Date: 2021-07-22 18:22:23 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 375969 rows and 530 columns.
#> Performed in total 68600 partitions.
#> There are 32 groups under the following parameters:
#> - min_samples: 6
#> - mean_silhouette_cutoff: 0.9
#> - min_n_signatures: 1000 (signatures are selected based on:)
#> - fdr_cutoff: 0.05
#> - group_diff: 0.25
#>
#> Hierarchy of the partition:
#> 0, 530 cols
#> |-- 01, 88 cols, 13116 signatures
#> | |-- 011, 32 cols, 675 signatures (c)
#> | |-- 012, 36 cols, 5644 signatures
#> | | |-- 0121, 12 cols, 1614 signatures
#> | | | |-- 01211, 5 cols (b)
#> | | | |-- 01212, 4 cols (b)
#> | | | `-- 01213, 3 cols (b)
#> | | |-- 0122, 13 cols, 593 signatures (c)
#> | | `-- 0123, 11 cols (b)
#> | |-- 013, 11 cols (b)
#> | `-- 014, 9 cols (b)
#> |-- 02, 431 cols, 9726 signatures
#> | |-- 021, 214 cols, 3432 signatures
#> | | |-- 0211, 80 cols, 374 signatures (c)
#> | | |-- 0212, 87 cols, 152 signatures (c)
#> | | `-- 0213, 47 cols, 254 signatures (c)
#> | |-- 022, 180 cols, 3536 signatures
#> | | |-- 0221, 80 cols, 1386 signatures
#> | | | |-- 02211, 46 cols, 10859 signatures
#> | | | | |-- 022111, 28 cols, 653 signatures (c)
#> | | | | |-- 022112, 6 cols (b)
#> | | | | `-- 022113, 12 cols, 0 signatures (c)
#> | | | `-- 02212, 34 cols, 8163 signatures
#> | | | |-- 022121, 19 cols, 2070 signatures
#> | | | | |-- 0221211, 8 cols (b)
#> | | | | |-- 0221212, 8 cols (b)
#> | | | | `-- 0221213, 3 cols (b)
#> | | | |-- 022122, 11 cols (b)
#> | | | `-- 022123, 4 cols (b)
#> | | `-- 0222, 100 cols, 7885 signatures
#> | | |-- 02221, 28 cols, 5170 signatures
#> | | | |-- 022211, 21 cols, 204 signatures (c)
#> | | | `-- 022212, 7 cols (b)
#> | | |-- 02222, 47 cols, 168 signatures (c)
#> | | `-- 02223, 25 cols, 2422 signatures
#> | | |-- 022231, 6 cols (b)
#> | | |-- 022232, 10 cols (b)
#> | | `-- 022233, 9 cols (b)
#> | `-- 023, 37 cols, 3040 signatures
#> | |-- 0231, 14 cols, 1373 signatures
#> | | |-- 02311, 8 cols (b)
#> | | |-- 02312, 4 cols (b)
#> | | `-- 02313, 2 cols (b)
#> | `-- 0232, 23 cols, 3007 signatures
#> | |-- 02321, 9 cols (b)
#> | |-- 02322, 9 cols (b)
#> | `-- 02323, 5 cols (b)
#> `-- 03, 11 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] 375969 530
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" "012" "0121" "01211" "01212" "01213" "0122"
#> [10] "0123" "013" "014" "02" "021" "0211" "0212" "0213" "022"
#> [19] "0221" "02211" "022111" "022112" "022113" "02212" "022121" "0221211" "0221212"
#> [28] "0221213" "022122" "022123" "0222" "02221" "022211" "022212" "02222" "02223"
#> [37] "022231" "022232" "022233" "023" "0231" "02311" "02312" "02313" "0232"
#> [46] "02321" "02322" "02323" "03"
all_leaves(res_rh)
#> [1] "011" "01211" "01212" "01213" "0122" "0123" "013" "014" "0211"
#> [10] "0212" "0213" "022111" "022112" "022113" "0221211" "0221212" "0221213" "022122"
#> [19] "022123" "022211" "022212" "02222" "022231" "022232" "022233" "02311" "02312"
#> [28] "02313" "02321" "02322" "02323" "03"
node_info(res_rh)
#> id best_method depth best_k n_columns n_signatures p_signatures is_leaf
#> 1 0 ATC:skmeans 1 3 530 36057 0.095904 FALSE
#> 2 01 SD:skmeans 2 4 88 13116 0.034886 FALSE
#> 3 011 ATC:skmeans 3 2 32 675 0.001795 TRUE
#> 4 012 ATC:kmeans 3 3 36 5644 0.015012 FALSE
#> 5 0121 ATC:kmeans 4 3 12 1614 0.004293 FALSE
#> 6 01211 not applied 5 NA 5 NA NA TRUE
#> 7 01212 not applied 5 NA 4 NA NA TRUE
#> 8 01213 not applied 5 NA 3 NA NA TRUE
#> 9 0122 ATC:kmeans 4 2 13 593 0.001577 TRUE
#> 10 0123 not applied 4 NA 11 NA NA TRUE
#> 11 013 not applied 3 NA 11 NA NA TRUE
#> 12 014 not applied 3 NA 9 NA NA TRUE
#> 13 02 ATC:skmeans 2 3 431 9726 0.025869 FALSE
#> 14 021 ATC:skmeans 3 3 214 3432 0.009128 FALSE
#> 15 0211 ATC:kmeans 4 2 80 374 0.000995 TRUE
#> 16 0212 SD:skmeans 4 2 87 152 0.000404 TRUE
#> 17 0213 ATC:skmeans 4 2 47 254 0.000676 TRUE
#> 18 022 SD:skmeans 3 2 180 3536 0.009405 FALSE
#> 19 0221 SD:kmeans 4 2 80 1386 0.003686 FALSE
#> 20 02211 ATC:skmeans 5 3 46 10859 0.028883 FALSE
#> 21 022111 ATC:skmeans 6 2 28 653 0.001737 TRUE
#> 22 022112 not applied 6 NA 6 NA NA TRUE
#> 23 022113 ATC:kmeans 6 2 12 0 0.000000 TRUE
#> 24 02212 ATC:kmeans 5 3 34 8163 0.021712 FALSE
#> 25 022121 ATC:kmeans 6 3 19 2070 0.005506 FALSE
#> 26 0221211 not applied 7 NA 8 NA NA TRUE
#> 27 0221212 not applied 7 NA 8 NA NA TRUE
#> 28 0221213 not applied 7 NA 3 NA NA TRUE
#> 29 022122 not applied 6 NA 11 NA NA TRUE
#> 30 022123 not applied 6 NA 4 NA NA TRUE
#> 31 0222 ATC:kmeans 4 3 100 7885 0.020972 FALSE
#> 32 02221 ATC:kmeans 5 2 28 5170 0.013751 FALSE
#> 33 022211 ATC:kmeans 6 2 21 204 0.000543 TRUE
#> 34 022212 not applied 6 NA 7 NA NA TRUE
#> 35 02222 ATC:kmeans 5 2 47 168 0.000447 TRUE
#> 36 02223 ATC:kmeans 5 3 25 2422 0.006442 FALSE
#> 37 022231 not applied 6 NA 6 NA NA TRUE
#> 38 022232 not applied 6 NA 10 NA NA TRUE
#> 39 022233 not applied 6 NA 9 NA NA TRUE
#> 40 023 ATC:kmeans 3 2 37 3040 0.008086 FALSE
#> 41 0231 ATC:skmeans 4 3 14 1373 0.003652 FALSE
#> 42 02311 not applied 5 NA 8 NA NA TRUE
#> 43 02312 not applied 5 NA 4 NA NA TRUE
#> 44 02313 not applied 5 NA 2 NA NA TRUE
#> 45 0232 ATC:kmeans 4 3 23 3007 0.007998 FALSE
#> 46 02321 not applied 5 NA 9 NA NA TRUE
#> 47 02322 not applied 5 NA 9 NA NA TRUE
#> 48 02323 not applied 5 NA 5 NA NA TRUE
#> 49 03 not applied 2 NA 11 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:skmeans | 4 | 0.94 | 0.89 | 0.95 | 530 | * | |
| Node01 | SD:skmeans | 4 | 1.00 | 0.97 | 0.99 | 88 | ** | |
| Node011-leaf | ATC:skmeans | ✓ (c) | 3 | 1.00 | 0.94 | 0.98 | 32 | ** |
| Node012 | ATC:kmeans | 3 | 1.00 | 1.00 | 1.00 | 36 | ** | |
| Node0121 | ATC:kmeans | 4 | 1.00 | 0.90 | 0.99 | 12 | ** | |
| Node01211-leaf | not applied | ✓ (b) | 5 | |||||
| Node01212-leaf | not applied | ✓ (b) | 4 | |||||
| Node01213-leaf | not applied | ✓ (b) | 3 | |||||
| Node0122-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 13 | ** |
| Node0123-leaf | not applied | ✓ (b) | 11 | |||||
| Node013-leaf | not applied | ✓ (b) | 11 | |||||
| Node014-leaf | not applied | ✓ (b) | 9 | |||||
| Node02 | ATC:skmeans | 5 | 0.93 | 0.90 | 0.96 | 431 | * | |
| Node021 | ATC:skmeans | 4 | 0.94 | 0.92 | 0.96 | 214 | * | |
| Node0211-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 0.99 | 1.00 | 80 | ** |
| Node0212-leaf | SD:skmeans | ✓ (c) | 2 | 1.00 | 0.97 | 0.99 | 87 | ** |
| Node0213-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 0.97 | 0.99 | 47 | ** |
| Node022 | SD:skmeans | 3 | 0.94 | 0.93 | 0.95 | 180 | * | |
| Node0221 | SD:kmeans | 2 | 1.00 | 1.00 | 1.00 | 80 | ** | |
| Node02211 | ATC:skmeans | 3 | 1.00 | 0.96 | 0.99 | 46 | ** | |
| Node022111-leaf | ATC:skmeans | ✓ (c) | 3 | 1.00 | 0.96 | 0.96 | 28 | ** |
| Node022112-leaf | not applied | ✓ (b) | 6 | |||||
| Node022113-leaf | ATC:kmeans | ✓ (c) | 4 | 0.88 | 0.88 | 0.98 | 12 | |
| Node02212 | ATC:kmeans | 6 | 0.95 | 0.96 | 0.95 | 34 | * | |
| Node022121 | ATC:kmeans | 7 | 0.91 | 0.68 | 0.78 | 19 | * | |
| Node0221211-leaf | not applied | ✓ (b) | 8 | |||||
| Node0221212-leaf | not applied | ✓ (b) | 8 | |||||
| Node0221213-leaf | not applied | ✓ (b) | 3 | |||||
| Node022122-leaf | not applied | ✓ (b) | 11 | |||||
| Node022123-leaf | not applied | ✓ (b) | 4 | |||||
| Node0222 | ATC:kmeans | 3 | 0.96 | 0.96 | 0.98 | 100 | ** | |
| Node02221 | ATC:kmeans | 8 | 0.93 | 0.70 | 0.88 | 28 | * | |
| Node022211-leaf | ATC:kmeans | ✓ (c) | 2 | 0.82 | 0.98 | 0.99 | 21 | |
| Node022212-leaf | not applied | ✓ (b) | 7 | |||||
| Node02222-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 47 | ** |
| Node02223 | ATC:kmeans | 3 | 1.00 | 1.00 | 1.00 | 25 | ** | |
| Node022231-leaf | not applied | ✓ (b) | 6 | |||||
| Node022232-leaf | not applied | ✓ (b) | 10 | |||||
| Node022233-leaf | not applied | ✓ (b) | 9 | |||||
| Node023 | ATC:kmeans | 2 | 1.00 | 0.99 | 0.99 | 37 | ** | |
| Node0231 | ATC:skmeans | 3 | 1.00 | 1.00 | 1.00 | 14 | ** | |
| Node02311-leaf | not applied | ✓ (b) | 8 | |||||
| Node02312-leaf | not applied | ✓ (b) | 4 | |||||
| Node02313-leaf | not applied | ✓ (b) | 2 | |||||
| Node0232 | ATC:kmeans | 3 | 1.00 | 1.00 | 1.00 | 23 | ** | |
| Node02321-leaf | not applied | ✓ (b) | 9 | |||||
| Node02322-leaf | not applied | ✓ (b) | 9 | |||||
| Node02323-leaf | not applied | ✓ (b) | 5 | |||||
| Node03-leaf | not applied | ✓ (b) | 11 |
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 = 1373))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1386))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1614))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2070))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2422))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3007))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3040))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3432))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3536))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5170))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5644))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7885))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8163))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 9726))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 10859))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 13116))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 36057))
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 = 1373))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "022111" "0212" "02311" "02222" "02311" "011"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.HT.A74L.01 TCGA.DU.A5TS.01 TCGA.DB.A4XA.01 TCGA.HT.A4DV.01
#> "02222" "0212" "022111" "0211" "022232" "022113"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01 TCGA.HT.8113.01
#> "013" "02222" "02312" "0211" "0211" "022113"
#> TCGA.DH.A66G.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01 TCGA.HT.7689.01 TCGA.HT.8109.01
#> "0212" "022231" "0212" "02222" "02321" "02222"
#> TCGA.E1.A7YE.01 TCGA.S9.A7R1.01 TCGA.FG.A710.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01
#> "02311" "02222" "022111" "02322" "022111" "022111"
#> TCGA.QH.A6CU.01 TCGA.HW.7486.01 TCGA.FG.7634.01 TCGA.DU.8163.01 TCGA.DU.6407.02 TCGA.DU.6407.01
#> "022113" "022233" "022232" "0211" "02311" "0212"
#> TCGA.S9.A7IX.01 TCGA.HT.8010.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0122" "022113" "0211" "0212" "0213" "022111"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.DU.7299.01 TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.DU.7011.01
#> "01213" "0211" "0211" "011" "0211" "0213"
#> TCGA.TM.A84Q.01 TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.DB.5270.01
#> "0211" "0211" "0123" "022233" "022111" "0212"
#> TCGA.S9.A6WQ.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.E1.A7YU.01 TCGA.W9.A837.01 TCGA.TM.A7C5.01
#> "0212" "0213" "02222" "02321" "02222" "022211"
#> TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01 TCGA.HT.7601.01 TCGA.P5.A5ET.01
#> "022111" "0211" "0211" "02322" "0212" "02222"
#> TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.HT.7873.01
#> "0213" "0213" "0212" "022112" "022211" "0213"
#> TCGA.CS.4938.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "0212" "02222" "022112" "0211" "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
#> "02321" "0123" "0211" "02312" "0212" "0123"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.DU.6403.01 TCGA.HW.7493.01
#> "014" "02222" "02222" "022113" "011" "0212"
#> TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01 TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01
#> "022232" "0212" "022232" "0211" "02322" "022211"
#> TCGA.DH.A7UT.01 TCGA.DU.7015.01 TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01
#> "0213" "0212" "0212" "013" "0211" "0212"
#> TCGA.FG.A60K.01 TCGA.HT.7856.01 TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01
#> "022111" "022231" "03" "03" "0212" "022112"
#> TCGA.S9.A6TY.01 TCGA.CS.5395.01 TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01
#> "022211" "0123" "0123" "011" "0211" "0213"
#> TCGA.TM.A84O.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.DU.5855.01 TCGA.HT.7884.01
#> "022111" "0213" "0211" "022113" "0212" "0212"
#> TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01 TCGA.WH.A86K.01
#> "022111" "03" "01211" "02222" "022123" "0211"
#> TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01 TCGA.HT.A618.01
#> "014" "022122" "013" "0212" "0212" "02321"
#> TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01
#> "0212" "022231" "0212" "0122" "0211" "022111"
#> TCGA.S9.A7IZ.01 TCGA.DU.A6S7.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "0212" "0212" "022123" "0211" "0221211" "0211"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.P5.A5F4.01 TCGA.QH.A65V.01
#> "02222" "02222" "0122" "022122" "0212" "022111"
#> TCGA.FG.8191.01 TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.CS.6666.01 TCGA.DU.7298.01
#> "0213" "0213" "022112" "0213" "0211" "0221212"
#> TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01 TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01
#> "022111" "011" "03" "0212" "0221211" "022211"
#> TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01 TCGA.DH.A66D.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01
#> "013" "0211" "0213" "0212" "02311" "022233"
#> TCGA.DU.A76K.01 TCGA.TQ.A7RR.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.P5.A735.01
#> "0122" "0213" "011" "0213" "022212" "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
#> "022122" "011" "022231" "013" "022111" "02313"
#> TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.S9.A6U5.01 TCGA.HT.7609.01 TCGA.DB.5274.01
#> "02323" "02222" "022233" "022232" "0211" "0221211"
#> TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01 TCGA.DU.A6S2.01 TCGA.S9.A7R7.01
#> "02222" "022211" "014" "0213" "022111" "0213"
#> TCGA.TM.A84R.01 TCGA.DB.A75M.01 TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.HT.7477.01 TCGA.HT.8012.01
#> "022231" "0211" "03" "0211" "02322" "0221212"
#> TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01 TCGA.S9.A7QZ.01
#> "0212" "0212" "0212" "022232" "0213" "022211"
#> TCGA.QH.A6X4.01 TCGA.P5.A77W.01 TCGA.DU.7302.01 TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.E1.5307.01
#> "02222" "0221212" "022122" "011" "0211" "0212"
#> TCGA.S9.A7QW.01 TCGA.DU.6402.01 TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01
#> "0212" "0122" "0211" "0212" "011" "0213"
#> TCGA.HW.7495.01 TCGA.QH.A65R.01 TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01
#> "022111" "0221213" "022231" "0211" "0211" "0213"
#> TCGA.HT.8104.01 TCGA.FG.A70Z.01 TCGA.DU.A7TC.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01
#> "011" "011" "0211" "0212" "02222" "0212"
#> TCGA.E1.5303.01 TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01
#> "0211" "0123" "022233" "0213" "0213" "0211"
#> TCGA.FG.A4MU.01 TCGA.HT.7875.01 TCGA.HT.7473.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01 TCGA.DU.7008.01
#> "01211" "02222" "0213" "011" "022113" "0212"
#> TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.FG.8189.01 TCGA.DB.A75O.01 TCGA.HT.7688.01
#> "013" "0122" "0213" "03" "0213" "0211"
#> TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01 TCGA.P5.A5EY.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01
#> "02322" "022211" "014" "013" "02222" "0212"
#> TCGA.DU.5872.02 TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01
#> "03" "0211" "0212" "011" "022211" "0122"
#> TCGA.DU.5874.01 TCGA.S9.A6WE.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "0221211" "02222" "0211" "0211" "014" "0122"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "022232" "022233" "02222" "0213" "0212" "02222"
#> TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01 TCGA.DB.A4XF.01
#> "011" "0221212" "0212" "014" "0212" "0212"
#> TCGA.HT.A74O.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01
#> "0211" "0211" "013" "02222" "0123" "0221211"
#> TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.E1.A7YJ.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.S9.A6TS.01
#> "0211" "022122" "01211" "022113" "022211" "02322"
#> TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01
#> "0211" "0212" "0212" "0212" "0123" "02311"
#> TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01 TCGA.DU.5849.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01
#> "014" "01212" "0211" "02222" "0211" "0122"
#> TCGA.HT.7468.01 TCGA.FG.6692.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01 TCGA.HW.7489.01
#> "02222" "01211" "022111" "022212" "0211" "0211"
#> TCGA.R8.A6YH.01 TCGA.DU.7018.01 TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01
#> "0211" "022122" "02222" "022113" "022122" "0211"
#> TCGA.HT.7690.01 TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01
#> "0213" "01213" "0213" "02323" "0212" "011"
#> TCGA.HT.A5RA.01 TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "011" "02322" "022233" "022212" "02222" "02222"
