.5273.01 8 0.1091 0.5772 0.00 0.00 0.00 0.00 0.06 0.00 0.00 0.94
#> TCGA.TM.A7C4.01 8 0.4588 0.0181 0.12 0.00 0.00 0.00 0.00 0.00 0.34 0.54
#> TCGA.HT.7607.01 5 0.0000 0.9218 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A736.01 8 0.1804 0.6158 0.08 0.00 0.00 0.00 0.00 0.00 0.02 0.90
#> TCGA.HT.7470.01 2 0.1557 0.8464 0.00 0.92 0.00 0.02 0.00 0.06 0.00 0.00
#> TCGA.P5.A781.01 1 0.0000 0.9245 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A7CF.02 5 0.2350 0.8970 0.00 0.00 0.00 0.00 0.86 0.10 0.00 0.04
#> TCGA.S9.A6U2.01 1 0.0000 0.9245 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WN.01 2 0.3570 0.7309 0.00 0.62 0.00 0.00 0.00 0.36 0.02 0.00
#> TCGA.DU.6396.01 2 0.0471 0.8729 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.DH.A7US.01 1 0.1947 0.8955 0.86 0.00 0.00 0.00 0.00 0.14 0.00 0.00
#> TCGA.FG.A87N.01 3 0.0941 0.9685 0.00 0.00 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.HT.7478.01 8 0.1341 0.6150 0.08 0.00 0.00 0.00 0.00 0.00 0.00 0.92
#> TCGA.HT.7603.01 8 0.2994 0.5364 0.00 0.00 0.00 0.00 0.14 0.06 0.00 0.80
#> TCGA.FG.5965.02 2 0.2020 0.8495 0.00 0.90 0.00 0.00 0.00 0.06 0.02 0.02
#> TCGA.FG.A70Y.01 7 0.3675 0.6474 0.00 0.00 0.00 0.02 0.00 0.08 0.76 0.14
#> TCGA.TQ.A7RV.02 5 0.1947 0.8334 0.00 0.00 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.HT.A5R7.01 2 0.0000 0.8789 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7474.01 8 0.2994 0.5364 0.00 0.00 0.00 0.00 0.14 0.06 0.00 0.80
#> TCGA.P5.A5EZ.01 4 0.2132 0.7694 0.00 0.00 0.00 0.88 0.00 0.04 0.08 0.00
#> TCGA.WY.A858.01 4 0.0808 0.8022 0.00 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.WY.A85A.01 7 0.2852 0.6500 0.00 0.00 0.00 0.00 0.00 0.00 0.72 0.28
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 , Node0112 , Node0113 , Node0121 , Node0122 , Node0123-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0141 , Node0142-leaf , Node0143 , Node0211-leaf , Node0212-leaf , Node0213-leaf , Node0214-leaf , Node0221 , Node0222 , Node0223 , Node0231 , Node0232-leaf , Node0233-leaf , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0323-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["031"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 78 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 0.4950 0.505 0.505
#> 3 3 1.000 1.000 1.000 0.3387 0.832 0.668
#> 4 4 0.886 0.967 0.934 0.1075 0.916 0.751
#> 5 5 0.938 0.934 0.952 0.0463 0.965 0.864
#> 6 6 0.952 0.873 0.950 0.0139 0.991 0.961
#> 7 7 0.903 0.812 0.907 0.0140 1.000 1.000
#> 8 8 0.873 0.682 0.859 0.0188 0.995 0.976
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.E1.5319.01 2 0 1 0 1
#> TCGA.DB.A4XA.01 1 0 1 1 0
#> TCGA.HT.A4DV.01 2 0 1 0 1
#> TCGA.HT.8113.01 2 0 1 0 1
#> TCGA.HT.7620.01 1 0 1 1 0
#> TCGA.HT.8109.01 1 0 1 1 0
#> TCGA.HT.7877.01 2 0 1 0 1
#> TCGA.QH.A6CU.01 2 0 1 0 1
#> TCGA.HW.7486.01 1 0 1 1 0
#> TCGA.DU.8163.01 1 0 1 1 0
#> TCGA.HT.8010.01 2 0 1 0 1
#> TCGA.DU.7011.01 1 0 1 1 0
#> TCGA.HT.7605.01 1 0 1 1 0
#> TCGA.DB.5270.01 2 0 1 0 1
#> TCGA.S9.A6WQ.01 2 0 1 0 1
#> TCGA.S9.A7QY.01 2 0 1 0 1
#> TCGA.HT.7880.01 1 0 1 1 0
#> TCGA.E1.A7Z3.01 2 0 1 0 1
#> TCGA.RY.A843.01 1 0 1 1 0
#> TCGA.QH.A6X5.01 2 0 1 0 1
#> TCGA.DH.A7UT.01 1 0 1 1 0
#> TCGA.HT.7856.01 1 0 1 1 0
#> TCGA.TM.A84O.01 2 0 1 0 1
#> TCGA.HT.A61A.01 2 0 1 0 1
#> TCGA.HT.A5R5.01 2 0 1 0 1
#> TCGA.HT.7467.01 1 0 1 1 0
#> TCGA.FG.A60L.01 2 0 1 0 1
#> TCGA.DB.5278.01 1 0 1 1 0
#> TCGA.HT.7881.01 1 0 1 1 0
#> TCGA.VM.A8CE.01 1 0 1 1 0
#> TCGA.CS.4944.01 1 0 1 1 0
#> TCGA.DU.A6S2.01 2 0 1 0 1
#> TCGA.TM.A84R.01 1 0 1 1 0
#> TCGA.FG.8187.01 1 0 1 1 0
#> TCGA.DU.A7TG.01 1 0 1 1 0
#> TCGA.HT.7610.01 2 0 1 0 1
#> TCGA.S9.A6TW.01 1 0 1 1 0
#> TCGA.HT.7481.01 1 0 1 1 0
#> TCGA.DU.A5TR.01 1 0 1 1 0
#> TCGA.S9.A7IQ.01 2 0 1 0 1
#> TCGA.S9.A6WG.01 1 0 1 1 0
#> TCGA.QH.A6CY.01 1 0 1 1 0
#> TCGA.P5.A72X.01 1 0 1 1 0
#> TCGA.S9.A6WI.01 2 0 1 0 1
#> TCGA.DU.5849.01 1 0 1 1 0
#> TCGA.HW.7489.01 1 0 1 1 0
#> TCGA.FG.A713.01 2 0 1 0 1
#> TCGA.DU.7300.01 2 0 1 0 1
#> TCGA.HT.7694.01 1 0 1 1 0
#> TCGA.DB.A64V.01 1 0 1 1 0
#> TCGA.E1.5302.01 1 0 1 1 0
#> TCGA.HT.A615.01 2 0 1 0 1
#> TCGA.DU.7309.01 2 0 1 0 1
#> TCGA.HT.7874.01 2 0 1 0 1
#> TCGA.E1.A7YY.01 2 0 1 0 1
#> TCGA.FG.5964.01 1 0 1 1 0
#> TCGA.DH.A7UR.01 2 0 1 0 1
#> TCGA.HT.7479.01 1 0 1 1 0
#> TCGA.HT.7602.01 1 0 1 1 0
#> TCGA.HT.7858.01 1 0 1 1 0
#> TCGA.CS.6290.01 1 0 1 1 0
#> TCGA.TM.A84S.01 1 0 1 1 0
#> TCGA.DB.5276.01 1 0 1 1 0
#> TCGA.TM.A84L.01 1 0 1 1 0
#> TCGA.DB.5273.01 1 0 1 1 0
#> TCGA.TM.A7C4.01 2 0 1 0 1
#> TCGA.HT.7607.01 2 0 1 0 1
#> TCGA.P5.A736.01 2 0 1 0 1
#> TCGA.P5.A781.01 2 0 1 0 1
#> TCGA.TM.A7CF.02 2 0 1 0 1
#> TCGA.S9.A6U2.01 2 0 1 0 1
#> TCGA.DH.A7US.01 1 0 1 1 0
#> TCGA.HT.7478.01 1 0 1 1 0
#> TCGA.HT.7603.01 1 0 1 1 0
#> TCGA.FG.A70Y.01 2 0 1 0 1
#> TCGA.TQ.A7RV.02 1 0 1 1 0
#> TCGA.HT.7474.01 1 0 1 1 0
#> TCGA.WY.A85A.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.E1.5319.01 2 0 1 0 1 0
#> TCGA.DB.A4XA.01 3 0 1 0 0 1
#> TCGA.HT.A4DV.01 2 0 1 0 1 0
#> TCGA.HT.8113.01 2 0 1 0 1 0
#> TCGA.HT.7620.01 3 0 1 0 0 1
#> TCGA.HT.8109.01 3 0 1 0 0 1
#> TCGA.HT.7877.01 2 0 1 0 1 0
#> TCGA.QH.A6CU.01 2 0 1 0 1 0
#> TCGA.HW.7486.01 3 0 1 0 0 1
#> TCGA.DU.8163.01 1 0 1 1 0 0
#> TCGA.HT.8010.01 2 0 1 0 1 0
#> TCGA.DU.7011.01 1 0 1 1 0 0
#> TCGA.HT.7605.01 3 0 1 0 0 1
#> TCGA.DB.5270.01 2 0 1 0 1 0
#> TCGA.S9.A6WQ.01 2 0 1 0 1 0
#> TCGA.S9.A7QY.01 2 0 1 0 1 0
#> TCGA.HT.7880.01 1 0 1 1 0 0
#> TCGA.E1.A7Z3.01 2 0 1 0 1 0
#> TCGA.RY.A843.01 1 0 1 1 0 0
#> TCGA.QH.A6X5.01 2 0 1 0 1 0
#> TCGA.DH.A7UT.01 1 0 1 1 0 0
#> TCGA.HT.7856.01 3 0 1 0 0 1
#> TCGA.TM.A84O.01 2 0 1 0 1 0
#> TCGA.HT.A61A.01 2 0 1 0 1 0
#> TCGA.HT.A5R5.01 2 0 1 0 1 0
#> TCGA.HT.7467.01 3 0 1 0 0 1
#> TCGA.FG.A60L.01 2 0 1 0 1 0
#> TCGA.DB.5278.01 1 0 1 1 0 0
#> TCGA.HT.7881.01 3 0 1 0 0 1
#> TCGA.VM.A8CE.01 3 0 1 0 0 1
#> TCGA.CS.4944.01 1 0 1 1 0 0