#> TCGA.HT.8013.01 TCGA.HW.7490.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01
#> "0212" "0211" "0212" "02222" "0221212" "0123"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.DB.A64V.01 TCGA.RY.A840.01 TCGA.E1.5302.01
#> "0212" "02322" "01211" "022233" "02222" "0213"
#> TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01 TCGA.DU.5847.01
#> "022211" "022111" "022211" "0212" "011" "011"
#> TCGA.E1.A7YK.01 TCGA.HT.7874.01 TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01
#> "02321" "022113" "0221212" "0122" "011" "0213"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.DU.6408.01 TCGA.DB.A4XB.01
#> "01212" "02323" "0212" "011" "0212" "0213"
#> TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01 TCGA.P5.A72U.01 TCGA.QH.A870.01
#> "03" "0212" "0212" "022211" "011" "0212"
#> TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01
#> "0221213" "011" "011" "022233" "022112" "013"
#> TCGA.DU.A7TA.01 TCGA.HW.8319.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01
#> "0213" "02321" "0221213" "0212" "0212" "0211"
#> TCGA.DU.6400.01 TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "0221211" "022211" "0221212" "0211" "022112" "02222"
#> TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01 TCGA.E1.A7YN.01
#> "0211" "0221211" "0213" "02323" "0211" "011"
#> TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.QH.A6XA.01 TCGA.HT.8111.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01
#> "022212" "0212" "0212" "0213" "011" "0213"
#> TCGA.VM.A8CD.01 TCGA.RY.A83Y.01 TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01
#> "0122" "02222" "0212" "0211" "0211" "0211"
#> TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.DB.A64W.01 TCGA.R8.A6MO.01 TCGA.DU.A7T8.01
#> "0213" "0123" "022111" "022122" "0221212" "0211"
#> TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01 TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01
#> "02222" "022123" "022123" "022111" "0211" "02222"
#> TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01 TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01
#> "0212" "013" "022211" "014" "02321" "022211"
#> TCGA.S9.A6U9.01 TCGA.CS.6290.01 TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01
#> "0211" "0213" "02222" "0211" "0212" "02311"
#> TCGA.HT.7860.01 TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.S9.A7J3.01 TCGA.P5.A5F2.01
#> "011" "0211" "0221211" "0213" "022122" "0212"
#> TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01
#> "02323" "011" "022232" "03" "0211" "022111"
#> TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01 TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.TM.A84L.01
#> "0212" "0211" "022211" "0211" "02222" "0211"
#> TCGA.DU.8161.01 TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01
#> "011" "0211" "022111" "022211" "0122" "0213"
#> TCGA.TM.A7C4.01 TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.HT.8108.01 TCGA.E1.A7YD.01
#> "0212" "02222" "022113" "022211" "0212" "01212"
#> TCGA.DU.7304.01 TCGA.S9.A7IY.01 TCGA.FG.7641.01 TCGA.P5.A736.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01
#> "0211" "022232" "02222" "0212" "0211" "0211"
#> TCGA.HT.7470.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.FG.A4MY.01 TCGA.TM.A7CF.01
#> "02321" "022111" "022111" "03" "0212" "0212"
#> TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01 TCGA.DU.7010.01
#> "0212" "022111" "0211" "013" "0212" "02311"
#> TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.DU.A7TD.01 TCGA.DU.6405.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "022111" "022113" "01212" "011" "0213" "0211"
#> TCGA.DU.6401.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01 TCGA.HT.A74H.01
#> "0212" "02321" "0212" "0211" "0213" "0123"
#> TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01 TCGA.DB.A64L.01
#> "022232" "02312" "0213" "011" "0212" "022122"
#> TCGA.VV.A829.01 TCGA.HT.A61B.01 TCGA.DH.A66B.01 TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01
#> "022212" "0213" "0211" "0211" "02222" "02222"
#> TCGA.HT.A4DS.01 TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01
#> "011" "0213" "02222" "0211" "022111" "01213"
#> TCGA.DB.A64P.01 TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01
#> "02222" "02312" "0212" "0211" "0213" "0212"
#> TCGA.HW.A5KL.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.QH.A6CZ.01 TCGA.DH.A669.02
#> "0212" "011" "0213" "02322" "02222" "022212"
#> TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01 TCGA.TQ.A7RJ.01 TCGA.WY.A858.01
#> "022212" "0212" "0211" "0212" "0212" "0212"
#> TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01
#> "03" "02222" "0211" "022211" "022122" "0212"
#> TCGA.TM.A84I.01 TCGA.CS.5394.01 TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01
#> "02313" "022211" "0122" "0211" "0212" "014"
#> TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0213" "02222"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1386))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "022111" "0212" "0231" "02222" "0231" "011"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.HT.A74L.01 TCGA.DU.A5TS.01 TCGA.DB.A4XA.01 TCGA.HT.A4DV.01
#> "02222" "0212" "022111" "0211" "022232" "022113"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01 TCGA.HT.8113.01
#> "013" "02222" "0231" "0211" "0211" "022113"
#> TCGA.DH.A66G.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01 TCGA.HT.7689.01 TCGA.HT.8109.01
#> "0212" "022231" "0212" "02222" "02321" "02222"
#> TCGA.E1.A7YE.01 TCGA.S9.A7R1.01 TCGA.FG.A710.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01
#> "0231" "02222" "022111" "02322" "022111" "022111"
#> TCGA.QH.A6CU.01 TCGA.HW.7486.01 TCGA.FG.7634.01 TCGA.DU.8163.01 TCGA.DU.6407.02 TCGA.DU.6407.01
#> "022113" "022233" "022232" "0211" "0231" "0212"
#> TCGA.S9.A7IX.01 TCGA.HT.8010.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0122" "022113" "0211" "0212" "0213" "022111"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.DU.7299.01 TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.DU.7011.01
#> "01213" "0211" "0211" "011" "0211" "0213"
#> TCGA.TM.A84Q.01 TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.DB.5270.01
#> "0211" "0211" "0123" "022233" "022111" "0212"
#> TCGA.S9.A6WQ.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.E1.A7YU.01 TCGA.W9.A837.01 TCGA.TM.A7C5.01
#> "0212" "0213" "02222" "02321" "02222" "022211"
#> TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01 TCGA.HT.7601.01 TCGA.P5.A5ET.01
#> "022111" "0211" "0211" "02322" "0212" "02222"
#> TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.HT.7873.01
#> "0213" "0213" "0212" "022112" "022211" "0213"
#> TCGA.CS.4938.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "0212" "02222" "022112" "0211" "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
#> "02321" "0123" "0211" "0231" "0212" "0123"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.DU.6403.01 TCGA.HW.7493.01
#> "014" "02222" "02222" "022113" "011" "0212"
#> TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01 TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01
#> "022232" "0212" "022232" "0211" "02322" "022211"
#> TCGA.DH.A7UT.01 TCGA.DU.7015.01 TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01
#> "0213" "0212" "0212" "013" "0211" "0212"
#> TCGA.FG.A60K.01 TCGA.HT.7856.01 TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01
#> "022111" "022231" "03" "03" "0212" "022112"
#> TCGA.S9.A6TY.01 TCGA.CS.5395.01 TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01
#> "022211" "0123" "0123" "011" "0211" "0213"
#> TCGA.TM.A84O.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.DU.5855.01 TCGA.HT.7884.01
#> "022111" "0213" "0211" "022113" "0212" "0212"
#> TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01 TCGA.WH.A86K.01
#> "022111" "03" "01211" "02222" "022123" "0211"
#> TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01 TCGA.HT.A618.01
#> "014" "022122" "013" "0212" "0212" "02321"
#> TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01
#> "0212" "022231" "0212" "0122" "0211" "022111"
#> TCGA.S9.A7IZ.01 TCGA.DU.A6S7.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "0212" "0212" "022123" "0211" "0221211" "0211"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.P5.A5F4.01 TCGA.QH.A65V.01
#> "02222" "02222" "0122" "022122" "0212" "022111"
#> TCGA.FG.8191.01 TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.CS.6666.01 TCGA.DU.7298.01
#> "0213" "0213" "022112" "0213" "0211" "0221212"
#> TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01 TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01
#> "022111" "011" "03" "0212" "0221211" "022211"
#> TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01 TCGA.DH.A66D.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01
#> "013" "0211" "0213" "0212" "0231" "022233"
#> TCGA.DU.A76K.01 TCGA.TQ.A7RR.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.P5.A735.01
#> "0122" "0213" "011" "0213" "022212" "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
#> "022122" "011" "022231" "013" "022111" "0231"
#> TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.S9.A6U5.01 TCGA.HT.7609.01 TCGA.DB.5274.01
#> "02323" "02222" "022233" "022232" "0211" "0221211"
#> TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01 TCGA.DU.A6S2.01 TCGA.S9.A7R7.01
#> "02222" "022211" "014" "0213" "022111" "0213"
#> TCGA.TM.A84R.01 TCGA.DB.A75M.01 TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.HT.7477.01 TCGA.HT.8012.01
#> "022231" "0211" "03" "0211" "02322" "0221212"
#> TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01 TCGA.S9.A7QZ.01
#> "0212" "0212" "0212" "022232" "0213" "022211"
#> TCGA.QH.A6X4.01 TCGA.P5.A77W.01 TCGA.DU.7302.01 TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.E1.5307.01
#> "02222" "0221212" "022122" "011" "0211" "0212"
#> TCGA.S9.A7QW.01 TCGA.DU.6402.01 TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01
#> "0212" "0122" "0211" "0212" "011" "0213"
#> TCGA.HW.7495.01 TCGA.QH.A65R.01 TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01
#> "022111" "0221213" "022231" "0211" "0211" "0213"
#> TCGA.HT.8104.01 TCGA.FG.A70Z.01 TCGA.DU.A7TC.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01
#> "011" "011" "0211" "0212" "02222" "0212"
#> TCGA.E1.5303.01 TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01
#> "0211" "0123" "022233" "0213" "0213" "0211"
#> TCGA.FG.A4MU.01 TCGA.HT.7875.01 TCGA.HT.7473.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01 TCGA.DU.7008.01
#> "01211" "02222" "0213" "011" "022113" "0212"
#> TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.FG.8189.01 TCGA.DB.A75O.01 TCGA.HT.7688.01
#> "013" "0122" "0213" "03" "0213" "0211"
#> TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01 TCGA.P5.A5EY.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01
#> "02322" "022211" "014" "013" "02222" "0212"
#> TCGA.DU.5872.02 TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01
#> "03" "0211" "0212" "011" "022211" "0122"
#> TCGA.DU.5874.01 TCGA.S9.A6WE.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "0221211" "02222" "0211" "0211" "014" "0122"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "022232" "022233" "02222" "0213" "0212" "02222"
#> TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01 TCGA.DB.A4XF.01
#> "011" "0221212" "0212" "014" "0212" "0212"
#> TCGA.HT.A74O.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01
#> "0211" "0211" "013" "02222" "0123" "0221211"
#> TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.E1.A7YJ.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.S9.A6TS.01
#> "0211" "022122" "01211" "022113" "022211" "02322"
#> TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01
#> "0211" "0212" "0212" "0212" "0123" "0231"
#> TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01 TCGA.DU.5849.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01
#> "014" "01212" "0211" "02222" "0211" "0122"
#> TCGA.HT.7468.01 TCGA.FG.6692.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01 TCGA.HW.7489.01
#> "02222" "01211" "022111" "022212" "0211" "0211"
#> TCGA.R8.A6YH.01 TCGA.DU.7018.01 TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01
#> "0211" "022122" "02222" "022113" "022122" "0211"
#> TCGA.HT.7690.01 TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01
#> "0213" "01213" "0213" "02323" "0212" "011"
#> TCGA.HT.A5RA.01 TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "011" "02322" "022233" "022212" "02222" "02222"
#> TCGA.HT.8013.01 TCGA.HW.7490.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01
#> "0212" "0211" "0212" "02222" "0221212" "0123"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.DB.A64V.01 TCGA.RY.A840.01 TCGA.E1.5302.01
#> "0212" "02322" "01211" "022233" "02222" "0213"
#> TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01 TCGA.DU.5847.01
#> "022211" "022111" "022211" "0212" "011" "011"
#> TCGA.E1.A7YK.01 TCGA.HT.7874.01 TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01
#> "02321" "022113" "0221212" "0122" "011" "0213"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.DU.6408.01 TCGA.DB.A4XB.01
#> "01212" "02323" "0212" "011" "0212" "0213"
#> TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01 TCGA.P5.A72U.01 TCGA.QH.A870.01
#> "03" "0212" "0212" "022211" "011" "0212"
#> TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01
#> "0221213" "011" "011" "022233" "022112" "013"
#> TCGA.DU.A7TA.01 TCGA.HW.8319.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01
#> "0213" "02321" "0221213" "0212" "0212" "0211"
#> TCGA.DU.6400.01 TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "0221211" "022211" "0221212" "0211" "022112" "02222"
#> TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01 TCGA.E1.A7YN.01
#> "0211" "0221211" "0213" "02323" "0211" "011"
#> TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.QH.A6XA.01 TCGA.HT.8111.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01
#> "022212" "0212" "0212" "0213" "011" "0213"
#> TCGA.VM.A8CD.01 TCGA.RY.A83Y.01 TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01
#> "0122" "02222" "0212" "0211" "0211" "0211"
#> TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.DB.A64W.01 TCGA.R8.A6MO.01 TCGA.DU.A7T8.01
#> "0213" "0123" "022111" "022122" "0221212" "0211"
#> TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01 TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01
#> "02222" "022123" "022123" "022111" "0211" "02222"
#> TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01 TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01
#> "0212" "013" "022211" "014" "02321" "022211"
#> TCGA.S9.A6U9.01 TCGA.CS.6290.01 TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01
#> "0211" "0213" "02222" "0211" "0212" "0231"
#> TCGA.HT.7860.01 TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.S9.A7J3.01 TCGA.P5.A5F2.01
#> "011" "0211" "0221211" "0213" "022122" "0212"
#> TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01
#> "02323" "011" "022232" "03" "0211" "022111"
#> TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01 TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.TM.A84L.01
#> "0212" "0211" "022211" "0211" "02222" "0211"
#> TCGA.DU.8161.01 TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01
#> "011" "0211" "022111" "022211" "0122" "0213"
#> TCGA.TM.A7C4.01 TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.HT.8108.01 TCGA.E1.A7YD.01
#> "0212" "02222" "022113" "022211" "0212" "01212"
#> TCGA.DU.7304.01 TCGA.S9.A7IY.01 TCGA.FG.7641.01 TCGA.P5.A736.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01
#> "0211" "022232" "02222" "0212" "0211" "0211"
#> TCGA.HT.7470.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.FG.A4MY.01 TCGA.TM.A7CF.01
#> "02321" "022111" "022111" "03" "0212" "0212"
#> TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01 TCGA.DU.7010.01
#> "0212" "022111" "0211" "013" "0212" "0231"
#> TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.DU.A7TD.01 TCGA.DU.6405.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "022111" "022113" "01212" "011" "0213" "0211"
#> TCGA.DU.6401.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01 TCGA.HT.A74H.01
#> "0212" "02321" "0212" "0211" "0213" "0123"
#> TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01 TCGA.DB.A64L.01
#> "022232" "0231" "0213" "011" "0212" "022122"
#> TCGA.VV.A829.01 TCGA.HT.A61B.01 TCGA.DH.A66B.01 TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01
#> "022212" "0213" "0211" "0211" "02222" "02222"
#> TCGA.HT.A4DS.01 TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01
#> "011" "0213" "02222" "0211" "022111" "01213"
#> TCGA.DB.A64P.01 TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01
#> "02222" "0231" "0212" "0211" "0213" "0212"
#> TCGA.HW.A5KL.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.QH.A6CZ.01 TCGA.DH.A669.02
#> "0212" "011" "0213" "02322" "02222" "022212"
#> TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01 TCGA.TQ.A7RJ.01 TCGA.WY.A858.01
#> "022212" "0212" "0211" "0212" "0212" "0212"
#> TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01
#> "03" "02222" "0211" "022211" "022122" "0212"
#> TCGA.TM.A84I.01 TCGA.CS.5394.01 TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01
#> "0231" "022211" "0122" "0211" "0212" "014"
#> TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0213" "02222"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1614))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "0221" "0212" "0231" "02222" "0231" "011"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.HT.A74L.01 TCGA.DU.A5TS.01 TCGA.DB.A4XA.01 TCGA.HT.A4DV.01
#> "02222" "0212" "0221" "0211" "022232" "0221"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01 TCGA.HT.8113.01
#> "013" "02222" "0231" "0211" "0211" "0221"
#> TCGA.DH.A66G.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01 TCGA.HT.7689.01 TCGA.HT.8109.01
#> "0212" "022231" "0212" "02222" "02321" "02222"
#> TCGA.E1.A7YE.01 TCGA.S9.A7R1.01 TCGA.FG.A710.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01
#> "0231" "02222" "0221" "02322" "0221" "0221"
#> TCGA.QH.A6CU.01 TCGA.HW.7486.01 TCGA.FG.7634.01 TCGA.DU.8163.01 TCGA.DU.6407.02 TCGA.DU.6407.01
#> "0221" "022233" "022232" "0211" "0231" "0212"
#> TCGA.S9.A7IX.01 TCGA.HT.8010.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0122" "0221" "0211" "0212" "0213" "0221"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.DU.7299.01 TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.DU.7011.01
#> "01213" "0211" "0211" "011" "0211" "0213"
#> TCGA.TM.A84Q.01 TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.DB.5270.01
#> "0211" "0211" "0123" "022233" "0221" "0212"
#> TCGA.S9.A6WQ.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.E1.A7YU.01 TCGA.W9.A837.01 TCGA.TM.A7C5.01
#> "0212" "0213" "02222" "02321" "02222" "022211"
#> TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01 TCGA.HT.7601.01 TCGA.P5.A5ET.01
#> "0221" "0211" "0211" "02322" "0212" "02222"
#> TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.HT.7873.01
#> "0213" "0213" "0212" "0221" "022211" "0213"
#> TCGA.CS.4938.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "0212" "02222" "0221" "0211" "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
#> "02321" "0123" "0211" "0231" "0212" "0123"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.DU.6403.01 TCGA.HW.7493.01
#> "014" "02222" "02222" "0221" "011" "0212"
#> TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01 TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01
#> "022232" "0212" "022232" "0211" "02322" "022211"
#> TCGA.DH.A7UT.01 TCGA.DU.7015.01 TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01
#> "0213" "0212" "0212" "013" "0211" "0212"
#> TCGA.FG.A60K.01 TCGA.HT.7856.01 TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01
#> "0221" "022231" "03" "03" "0212" "0221"
#> TCGA.S9.A6TY.01 TCGA.CS.5395.01 TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01
#> "022211" "0123" "0123" "011" "0211" "0213"
#> TCGA.TM.A84O.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.DU.5855.01 TCGA.HT.7884.01
#> "0221" "0213" "0211" "0221" "0212" "0212"
#> TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01 TCGA.WH.A86K.01
#> "0221" "03" "01211" "02222" "0221" "0211"
#> TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01 TCGA.HT.A618.01
#> "014" "0221" "013" "0212" "0212" "02321"
#> TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01
#> "0212" "022231" "0212" "0122" "0211" "0221"
#> TCGA.S9.A7IZ.01 TCGA.DU.A6S7.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "0212" "0212" "0221" "0211" "0221211" "0211"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.P5.A5F4.01 TCGA.QH.A65V.01
#> "02222" "02222" "0122" "0221" "0212" "0221"
#> TCGA.FG.8191.01 TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.CS.6666.01 TCGA.DU.7298.01
#> "0213" "0213" "0221" "0213" "0211" "0221212"
#> TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01 TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01
#> "0221" "011" "03" "0212" "0221211" "022211"
#> TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01 TCGA.DH.A66D.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01
#> "013" "0211" "0213" "0212" "0231" "022233"
#> TCGA.DU.A76K.01 TCGA.TQ.A7RR.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.P5.A735.01
#> "0122" "0213" "011" "0213" "022212" "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
#> "0221" "011" "022231" "013" "0221" "0231"
#> TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.S9.A6U5.01 TCGA.HT.7609.01 TCGA.DB.5274.01
#> "02323" "02222" "022233" "022232" "0211" "0221211"
#> TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01 TCGA.DU.A6S2.01 TCGA.S9.A7R7.01
#> "02222" "022211" "014" "0213" "0221" "0213"
#> TCGA.TM.A84R.01 TCGA.DB.A75M.01 TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.HT.7477.01 TCGA.HT.8012.01
#> "022231" "0211" "03" "0211" "02322" "0221212"
#> TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01 TCGA.S9.A7QZ.01
#> "0212" "0212" "0212" "022232" "0213" "022211"
#> TCGA.QH.A6X4.01 TCGA.P5.A77W.01 TCGA.DU.7302.01 TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.E1.5307.01
#> "02222" "0221212" "0221" "011" "0211" "0212"
#> TCGA.S9.A7QW.01 TCGA.DU.6402.01 TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01
#> "0212" "0122" "0211" "0212" "011" "0213"
#> TCGA.HW.7495.01 TCGA.QH.A65R.01 TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01
#> "0221" "0221213" "022231" "0211" "0211" "0213"
#> TCGA.HT.8104.01 TCGA.FG.A70Z.01 TCGA.DU.A7TC.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01
#> "011" "011" "0211" "0212" "02222" "0212"
#> TCGA.E1.5303.01 TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01
#> "0211" "0123" "022233" "0213" "0213" "0211"
#> TCGA.FG.A4MU.01 TCGA.HT.7875.01 TCGA.HT.7473.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01 TCGA.DU.7008.01
#> "01211" "02222" "0213" "011" "0221" "0212"
#> TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.FG.8189.01 TCGA.DB.A75O.01 TCGA.HT.7688.01
#> "013" "0122" "0213" "03" "0213" "0211"
#> TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01 TCGA.P5.A5EY.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01
#> "02322" "022211" "014" "013" "02222" "0212"
#> TCGA.DU.5872.02 TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01
#> "03" "0211" "0212" "011" "022211" "0122"
#> TCGA.DU.5874.01 TCGA.S9.A6WE.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "0221211" "02222" "0211" "0211" "014" "0122"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "022232" "022233" "02222" "0213" "0212" "02222"
#> TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01 TCGA.DB.A4XF.01
#> "011" "0221212" "0212" "014" "0212" "0212"
#> TCGA.HT.A74O.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01
#> "0211" "0211" "013" "02222" "0123" "0221211"
#> TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.E1.A7YJ.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.S9.A6TS.01
#> "0211" "0221" "01211" "0221" "022211" "02322"
#> TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01
#> "0211" "0212" "0212" "0212" "0123" "0231"
#> TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01 TCGA.DU.5849.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01
#> "014" "01212" "0211" "02222" "0211" "0122"
#> TCGA.HT.7468.01 TCGA.FG.6692.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01 TCGA.HW.7489.01
#> "02222" "01211" "0221" "022212" "0211" "0211"
#> TCGA.R8.A6YH.01 TCGA.DU.7018.01 TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01
#> "0211" "0221" "02222" "0221" "0221" "0211"
#> TCGA.HT.7690.01 TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01
#> "0213" "01213" "0213" "02323" "0212" "011"
#> TCGA.HT.A5RA.01 TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "011" "02322" "022233" "022212" "02222" "02222"
#> TCGA.HT.8013.01 TCGA.HW.7490.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01
#> "0212" "0211" "0212" "02222" "0221212" "0123"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.DB.A64V.01 TCGA.RY.A840.01 TCGA.E1.5302.01
#> "0212" "02322" "01211" "022233" "02222" "0213"
#> TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01 TCGA.DU.5847.01
#> "022211" "0221" "022211" "0212" "011" "011"
#> TCGA.E1.A7YK.01 TCGA.HT.7874.01 TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01
#> "02321" "0221" "0221212" "0122" "011" "0213"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.DU.6408.01 TCGA.DB.A4XB.01
#> "01212" "02323" "0212" "011" "0212" "0213"
#> TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01 TCGA.P5.A72U.01 TCGA.QH.A870.01
#> "03" "0212" "0212" "022211" "011" "0212"
#> TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01
#> "0221213" "011" "011" "022233" "0221" "013"
#> TCGA.DU.A7TA.01 TCGA.HW.8319.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01
#> "0213" "02321" "0221213" "0212" "0212" "0211"
#> TCGA.DU.6400.01 TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "0221211" "022211" "0221212" "0211" "0221" "02222"
#> TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01 TCGA.E1.A7YN.01
#> "0211" "0221211" "0213" "02323" "0211" "011"
#> TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.QH.A6XA.01 TCGA.HT.8111.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01
#> "022212" "0212" "0212" "0213" "011" "0213"
#> TCGA.VM.A8CD.01 TCGA.RY.A83Y.01 TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01
#> "0122" "02222" "0212" "0211" "0211" "0211"
#> TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.DB.A64W.01 TCGA.R8.A6MO.01 TCGA.DU.A7T8.01
#> "0213" "0123" "0221" "0221" "0221212" "0211"
#> TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01 TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01
#> "02222" "0221" "0221" "0221" "0211" "02222"
#> TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01 TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01
#> "0212" "013" "022211" "014" "02321" "022211"
#> TCGA.S9.A6U9.01 TCGA.CS.6290.01 TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01
#> "0211" "0213" "02222" "0211" "0212" "0231"
#> TCGA.HT.7860.01 TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.S9.A7J3.01 TCGA.P5.A5F2.01
#> "011" "0211" "0221211" "0213" "0221" "0212"
#> TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01
#> "02323" "011" "022232" "03" "0211" "0221"
#> TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01 TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.TM.A84L.01
#> "0212" "0211" "022211" "0211" "02222" "0211"
#> TCGA.DU.8161.01 TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01
#> "011" "0211" "0221" "022211" "0122" "0213"
#> TCGA.TM.A7C4.01 TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.HT.8108.01 TCGA.E1.A7YD.01
#> "0212" "02222" "0221" "022211" "0212" "01212"
#> TCGA.DU.7304.01 TCGA.S9.A7IY.01 TCGA.FG.7641.01 TCGA.P5.A736.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01
#> "0211" "022232" "02222" "0212" "0211" "0211"
#> TCGA.HT.7470.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.FG.A4MY.01 TCGA.TM.A7CF.01
#> "02321" "0221" "0221" "03" "0212" "0212"
#> TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01 TCGA.DU.7010.01
#> "0212" "0221" "0211" "013" "0212" "0231"
#> TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.DU.A7TD.01 TCGA.DU.6405.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "0221" "0221" "01212" "011" "0213" "0211"
#> TCGA.DU.6401.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01 TCGA.HT.A74H.01
#> "0212" "02321" "0212" "0211" "0213" "0123"
#> TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01 TCGA.DB.A64L.01
#> "022232" "0231" "0213" "011" "0212" "0221"
#> TCGA.VV.A829.01 TCGA.HT.A61B.01 TCGA.DH.A66B.01 TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01
#> "022212" "0213" "0211" "0211" "02222" "02222"
#> TCGA.HT.A4DS.01 TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01
#> "011" "0213" "02222" "0211" "0221" "01213"
#> TCGA.DB.A64P.01 TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01
#> "02222" "0231" "0212" "0211" "0213" "0212"
#> TCGA.HW.A5KL.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.QH.A6CZ.01 TCGA.DH.A669.02
#> "0212" "011" "0213" "02322" "02222" "022212"
#> TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01 TCGA.TQ.A7RJ.01 TCGA.WY.A858.01
#> "022212" "0212" "0211" "0212" "0212" "0212"
#> TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01
#> "03" "02222" "0211" "022211" "0221" "0212"
#> TCGA.TM.A84I.01 TCGA.CS.5394.01 TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01
#> "0231" "022211" "0122" "0211" "0212" "014"
#> TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0213" "02222"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2070))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "0221" "0212" "0231" "02222" "0231" "011"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.HT.A74L.01 TCGA.DU.A5TS.01 TCGA.DB.A4XA.01 TCGA.HT.A4DV.01
#> "02222" "0212" "0221" "0211" "022232" "0221"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01 TCGA.HT.8113.01
#> "013" "02222" "0231" "0211" "0211" "0221"
#> TCGA.DH.A66G.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01 TCGA.HT.7689.01 TCGA.HT.8109.01
#> "0212" "022231" "0212" "02222" "02321" "02222"
#> TCGA.E1.A7YE.01 TCGA.S9.A7R1.01 TCGA.FG.A710.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01
#> "0231" "02222" "0221" "02322" "0221" "0221"
#> TCGA.QH.A6CU.01 TCGA.HW.7486.01 TCGA.FG.7634.01 TCGA.DU.8163.01 TCGA.DU.6407.02 TCGA.DU.6407.01
#> "0221" "022233" "022232" "0211" "0231" "0212"
#> TCGA.S9.A7IX.01 TCGA.HT.8010.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0122" "0221" "0211" "0212" "0213" "0221"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.DU.7299.01 TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.DU.7011.01
#> "0121" "0211" "0211" "011" "0211" "0213"
#> TCGA.TM.A84Q.01 TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.DB.5270.01
#> "0211" "0211" "0123" "022233" "0221" "0212"
#> TCGA.S9.A6WQ.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.E1.A7YU.01 TCGA.W9.A837.01 TCGA.TM.A7C5.01
#> "0212" "0213" "02222" "02321" "02222" "022211"
#> TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01 TCGA.HT.7601.01 TCGA.P5.A5ET.01
#> "0221" "0211" "0211" "02322" "0212" "02222"
#> TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.HT.7873.01
#> "0213" "0213" "0212" "0221" "022211" "0213"
#> TCGA.CS.4938.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "0212" "02222" "0221" "0211" "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
#> "02321" "0123" "0211" "0231" "0212" "0123"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.DU.6403.01 TCGA.HW.7493.01
#> "014" "02222" "02222" "0221" "011" "0212"
#> TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01 TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01
#> "022232" "0212" "022232" "0211" "02322" "022211"
#> TCGA.DH.A7UT.01 TCGA.DU.7015.01 TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01
#> "0213" "0212" "0212" "013" "0211" "0212"
#> TCGA.FG.A60K.01 TCGA.HT.7856.01 TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01
#> "0221" "022231" "03" "03" "0212" "0221"
#> TCGA.S9.A6TY.01 TCGA.CS.5395.01 TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01
#> "022211" "0123" "0123" "011" "0211" "0213"
#> TCGA.TM.A84O.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.DU.5855.01 TCGA.HT.7884.01
#> "0221" "0213" "0211" "0221" "0212" "0212"
#> TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01 TCGA.WH.A86K.01
#> "0221" "03" "0121" "02222" "0221" "0211"
#> TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01 TCGA.HT.A618.01
#> "014" "0221" "013" "0212" "0212" "02321"
#> TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01
#> "0212" "022231" "0212" "0122" "0211" "0221"
#> TCGA.S9.A7IZ.01 TCGA.DU.A6S7.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "0212" "0212" "0221" "0211" "0221211" "0211"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.P5.A5F4.01 TCGA.QH.A65V.01
#> "02222" "02222" "0122" "0221" "0212" "0221"
#> TCGA.FG.8191.01 TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.CS.6666.01 TCGA.DU.7298.01
#> "0213" "0213" "0221" "0213" "0211" "0221212"
#> TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01 TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01
#> "0221" "011" "03" "0212" "0221211" "022211"
#> TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01 TCGA.DH.A66D.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01
#> "013" "0211" "0213" "0212" "0231" "022233"
#> TCGA.DU.A76K.01 TCGA.TQ.A7RR.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.P5.A735.01
#> "0122" "0213" "011" "0213" "022212" "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
#> "0221" "011" "022231" "013" "0221" "0231"
#> TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.S9.A6U5.01 TCGA.HT.7609.01 TCGA.DB.5274.01
#> "02323" "02222" "022233" "022232" "0211" "0221211"
#> TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01 TCGA.DU.A6S2.01 TCGA.S9.A7R7.01
#> "02222" "022211" "014" "0213" "0221" "0213"
#> TCGA.TM.A84R.01 TCGA.DB.A75M.01 TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.HT.7477.01 TCGA.HT.8012.01
#> "022231" "0211" "03" "0211" "02322" "0221212"
#> TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01 TCGA.S9.A7QZ.01
#> "0212" "0212" "0212" "022232" "0213" "022211"
#> TCGA.QH.A6X4.01 TCGA.P5.A77W.01 TCGA.DU.7302.01 TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.E1.5307.01
#> "02222" "0221212" "0221" "011" "0211" "0212"
#> TCGA.S9.A7QW.01 TCGA.DU.6402.01 TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01
#> "0212" "0122" "0211" "0212" "011" "0213"
#> TCGA.HW.7495.01 TCGA.QH.A65R.01 TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01
#> "0221" "0221213" "022231" "0211" "0211" "0213"
#> TCGA.HT.8104.01 TCGA.FG.A70Z.01 TCGA.DU.A7TC.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01
#> "011" "011" "0211" "0212" "02222" "0212"
#> TCGA.E1.5303.01 TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01
#> "0211" "0123" "022233" "0213" "0213" "0211"
#> TCGA.FG.A4MU.01 TCGA.HT.7875.01 TCGA.HT.7473.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01 TCGA.DU.7008.01
#> "0121" "02222" "0213" "011" "0221" "0212"
#> TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.FG.8189.01 TCGA.DB.A75O.01 TCGA.HT.7688.01
#> "013" "0122" "0213" "03" "0213" "0211"
#> TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01 TCGA.P5.A5EY.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01
#> "02322" "022211" "014" "013" "02222" "0212"
#> TCGA.DU.5872.02 TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01
#> "03" "0211" "0212" "011" "022211" "0122"
#> TCGA.DU.5874.01 TCGA.S9.A6WE.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "0221211" "02222" "0211" "0211" "014" "0122"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "022232" "022233" "02222" "0213" "0212" "02222"
#> TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01 TCGA.DB.A4XF.01
#> "011" "0221212" "0212" "014" "0212" "0212"
#> TCGA.HT.A74O.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01
#> "0211" "0211" "013" "02222" "0123" "0221211"
#> TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.E1.A7YJ.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.S9.A6TS.01
#> "0211" "0221" "0121" "0221" "022211" "02322"
#> TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01
#> "0211" "0212" "0212" "0212" "0123" "0231"
#> TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01 TCGA.DU.5849.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01
#> "014" "0121" "0211" "02222" "0211" "0122"
#> TCGA.HT.7468.01 TCGA.FG.6692.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01 TCGA.HW.7489.01
#> "02222" "0121" "0221" "022212" "0211" "0211"
#> TCGA.R8.A6YH.01 TCGA.DU.7018.01 TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01
#> "0211" "0221" "02222" "0221" "0221" "0211"
#> TCGA.HT.7690.01 TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01
#> "0213" "0121" "0213" "02323" "0212" "011"
#> TCGA.HT.A5RA.01 TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "011" "02322" "022233" "022212" "02222" "02222"
#> TCGA.HT.8013.01 TCGA.HW.7490.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01
#> "0212" "0211" "0212" "02222" "0221212" "0123"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.DB.A64V.01 TCGA.RY.A840.01 TCGA.E1.5302.01
#> "0212" "02322" "0121" "022233" "02222" "0213"
#> TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01 TCGA.DU.5847.01
#> "022211" "0221" "022211" "0212" "011" "011"
#> TCGA.E1.A7YK.01 TCGA.HT.7874.01 TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01
#> "02321" "0221" "0221212" "0122" "011" "0213"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.DU.6408.01 TCGA.DB.A4XB.01
#> "0121" "02323" "0212" "011" "0212" "0213"
#> TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01 TCGA.P5.A72U.01 TCGA.QH.A870.01
#> "03" "0212" "0212" "022211" "011" "0212"
#> TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01
#> "0221213" "011" "011" "022233" "0221" "013"
#> TCGA.DU.A7TA.01 TCGA.HW.8319.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01
#> "0213" "02321" "0221213" "0212" "0212" "0211"
#> TCGA.DU.6400.01 TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "0221211" "022211" "0221212" "0211" "0221" "02222"
#> TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01 TCGA.E1.A7YN.01
#> "0211" "0221211" "0213" "02323" "0211" "011"
#> TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.QH.A6XA.01 TCGA.HT.8111.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01
#> "022212" "0212" "0212" "0213" "011" "0213"
#> TCGA.VM.A8CD.01 TCGA.RY.A83Y.01 TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01
#> "0122" "02222" "0212" "0211" "0211" "0211"
#> TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.DB.A64W.01 TCGA.R8.A6MO.01 TCGA.DU.A7T8.01
#> "0213" "0123" "0221" "0221" "0221212" "0211"
#> TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01 TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01
#> "02222" "0221" "0221" "0221" "0211" "02222"
#> TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01 TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01
#> "0212" "013" "022211" "014" "02321" "022211"
#> TCGA.S9.A6U9.01 TCGA.CS.6290.01 TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01
#> "0211" "0213" "02222" "0211" "0212" "0231"
#> TCGA.HT.7860.01 TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.S9.A7J3.01 TCGA.P5.A5F2.01
#> "011" "0211" "0221211" "0213" "0221" "0212"
#> TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01
#> "02323" "011" "022232" "03" "0211" "0221"
#> TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01 TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.TM.A84L.01
#> "0212" "0211" "022211" "0211" "02222" "0211"
#> TCGA.DU.8161.01 TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01
#> "011" "0211" "0221" "022211" "0122" "0213"
#> TCGA.TM.A7C4.01 TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.HT.8108.01 TCGA.E1.A7YD.01
#> "0212" "02222" "0221" "022211" "0212" "0121"
#> TCGA.DU.7304.01 TCGA.S9.A7IY.01 TCGA.FG.7641.01 TCGA.P5.A736.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01
#> "0211" "022232" "02222" "0212" "0211" "0211"
#> TCGA.HT.7470.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.FG.A4MY.01 TCGA.TM.A7CF.01
#> "02321" "0221" "0221" "03" "0212" "0212"
#> TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01 TCGA.DU.7010.01
#> "0212" "0221" "0211" "013" "0212" "0231"
#> TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.DU.A7TD.01 TCGA.DU.6405.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "0221" "0221" "0121" "011" "0213" "0211"
#> TCGA.DU.6401.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01 TCGA.HT.A74H.01
#> "0212" "02321" "0212" "0211" "0213" "0123"
#> TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01 TCGA.DB.A64L.01
#> "022232" "0231" "0213" "011" "0212" "0221"
#> TCGA.VV.A829.01 TCGA.HT.A61B.01 TCGA.DH.A66B.01 TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01
#> "022212" "0213" "0211" "0211" "02222" "02222"
#> TCGA.HT.A4DS.01 TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01
#> "011" "0213" "02222" "0211" "0221" "0121"
#> TCGA.DB.A64P.01 TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01
#> "02222" "0231" "0212" "0211" "0213" "0212"
#> TCGA.HW.A5KL.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.QH.A6CZ.01 TCGA.DH.A669.02
#> "0212" "011" "0213" "02322" "02222" "022212"
#> TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01 TCGA.TQ.A7RJ.01 TCGA.WY.A858.01
#> "022212" "0212" "0211" "0212" "0212" "0212"
#> TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01
#> "03" "02222" "0211" "022211" "0221" "0212"
#> TCGA.TM.A84I.01 TCGA.CS.5394.01 TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01
#> "0231" "022211" "0122" "0211" "0212" "014"
#> TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0213" "02222"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2422))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "0221" "0212" "0231" "02222" "0231" "011"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.HT.A74L.01 TCGA.DU.A5TS.01 TCGA.DB.A4XA.01 TCGA.HT.A4DV.01
#> "02222" "0212" "0221" "0211" "022232" "0221"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01 TCGA.HT.8113.01
#> "013" "02222" "0231" "0211" "0211" "0221"
#> TCGA.DH.A66G.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01 TCGA.HT.7689.01 TCGA.HT.8109.01
#> "0212" "022231" "0212" "02222" "02321" "02222"
#> TCGA.E1.A7YE.01 TCGA.S9.A7R1.01 TCGA.FG.A710.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01
#> "0231" "02222" "0221" "02322" "0221" "0221"
#> TCGA.QH.A6CU.01 TCGA.HW.7486.01 TCGA.FG.7634.01 TCGA.DU.8163.01 TCGA.DU.6407.02 TCGA.DU.6407.01
#> "0221" "022233" "022232" "0211" "0231" "0212"
#> TCGA.S9.A7IX.01 TCGA.HT.8010.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0122" "0221" "0211" "0212" "0213" "0221"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.DU.7299.01 TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.DU.7011.01
#> "0121" "0211" "0211" "011" "0211" "0213"
#> TCGA.TM.A84Q.01 TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.DB.5270.01
#> "0211" "0211" "0123" "022233" "0221" "0212"
#> TCGA.S9.A6WQ.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.E1.A7YU.01 TCGA.W9.A837.01 TCGA.TM.A7C5.01
#> "0212" "0213" "02222" "02321" "02222" "022211"
#> TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01 TCGA.HT.7601.01 TCGA.P5.A5ET.01
#> "0221" "0211" "0211" "02322" "0212" "02222"
#> TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.HT.7873.01
#> "0213" "0213" "0212" "0221" "022211" "0213"
#> TCGA.CS.4938.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "0212" "02222" "0221" "0211" "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
#> "02321" "0123" "0211" "0231" "0212" "0123"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.DU.6403.01 TCGA.HW.7493.01
#> "014" "02222" "02222" "0221" "011" "0212"
#> TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01 TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01
#> "022232" "0212" "022232" "0211" "02322" "022211"
#> TCGA.DH.A7UT.01 TCGA.DU.7015.01 TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01
#> "0213" "0212" "0212" "013" "0211" "0212"
#> TCGA.FG.A60K.01 TCGA.HT.7856.01 TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01
#> "0221" "022231" "03" "03" "0212" "0221"
#> TCGA.S9.A6TY.01 TCGA.CS.5395.01 TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01
#> "022211" "0123" "0123" "011" "0211" "0213"
#> TCGA.TM.A84O.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.DU.5855.01 TCGA.HT.7884.01
#> "0221" "0213" "0211" "0221" "0212" "0212"
#> TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01 TCGA.WH.A86K.01
#> "0221" "03" "0121" "02222" "0221" "0211"
#> TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01 TCGA.HT.A618.01
#> "014" "0221" "013" "0212" "0212" "02321"
#> TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01
#> "0212" "022231" "0212" "0122" "0211" "0221"
#> TCGA.S9.A7IZ.01 TCGA.DU.A6S7.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "0212" "0212" "0221" "0211" "0221" "0211"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.P5.A5F4.01 TCGA.QH.A65V.01
#> "02222" "02222" "0122" "0221" "0212" "0221"
#> TCGA.FG.8191.01 TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.CS.6666.01 TCGA.DU.7298.01
#> "0213" "0213" "0221" "0213" "0211" "0221"
#> TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01 TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01
#> "0221" "011" "03" "0212" "0221" "022211"
#> TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01 TCGA.DH.A66D.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01
#> "013" "0211" "0213" "0212" "0231" "022233"
#> TCGA.DU.A76K.01 TCGA.TQ.A7RR.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.P5.A735.01
#> "0122" "0213" "011" "0213" "022212" "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
#> "0221" "011" "022231" "013" "0221" "0231"
#> TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.S9.A6U5.01 TCGA.HT.7609.01 TCGA.DB.5274.01
#> "02323" "02222" "022233" "022232" "0211" "0221"
#> TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01 TCGA.DU.A6S2.01 TCGA.S9.A7R7.01
#> "02222" "022211" "014" "0213" "0221" "0213"
#> TCGA.TM.A84R.01 TCGA.DB.A75M.01 TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.HT.7477.01 TCGA.HT.8012.01
#> "022231" "0211" "03" "0211" "02322" "0221"
#> TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01 TCGA.S9.A7QZ.01
#> "0212" "0212" "0212" "022232" "0213" "022211"
#> TCGA.QH.A6X4.01 TCGA.P5.A77W.01 TCGA.DU.7302.01 TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.E1.5307.01
#> "02222" "0221" "0221" "011" "0211" "0212"
#> TCGA.S9.A7QW.01 TCGA.DU.6402.01 TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01
#> "0212" "0122" "0211" "0212" "011" "0213"
#> TCGA.HW.7495.01 TCGA.QH.A65R.01 TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01
#> "0221" "0221" "022231" "0211" "0211" "0213"
#> TCGA.HT.8104.01 TCGA.FG.A70Z.01 TCGA.DU.A7TC.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01
#> "011" "011" "0211" "0212" "02222" "0212"
#> TCGA.E1.5303.01 TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01
#> "0211" "0123" "022233" "0213" "0213" "0211"
#> TCGA.FG.A4MU.01 TCGA.HT.7875.01 TCGA.HT.7473.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01 TCGA.DU.7008.01
#> "0121" "02222" "0213" "011" "0221" "0212"
#> TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.FG.8189.01 TCGA.DB.A75O.01 TCGA.HT.7688.01
#> "013" "0122" "0213" "03" "0213" "0211"
#> TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01 TCGA.P5.A5EY.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01
#> "02322" "022211" "014" "013" "02222" "0212"
#> TCGA.DU.5872.02 TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01
#> "03" "0211" "0212" "011" "022211" "0122"
#> TCGA.DU.5874.01 TCGA.S9.A6WE.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "0221" "02222" "0211" "0211" "014" "0122"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "022232" "022233" "02222" "0213" "0212" "02222"
#> TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01 TCGA.DB.A4XF.01
#> "011" "0221" "0212" "014" "0212" "0212"
#> TCGA.HT.A74O.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01
#> "0211" "0211" "013" "02222" "0123" "0221"
#> TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.E1.A7YJ.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.S9.A6TS.01
#> "0211" "0221" "0121" "0221" "022211" "02322"
#> TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01
#> "0211" "0212" "0212" "0212" "0123" "0231"
#> TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01 TCGA.DU.5849.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01
#> "014" "0121" "0211" "02222" "0211" "0122"
#> TCGA.HT.7468.01 TCGA.FG.6692.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01 TCGA.HW.7489.01
#> "02222" "0121" "0221" "022212" "0211" "0211"
#> TCGA.R8.A6YH.01 TCGA.DU.7018.01 TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01
#> "0211" "0221" "02222" "0221" "0221" "0211"
#> TCGA.HT.7690.01 TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01
#> "0213" "0121" "0213" "02323" "0212" "011"
#> TCGA.HT.A5RA.01 TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "011" "02322" "022233" "022212" "02222" "02222"
#> TCGA.HT.8013.01 TCGA.HW.7490.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01
#> "0212" "0211" "0212" "02222" "0221" "0123"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.DB.A64V.01 TCGA.RY.A840.01 TCGA.E1.5302.01
#> "0212" "02322" "0121" "022233" "02222" "0213"
#> TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01 TCGA.DU.5847.01
#> "022211" "0221" "022211" "0212" "011" "011"
#> TCGA.E1.A7YK.01 TCGA.HT.7874.01 TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01
#> "02321" "0221" "0221" "0122" "011" "0213"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.DU.6408.01 TCGA.DB.A4XB.01
#> "0121" "02323" "0212" "011" "0212" "0213"
#> TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01 TCGA.P5.A72U.01 TCGA.QH.A870.01
#> "03" "0212" "0212" "022211" "011" "0212"
#> TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01
#> "0221" "011" "011" "022233" "0221" "013"
#> TCGA.DU.A7TA.01 TCGA.HW.8319.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01
#> "0213" "02321" "0221" "0212" "0212" "0211"
#> TCGA.DU.6400.01 TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "0221" "022211" "0221" "0211" "0221" "02222"
#> TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01 TCGA.E1.A7YN.01
#> "0211" "0221" "0213" "02323" "0211" "011"
#> TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.QH.A6XA.01 TCGA.HT.8111.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01
#> "022212" "0212" "0212" "0213" "011" "0213"