#> TCGA.DU.A6S2.01 2 0 1 0 1 0
#> TCGA.TM.A84R.01 3 0 1 0 0 1
#> TCGA.FG.8187.01 3 0 1 0 0 1
#> TCGA.DU.A7TG.01 3 0 1 0 0 1
#> TCGA.HT.7610.01 2 0 1 0 1 0
#> TCGA.S9.A6TW.01 3 0 1 0 0 1
#> TCGA.HT.7481.01 3 0 1 0 0 1
#> TCGA.DU.A5TR.01 1 0 1 1 0 0
#> TCGA.S9.A7IQ.01 2 0 1 0 1 0
#> TCGA.S9.A6WG.01 1 0 1 1 0 0
#> TCGA.QH.A6CY.01 3 0 1 0 0 1
#> TCGA.P5.A72X.01 1 0 1 1 0 0
#> TCGA.S9.A6WI.01 2 0 1 0 1 0
#> TCGA.DU.5849.01 3 0 1 0 0 1
#> TCGA.HW.7489.01 1 0 1 1 0 0
#> TCGA.FG.A713.01 2 0 1 0 1 0
#> TCGA.DU.7300.01 2 0 1 0 1 0
#> TCGA.HT.7694.01 3 0 1 0 0 1
#> TCGA.DB.A64V.01 3 0 1 0 0 1
#> TCGA.E1.5302.01 1 0 1 1 0 0
#> TCGA.HT.A615.01 2 0 1 0 1 0
#> TCGA.DU.7309.01 2 0 1 0 1 0
#> TCGA.HT.7874.01 2 0 1 0 1 0
#> TCGA.E1.A7YY.01 2 0 1 0 1 0
#> TCGA.FG.5964.01 3 0 1 0 0 1
#> TCGA.DH.A7UR.01 2 0 1 0 1 0
#> TCGA.HT.7479.01 1 0 1 1 0 0
#> TCGA.HT.7602.01 1 0 1 1 0 0
#> TCGA.HT.7858.01 1 0 1 1 0 0
#> TCGA.CS.6290.01 1 0 1 1 0 0
#> TCGA.TM.A84S.01 3 0 1 0 0 1
#> TCGA.DB.5276.01 1 0 1 1 0 0
#> TCGA.TM.A84L.01 1 0 1 1 0 0
#> TCGA.DB.5273.01 1 0 1 1 0 0
#> TCGA.TM.A7C4.01 2 0 1 0 1 0
#> TCGA.HT.7607.01 2 0 1 0 1 0
#> TCGA.P5.A736.01 2 0 1 0 1 0
#> TCGA.P5.A781.01 2 0 1 0 1 0
#> TCGA.TM.A7CF.02 2 0 1 0 1 0
#> TCGA.S9.A6U2.01 2 0 1 0 1 0
#> TCGA.DH.A7US.01 3 0 1 0 0 1
#> TCGA.HT.7478.01 1 0 1 1 0 0
#> TCGA.HT.7603.01 1 0 1 1 0 0
#> TCGA.FG.A70Y.01 2 0 1 0 1 0
#> TCGA.TQ.A7RV.02 1 0 1 1 0 0
#> TCGA.HT.7474.01 1 0 1 1 0 0
#> TCGA.WY.A85A.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.E1.5319.01 2 0.0000 0.999 0.00 1.00 0.00 0.00
#> TCGA.DB.A4XA.01 3 0.3610 0.892 0.00 0.00 0.80 0.20
#> TCGA.HT.A4DV.01 2 0.0000 0.999 0.00 1.00 0.00 0.00
#> TCGA.HT.8113.01 2 0.0000 0.999 0.00 1.00 0.00 0.00
#> TCGA.HT.7620.01 3 0.0000 0.917 0.00 0.00 1.00 0.00
#> TCGA.HT.8109.01 3 0.3975 0.879 0.00 0.00 0.76 0.24
#> TCGA.HT.7877.01 2 0.0000 0.999 0.00 1.00 0.00 0.00
#> TCGA.QH.A6CU.01 2 0.0000 0.999 0.00 1.00 0.00 0.00
#> TCGA.HW.7486.01 3 0.0707 0.916 0.00 0.00 0.98 0.02
#> TCGA.DU.8163.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HT.8010.01 2 0.0000 0.999 0.00 1.00 0.00 0.00
#> TCGA.DU.7011.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HT.7605.01 3 0.0000 0.917 0.00 0.00 1.00 0.00
#> TCGA.DB.5270.01 4 0.3975 0.978 0.00 0.24 0.00 0.76
#> TCGA.S9.A6WQ.01 4 0.4406 0.914 0.00 0.30 0.00 0.70
#> TCGA.S9.A7QY.01 2 0.0000 0.999 0.00 1.00 0.00 0.00
#> TCGA.HT.7880.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.E1.A7Z3.01 4 0.3975 0.978 0.00 0.24 0.00 0.76
#> TCGA.RY.A843.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.QH.A6X5.01 2 0.0000 0.999 0.00 1.00 0.00 0.00
#> TCGA.DH.A7UT.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HT.7856.01 3 0.0000 0.917 0.00 0.00 1.00 0.00
#> TCGA.TM.A84O.01 2 0.0000 0.999 0.00 1.00 0.00 0.00
#> TCGA.HT.A61A.01 2 0.0707 0.972 0.00 0.98 0.00 0.02
#> TCGA.HT.A5R5.01 4 0.3975 0.978 0.00 0.24 0.00 0.76
#> TCGA.HT.7467.01 3 0.0000 0.917 0.00 0.00 1.00 0.00
#> TCGA.FG.A60L.01 4 0.3975 0.978 0.00 0.24 0.00 0.76
#> TCGA.DB.5278.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HT.7881.01 3 0.0707 0.904 0.02 0.00 0.98 0.00
#> TCGA.VM.A8CE.01 3 0.0000 0.917 0.00 0.00 1.00 0.00
#> TCGA.CS.4944.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DU.A6S2.01 2 0.0000 0.999 0.00 1.00 0.00 0.00
#> TCGA.TM.A84R.01 3 0.0000 0.917 0.00 0.00 1.00 0.00
#> TCGA.FG.8187.01 3 0.0000 0.917 0.00 0.00 1.00 0.00
#> TCGA.DU.A7TG.01 3 0.0000 0.917 0.00 0.00 1.00 0.00
#> TCGA.HT.7610.01 4 0.3975 0.978 0.00 0.24 0.00 0.76
#> TCGA.S9.A6TW.01 3 0.3801 0.888 0.00 0.00 0.78 0.22
#> TCGA.HT.7481.01 3 0.0000 0.917 0.00 0.00 1.00 0.00
#> TCGA.DU.A5TR.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.S9.A7IQ.01 2 0.0000 0.999 0.00 1.00 0.00 0.00
#> TCGA.S9.A6WG.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.QH.A6CY.01 3 0.3801 0.888 0.00 0.00 0.78 0.22
#> TCGA.P5.A72X.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.S9.A6WI.01 2 0.0000 0.999 0.00 1.00 0.00 0.00
#> TCGA.DU.5849.01 3 0.3975 0.879 0.00 0.00 0.76 0.24
#> TCGA.HW.7489.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.FG.A713.01 2 0.0000 0.999 0.00 1.00 0.00 0.00
#> TCGA.DU.7300.01 2 0.0000 0.999 0.00 1.00 0.00 0.00
#> TCGA.HT.7694.01 3 0.3801 0.888 0.00 0.00 0.78 0.22
#> TCGA.DB.A64V.01 3 0.3801 0.888 0.00 0.00 0.78 0.22
#> TCGA.E1.5302.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HT.A615.01 2 0.0000 0.999 0.00 1.00 0.00 0.00
#> TCGA.DU.7309.01 4 0.3975 0.978 0.00 0.24 0.00 0.76
#> TCGA.HT.7874.01 2 0.0000 0.999 0.00 1.00 0.00 0.00
#> TCGA.E1.A7YY.01 4 0.4713 0.823 0.00 0.36 0.00 0.64
#> TCGA.FG.5964.01 3 0.3801 0.888 0.00 0.00 0.78 0.22
#> TCGA.DH.A7UR.01 2 0.0000 0.999 0.00 1.00 0.00 0.00
#> TCGA.HT.7479.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HT.7602.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HT.7858.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CS.6290.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.TM.A84S.01 3 0.0000 0.917 0.00 0.00 1.00 0.00
#> TCGA.DB.5276.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.TM.A84L.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DB.5273.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.TM.A7C4.01 4 0.3975 0.978 0.00 0.24 0.00 0.76
#> TCGA.HT.7607.01 2 0.0000 0.999 0.00 1.00 0.00 0.00
#> TCGA.P5.A736.01 4 0.3975 0.978 0.00 0.24 0.00 0.76
#> TCGA.P5.A781.01 2 0.0000 0.999 0.00 1.00 0.00 0.00
#> TCGA.TM.A7CF.02 4 0.3975 0.978 0.00 0.24 0.00 0.76
#> TCGA.S9.A6U2.01 2 0.0000 0.999 0.00 1.00 0.00 0.00
#> TCGA.DH.A7US.01 3 0.3801 0.888 0.00 0.00 0.78 0.22
#> TCGA.HT.7478.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HT.7603.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.FG.A70Y.01 4 0.3975 0.978 0.00 0.24 0.00 0.76
#> TCGA.TQ.A7RV.02 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HT.7474.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.WY.A85A.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.E1.5319.01 2 0.0000 0.996 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.A4XA.01 3 0.4767 -0.235 0.00 0.00 0.56 0.02 0.42
#> TCGA.HT.A4DV.01 2 0.0000 0.996 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.8113.01 2 0.0000 0.996 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7620.01 3 0.0000 0.951 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.8109.01 5 0.0609 0.722 0.00 0.00 0.00 0.02 0.98
#> TCGA.HT.7877.01 2 0.0000 0.996 0.00 1.00 0.00 0.00 0.00
#> TCGA.QH.A6CU.01 2 0.0609 0.979 0.00 0.98 0.00 0.02 0.00
#> TCGA.HW.7486.01 3 0.0000 0.951 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.8163.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8010.01 2 0.0000 0.996 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7011.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7605.01 3 0.0000 0.951 0.00 0.00 1.00 0.00 0.00
#> TCGA.DB.5270.01 4 0.2280 0.910 0.00 0.12 0.00 0.88 0.00
#> TCGA.S9.A6WQ.01 4 0.3561 0.768 0.00 0.26 0.00 0.74 0.00
#> TCGA.S9.A7QY.01 2 0.0000 0.996 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7880.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7Z3.01 4 0.1732 0.935 0.00 0.08 0.00 0.92 0.00
#> TCGA.RY.A843.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6X5.01 2 0.0000 0.996 0.00 1.00 0.00 0.00 0.00
#> TCGA.DH.A7UT.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7856.01 3 0.0000 0.951 0.00 0.00 1.00 0.00 0.00
#> TCGA.TM.A84O.01 2 0.0000 0.996 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.A61A.01 2 0.0609 0.979 0.00 0.98 0.00 0.02 0.00
#> TCGA.HT.A5R5.01 4 0.1732 0.935 0.00 0.08 0.00 0.92 0.00
#> TCGA.HT.7467.01 3 0.0000 0.951 0.00 0.00 1.00 0.00 0.00
#> TCGA.FG.A60L.01 4 0.1732 0.935 0.00 0.08 0.00 0.92 0.00
#> TCGA.DB.5278.01 1 0.0609 0.979 0.98 0.00 0.02 0.00 0.00
#> TCGA.HT.7881.01 3 0.0000 0.951 0.00 0.00 1.00 0.00 0.00
#> TCGA.VM.A8CE.01 3 0.0000 0.951 0.00 0.00 1.00 0.00 0.00
#> TCGA.CS.4944.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A6S2.01 2 0.0000 0.996 0.00 1.00 0.00 0.00 0.00
#> TCGA.TM.A84R.01 3 0.0000 0.951 0.00 0.00 1.00 0.00 0.00
#> TCGA.FG.8187.01 3 0.0000 0.951 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.A7TG.01 3 0.0000 0.951 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7610.01 4 0.1410 0.913 0.00 0.06 0.00 0.94 0.00
#> TCGA.S9.A6TW.01 5 0.2929 0.838 0.00 0.00 0.18 0.00 0.82
#> TCGA.HT.7481.01 3 0.0000 0.951 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.A5TR.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IQ.01 2 0.0609 0.979 0.00 0.98 0.00 0.02 0.00
#> TCGA.S9.A6WG.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CY.01 5 0.4126 0.694 0.00 0.00 0.38 0.00 0.62
#> TCGA.P5.A72X.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WI.01 2 0.0000 0.996 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.5849.01 5 0.2616 0.796 0.00 0.00 0.10 0.02 0.88
#> TCGA.HW.7489.01 1 0.0609 0.979 0.98 0.00 0.02 0.00 0.00
#> TCGA.FG.A713.01 2 0.0000 0.996 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7300.01 2 0.0000 0.996 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7694.01 5 0.3109 0.843 0.00 0.00 0.20 0.00 0.80
#> TCGA.DB.A64V.01 5 0.3274 0.841 0.00 0.00 0.22 0.00 0.78
#> TCGA.E1.5302.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A615.01 2 0.0000 0.996 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7309.01 4 0.1732 0.935 0.00 0.08 0.00 0.92 0.00
#> TCGA.HT.7874.01 2 0.0000 0.996 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YY.01 4 0.4060 0.601 0.00 0.36 0.00 0.64 0.00
#> TCGA.FG.5964.01 5 0.4126 0.683 0.00 0.00 0.38 0.00 0.62
#> TCGA.DH.A7UR.01 2 0.0000 0.996 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7479.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7602.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7858.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6290.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84S.01 3 0.0000 0.951 0.00 0.00 1.00 0.00 0.00
#> TCGA.DB.5276.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84L.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5273.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A7C4.01 4 0.1732 0.935 0.00 0.08 0.00 0.92 0.00
#> TCGA.HT.7607.01 2 0.0000 0.996 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A736.01 4 0.1732 0.935 0.00 0.08 0.00 0.92 0.00
#> TCGA.P5.A781.01 2 0.0000 0.996 0.00 1.00 0.00 0.00 0.00
#> TCGA.TM.A7CF.02 4 0.2020 0.925 0.00 0.10 0.00 0.90 0.00
#> TCGA.S9.A6U2.01 2 0.0000 0.996 0.00 1.00 0.00 0.00 0.00
#> TCGA.DH.A7US.01 5 0.3684 0.807 0.00 0.00 0.28 0.00 0.72
#> TCGA.HT.7478.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7603.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A70Y.01 4 0.1732 0.935 0.00 0.08 0.00 0.92 0.00
#> TCGA.TQ.A7RV.02 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7474.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.WY.A85A.01 1 0.0000 0.998 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.E1.5319.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4XA.01 3 0.4576 -0.0798 0.00 0.00 0.56 0.00 0.40 0.04
#> TCGA.HT.A4DV.01 2 0.1807 0.9470 0.00 0.92 0.00 0.06 0.00 0.02
#> TCGA.HT.8113.01 2 0.1807 0.9470 0.00 0.92 0.00 0.06 0.00 0.02
#> TCGA.HT.7620.01 3 0.0000 0.9051 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.8109.01 6 0.2941 0.0000 0.00 0.00 0.00 0.00 0.22 0.78
#> TCGA.HT.7877.01 2 0.1807 0.9470 0.00 0.92 0.00 0.06 0.00 0.02
#> TCGA.QH.A6CU.01 2 0.1807 0.9470 0.00 0.92 0.00 0.06 0.00 0.02
#> TCGA.HW.7486.01 3 0.0000 0.9051 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.8163.01 1 0.0000 0.9959 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8010.01 2 0.1807 0.9470 0.00 0.92 0.00 0.06 0.00 0.02
#> TCGA.DU.7011.01 1 0.0000 0.9959 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7605.01 3 0.0000 0.9051 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.5270.01 4 0.0547 0.9183 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.S9.A6WQ.01 4 0.2793 0.6863 0.00 0.20 0.00 0.80 0.00 0.00