#> TCGA.VM.A8CD.01 TCGA.RY.A83Y.01 TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01
#> "0122" "02222" "0212" "0211" "0211" "0211"
#> TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.DB.A64W.01 TCGA.R8.A6MO.01 TCGA.DU.A7T8.01
#> "0213" "0123" "0221" "0221" "0221" "0211"
#> TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01 TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01
#> "02222" "0221" "0221" "0221" "0211" "02222"
#> TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01 TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01
#> "0212" "013" "022211" "014" "02321" "022211"
#> TCGA.S9.A6U9.01 TCGA.CS.6290.01 TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01
#> "0211" "0213" "02222" "0211" "0212" "0231"
#> TCGA.HT.7860.01 TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.S9.A7J3.01 TCGA.P5.A5F2.01
#> "011" "0211" "0221" "0213" "0221" "0212"
#> TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01
#> "02323" "011" "022232" "03" "0211" "0221"
#> TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01 TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.TM.A84L.01
#> "0212" "0211" "022211" "0211" "02222" "0211"
#> TCGA.DU.8161.01 TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01
#> "011" "0211" "0221" "022211" "0122" "0213"
#> TCGA.TM.A7C4.01 TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.HT.8108.01 TCGA.E1.A7YD.01
#> "0212" "02222" "0221" "022211" "0212" "0121"
#> TCGA.DU.7304.01 TCGA.S9.A7IY.01 TCGA.FG.7641.01 TCGA.P5.A736.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01
#> "0211" "022232" "02222" "0212" "0211" "0211"
#> TCGA.HT.7470.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.FG.A4MY.01 TCGA.TM.A7CF.01
#> "02321" "0221" "0221" "03" "0212" "0212"
#> TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01 TCGA.DU.7010.01
#> "0212" "0221" "0211" "013" "0212" "0231"
#> TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.DU.A7TD.01 TCGA.DU.6405.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "0221" "0221" "0121" "011" "0213" "0211"
#> TCGA.DU.6401.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01 TCGA.HT.A74H.01
#> "0212" "02321" "0212" "0211" "0213" "0123"
#> TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01 TCGA.DB.A64L.01
#> "022232" "0231" "0213" "011" "0212" "0221"
#> TCGA.VV.A829.01 TCGA.HT.A61B.01 TCGA.DH.A66B.01 TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01
#> "022212" "0213" "0211" "0211" "02222" "02222"
#> TCGA.HT.A4DS.01 TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01
#> "011" "0213" "02222" "0211" "0221" "0121"
#> TCGA.DB.A64P.01 TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01
#> "02222" "0231" "0212" "0211" "0213" "0212"
#> TCGA.HW.A5KL.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.QH.A6CZ.01 TCGA.DH.A669.02
#> "0212" "011" "0213" "02322" "02222" "022212"
#> TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01 TCGA.TQ.A7RJ.01 TCGA.WY.A858.01
#> "022212" "0212" "0211" "0212" "0212" "0212"
#> TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01
#> "03" "02222" "0211" "022211" "0221" "0212"
#> TCGA.TM.A84I.01 TCGA.CS.5394.01 TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01
#> "0231" "022211" "0122" "0211" "0212" "014"
#> TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0213" "02222"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3007))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "0221" "0212" "0231" "02222" "0231" "011"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.HT.A74L.01 TCGA.DU.A5TS.01 TCGA.DB.A4XA.01 TCGA.HT.A4DV.01
#> "02222" "0212" "0221" "0211" "02223" "0221"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01 TCGA.HT.8113.01
#> "013" "02222" "0231" "0211" "0211" "0221"
#> TCGA.DH.A66G.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01 TCGA.HT.7689.01 TCGA.HT.8109.01
#> "0212" "02223" "0212" "02222" "02321" "02222"
#> TCGA.E1.A7YE.01 TCGA.S9.A7R1.01 TCGA.FG.A710.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01
#> "0231" "02222" "0221" "02322" "0221" "0221"
#> TCGA.QH.A6CU.01 TCGA.HW.7486.01 TCGA.FG.7634.01 TCGA.DU.8163.01 TCGA.DU.6407.02 TCGA.DU.6407.01
#> "0221" "02223" "02223" "0211" "0231" "0212"
#> TCGA.S9.A7IX.01 TCGA.HT.8010.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0122" "0221" "0211" "0212" "0213" "0221"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.DU.7299.01 TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.DU.7011.01
#> "0121" "0211" "0211" "011" "0211" "0213"
#> TCGA.TM.A84Q.01 TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.DB.5270.01
#> "0211" "0211" "0123" "02223" "0221" "0212"
#> TCGA.S9.A6WQ.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.E1.A7YU.01 TCGA.W9.A837.01 TCGA.TM.A7C5.01
#> "0212" "0213" "02222" "02321" "02222" "022211"
#> TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01 TCGA.HT.7601.01 TCGA.P5.A5ET.01
#> "0221" "0211" "0211" "02322" "0212" "02222"
#> TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.HT.7873.01
#> "0213" "0213" "0212" "0221" "022211" "0213"
#> TCGA.CS.4938.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "0212" "02222" "0221" "0211" "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
#> "02321" "0123" "0211" "0231" "0212" "0123"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.DU.6403.01 TCGA.HW.7493.01
#> "014" "02222" "02222" "0221" "011" "0212"
#> TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01 TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01
#> "02223" "0212" "02223" "0211" "02322" "022211"
#> TCGA.DH.A7UT.01 TCGA.DU.7015.01 TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01
#> "0213" "0212" "0212" "013" "0211" "0212"
#> TCGA.FG.A60K.01 TCGA.HT.7856.01 TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01
#> "0221" "02223" "03" "03" "0212" "0221"
#> TCGA.S9.A6TY.01 TCGA.CS.5395.01 TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01
#> "022211" "0123" "0123" "011" "0211" "0213"
#> TCGA.TM.A84O.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.DU.5855.01 TCGA.HT.7884.01
#> "0221" "0213" "0211" "0221" "0212" "0212"
#> TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01 TCGA.WH.A86K.01
#> "0221" "03" "0121" "02222" "0221" "0211"
#> TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01 TCGA.HT.A618.01
#> "014" "0221" "013" "0212" "0212" "02321"
#> TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01
#> "0212" "02223" "0212" "0122" "0211" "0221"
#> TCGA.S9.A7IZ.01 TCGA.DU.A6S7.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "0212" "0212" "0221" "0211" "0221" "0211"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.P5.A5F4.01 TCGA.QH.A65V.01
#> "02222" "02222" "0122" "0221" "0212" "0221"
#> TCGA.FG.8191.01 TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.CS.6666.01 TCGA.DU.7298.01
#> "0213" "0213" "0221" "0213" "0211" "0221"
#> TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01 TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01
#> "0221" "011" "03" "0212" "0221" "022211"
#> TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01 TCGA.DH.A66D.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01
#> "013" "0211" "0213" "0212" "0231" "02223"
#> TCGA.DU.A76K.01 TCGA.TQ.A7RR.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.P5.A735.01
#> "0122" "0213" "011" "0213" "022212" "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
#> "0221" "011" "02223" "013" "0221" "0231"
#> TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.S9.A6U5.01 TCGA.HT.7609.01 TCGA.DB.5274.01
#> "02323" "02222" "02223" "02223" "0211" "0221"
#> TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01 TCGA.DU.A6S2.01 TCGA.S9.A7R7.01
#> "02222" "022211" "014" "0213" "0221" "0213"
#> TCGA.TM.A84R.01 TCGA.DB.A75M.01 TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.HT.7477.01 TCGA.HT.8012.01
#> "02223" "0211" "03" "0211" "02322" "0221"
#> TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01 TCGA.S9.A7QZ.01
#> "0212" "0212" "0212" "02223" "0213" "022211"
#> TCGA.QH.A6X4.01 TCGA.P5.A77W.01 TCGA.DU.7302.01 TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.E1.5307.01
#> "02222" "0221" "0221" "011" "0211" "0212"
#> TCGA.S9.A7QW.01 TCGA.DU.6402.01 TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01
#> "0212" "0122" "0211" "0212" "011" "0213"
#> TCGA.HW.7495.01 TCGA.QH.A65R.01 TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01
#> "0221" "0221" "02223" "0211" "0211" "0213"
#> TCGA.HT.8104.01 TCGA.FG.A70Z.01 TCGA.DU.A7TC.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01
#> "011" "011" "0211" "0212" "02222" "0212"
#> TCGA.E1.5303.01 TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01
#> "0211" "0123" "02223" "0213" "0213" "0211"
#> TCGA.FG.A4MU.01 TCGA.HT.7875.01 TCGA.HT.7473.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01 TCGA.DU.7008.01
#> "0121" "02222" "0213" "011" "0221" "0212"
#> TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.FG.8189.01 TCGA.DB.A75O.01 TCGA.HT.7688.01
#> "013" "0122" "0213" "03" "0213" "0211"
#> TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01 TCGA.P5.A5EY.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01
#> "02322" "022211" "014" "013" "02222" "0212"
#> TCGA.DU.5872.02 TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01
#> "03" "0211" "0212" "011" "022211" "0122"
#> TCGA.DU.5874.01 TCGA.S9.A6WE.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "0221" "02222" "0211" "0211" "014" "0122"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "02223" "02223" "02222" "0213" "0212" "02222"
#> TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01 TCGA.DB.A4XF.01
#> "011" "0221" "0212" "014" "0212" "0212"
#> TCGA.HT.A74O.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01
#> "0211" "0211" "013" "02222" "0123" "0221"
#> TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.E1.A7YJ.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.S9.A6TS.01
#> "0211" "0221" "0121" "0221" "022211" "02322"
#> TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01
#> "0211" "0212" "0212" "0212" "0123" "0231"
#> TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01 TCGA.DU.5849.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01
#> "014" "0121" "0211" "02222" "0211" "0122"
#> TCGA.HT.7468.01 TCGA.FG.6692.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01 TCGA.HW.7489.01
#> "02222" "0121" "0221" "022212" "0211" "0211"
#> TCGA.R8.A6YH.01 TCGA.DU.7018.01 TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01
#> "0211" "0221" "02222" "0221" "0221" "0211"
#> TCGA.HT.7690.01 TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01
#> "0213" "0121" "0213" "02323" "0212" "011"
#> TCGA.HT.A5RA.01 TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "011" "02322" "02223" "022212" "02222" "02222"
#> TCGA.HT.8013.01 TCGA.HW.7490.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01
#> "0212" "0211" "0212" "02222" "0221" "0123"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.DB.A64V.01 TCGA.RY.A840.01 TCGA.E1.5302.01
#> "0212" "02322" "0121" "02223" "02222" "0213"
#> TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01 TCGA.DU.5847.01
#> "022211" "0221" "022211" "0212" "011" "011"
#> TCGA.E1.A7YK.01 TCGA.HT.7874.01 TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01
#> "02321" "0221" "0221" "0122" "011" "0213"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.DU.6408.01 TCGA.DB.A4XB.01
#> "0121" "02323" "0212" "011" "0212" "0213"
#> TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01 TCGA.P5.A72U.01 TCGA.QH.A870.01
#> "03" "0212" "0212" "022211" "011" "0212"
#> TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01
#> "0221" "011" "011" "02223" "0221" "013"
#> TCGA.DU.A7TA.01 TCGA.HW.8319.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01
#> "0213" "02321" "0221" "0212" "0212" "0211"
#> TCGA.DU.6400.01 TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "0221" "022211" "0221" "0211" "0221" "02222"
#> TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01 TCGA.E1.A7YN.01
#> "0211" "0221" "0213" "02323" "0211" "011"
#> TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.QH.A6XA.01 TCGA.HT.8111.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01
#> "022212" "0212" "0212" "0213" "011" "0213"
#> TCGA.VM.A8CD.01 TCGA.RY.A83Y.01 TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01
#> "0122" "02222" "0212" "0211" "0211" "0211"
#> TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.DB.A64W.01 TCGA.R8.A6MO.01 TCGA.DU.A7T8.01
#> "0213" "0123" "0221" "0221" "0221" "0211"
#> TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01 TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01
#> "02222" "0221" "0221" "0221" "0211" "02222"
#> TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01 TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01
#> "0212" "013" "022211" "014" "02321" "022211"
#> TCGA.S9.A6U9.01 TCGA.CS.6290.01 TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01
#> "0211" "0213" "02222" "0211" "0212" "0231"
#> TCGA.HT.7860.01 TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.S9.A7J3.01 TCGA.P5.A5F2.01
#> "011" "0211" "0221" "0213" "0221" "0212"
#> TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01
#> "02323" "011" "02223" "03" "0211" "0221"
#> TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01 TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.TM.A84L.01
#> "0212" "0211" "022211" "0211" "02222" "0211"
#> TCGA.DU.8161.01 TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01
#> "011" "0211" "0221" "022211" "0122" "0213"
#> TCGA.TM.A7C4.01 TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.HT.8108.01 TCGA.E1.A7YD.01
#> "0212" "02222" "0221" "022211" "0212" "0121"
#> TCGA.DU.7304.01 TCGA.S9.A7IY.01 TCGA.FG.7641.01 TCGA.P5.A736.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01
#> "0211" "02223" "02222" "0212" "0211" "0211"
#> TCGA.HT.7470.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.FG.A4MY.01 TCGA.TM.A7CF.01
#> "02321" "0221" "0221" "03" "0212" "0212"
#> TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01 TCGA.DU.7010.01
#> "0212" "0221" "0211" "013" "0212" "0231"
#> TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.DU.A7TD.01 TCGA.DU.6405.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "0221" "0221" "0121" "011" "0213" "0211"
#> TCGA.DU.6401.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01 TCGA.HT.A74H.01
#> "0212" "02321" "0212" "0211" "0213" "0123"
#> TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01 TCGA.DB.A64L.01
#> "02223" "0231" "0213" "011" "0212" "0221"
#> TCGA.VV.A829.01 TCGA.HT.A61B.01 TCGA.DH.A66B.01 TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01
#> "022212" "0213" "0211" "0211" "02222" "02222"
#> TCGA.HT.A4DS.01 TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01
#> "011" "0213" "02222" "0211" "0221" "0121"
#> TCGA.DB.A64P.01 TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01
#> "02222" "0231" "0212" "0211" "0213" "0212"
#> TCGA.HW.A5KL.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.QH.A6CZ.01 TCGA.DH.A669.02
#> "0212" "011" "0213" "02322" "02222" "022212"
#> TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01 TCGA.TQ.A7RJ.01 TCGA.WY.A858.01
#> "022212" "0212" "0211" "0212" "0212" "0212"
#> TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01
#> "03" "02222" "0211" "022211" "0221" "0212"
#> TCGA.TM.A84I.01 TCGA.CS.5394.01 TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01
#> "0231" "022211" "0122" "0211" "0212" "014"
#> TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0213" "02222"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3040))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "0221" "0212" "0231" "02222" "0231" "011"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.HT.A74L.01 TCGA.DU.A5TS.01 TCGA.DB.A4XA.01 TCGA.HT.A4DV.01
#> "02222" "0212" "0221" "0211" "02223" "0221"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01 TCGA.HT.8113.01
#> "013" "02222" "0231" "0211" "0211" "0221"
#> TCGA.DH.A66G.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01 TCGA.HT.7689.01 TCGA.HT.8109.01
#> "0212" "02223" "0212" "02222" "0232" "02222"
#> TCGA.E1.A7YE.01 TCGA.S9.A7R1.01 TCGA.FG.A710.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01
#> "0231" "02222" "0221" "0232" "0221" "0221"
#> TCGA.QH.A6CU.01 TCGA.HW.7486.01 TCGA.FG.7634.01 TCGA.DU.8163.01 TCGA.DU.6407.02 TCGA.DU.6407.01
#> "0221" "02223" "02223" "0211" "0231" "0212"
#> TCGA.S9.A7IX.01 TCGA.HT.8010.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0122" "0221" "0211" "0212" "0213" "0221"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.DU.7299.01 TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.DU.7011.01
#> "0121" "0211" "0211" "011" "0211" "0213"
#> TCGA.TM.A84Q.01 TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.DB.5270.01
#> "0211" "0211" "0123" "02223" "0221" "0212"
#> TCGA.S9.A6WQ.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.E1.A7YU.01 TCGA.W9.A837.01 TCGA.TM.A7C5.01
#> "0212" "0213" "02222" "0232" "02222" "022211"
#> TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01 TCGA.HT.7601.01 TCGA.P5.A5ET.01
#> "0221" "0211" "0211" "0232" "0212" "02222"
#> TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.HT.7873.01
#> "0213" "0213" "0212" "0221" "022211" "0213"
#> TCGA.CS.4938.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "0212" "02222" "0221" "0211" "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
#> "0232" "0123" "0211" "0231" "0212" "0123"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.DU.6403.01 TCGA.HW.7493.01
#> "014" "02222" "02222" "0221" "011" "0212"
#> TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01 TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01
#> "02223" "0212" "02223" "0211" "0232" "022211"
#> TCGA.DH.A7UT.01 TCGA.DU.7015.01 TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01
#> "0213" "0212" "0212" "013" "0211" "0212"
#> TCGA.FG.A60K.01 TCGA.HT.7856.01 TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01
#> "0221" "02223" "03" "03" "0212" "0221"
#> TCGA.S9.A6TY.01 TCGA.CS.5395.01 TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01
#> "022211" "0123" "0123" "011" "0211" "0213"
#> TCGA.TM.A84O.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.DU.5855.01 TCGA.HT.7884.01
#> "0221" "0213" "0211" "0221" "0212" "0212"
#> TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01 TCGA.WH.A86K.01
#> "0221" "03" "0121" "02222" "0221" "0211"
#> TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01 TCGA.HT.A618.01
#> "014" "0221" "013" "0212" "0212" "0232"
#> TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01
#> "0212" "02223" "0212" "0122" "0211" "0221"
#> TCGA.S9.A7IZ.01 TCGA.DU.A6S7.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "0212" "0212" "0221" "0211" "0221" "0211"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.P5.A5F4.01 TCGA.QH.A65V.01
#> "02222" "02222" "0122" "0221" "0212" "0221"
#> TCGA.FG.8191.01 TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.CS.6666.01 TCGA.DU.7298.01
#> "0213" "0213" "0221" "0213" "0211" "0221"
#> TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01 TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01
#> "0221" "011" "03" "0212" "0221" "022211"
#> TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01 TCGA.DH.A66D.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01
#> "013" "0211" "0213" "0212" "0231" "02223"
#> TCGA.DU.A76K.01 TCGA.TQ.A7RR.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.P5.A735.01
#> "0122" "0213" "011" "0213" "022212" "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
#> "0221" "011" "02223" "013" "0221" "0231"
#> TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.S9.A6U5.01 TCGA.HT.7609.01 TCGA.DB.5274.01
#> "0232" "02222" "02223" "02223" "0211" "0221"
#> TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01 TCGA.DU.A6S2.01 TCGA.S9.A7R7.01
#> "02222" "022211" "014" "0213" "0221" "0213"
#> TCGA.TM.A84R.01 TCGA.DB.A75M.01 TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.HT.7477.01 TCGA.HT.8012.01
#> "02223" "0211" "03" "0211" "0232" "0221"
#> TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01 TCGA.S9.A7QZ.01
#> "0212" "0212" "0212" "02223" "0213" "022211"
#> TCGA.QH.A6X4.01 TCGA.P5.A77W.01 TCGA.DU.7302.01 TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.E1.5307.01
#> "02222" "0221" "0221" "011" "0211" "0212"
#> TCGA.S9.A7QW.01 TCGA.DU.6402.01 TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01
#> "0212" "0122" "0211" "0212" "011" "0213"
#> TCGA.HW.7495.01 TCGA.QH.A65R.01 TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01
#> "0221" "0221" "02223" "0211" "0211" "0213"
#> TCGA.HT.8104.01 TCGA.FG.A70Z.01 TCGA.DU.A7TC.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01
#> "011" "011" "0211" "0212" "02222" "0212"
#> TCGA.E1.5303.01 TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01
#> "0211" "0123" "02223" "0213" "0213" "0211"
#> TCGA.FG.A4MU.01 TCGA.HT.7875.01 TCGA.HT.7473.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01 TCGA.DU.7008.01
#> "0121" "02222" "0213" "011" "0221" "0212"
#> TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.FG.8189.01 TCGA.DB.A75O.01 TCGA.HT.7688.01
#> "013" "0122" "0213" "03" "0213" "0211"
#> TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01 TCGA.P5.A5EY.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01
#> "0232" "022211" "014" "013" "02222" "0212"
#> TCGA.DU.5872.02 TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01
#> "03" "0211" "0212" "011" "022211" "0122"
#> TCGA.DU.5874.01 TCGA.S9.A6WE.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "0221" "02222" "0211" "0211" "014" "0122"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "02223" "02223" "02222" "0213" "0212" "02222"
#> TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01 TCGA.DB.A4XF.01
#> "011" "0221" "0212" "014" "0212" "0212"
#> TCGA.HT.A74O.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01
#> "0211" "0211" "013" "02222" "0123" "0221"
#> TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.E1.A7YJ.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.S9.A6TS.01
#> "0211" "0221" "0121" "0221" "022211" "0232"
#> TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01
#> "0211" "0212" "0212" "0212" "0123" "0231"
#> TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01 TCGA.DU.5849.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01
#> "014" "0121" "0211" "02222" "0211" "0122"
#> TCGA.HT.7468.01 TCGA.FG.6692.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01 TCGA.HW.7489.01
#> "02222" "0121" "0221" "022212" "0211" "0211"
#> TCGA.R8.A6YH.01 TCGA.DU.7018.01 TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01
#> "0211" "0221" "02222" "0221" "0221" "0211"
#> TCGA.HT.7690.01 TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01
#> "0213" "0121" "0213" "0232" "0212" "011"
#> TCGA.HT.A5RA.01 TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "011" "0232" "02223" "022212" "02222" "02222"
#> TCGA.HT.8013.01 TCGA.HW.7490.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01
#> "0212" "0211" "0212" "02222" "0221" "0123"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.DB.A64V.01 TCGA.RY.A840.01 TCGA.E1.5302.01
#> "0212" "0232" "0121" "02223" "02222" "0213"
#> TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01 TCGA.DU.5847.01
#> "022211" "0221" "022211" "0212" "011" "011"
#> TCGA.E1.A7YK.01 TCGA.HT.7874.01 TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01
#> "0232" "0221" "0221" "0122" "011" "0213"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.DU.6408.01 TCGA.DB.A4XB.01
#> "0121" "0232" "0212" "011" "0212" "0213"
#> TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01 TCGA.P5.A72U.01 TCGA.QH.A870.01
#> "03" "0212" "0212" "022211" "011" "0212"
#> TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01
#> "0221" "011" "011" "02223" "0221" "013"
#> TCGA.DU.A7TA.01 TCGA.HW.8319.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01
#> "0213" "0232" "0221" "0212" "0212" "0211"
#> TCGA.DU.6400.01 TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "0221" "022211" "0221" "0211" "0221" "02222"
#> TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01 TCGA.E1.A7YN.01
#> "0211" "0221" "0213" "0232" "0211" "011"
#> TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.QH.A6XA.01 TCGA.HT.8111.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01
#> "022212" "0212" "0212" "0213" "011" "0213"
#> TCGA.VM.A8CD.01 TCGA.RY.A83Y.01 TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01
#> "0122" "02222" "0212" "0211" "0211" "0211"
#> TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.DB.A64W.01 TCGA.R8.A6MO.01 TCGA.DU.A7T8.01
#> "0213" "0123" "0221" "0221" "0221" "0211"
#> TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01 TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01
#> "02222" "0221" "0221" "0221" "0211" "02222"
#> TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01 TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01
#> "0212" "013" "022211" "014" "0232" "022211"
#> TCGA.S9.A6U9.01 TCGA.CS.6290.01 TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01
#> "0211" "0213" "02222" "0211" "0212" "0231"
#> TCGA.HT.7860.01 TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.S9.A7J3.01 TCGA.P5.A5F2.01
#> "011" "0211" "0221" "0213" "0221" "0212"
#> TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01
#> "0232" "011" "02223" "03" "0211" "0221"
#> TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01 TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.TM.A84L.01
#> "0212" "0211" "022211" "0211" "02222" "0211"
#> TCGA.DU.8161.01 TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01
#> "011" "0211" "0221" "022211" "0122" "0213"
#> TCGA.TM.A7C4.01 TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.HT.8108.01 TCGA.E1.A7YD.01
#> "0212" "02222" "0221" "022211" "0212" "0121"
#> TCGA.DU.7304.01 TCGA.S9.A7IY.01 TCGA.FG.7641.01 TCGA.P5.A736.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01
#> "0211" "02223" "02222" "0212" "0211" "0211"
#> TCGA.HT.7470.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.FG.A4MY.01 TCGA.TM.A7CF.01
#> "0232" "0221" "0221" "03" "0212" "0212"
#> TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01 TCGA.DU.7010.01
#> "0212" "0221" "0211" "013" "0212" "0231"
#> TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.DU.A7TD.01 TCGA.DU.6405.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "0221" "0221" "0121" "011" "0213" "0211"
#> TCGA.DU.6401.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01 TCGA.HT.A74H.01
#> "0212" "0232" "0212" "0211" "0213" "0123"
#> TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01 TCGA.DB.A64L.01
#> "02223" "0231" "0213" "011" "0212" "0221"
#> TCGA.VV.A829.01 TCGA.HT.A61B.01 TCGA.DH.A66B.01 TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01
#> "022212" "0213" "0211" "0211" "02222" "02222"
#> TCGA.HT.A4DS.01 TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01
#> "011" "0213" "02222" "0211" "0221" "0121"
#> TCGA.DB.A64P.01 TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01
#> "02222" "0231" "0212" "0211" "0213" "0212"
#> TCGA.HW.A5KL.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.QH.A6CZ.01 TCGA.DH.A669.02
#> "0212" "011" "0213" "0232" "02222" "022212"
#> TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01 TCGA.TQ.A7RJ.01 TCGA.WY.A858.01
#> "022212" "0212" "0211" "0212" "0212" "0212"
#> TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01
#> "03" "02222" "0211" "022211" "0221" "0212"
#> TCGA.TM.A84I.01 TCGA.CS.5394.01 TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01
#> "0231" "022211" "0122" "0211" "0212" "014"
#> TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0213" "02222"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3432))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "0221" "0212" "023" "02222" "023" "011"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.HT.A74L.01 TCGA.DU.A5TS.01 TCGA.DB.A4XA.01 TCGA.HT.A4DV.01
#> "02222" "0212" "0221" "0211" "02223" "0221"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01 TCGA.HT.8113.01
#> "013" "02222" "023" "0211" "0211" "0221"
#> TCGA.DH.A66G.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01 TCGA.HT.7689.01 TCGA.HT.8109.01
#> "0212" "02223" "0212" "02222" "023" "02222"
#> TCGA.E1.A7YE.01 TCGA.S9.A7R1.01 TCGA.FG.A710.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01
#> "023" "02222" "0221" "023" "0221" "0221"
#> TCGA.QH.A6CU.01 TCGA.HW.7486.01 TCGA.FG.7634.01 TCGA.DU.8163.01 TCGA.DU.6407.02 TCGA.DU.6407.01
#> "0221" "02223" "02223" "0211" "023" "0212"
#> TCGA.S9.A7IX.01 TCGA.HT.8010.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0122" "0221" "0211" "0212" "0213" "0221"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.DU.7299.01 TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.DU.7011.01
#> "0121" "0211" "0211" "011" "0211" "0213"
#> TCGA.TM.A84Q.01 TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.DB.5270.01
#> "0211" "0211" "0123" "02223" "0221" "0212"
#> TCGA.S9.A6WQ.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.E1.A7YU.01 TCGA.W9.A837.01 TCGA.TM.A7C5.01
#> "0212" "0213" "02222" "023" "02222" "022211"
#> TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01 TCGA.HT.7601.01 TCGA.P5.A5ET.01
#> "0221" "0211" "0211" "023" "0212" "02222"
#> TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.HT.7873.01
#> "0213" "0213" "0212" "0221" "022211" "0213"
#> TCGA.CS.4938.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "0212" "02222" "0221" "0211" "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
#> "023" "0123" "0211" "023" "0212" "0123"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.DU.6403.01 TCGA.HW.7493.01
#> "014" "02222" "02222" "0221" "011" "0212"
#> TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01 TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01
#> "02223" "0212" "02223" "0211" "023" "022211"
#> TCGA.DH.A7UT.01 TCGA.DU.7015.01 TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01
#> "0213" "0212" "0212" "013" "0211" "0212"
#> TCGA.FG.A60K.01 TCGA.HT.7856.01 TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01
#> "0221" "02223" "03" "03" "0212" "0221"
#> TCGA.S9.A6TY.01 TCGA.CS.5395.01 TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01
#> "022211" "0123" "0123" "011" "0211" "0213"
#> TCGA.TM.A84O.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.DU.5855.01 TCGA.HT.7884.01
#> "0221" "0213" "0211" "0221" "0212" "0212"
#> TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01 TCGA.WH.A86K.01
#> "0221" "03" "0121" "02222" "0221" "0211"
#> TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01 TCGA.HT.A618.01
#> "014" "0221" "013" "0212" "0212" "023"
#> TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01
#> "0212" "02223" "0212" "0122" "0211" "0221"
#> TCGA.S9.A7IZ.01 TCGA.DU.A6S7.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "0212" "0212" "0221" "0211" "0221" "0211"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.P5.A5F4.01 TCGA.QH.A65V.01
#> "02222" "02222" "0122" "0221" "0212" "0221"
#> TCGA.FG.8191.01 TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.CS.6666.01 TCGA.DU.7298.01
#> "0213" "0213" "0221" "0213" "0211" "0221"
#> TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01 TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01
#> "0221" "011" "03" "0212" "0221" "022211"
#> TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01 TCGA.DH.A66D.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01
#> "013" "0211" "0213" "0212" "023" "02223"
#> TCGA.DU.A76K.01 TCGA.TQ.A7RR.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.P5.A735.01
#> "0122" "0213" "011" "0213" "022212" "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
#> "0221" "011" "02223" "013" "0221" "023"
#> TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.S9.A6U5.01 TCGA.HT.7609.01 TCGA.DB.5274.01
#> "023" "02222" "02223" "02223" "0211" "0221"
#> TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01 TCGA.DU.A6S2.01 TCGA.S9.A7R7.01
#> "02222" "022211" "014" "0213" "0221" "0213"
#> TCGA.TM.A84R.01 TCGA.DB.A75M.01 TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.HT.7477.01 TCGA.HT.8012.01
#> "02223" "0211" "03" "0211" "023" "0221"
#> TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01 TCGA.S9.A7QZ.01
#> "0212" "0212" "0212" "02223" "0213" "022211"
#> TCGA.QH.A6X4.01 TCGA.P5.A77W.01 TCGA.DU.7302.01 TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.E1.5307.01
#> "02222" "0221" "0221" "011" "0211" "0212"
#> TCGA.S9.A7QW.01 TCGA.DU.6402.01 TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01
#> "0212" "0122" "0211" "0212" "011" "0213"
#> TCGA.HW.7495.01 TCGA.QH.A65R.01 TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01
#> "0221" "0221" "02223" "0211" "0211" "0213"
#> TCGA.HT.8104.01 TCGA.FG.A70Z.01 TCGA.DU.A7TC.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01
#> "011" "011" "0211" "0212" "02222" "0212"
#> TCGA.E1.5303.01 TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01
#> "0211" "0123" "02223" "0213" "0213" "0211"
#> TCGA.FG.A4MU.01 TCGA.HT.7875.01 TCGA.HT.7473.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01 TCGA.DU.7008.01
#> "0121" "02222" "0213" "011" "0221" "0212"
#> TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.FG.8189.01 TCGA.DB.A75O.01 TCGA.HT.7688.01
#> "013" "0122" "0213" "03" "0213" "0211"
#> TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01 TCGA.P5.A5EY.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01
#> "023" "022211" "014" "013" "02222" "0212"
#> TCGA.DU.5872.02 TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01
#> "03" "0211" "0212" "011" "022211" "0122"
#> TCGA.DU.5874.01 TCGA.S9.A6WE.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "0221" "02222" "0211" "0211" "014" "0122"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "02223" "02223" "02222" "0213" "0212" "02222"
#> TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01 TCGA.DB.A4XF.01
#> "011" "0221" "0212" "014" "0212" "0212"
#> TCGA.HT.A74O.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01
#> "0211" "0211" "013" "02222" "0123" "0221"
#> TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.E1.A7YJ.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.S9.A6TS.01
#> "0211" "0221" "0121" "0221" "022211" "023"
#> TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01
#> "0211" "0212" "0212" "0212" "0123" "023"
#> TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01 TCGA.DU.5849.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01
#> "014" "0121" "0211" "02222" "0211" "0122"
#> TCGA.HT.7468.01 TCGA.FG.6692.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01 TCGA.HW.7489.01
#> "02222" "0121" "0221" "022212" "0211" "0211"
#> TCGA.R8.A6YH.01 TCGA.DU.7018.01 TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01
#> "0211" "0221" "02222" "0221" "0221" "0211"
#> TCGA.HT.7690.01 TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01
#> "0213" "0121" "0213" "023" "0212" "011"
#> TCGA.HT.A5RA.01 TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "011" "023" "02223" "022212" "02222" "02222"
#> TCGA.HT.8013.01 TCGA.HW.7490.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01
#> "0212" "0211" "0212" "02222" "0221" "0123"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.DB.A64V.01 TCGA.RY.A840.01 TCGA.E1.5302.01
#> "0212" "023" "0121" "02223" "02222" "0213"
#> TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01 TCGA.DU.5847.01
#> "022211" "0221" "022211" "0212" "011" "011"
#> TCGA.E1.A7YK.01 TCGA.HT.7874.01 TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01
#> "023" "0221" "0221" "0122" "011" "0213"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.DU.6408.01 TCGA.DB.A4XB.01
#> "0121" "023" "0212" "011" "0212" "0213"
#> TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01 TCGA.P5.A72U.01 TCGA.QH.A870.01
#> "03" "0212" "0212" "022211" "011" "0212"
#> TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01
#> "0221" "011" "011" "02223" "0221" "013"
#> TCGA.DU.A7TA.01 TCGA.HW.8319.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01
#> "0213" "023" "0221" "0212" "0212" "0211"
#> TCGA.DU.6400.01 TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "0221" "022211" "0221" "0211" "0221" "02222"
#> TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01 TCGA.E1.A7YN.01
#> "0211" "0221" "0213" "023" "0211" "011"
#> TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.QH.A6XA.01 TCGA.HT.8111.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01
#> "022212" "0212" "0212" "0213" "011" "0213"
#> TCGA.VM.A8CD.01 TCGA.RY.A83Y.01 TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01
#> "0122" "02222" "0212" "0211" "0211" "0211"
#> TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.DB.A64W.01 TCGA.R8.A6MO.01 TCGA.DU.A7T8.01
#> "0213" "0123" "0221" "0221" "0221" "0211"
#> TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01 TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01
#> "02222" "0221" "0221" "0221" "0211" "02222"
#> TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01 TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01
#> "0212" "013" "022211" "014" "023" "022211"
#> TCGA.S9.A6U9.01 TCGA.CS.6290.01 TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01
#> "0211" "0213" "02222" "0211" "0212" "023"
#> TCGA.HT.7860.01 TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.S9.A7J3.01 TCGA.P5.A5F2.01
#> "011" "0211" "0221" "0213" "0221" "0212"
#> TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01
#> "023" "011" "02223" "03" "0211" "0221"
#> TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01 TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.TM.A84L.01
#> "0212" "0211" "022211" "0211" "02222" "0211"
#> TCGA.DU.8161.01 TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01
#> "011" "0211" "0221" "022211" "0122" "0213"
#> TCGA.TM.A7C4.01 TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.HT.8108.01 TCGA.E1.A7YD.01
#> "0212" "02222" "0221" "022211" "0212" "0121"
#> TCGA.DU.7304.01 TCGA.S9.A7IY.01 TCGA.FG.7641.01 TCGA.P5.A736.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01
#> "0211" "02223" "02222" "0212" "0211" "0211"
#> TCGA.HT.7470.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.FG.A4MY.01 TCGA.TM.A7CF.01
#> "023" "0221" "0221" "03" "0212" "0212"
#> TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01 TCGA.DU.7010.01
#> "0212" "0221" "0211" "013" "0212" "023"
#> TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.DU.A7TD.01 TCGA.DU.6405.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "0221" "0221" "0121" "011" "0213" "0211"
#> TCGA.DU.6401.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01 TCGA.HT.A74H.01
#> "0212" "023" "0212" "0211" "0213" "0123"
#> TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01 TCGA.DB.A64L.01
#> "02223" "023" "0213" "011" "0212" "0221"
#> TCGA.VV.A829.01 TCGA.HT.A61B.01 TCGA.DH.A66B.01 TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01
#> "022212" "0213" "0211" "0211" "02222" "02222"
#> TCGA.HT.A4DS.01 TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01
#> "011" "0213" "02222" "0211" "0221" "0121"
#> TCGA.DB.A64P.01 TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01
#> "02222" "023" "0212" "0211" "0213" "0212"
#> TCGA.HW.A5KL.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.QH.A6CZ.01 TCGA.DH.A669.02
#> "0212" "011" "0213" "023" "02222" "022212"
#> TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01 TCGA.TQ.A7RJ.01 TCGA.WY.A858.01
#> "022212" "0212" "0211" "0212" "0212" "0212"
#> TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01
#> "03" "02222" "0211" "022211" "0221" "0212"
#> TCGA.TM.A84I.01 TCGA.CS.5394.01 TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01
#> "023" "022211" "0122" "0211" "0212" "014"
#> TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "0213" "02222"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3536))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "0221" "021" "023" "02222" "023" "011"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.HT.A74L.01 TCGA.DU.A5TS.01 TCGA.DB.A4XA.01 TCGA.HT.A4DV.01
#> "02222" "021" "0221" "021" "02223" "0221"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01 TCGA.HT.8113.01
#> "013" "02222" "023" "021" "021" "0221"
#> TCGA.DH.A66G.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01 TCGA.HT.7689.01 TCGA.HT.8109.01
#> "021" "02223" "021" "02222" "023" "02222"
#> TCGA.E1.A7YE.01 TCGA.S9.A7R1.01 TCGA.FG.A710.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01
#> "023" "02222" "0221" "023" "0221" "0221"
#> TCGA.QH.A6CU.01 TCGA.HW.7486.01 TCGA.FG.7634.01 TCGA.DU.8163.01 TCGA.DU.6407.02 TCGA.DU.6407.01
#> "0221" "02223" "02223" "021" "023" "021"
#> TCGA.S9.A7IX.01 TCGA.HT.8010.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0122" "0221" "021" "021" "021" "0221"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.DU.7299.01 TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.DU.7011.01
#> "0121" "021" "021" "011" "021" "021"
#> TCGA.TM.A84Q.01 TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.DB.5270.01
#> "021" "021" "0123" "02223" "0221" "021"
#> TCGA.S9.A6WQ.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.E1.A7YU.01 TCGA.W9.A837.01 TCGA.TM.A7C5.01
#> "021" "021" "02222" "023" "02222" "022211"
#> TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01 TCGA.HT.7601.01 TCGA.P5.A5ET.01
#> "0221" "021" "021" "023" "021" "02222"
#> TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.HT.7873.01
#> "021" "021" "021" "0221" "022211" "021"
#> TCGA.CS.4938.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "021" "02222" "0221" "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
#> "023" "0123" "021" "023" "021" "0123"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.DU.6403.01 TCGA.HW.7493.01
#> "014" "02222" "02222" "0221" "011" "021"
#> TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01 TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01
#> "02223" "021" "02223" "021" "023" "022211"
#> TCGA.DH.A7UT.01 TCGA.DU.7015.01 TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01
#> "021" "021" "021" "013" "021" "021"
#> TCGA.FG.A60K.01 TCGA.HT.7856.01 TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01
#> "0221" "02223" "03" "03" "021" "0221"
#> TCGA.S9.A6TY.01 TCGA.CS.5395.01 TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01
#> "022211" "0123" "0123" "011" "021" "021"
#> TCGA.TM.A84O.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.DU.5855.01 TCGA.HT.7884.01
#> "0221" "021" "021" "0221" "021" "021"
#> TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01 TCGA.WH.A86K.01
#> "0221" "03" "0121" "02222" "0221" "021"
#> TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01 TCGA.HT.A618.01
#> "014" "0221" "013" "021" "021" "023"
#> TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01
#> "021" "02223" "021" "0122" "021" "0221"
#> TCGA.S9.A7IZ.01 TCGA.DU.A6S7.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "021" "021" "0221" "021" "0221" "021"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.P5.A5F4.01 TCGA.QH.A65V.01
#> "02222" "02222" "0122" "0221" "021" "0221"
#> TCGA.FG.8191.01 TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.CS.6666.01 TCGA.DU.7298.01
#> "021" "021" "0221" "021" "021" "0221"
#> TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01 TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01
#> "0221" "011" "03" "021" "0221" "022211"
#> TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01 TCGA.DH.A66D.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01
#> "013" "021" "021" "021" "023" "02223"
#> TCGA.DU.A76K.01 TCGA.TQ.A7RR.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.P5.A735.01
#> "0122" "021" "011" "021" "022212" "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
#> "0221" "011" "02223" "013" "0221" "023"
#> TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.S9.A6U5.01 TCGA.HT.7609.01 TCGA.DB.5274.01
#> "023" "02222" "02223" "02223" "021" "0221"
#> TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01 TCGA.DU.A6S2.01 TCGA.S9.A7R7.01
#> "02222" "022211" "014" "021" "0221" "021"
#> TCGA.TM.A84R.01 TCGA.DB.A75M.01 TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.HT.7477.01 TCGA.HT.8012.01
#> "02223" "021" "03" "021" "023" "0221"
#> TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01 TCGA.S9.A7QZ.01
#> "021" "021" "021" "02223" "021" "022211"
#> TCGA.QH.A6X4.01 TCGA.P5.A77W.01 TCGA.DU.7302.01 TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.E1.5307.01
#> "02222" "0221" "0221" "011" "021" "021"
#> TCGA.S9.A7QW.01 TCGA.DU.6402.01 TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01
#> "021" "0122" "021" "021" "011" "021"
#> TCGA.HW.7495.01 TCGA.QH.A65R.01 TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01
#> "0221" "0221" "02223" "021" "021" "021"
#> TCGA.HT.8104.01 TCGA.FG.A70Z.01 TCGA.DU.A7TC.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01
#> "011" "011" "021" "021" "02222" "021"
#> TCGA.E1.5303.01 TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01
#> "021" "0123" "02223" "021" "021" "021"
#> TCGA.FG.A4MU.01 TCGA.HT.7875.01 TCGA.HT.7473.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01 TCGA.DU.7008.01
#> "0121" "02222" "021" "011" "0221" "021"
#> TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.FG.8189.01 TCGA.DB.A75O.01 TCGA.HT.7688.01
#> "013" "0122" "021" "03" "021" "021"
#> TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01 TCGA.P5.A5EY.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01
#> "023" "022211" "014" "013" "02222" "021"
#> TCGA.DU.5872.02 TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01
#> "03" "021" "021" "011" "022211" "0122"
#> TCGA.DU.5874.01 TCGA.S9.A6WE.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "0221" "02222" "021" "021" "014" "0122"
#> TCGA.R8.A6MK.01 TCGA.QH.A6CY.01 TCGA.S9.A7J1.01 TCGA.P5.A72X.01 TCGA.E1.5322.01 TCGA.P5.A5F0.01
#> "02223" "02223" "02222" "021" "021" "02222"
#> TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01 TCGA.DB.A4XF.01
#> "011" "0221" "021" "014" "021" "021"
#> TCGA.HT.A74O.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01
#> "021" "021" "013" "02222" "0123" "0221"
#> TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.E1.A7YJ.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.S9.A6TS.01
#> "021" "0221" "0121" "0221" "022211" "023"
#> TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01
#> "021" "021" "021" "021" "0123" "023"
#> TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01 TCGA.DU.5849.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01
#> "014" "0121" "021" "02222" "021" "0122"
#> TCGA.HT.7468.01 TCGA.FG.6692.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01 TCGA.HW.7489.01
#> "02222" "0121" "0221" "022212" "021" "021"
#> TCGA.R8.A6YH.01 TCGA.DU.7018.01 TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01
#> "021" "0221" "02222" "0221" "0221" "021"
#> TCGA.HT.7690.01 TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01
#> "021" "0121" "021" "023" "021" "011"
#> TCGA.HT.A5RA.01 TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "011" "023" "02223" "022212" "02222" "02222"
#> TCGA.HT.8013.01 TCGA.HW.7490.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01
#> "021" "021" "021" "02222" "0221" "0123"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.DB.A64V.01 TCGA.RY.A840.01 TCGA.E1.5302.01
#> "021" "023" "0121" "02223" "02222" "021"
#> TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01 TCGA.DU.5847.01
#> "022211" "0221" "022211" "021" "011" "011"
#> TCGA.E1.A7YK.01 TCGA.HT.7874.01 TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01
#> "023" "0221" "0221" "0122" "011" "021"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.DU.6408.01 TCGA.DB.A4XB.01
#> "0121" "023" "021" "011" "021" "021"
#> TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01 TCGA.P5.A72U.01 TCGA.QH.A870.01
#> "03" "021" "021" "022211" "011" "021"
#> TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01
#> "0221" "011" "011" "02223" "0221" "013"
#> TCGA.DU.A7TA.01 TCGA.HW.8319.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01
#> "021" "023" "0221" "021" "021" "021"
#> TCGA.DU.6400.01 TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "0221" "022211" "0221" "021" "0221" "02222"
#> TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01 TCGA.E1.A7YN.01
#> "021" "0221" "021" "023" "021" "011"
#> TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.QH.A6XA.01 TCGA.HT.8111.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01
#> "022212" "021" "021" "021" "011" "021"
#> TCGA.VM.A8CD.01 TCGA.RY.A83Y.01 TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01
#> "0122" "02222" "021" "021" "021" "021"
#> TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.DB.A64W.01 TCGA.R8.A6MO.01 TCGA.DU.A7T8.01
#> "021" "0123" "0221" "0221" "0221" "021"
#> TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01 TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01
#> "02222" "0221" "0221" "0221" "021" "02222"
#> TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01 TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01
#> "021" "013" "022211" "014" "023" "022211"
#> TCGA.S9.A6U9.01 TCGA.CS.6290.01 TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01
#> "021" "021" "02222" "021" "021" "023"
#> TCGA.HT.7860.01 TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.S9.A7J3.01 TCGA.P5.A5F2.01
#> "011" "021" "0221" "021" "0221" "021"
#> TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01
#> "023" "011" "02223" "03" "021" "0221"
#> TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01 TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.TM.A84L.01
#> "021" "021" "022211" "021" "02222" "021"
#> TCGA.DU.8161.01 TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01
#> "011" "021" "0221" "022211" "0122" "021"
#> TCGA.TM.A7C4.01 TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.HT.8108.01 TCGA.E1.A7YD.01
#> "021" "02222" "0221" "022211" "021" "0121"
#> TCGA.DU.7304.01 TCGA.S9.A7IY.01 TCGA.FG.7641.01 TCGA.P5.A736.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01
#> "021" "02223" "02222" "021" "021" "021"
#> TCGA.HT.7470.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.FG.A4MY.01 TCGA.TM.A7CF.01
#> "023" "0221" "0221" "03" "021" "021"
#> TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01 TCGA.DU.7010.01
#> "021" "0221" "021" "013" "021" "023"
#> TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.DU.A7TD.01 TCGA.DU.6405.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "0221" "0221" "0121" "011" "021" "021"
#> TCGA.DU.6401.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01 TCGA.HT.A74H.01
#> "021" "023" "021" "021" "021" "0123"
#> TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01 TCGA.DB.A64L.01