#> TCGA.S9.A7QY.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7880.01 1 0.0000 0.9959 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7Z3.01 4 0.0000 0.9298 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.RY.A843.01 1 0.0000 0.9959 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6X5.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A7UT.01 1 0.0000 0.9959 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7856.01 3 0.0000 0.9051 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.TM.A84O.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A61A.01 2 0.1807 0.9470 0.00 0.92 0.00 0.06 0.00 0.02
#> TCGA.HT.A5R5.01 4 0.0000 0.9298 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7467.01 3 0.0000 0.9051 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.A60L.01 4 0.0000 0.9298 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DB.5278.01 1 0.0937 0.9521 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.HT.7881.01 3 0.0000 0.9051 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VM.A8CE.01 3 0.0000 0.9051 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CS.4944.01 1 0.0000 0.9959 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A6S2.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84R.01 3 0.0000 0.9051 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.8187.01 3 0.0000 0.9051 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.A7TG.01 3 0.0000 0.9051 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7610.01 4 0.0547 0.9202 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.S9.A6TW.01 5 0.3746 0.5795 0.00 0.00 0.08 0.00 0.78 0.14
#> TCGA.HT.7481.01 3 0.0000 0.9051 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.A5TR.01 1 0.0000 0.9959 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IQ.01 2 0.1807 0.9470 0.00 0.92 0.00 0.06 0.00 0.02
#> TCGA.S9.A6WG.01 1 0.0000 0.9959 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CY.01 3 0.3869 -0.3334 0.00 0.00 0.50 0.00 0.50 0.00
#> TCGA.P5.A72X.01 1 0.0000 0.9959 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WI.01 2 0.1807 0.9470 0.00 0.92 0.00 0.06 0.00 0.02
#> TCGA.DU.5849.01 5 0.1556 0.3852 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.HW.7489.01 1 0.0937 0.9526 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.FG.A713.01 2 0.0547 0.9551 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.DU.7300.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7694.01 5 0.2581 0.6708 0.00 0.00 0.12 0.00 0.86 0.02
#> TCGA.DB.A64V.01 5 0.2260 0.6821 0.00 0.00 0.14 0.00 0.86 0.00
#> TCGA.E1.5302.01 1 0.0000 0.9959 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A615.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7309.01 4 0.0000 0.9298 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7874.01 2 0.1807 0.9470 0.00 0.92 0.00 0.06 0.00 0.02
#> TCGA.E1.A7YY.01 4 0.3460 0.6294 0.00 0.22 0.00 0.76 0.00 0.02
#> TCGA.FG.5964.01 5 0.3828 0.3978 0.00 0.00 0.44 0.00 0.56 0.00
#> TCGA.DH.A7UR.01 2 0.0937 0.9302 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.HT.7479.01 1 0.0000 0.9959 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7602.01 1 0.0000 0.9959 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7858.01 1 0.0000 0.9959 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6290.01 1 0.0000 0.9959 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84S.01 3 0.0000 0.9051 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.5276.01 1 0.0000 0.9959 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84L.01 1 0.0000 0.9959 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5273.01 1 0.0000 0.9959 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A7C4.01 4 0.0000 0.9298 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7607.01 2 0.0547 0.9539 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.P5.A736.01 4 0.0000 0.9298 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.P5.A781.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A7CF.02 4 0.0547 0.9183 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.S9.A6U2.01 2 0.0000 0.9550 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A7US.01 5 0.3916 0.6101 0.00 0.00 0.30 0.00 0.68 0.02
#> TCGA.HT.7478.01 1 0.0000 0.9959 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7603.01 1 0.0000 0.9959 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A70Y.01 4 0.0000 0.9298 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.TQ.A7RV.02 1 0.0000 0.9959 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7474.01 1 0.0000 0.9959 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WY.A85A.01 1 0.0000 0.9959 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.E1.5319.01 2 0.1166 0.862 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.DB.A4XA.01 3 0.5536 0.171 0.00 0.00 0.54 0.00 0.22 0.02 0.22
#> TCGA.HT.A4DV.01 2 0.2259 0.876 0.00 0.84 0.00 0.00 0.00 0.16 0.00
#> TCGA.HT.8113.01 2 0.2259 0.876 0.00 0.84 0.00 0.00 0.00 0.16 0.00
#> TCGA.HT.7620.01 3 0.0504 0.900 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.HT.8109.01 6 0.5016 0.000 0.00 0.00 0.00 0.00 0.42 0.46 0.12
#> TCGA.HT.7877.01 2 0.1886 0.881 0.00 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.QH.A6CU.01 2 0.2259 0.876 0.00 0.84 0.00 0.00 0.00 0.16 0.00
#> TCGA.HW.7486.01 3 0.0504 0.900 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.DU.8163.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8010.01 2 0.2259 0.876 0.00 0.84 0.00 0.00 0.00 0.16 0.00
#> TCGA.DU.7011.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7605.01 3 0.0000 0.903 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5270.01 4 0.3670 0.670 0.00 0.14 0.00 0.76 0.00 0.10 0.00
#> TCGA.S9.A6WQ.01 4 0.4615 0.471 0.00 0.30 0.00 0.60 0.00 0.10 0.00
#> TCGA.S9.A7QY.01 2 0.1166 0.862 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.HT.7880.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7Z3.01 4 0.0504 0.836 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.RY.A843.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6X5.01 2 0.0863 0.867 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.DH.A7UT.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7856.01 3 0.0504 0.900 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.TM.A84O.01 2 0.1166 0.862 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.HT.A61A.01 2 0.3086 0.844 0.00 0.80 0.00 0.04 0.00 0.16 0.00
#> TCGA.HT.A5R5.01 4 0.1006 0.834 0.00 0.02 0.00 0.96 0.00 0.02 0.00
#> TCGA.HT.7467.01 3 0.0504 0.900 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.FG.A60L.01 4 0.1006 0.834 0.00 0.02 0.00 0.96 0.00 0.02 0.00
#> TCGA.DB.5278.01 1 0.0863 0.946 0.96 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.HT.7881.01 3 0.0000 0.903 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8CE.01 3 0.0000 0.903 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.4944.01 1 0.1433 0.935 0.92 0.00 0.00 0.00 0.00 0.08 0.00
#> TCGA.DU.A6S2.01 2 0.1166 0.862 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.TM.A84R.01 3 0.0504 0.900 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.FG.8187.01 3 0.0000 0.903 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A7TG.01 3 0.0000 0.903 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7610.01 4 0.1363 0.820 0.00 0.02 0.00 0.94 0.04 0.00 0.00
#> TCGA.S9.A6TW.01 7 0.3691 0.446 0.00 0.00 0.02 0.02 0.04 0.12 0.80
#> TCGA.HT.7481.01 3 0.0000 0.903 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TR.01 1 0.1433 0.935 0.92 0.00 0.00 0.00 0.00 0.08 0.00
#> TCGA.S9.A7IQ.01 2 0.2259 0.876 0.00 0.84 0.00 0.00 0.00 0.16 0.00
#> TCGA.S9.A6WG.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CY.01 3 0.3994 -0.204 0.00 0.00 0.50 0.00 0.02 0.00 0.48
#> TCGA.P5.A72X.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WI.01 2 0.2259 0.876 0.00 0.84 0.00 0.00 0.00 0.16 0.00
#> TCGA.DU.5849.01 7 0.3546 0.060 0.00 0.00 0.00 0.00 0.46 0.00 0.54
#> TCGA.HW.7489.01 1 0.2572 0.876 0.86 0.00 0.06 0.00 0.00 0.08 0.00
#> TCGA.FG.A713.01 2 0.2081 0.879 0.00 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.DU.7300.01 2 0.1166 0.862 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.HT.7694.01 7 0.2572 0.560 0.00 0.00 0.06 0.00 0.08 0.00 0.86
#> TCGA.DB.A64V.01 7 0.2313 0.569 0.00 0.00 0.06 0.00 0.06 0.00 0.88
#> TCGA.E1.5302.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A615.01 2 0.0504 0.870 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DU.7309.01 4 0.0504 0.836 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.HT.7874.01 2 0.2259 0.876 0.00 0.84 0.00 0.00 0.00 0.16 0.00
#> TCGA.E1.A7YY.01 4 0.5232 0.179 0.00 0.38 0.00 0.46 0.00 0.16 0.00
#> TCGA.FG.5964.01 7 0.3909 0.359 0.00 0.00 0.40 0.00 0.00 0.02 0.58
#> TCGA.DH.A7UR.01 2 0.2422 0.755 0.00 0.82 0.00 0.00 0.00 0.18 0.00
#> TCGA.HT.7479.01 1 0.1166 0.948 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.HT.7602.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7858.01 1 0.1433 0.935 0.92 0.00 0.00 0.00 0.00 0.08 0.00
#> TCGA.CS.6290.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84S.01 3 0.0000 0.903 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5276.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84L.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5273.01 1 0.0863 0.958 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.TM.A7C4.01 4 0.0504 0.836 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.HT.7607.01 2 0.2081 0.879 0.00 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.P5.A736.01 4 0.0504 0.836 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.P5.A781.01 2 0.1166 0.862 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.TM.A7CF.02 4 0.1664 0.806 0.00 0.06 0.00 0.92 0.00 0.02 0.00
#> TCGA.S9.A6U2.01 2 0.1166 0.862 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.DH.A7US.01 7 0.3047 0.521 0.00 0.00 0.28 0.00 0.00 0.00 0.72
#> TCGA.HT.7478.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7603.01 1 0.1166 0.948 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.FG.A70Y.01 4 0.0504 0.836 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.TQ.A7RV.02 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7474.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WY.A85A.01 1 0.0000 0.976 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.E1.5319.01 2 0.0000 0.5886 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4XA.01 3 0.6018 -0.0669 0.00 0.00 0.44 0.00 0.20 0.04 0.30 0.02
#> TCGA.HT.A4DV.01 2 0.3272 0.4613 0.00 0.58 0.00 0.00 0.00 0.00 0.00 0.42
#> TCGA.HT.8113.01 2 0.3272 0.4613 0.00 0.58 0.00 0.00 0.00 0.00 0.00 0.42
#> TCGA.HT.7620.01 3 0.1607 0.8451 0.00 0.00 0.92 0.00 0.00 0.00 0.04 0.04
#> TCGA.HT.8109.01 6 0.1947 0.0000 0.00 0.00 0.00 0.00 0.00 0.86 0.14 0.00
#> TCGA.HT.7877.01 2 0.3193 0.4943 0.00 0.62 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.QH.A6CU.01 2 0.3690 0.4224 0.00 0.56 0.00 0.02 0.00 0.00 0.00 0.42
#> TCGA.HW.7486.01 3 0.1557 0.8499 0.00 0.00 0.92 0.00 0.00 0.00 0.06 0.02
#> TCGA.DU.8163.01 1 0.0000 0.9708 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8010.01 2 0.3690 0.4224 0.00 0.56 0.00 0.02 0.00 0.00 0.00 0.42
#> TCGA.DU.7011.01 1 0.0000 0.9708 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7605.01 3 0.1408 0.8542 0.00 0.00 0.94 0.00 0.02 0.00 0.02 0.02
#> TCGA.DB.5270.01 4 0.3095 0.4346 0.00 0.02 0.00 0.74 0.00 0.00 0.00 0.24
#> TCGA.S9.A6WQ.01 4 0.4396 -0.1627 0.00 0.14 0.00 0.62 0.00 0.00 0.00 0.24
#> TCGA.S9.A7QY.01 2 0.0000 0.5886 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7880.01 1 0.0000 0.9708 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7Z3.01 4 0.0000 0.8827 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RY.A843.01 1 0.0000 0.9708 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6X5.01 2 0.1091 0.5874 0.00 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.DH.A7UT.01 1 0.0000 0.9708 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7856.01 3 0.1275 0.8543 0.00 0.00 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.TM.A84O.01 2 0.0000 0.5886 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A61A.01 2 0.4391 0.1770 0.00 0.50 0.00 0.08 0.00 0.00 0.00 0.42
#> TCGA.HT.A5R5.01 4 0.0000 0.8827 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7467.01 3 0.1275 0.8543 0.00 0.00 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.FG.A60L.01 4 0.0000 0.8827 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5278.01 1 0.1275 0.9281 0.94 0.00 0.04 0.00 0.02 0.00 0.00 0.00
#> TCGA.HT.7881.01 3 0.0471 0.8594 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.VM.A8CE.01 3 0.1741 0.8430 0.00 0.00 0.92 0.00 0.04 0.00 0.02 0.02
#> TCGA.CS.4944.01 1 0.2132 0.9019 0.88 0.00 0.00 0.00 0.04 0.00 0.00 0.08
#> TCGA.DU.A6S2.01 2 0.0000 0.5886 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84R.01 3 0.0808 0.8577 0.00 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.FG.8187.01 3 0.1408 0.8542 0.00 0.00 0.94 0.00 0.02 0.00 0.02 0.02
#> TCGA.DU.A7TG.01 3 0.0808 0.8577 0.00 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.HT.7610.01 4 0.2071 0.8150 0.00 0.00 0.00 0.90 0.04 0.04 0.00 0.02
#> TCGA.S9.A6TW.01 7 0.5819 0.1799 0.00 0.00 0.02 0.00 0.12 0.08 0.54 0.24
#> TCGA.HT.7481.01 3 0.0471 0.8618 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DU.A5TR.01 1 0.2132 0.9019 0.88 0.00 0.00 0.00 0.04 0.00 0.00 0.08
#> TCGA.S9.A7IQ.01 2 0.3690 0.4224 0.00 0.56 0.00 0.02 0.00 0.00 0.00 0.42
#> TCGA.S9.A6WG.01 1 0.0000 0.9708 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CY.01 3 0.3299 0.0706 0.00 0.00 0.56 0.00 0.00 0.00 0.44 0.00
#> TCGA.P5.A72X.01 1 0.0000 0.9708 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WI.01 2 0.3690 0.4224 0.00 0.56 0.00 0.02 0.00 0.00 0.00 0.42
#> TCGA.DU.5849.01 5 0.3729 0.0000 0.00 0.00 0.00 0.00 0.52 0.02 0.46 0.00
#> TCGA.HW.7489.01 1 0.2674 0.8777 0.86 0.00 0.04 0.00 0.04 0.00 0.00 0.06
#> TCGA.FG.A713.01 2 0.3015 0.5176 0.00 0.68 0.00 0.00 0.00 0.00 0.00 0.32
#> TCGA.DU.7300.01 2 0.0000 0.5886 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7694.01 7 0.1275 0.3237 0.00 0.00 0.04 0.00 0.00 0.02 0.94 0.00
#> TCGA.DB.A64V.01 7 0.1887 0.3479 0.00 0.00 0.06 0.00 0.04 0.00 0.90 0.00
#> TCGA.E1.5302.01 1 0.0000 0.9708 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A615.01 2 0.1947 0.5728 0.00 0.86 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.DU.7309.01 4 0.0000 0.8827 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7874.01 2 0.3272 0.4613 0.00 0.58 0.00 0.00 0.00 0.00 0.00 0.42
#> TCGA.E1.A7YY.01 8 0.5163 0.0000 0.00 0.24 0.00 0.34 0.00 0.00 0.00 0.42
#> TCGA.FG.5964.01 7 0.4655 0.3890 0.00 0.00 0.34 0.00 0.02 0.02 0.58 0.04
#> TCGA.DH.A7UR.01 2 0.3934 0.2345 0.00 0.70 0.00 0.00 0.14 0.00 0.00 0.16
#> TCGA.HT.7479.01 1 0.0941 0.9548 0.96 0.00 0.00 0.00 0.02 0.00 0.00 0.02
#> TCGA.HT.7602.01 1 0.0000 0.9708 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7858.01 1 0.2132 0.9019 0.88 0.00 0.00 0.00 0.04 0.00 0.00 0.08
#> TCGA.CS.6290.01 1 0.0000 0.9708 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84S.01 3 0.1408 0.8542 0.00 0.00 0.94 0.00 0.02 0.00 0.02 0.02
#> TCGA.DB.5276.01 1 0.0000 0.9708 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84L.01 1 0.0471 0.9632 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DB.5273.01 1 0.1275 0.9421 0.94 0.00 0.00 0.00 0.04 0.00 0.00 0.02
#> TCGA.TM.A7C4.01 4 0.0000 0.8827 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7607.01 2 0.3193 0.4948 0.00 0.62 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.P5.A736.01 4 0.0000 0.8827 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A781.01 2 0.0000 0.5886 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A7CF.02 4 0.1091 0.8281 0.00 0.00 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.S9.A6U2.01 2 0.0000 0.5886 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A7US.01 7 0.3868 0.4540 0.00 0.00 0.22 0.00 0.02 0.02 0.72 0.02
#> TCGA.HT.7478.01 1 0.0000 0.9708 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7603.01 1 0.0941 0.9548 0.96 0.00 0.00 0.00 0.02 0.00 0.00 0.02
#> TCGA.FG.A70Y.01 4 0.0000 0.8827 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RV.02 1 0.0000 0.9708 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7474.01 1 0.0000 0.9708 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WY.A85A.01 1 0.0000 0.9708 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: Node03. Child nodes: Node0111 , Node0112 , Node0113 , Node0121 , Node0122 , Node0123-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0134-leaf , Node0141 , Node0142-leaf , Node0143 , Node0211-leaf , Node0212-leaf , Node0213-leaf , Node0214-leaf , Node0221 , Node0222 , Node0223 , Node0231 , Node0232-leaf , Node0233-leaf , Node0311-leaf , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0321-leaf , Node0322-leaf , Node0323-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["032"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 27 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 8.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.5019 0.499 0.499
#> 3 3 1.000 1.000 1.000 0.2211 0.889 0.777
#> 4 4 1.000 0.963 1.000 0.0557 0.966 0.912
#> 5 5 0.917 0.914 0.959 0.1048 0.923 0.782
#> 6 6 0.853 0.789 0.927 0.0486 0.977 0.918
#> 7 7 0.887 0.735 0.913 0.0313 0.949 0.800
#> 8 8 0.917 0.769 0.955 0.0234 0.972 0.875
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 8
#> attr(,"optional")
#> [1] 2 3 5
There is also optional best \(k\) = 2 3 5 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.HT.7689.01 2 0 1 0 1
#> TCGA.HT.8106.01 1 0 1 1 0
#> TCGA.HT.7601.01 2 0 1 0 1
#> TCGA.26.1442.01 1 0 1 1 0
#> TCGA.P5.A5EX.01 2 0 1 0 1
#> TCGA.HT.8563.01 2 0 1 0 1
#> TCGA.HT.8018.01 2 0 1 0 1
#> TCGA.DU.5851.01 2 0 1 0 1
#> TCGA.DU.A7T6.01 2 0 1 0 1
#> TCGA.HT.A618.01 2 0 1 0 1
#> TCGA.TQ.A7RR.01 1 0 1 1 0
#> TCGA.15.1444.01 1 0 1 1 0
#> TCGA.S9.A7R7.01 1 0 1 1 0
#> TCGA.TM.A84F.01 1 0 1 1 0
#> TCGA.HT.7688.01 1 0 1 1 0
#> TCGA.HT.7902.01 2 0 1 0 1
#> TCGA.P5.A780.01 2 0 1 0 1
#> TCGA.E1.A7YK.01 1 0 1 1 0
#> TCGA.HT.8111.01 1 0 1 1 0
#> TCGA.HT.7686.01 2 0 1 0 1
#> TCGA.FG.A711.01 2 0 1 0 1
#> TCGA.HT.7470.01 1 0 1 1 0
#> TCGA.S9.A6WN.01 2 0 1 0 1
#> TCGA.DU.6396.01 2 0 1 0 1
#> TCGA.HT.A5R7.01 2 0 1 0 1
#> TCGA.P5.A5EZ.01 1 0 1 1 0
#> TCGA.WY.A858.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.HT.7689.01 2 0 1 0 1 0
#> TCGA.HT.8106.01 1 0 1 1 0 0
#> TCGA.HT.7601.01 2 0 1 0 1 0
#> TCGA.26.1442.01 1 0 1 1 0 0
#> TCGA.P5.A5EX.01 3 0 1 0 0 1
#> TCGA.HT.8563.01 2 0 1 0 1 0
#> TCGA.HT.8018.01 2 0 1 0 1 0
#> TCGA.DU.5851.01 2 0 1 0 1 0
#> TCGA.DU.A7T6.01 3 0 1 0 0 1
#> TCGA.HT.A618.01 2 0 1 0 1 0
#> TCGA.TQ.A7RR.01 1 0 1 1 0 0
#> TCGA.15.1444.01 1 0 1 1 0 0
#> TCGA.S9.A7R7.01 1 0 1 1 0 0
#> TCGA.TM.A84F.01 1 0 1 1 0 0
#> TCGA.HT.7688.01 1 0 1 1 0 0
#> TCGA.HT.7902.01 2 0 1 0 1 0
#> TCGA.P5.A780.01 2 0 1 0 1 0
#> TCGA.E1.A7YK.01 1 0 1 1 0 0
#> TCGA.HT.8111.01 1 0 1 1 0 0
#> TCGA.HT.7686.01 2 0 1 0 1 0
#> TCGA.FG.A711.01 2 0 1 0 1 0
#> TCGA.HT.7470.01 1 0 1 1 0 0
#> TCGA.S9.A6WN.01 3 0 1 0 0 1
#> TCGA.DU.6396.01 2 0 1 0 1 0
#> TCGA.HT.A5R7.01 2 0 1 0 1 0
#> TCGA.P5.A5EZ.01 1 0 1 1 0 0
#> TCGA.WY.A858.01 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.HT.7689.01 2 0 1 0 1 0 0
#> TCGA.HT.8106.01 1 0 1 1 0 0 0
#> TCGA.HT.7601.01 2 0 1 0 1 0 0
#> TCGA.26.1442.01 1 0 1 1 0 0 0
#> TCGA.P5.A5EX.01 3 0 1 0 0 1 0
#> TCGA.HT.8563.01 2 0 1 0 1 0 0
#> TCGA.HT.8018.01 2 0 1 0 1 0 0
#> TCGA.DU.5851.01 2 0 1 0 1 0 0
#> TCGA.DU.A7T6.01 3 0 1 0 0 1 0
#> TCGA.HT.A618.01 2 0 1 0 1 0 0
#> TCGA.TQ.A7RR.01 1 0 1 1 0 0 0
#> TCGA.15.1444.01 1 0 1 1 0 0 0
#> TCGA.S9.A7R7.01 1 0 1 1 0 0 0
#> TCGA.TM.A84F.01 1 0 1 1 0 0 0
#> TCGA.HT.7688.01 1 0 1 1 0 0 0
#> TCGA.HT.7902.01 2 0 1 0 1 0 0
#> TCGA.P5.A780.01 2 0 1 0 1 0 0
#> TCGA.E1.A7YK.01 1 0 1 1 0 0 0
#> TCGA.HT.8111.01 1 0 1 1 0 0 0
#> TCGA.HT.7686.01 2 0 1 0 1 0 0
#> TCGA.FG.A711.01 2 0 1 0 1 0 0
#> TCGA.HT.7470.01 1 0 1 1 0 0 0
#> TCGA.S9.A6WN.01 3 0 1 0 0 1 0
#> TCGA.DU.6396.01 4 0 0 0 0 0 1
#> TCGA.HT.A5R7.01 2 0 1 0 1 0 0
#> TCGA.P5.A5EZ.01 1 0 1 1 0 0 0
#> TCGA.WY.A858.01 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.HT.7689.01 2 0.2732 0.792 0.00 0.84 0 0 0.16
#> TCGA.HT.8106.01 1 0.0609 0.983 0.98 0.00 0 0 0.02
#> TCGA.HT.7601.01 5 0.3983 0.775 0.00 0.34 0 0 0.66
#> TCGA.26.1442.01 1 0.0000 0.996 1.00 0.00 0 0 0.00
#> TCGA.P5.A5EX.01 3 0.0000 1.000 0.00 0.00 1 0 0.00
#> TCGA.HT.8563.01 2 0.0000 0.946 0.00 1.00 0 0 0.00
#> TCGA.HT.8018.01 2 0.0000 0.946 0.00 1.00 0 0 0.00
#> TCGA.DU.5851.01 2 0.0000 0.946 0.00 1.00 0 0 0.00
#> TCGA.DU.A7T6.01 3 0.0000 1.000 0.00 0.00 1 0 0.00
#> TCGA.HT.A618.01 2 0.0000 0.946 0.00 1.00 0 0 0.00
#> TCGA.TQ.A7RR.01 1 0.0000 0.996 1.00 0.00 0 0 0.00
#> TCGA.15.1444.01 1 0.0000 0.996 1.00 0.00 0 0 0.00
#> TCGA.S9.A7R7.01 1 0.0000 0.996 1.00 0.00 0 0 0.00
#> TCGA.TM.A84F.01 1 0.0609 0.983 0.98 0.00 0 0 0.02
#> TCGA.HT.7688.01 1 0.0000 0.996 1.00 0.00 0 0 0.00
#> TCGA.HT.7902.01 2 0.0000 0.946 0.00 1.00 0 0 0.00
#> TCGA.P5.A780.01 5 0.3109 0.867 0.00 0.20 0 0 0.80
#> TCGA.E1.A7YK.01 1 0.0000 0.996 1.00 0.00 0 0 0.00
#> TCGA.HT.8111.01 1 0.0000 0.996 1.00 0.00 0 0 0.00
#> TCGA.HT.7686.01 2 0.1410 0.891 0.00 0.94 0 0 0.06
#> TCGA.FG.A711.01 2 0.1732 0.883 0.00 0.92 0 0 0.08
#> TCGA.HT.7470.01 1 0.0000 0.996 1.00 0.00 0 0 0.00
#> TCGA.S9.A6WN.01 3 0.0000 1.000 0.00 0.00 1 0 0.00
#> TCGA.DU.6396.01 4 0.0000 0.000 0.00 0.00 0 1 0.00
#> TCGA.HT.A5R7.01 2 0.0609 0.933 0.00 0.98 0 0 0.02
#> TCGA.P5.A5EZ.01 1 0.0000 0.996 1.00 0.00 0 0 0.00
#> TCGA.WY.A858.01 5 0.3109 0.867 0.00 0.20 0 0 0.80
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.HT.7689.01 6 0.3756 0.000 0.00 0.40 0 0 0.00 0.60
#> TCGA.HT.8106.01 1 0.3679 0.741 0.76 0.00 0 0 0.04 0.20
#> TCGA.HT.7601.01 5 0.4246 0.343 0.00 0.40 0 0 0.58 0.02
#> TCGA.26.1442.01 1 0.0000 0.937 1.00 0.00 0 0 0.00 0.00
#> TCGA.P5.A5EX.01 3 0.0000 1.000 0.00 0.00 1 0 0.00 0.00
#> TCGA.HT.8563.01 2 0.0000 0.924 0.00 1.00 0 0 0.00 0.00
#> TCGA.HT.8018.01 2 0.0000 0.924 0.00 1.00 0 0 0.00 0.00
#> TCGA.DU.5851.01 2 0.0547 0.907 0.00 0.98 0 0 0.00 0.02
#> TCGA.DU.A7T6.01 3 0.0000 1.000 0.00 0.00 1 0 0.00 0.00
#> TCGA.HT.A618.01 2 0.0000 0.924 0.00 1.00 0 0 0.00 0.00
#> TCGA.TQ.A7RR.01 1 0.0000 0.937 1.00 0.00 0 0 0.00 0.00
#> TCGA.15.1444.01 1 0.0000 0.937 1.00 0.00 0 0 0.00 0.00
#> TCGA.S9.A7R7.01 1 0.0547 0.929 0.98 0.00 0 0 0.00 0.02
#> TCGA.TM.A84F.01 1 0.4420 0.559 0.62 0.00 0 0 0.04 0.34
#> TCGA.HT.7688.01 1 0.0000 0.937 1.00 0.00 0 0 0.00 0.00
#> TCGA.HT.7902.01 2 0.0000 0.924 0.00 1.00 0 0 0.00 0.00
#> TCGA.P5.A780.01 5 0.2094 0.681 0.00 0.08 0 0 0.90 0.02
#> TCGA.E1.A7YK.01 1 0.0547 0.929 0.98 0.00 0 0 0.00 0.02
#> TCGA.HT.8111.01 1 0.0000 0.937 1.00 0.00 0 0 0.00 0.00
#> TCGA.HT.7686.01 2 0.2094 0.784 0.00 0.90 0 0 0.08 0.02
#> TCGA.FG.A711.01 2 0.2981 0.582 0.00 0.82 0 0 0.02 0.16
#> TCGA.HT.7470.01 1 0.0000 0.937 1.00 0.00 0 0 0.00 0.00
#> TCGA.S9.A6WN.01 3 0.0000 1.000 0.00 0.00 1 0 0.00 0.00
#> TCGA.DU.6396.01 4 0.0000 0.000 0.00 0.00 0 1 0.00 0.00
#> TCGA.HT.A5R7.01 2 0.0000 0.924 0.00 1.00 0 0 0.00 0.00
#> TCGA.P5.A5EZ.01 1 0.0000 0.937 1.00 0.00 0 0 0.00 0.00
#> TCGA.WY.A858.01 5 0.1807 0.658 0.00 0.06 0 0 0.92 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.HT.7689.01 6 0.4978 0.1740 0.00 0.12 0 0 0.00 0.50 0.38
#> TCGA.HT.8106.01 1 0.2945 0.0714 0.74 0.00 0 0 0.00 0.00 0.26
#> TCGA.HT.7601.01 5 0.4710 0.0320 0.00 0.46 0 0 0.46 0.08 0.00
#> TCGA.26.1442.01 1 0.0000 0.9439 1.00 0.00 0 0 0.00 0.00 0.00
#> TCGA.P5.A5EX.01 3 0.0000 1.0000 0.00 0.00 1 0 0.00 0.00 0.00
#> TCGA.HT.8563.01 2 0.0000 0.9770 0.00 1.00 0 0 0.00 0.00 0.00
#> TCGA.HT.8018.01 2 0.0000 0.9770 0.00 1.00 0 0 0.00 0.00 0.00
#> TCGA.DU.5851.01 2 0.0863 0.9365 0.00 0.96 0 0 0.00 0.04 0.00
#> TCGA.DU.A7T6.01 3 0.0000 1.0000 0.00 0.00 1 0 0.00 0.00 0.00
#> TCGA.HT.A618.01 2 0.0000 0.9770 0.00 1.00 0 0 0.00 0.00 0.00
#> TCGA.TQ.A7RR.01 1 0.0000 0.9439 1.00 0.00 0 0 0.00 0.00 0.00
#> TCGA.15.1444.01 1 0.0000 0.9439 1.00 0.00 0 0 0.00 0.00 0.00
#> TCGA.S9.A7R7.01 1 0.0000 0.9439 1.00 0.00 0 0 0.00 0.00 0.00
#> TCGA.TM.A84F.01 7 0.3546 0.0000 0.46 0.00 0 0 0.00 0.00 0.54
#> TCGA.HT.7688.01 1 0.0000 0.9439 1.00 0.00 0 0 0.00 0.00 0.00
#> TCGA.HT.7902.01 2 0.0000 0.9770 0.00 1.00 0 0 0.00 0.00 0.00
#> TCGA.P5.A780.01 5 0.1166 0.5267 0.00 0.00 0 0 0.94 0.00 0.06
#> TCGA.E1.A7YK.01 1 0.0000 0.9439 1.00 0.00 0 0 0.00 0.00 0.00
#> TCGA.HT.8111.01 1 0.0000 0.9439 1.00 0.00 0 0 0.00 0.00 0.00
#> TCGA.HT.7686.01 2 0.1166 0.9128 0.00 0.94 0 0 0.00 0.06 0.00
#> TCGA.FG.A711.01 6 0.3755 0.2880 0.00 0.34 0 0 0.02 0.64 0.00
#> TCGA.HT.7470.01 1 0.0000 0.9439 1.00 0.00 0 0 0.00 0.00 0.00
#> TCGA.S9.A6WN.01 3 0.0000 1.0000 0.00 0.00 1 0 0.00 0.00 0.00
#> TCGA.DU.6396.01 4 0.0000 0.0000 0.00 0.00 0 1 0.00 0.00 0.00
#> TCGA.HT.A5R7.01 2 0.0000 0.9770 0.00 1.00 0 0 0.00 0.00 0.00
#> TCGA.P5.A5EZ.01 1 0.0000 0.9439 1.00 0.00 0 0 0.00 0.00 0.00
#> TCGA.WY.A858.01 5 0.0504 0.5230 0.00 0.00 0 0 0.98 0.00 0.02
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.HT.7689.01 6 0.0941 0.000 0.00 0.02 0.00 0 0.00 0.96 0.00 0.02
#> TCGA.HT.8106.01 1 0.2852 0.565 0.72 0.00 0.00 0 0.00 0.00 0.28 0.00
#> TCGA.HT.7601.01 2 0.4397 0.531 0.00 0.66 0.00 0 0.24 0.00 0.06 0.04
#> TCGA.26.1442.01 1 0.0000 0.954 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.P5.A5EX.01 3 0.0000 0.983 0.00 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.HT.8563.01 2 0.0941 0.915 0.00 0.96 0.00 0 0.00 0.02 0.00 0.02
#> TCGA.HT.8018.01 2 0.0000 0.930 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.DU.5851.01 2 0.0000 0.930 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.DU.A7T6.01 3 0.0941 0.965 0.00 0.00 0.96 0 0.00 0.00 0.02 0.02
#> TCGA.HT.A618.01 2 0.0000 0.930 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RR.01 1 0.0000 0.954 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.15.1444.01 1 0.0000 0.954 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.S9.A7R7.01 1 0.1091 0.907 0.94 0.00 0.00 0 0.00 0.00 0.06 0.00
#> TCGA.TM.A84F.01 7 0.1765 0.000 0.12 0.00 0.00 0 0.00 0.00 0.88 0.00
#> TCGA.HT.7688.01 1 0.0000 0.954 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.HT.7902.01 2 0.0941 0.915 0.00 0.96 0.00 0 0.00 0.02 0.00 0.02
#> TCGA.P5.A780.01 5 0.2674 0.870 0.00 0.00 0.00 0 0.86 0.04 0.06 0.04
#> TCGA.E1.A7YK.01 1 0.0471 0.941 0.98 0.00 0.00 0 0.00 0.00 0.02 0.00
#> TCGA.HT.8111.01 1 0.0000 0.954 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.HT.7686.01 2 0.0941 0.910 0.00 0.96 0.00 0 0.00 0.00 0.02 0.02
#> TCGA.FG.A711.01 8 0.1275 0.000 0.00 0.04 0.00 0 0.02 0.00 0.00 0.94
#> TCGA.HT.7470.01 1 0.0000 0.954 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WN.01 3 0.0000 0.983 0.00 0.00 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.DU.6396.01 4 0.0000 0.000 0.00 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.HT.A5R7.01 2 0.0000 0.930 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.P5.A5EZ.01 1 0.0000 0.954 1.00 0.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.WY.A858.01 5 0.0000 0.872 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.
sessionInfo()
#> R version 4.1.0 (2021-05-18)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: CentOS Linux 7 (Core)
#>
#> Matrix products: default
#> BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
#> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
#> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] grid stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] genefilter_1.74.0 ComplexHeatmap_2.8.0 markdown_1.1 knitr_1.33
#> [5] matrixStats_0.59.0 cola_1.9.4
#>
#> loaded via a namespace (and not attached):
#> [1] bitops_1.0-7 bit64_4.0.5 doParallel_1.0.16 RColorBrewer_1.1-2
#> [5] httr_1.4.2 GenomeInfoDb_1.28.1 data.tree_1.0.0 tools_4.1.0
#> [9] utf8_1.2.1 R6_2.5.0 irlba_2.3.3 DBI_1.1.1
#> [13] BiocGenerics_0.38.0 colorspace_2.0-2 GetoptLong_1.0.5 gridExtra_2.3
#> [17] tidyselect_1.1.1 bit_4.0.4 compiler_4.1.0 Biobase_2.52.0
#> [21] Cairo_1.5-12.2 xml2_1.3.2 microbenchmark_1.4-7 slam_0.1-48
#> [25] scales_1.1.1 askpass_1.1 stringr_1.4.0 digest_0.6.27
#> [29] XVector_0.32.0 pkgconfig_2.0.3 umap_0.2.7.0 fastmap_1.1.0
#> [33] highr_0.9 rlang_0.4.11 GlobalOptions_0.1.2 rstudioapi_0.13
#> [37] RSQLite_2.2.7 impute_1.66.0 generics_0.1.0 shape_1.4.6
#> [41] jsonlite_1.7.2 mclust_5.4.7 dplyr_1.0.7 dendextend_1.15.1
#> [45] RCurl_1.98-1.3 magrittr_2.0.1 GenomeInfoDbData_1.2.6 Matrix_1.3-4
#> [49] fansi_0.5.0 Rcpp_1.0.7 munsell_0.5.0 S4Vectors_0.30.0
#> [53] viridis_0.6.1 reticulate_1.20 lifecycle_1.0.0 scatterplot3d_0.3-41
#> [57] stringi_1.7.3 zlibbioc_1.38.0 blob_1.2.1 parallel_4.1.0
#> [61] crayon_1.4.1 lattice_0.20-44 Biostrings_2.60.1 splines_4.1.0
#> [65] annotate_1.70.0 circlize_0.4.13 KEGGREST_1.32.0 polylabelr_0.2.0
#> [69] pillar_1.6.1 rjson_0.2.20 codetools_0.2-18 stats4_4.1.0
#> [73] XML_3.99-0.6 glue_1.4.2 evaluate_0.14 png_0.1-7
#> [77] vctrs_0.3.8 foreach_1.5.1 polyclip_1.10-0 purrr_0.3.4
#> [81] gtable_0.3.0 openssl_1.4.4 assertthat_0.2.1 clue_0.3-59
#> [85] cachem_1.0.5 ggplot2_3.3.5 xfun_0.24 eulerr_6.1.0
#> [89] xtable_1.8-4 skmeans_0.2-13 RSpectra_0.16-0 viridisLite_0.4.0
#> [93] survival_3.2-11 tibble_3.1.2 Polychrome_1.3.1 iterators_1.0.13
#> [97] AnnotationDbi_1.54.1 memoise_2.0.0 IRanges_2.26.0 cluster_2.1.2
#> [101] ellipsis_0.3.2 brew_1.0-6