#> "02223" "023" "021" "011" "021" "0221"
#> TCGA.VV.A829.01 TCGA.HT.A61B.01 TCGA.DH.A66B.01 TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01
#> "022212" "021" "021" "021" "02222" "02222"
#> TCGA.HT.A4DS.01 TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01
#> "011" "021" "02222" "021" "0221" "0121"
#> TCGA.DB.A64P.01 TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01
#> "02222" "023" "021" "021" "021" "021"
#> TCGA.HW.A5KL.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.QH.A6CZ.01 TCGA.DH.A669.02
#> "021" "011" "021" "023" "02222" "022212"
#> TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01 TCGA.TQ.A7RJ.01 TCGA.WY.A858.01
#> "022212" "021" "021" "021" "021" "021"
#> TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01
#> "03" "02222" "021" "022211" "0221" "021"
#> TCGA.TM.A84I.01 TCGA.CS.5394.01 TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01
#> "023" "022211" "0122" "021" "021" "014"
#> TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "021" "02222"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5170))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "022" "021" "023" "022" "023" "011"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.HT.A74L.01 TCGA.DU.A5TS.01 TCGA.DB.A4XA.01 TCGA.HT.A4DV.01
#> "022" "021" "022" "021" "022" "022"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01 TCGA.HT.8113.01
#> "013" "022" "023" "021" "021" "022"
#> TCGA.DH.A66G.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01 TCGA.HT.7689.01 TCGA.HT.8109.01
#> "021" "022" "021" "022" "023" "022"
#> TCGA.E1.A7YE.01 TCGA.S9.A7R1.01 TCGA.FG.A710.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01
#> "023" "022" "022" "023" "022" "022"
#> TCGA.QH.A6CU.01 TCGA.HW.7486.01 TCGA.FG.7634.01 TCGA.DU.8163.01 TCGA.DU.6407.02 TCGA.DU.6407.01
#> "022" "022" "022" "021" "023" "021"
#> TCGA.S9.A7IX.01 TCGA.HT.8010.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0122" "022" "021" "021" "021" "022"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.DU.7299.01 TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.DU.7011.01
#> "0121" "021" "021" "011" "021" "021"
#> TCGA.TM.A84Q.01 TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.DB.5270.01
#> "021" "021" "0123" "022" "022" "021"
#> TCGA.S9.A6WQ.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.E1.A7YU.01 TCGA.W9.A837.01 TCGA.TM.A7C5.01
#> "021" "021" "022" "023" "022" "022211"
#> TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01 TCGA.HT.7601.01 TCGA.P5.A5ET.01
#> "022" "021" "021" "023" "021" "022"
#> TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.HT.7873.01
#> "021" "021" "021" "022" "022211" "021"
#> TCGA.CS.4938.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "021" "022" "022" "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
#> "023" "0123" "021" "023" "021" "0123"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.DU.6403.01 TCGA.HW.7493.01
#> "014" "022" "022" "022" "011" "021"
#> TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01 TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01
#> "022" "021" "022" "021" "023" "022211"
#> TCGA.DH.A7UT.01 TCGA.DU.7015.01 TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01
#> "021" "021" "021" "013" "021" "021"
#> TCGA.FG.A60K.01 TCGA.HT.7856.01 TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01
#> "022" "022" "03" "03" "021" "022"
#> TCGA.S9.A6TY.01 TCGA.CS.5395.01 TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01
#> "022211" "0123" "0123" "011" "021" "021"
#> TCGA.TM.A84O.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.DU.5855.01 TCGA.HT.7884.01
#> "022" "021" "021" "022" "021" "021"
#> TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01 TCGA.WH.A86K.01
#> "022" "03" "0121" "022" "022" "021"
#> TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01 TCGA.HT.A618.01
#> "014" "022" "013" "021" "021" "023"
#> TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01
#> "021" "022" "021" "0122" "021" "022"
#> TCGA.S9.A7IZ.01 TCGA.DU.A6S7.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "021" "021" "022" "021" "022" "021"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.P5.A5F4.01 TCGA.QH.A65V.01
#> "022" "022" "0122" "022" "021" "022"
#> TCGA.FG.8191.01 TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.CS.6666.01 TCGA.DU.7298.01
#> "021" "021" "022" "021" "021" "022"
#> TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01 TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01
#> "022" "011" "03" "021" "022" "022211"
#> TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01 TCGA.DH.A66D.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01
#> "013" "021" "021" "021" "023" "022"
#> TCGA.DU.A76K.01 TCGA.TQ.A7RR.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.P5.A735.01
#> "0122" "021" "011" "021" "022212" "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" "011" "022" "013" "022" "023"
#> TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.S9.A6U5.01 TCGA.HT.7609.01 TCGA.DB.5274.01
#> "023" "022" "022" "022" "021" "022"
#> TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01 TCGA.DU.A6S2.01 TCGA.S9.A7R7.01
#> "022" "022211" "014" "021" "022" "021"
#> TCGA.TM.A84R.01 TCGA.DB.A75M.01 TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.HT.7477.01 TCGA.HT.8012.01
#> "022" "021" "03" "021" "023" "022"
#> TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01 TCGA.S9.A7QZ.01
#> "021" "021" "021" "022" "021" "022211"
#> TCGA.QH.A6X4.01 TCGA.P5.A77W.01 TCGA.DU.7302.01 TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.E1.5307.01
#> "022" "022" "022" "011" "021" "021"
#> TCGA.S9.A7QW.01 TCGA.DU.6402.01 TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01
#> "021" "0122" "021" "021" "011" "021"
#> TCGA.HW.7495.01 TCGA.QH.A65R.01 TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01
#> "022" "022" "022" "021" "021" "021"
#> TCGA.HT.8104.01 TCGA.FG.A70Z.01 TCGA.DU.A7TC.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01
#> "011" "011" "021" "021" "022" "021"
#> TCGA.E1.5303.01 TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01
#> "021" "0123" "022" "021" "021" "021"
#> TCGA.FG.A4MU.01 TCGA.HT.7875.01 TCGA.HT.7473.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01 TCGA.DU.7008.01
#> "0121" "022" "021" "011" "022" "021"
#> TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.FG.8189.01 TCGA.DB.A75O.01 TCGA.HT.7688.01
#> "013" "0122" "021" "03" "021" "021"
#> TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01 TCGA.P5.A5EY.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01
#> "023" "022211" "014" "013" "022" "021"
#> TCGA.DU.5872.02 TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01
#> "03" "021" "021" "011" "022211" "0122"
#> TCGA.DU.5874.01 TCGA.S9.A6WE.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "022" "022" "021" "021" "014" "0122"
#> 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" "022" "022" "021" "021" "022"
#> TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01 TCGA.DB.A4XF.01
#> "011" "022" "021" "014" "021" "021"
#> TCGA.HT.A74O.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01
#> "021" "021" "013" "022" "0123" "022"
#> TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.E1.A7YJ.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.S9.A6TS.01
#> "021" "022" "0121" "022" "022211" "023"
#> TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01
#> "021" "021" "021" "021" "0123" "023"
#> TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01 TCGA.DU.5849.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01
#> "014" "0121" "021" "022" "021" "0122"
#> TCGA.HT.7468.01 TCGA.FG.6692.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01 TCGA.HW.7489.01
#> "022" "0121" "022" "022212" "021" "021"
#> TCGA.R8.A6YH.01 TCGA.DU.7018.01 TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01
#> "021" "022" "022" "022" "022" "021"
#> TCGA.HT.7690.01 TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01
#> "021" "0121" "021" "023" "021" "011"
#> TCGA.HT.A5RA.01 TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "011" "023" "022" "022212" "022" "022"
#> TCGA.HT.8013.01 TCGA.HW.7490.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01
#> "021" "021" "021" "022" "022" "0123"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.DB.A64V.01 TCGA.RY.A840.01 TCGA.E1.5302.01
#> "021" "023" "0121" "022" "022" "021"
#> TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01 TCGA.DU.5847.01
#> "022211" "022" "022211" "021" "011" "011"
#> TCGA.E1.A7YK.01 TCGA.HT.7874.01 TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01
#> "023" "022" "022" "0122" "011" "021"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.DU.6408.01 TCGA.DB.A4XB.01
#> "0121" "023" "021" "011" "021" "021"
#> TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01 TCGA.P5.A72U.01 TCGA.QH.A870.01
#> "03" "021" "021" "022211" "011" "021"
#> TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01
#> "022" "011" "011" "022" "022" "013"
#> TCGA.DU.A7TA.01 TCGA.HW.8319.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01
#> "021" "023" "022" "021" "021" "021"
#> TCGA.DU.6400.01 TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "022" "022211" "022" "021" "022" "022"
#> TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01 TCGA.E1.A7YN.01
#> "021" "022" "021" "023" "021" "011"
#> TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.QH.A6XA.01 TCGA.HT.8111.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01
#> "022212" "021" "021" "021" "011" "021"
#> TCGA.VM.A8CD.01 TCGA.RY.A83Y.01 TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01
#> "0122" "022" "021" "021" "021" "021"
#> TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.DB.A64W.01 TCGA.R8.A6MO.01 TCGA.DU.A7T8.01
#> "021" "0123" "022" "022" "022" "021"
#> TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01 TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01
#> "022" "022" "022" "022" "021" "022"
#> TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01 TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01
#> "021" "013" "022211" "014" "023" "022211"
#> TCGA.S9.A6U9.01 TCGA.CS.6290.01 TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01
#> "021" "021" "022" "021" "021" "023"
#> TCGA.HT.7860.01 TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.S9.A7J3.01 TCGA.P5.A5F2.01
#> "011" "021" "022" "021" "022" "021"
#> TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01
#> "023" "011" "022" "03" "021" "022"
#> TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01 TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.TM.A84L.01
#> "021" "021" "022211" "021" "022" "021"
#> TCGA.DU.8161.01 TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01
#> "011" "021" "022" "022211" "0122" "021"
#> TCGA.TM.A7C4.01 TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.HT.8108.01 TCGA.E1.A7YD.01
#> "021" "022" "022" "022211" "021" "0121"
#> TCGA.DU.7304.01 TCGA.S9.A7IY.01 TCGA.FG.7641.01 TCGA.P5.A736.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01
#> "021" "022" "022" "021" "021" "021"
#> TCGA.HT.7470.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.FG.A4MY.01 TCGA.TM.A7CF.01
#> "023" "022" "022" "03" "021" "021"
#> TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01 TCGA.DU.7010.01
#> "021" "022" "021" "013" "021" "023"
#> TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.DU.A7TD.01 TCGA.DU.6405.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "022" "022" "0121" "011" "021" "021"
#> TCGA.DU.6401.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01 TCGA.HT.A74H.01
#> "021" "023" "021" "021" "021" "0123"
#> TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01 TCGA.DB.A64L.01
#> "022" "023" "021" "011" "021" "022"
#> TCGA.VV.A829.01 TCGA.HT.A61B.01 TCGA.DH.A66B.01 TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01
#> "022212" "021" "021" "021" "022" "022"
#> TCGA.HT.A4DS.01 TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01
#> "011" "021" "022" "021" "022" "0121"
#> TCGA.DB.A64P.01 TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01
#> "022" "023" "021" "021" "021" "021"
#> TCGA.HW.A5KL.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.QH.A6CZ.01 TCGA.DH.A669.02
#> "021" "011" "021" "023" "022" "022212"
#> TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01 TCGA.TQ.A7RJ.01 TCGA.WY.A858.01
#> "022212" "021" "021" "021" "021" "021"
#> TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01
#> "03" "022" "021" "022211" "022" "021"
#> TCGA.TM.A84I.01 TCGA.CS.5394.01 TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01
#> "023" "022211" "0122" "021" "021" "014"
#> TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "021" "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5644))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "022" "021" "023" "022" "023" "011"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.HT.A74L.01 TCGA.DU.A5TS.01 TCGA.DB.A4XA.01 TCGA.HT.A4DV.01
#> "022" "021" "022" "021" "022" "022"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01 TCGA.HT.8113.01
#> "013" "022" "023" "021" "021" "022"
#> TCGA.DH.A66G.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01 TCGA.HT.7689.01 TCGA.HT.8109.01
#> "021" "022" "021" "022" "023" "022"
#> TCGA.E1.A7YE.01 TCGA.S9.A7R1.01 TCGA.FG.A710.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01
#> "023" "022" "022" "023" "022" "022"
#> TCGA.QH.A6CU.01 TCGA.HW.7486.01 TCGA.FG.7634.01 TCGA.DU.8163.01 TCGA.DU.6407.02 TCGA.DU.6407.01
#> "022" "022" "022" "021" "023" "021"
#> TCGA.S9.A7IX.01 TCGA.HT.8010.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "0122" "022" "021" "021" "021" "022"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.DU.7299.01 TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.DU.7011.01
#> "0121" "021" "021" "011" "021" "021"
#> TCGA.TM.A84Q.01 TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.DB.5270.01
#> "021" "021" "0123" "022" "022" "021"
#> TCGA.S9.A6WQ.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.E1.A7YU.01 TCGA.W9.A837.01 TCGA.TM.A7C5.01
#> "021" "021" "022" "023" "022" "022"
#> TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01 TCGA.HT.7601.01 TCGA.P5.A5ET.01
#> "022" "021" "021" "023" "021" "022"
#> TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.HT.7873.01
#> "021" "021" "021" "022" "022" "021"
#> TCGA.CS.4938.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "021" "022" "022" "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
#> "023" "0123" "021" "023" "021" "0123"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.DU.6403.01 TCGA.HW.7493.01
#> "014" "022" "022" "022" "011" "021"
#> TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01 TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01
#> "022" "021" "022" "021" "023" "022"
#> TCGA.DH.A7UT.01 TCGA.DU.7015.01 TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01
#> "021" "021" "021" "013" "021" "021"
#> TCGA.FG.A60K.01 TCGA.HT.7856.01 TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01
#> "022" "022" "03" "03" "021" "022"
#> TCGA.S9.A6TY.01 TCGA.CS.5395.01 TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01
#> "022" "0123" "0123" "011" "021" "021"
#> TCGA.TM.A84O.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.DU.5855.01 TCGA.HT.7884.01
#> "022" "021" "021" "022" "021" "021"
#> TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01 TCGA.WH.A86K.01
#> "022" "03" "0121" "022" "022" "021"
#> TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01 TCGA.HT.A618.01
#> "014" "022" "013" "021" "021" "023"
#> TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01
#> "021" "022" "021" "0122" "021" "022"
#> TCGA.S9.A7IZ.01 TCGA.DU.A6S7.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "021" "021" "022" "021" "022" "021"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.P5.A5F4.01 TCGA.QH.A65V.01
#> "022" "022" "0122" "022" "021" "022"
#> TCGA.FG.8191.01 TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.CS.6666.01 TCGA.DU.7298.01
#> "021" "021" "022" "021" "021" "022"
#> TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01 TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01
#> "022" "011" "03" "021" "022" "022"
#> TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01 TCGA.DH.A66D.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01
#> "013" "021" "021" "021" "023" "022"
#> TCGA.DU.A76K.01 TCGA.TQ.A7RR.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.P5.A735.01
#> "0122" "021" "011" "021" "022" "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" "011" "022" "013" "022" "023"
#> TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.S9.A6U5.01 TCGA.HT.7609.01 TCGA.DB.5274.01
#> "023" "022" "022" "022" "021" "022"
#> TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01 TCGA.DU.A6S2.01 TCGA.S9.A7R7.01
#> "022" "022" "014" "021" "022" "021"
#> TCGA.TM.A84R.01 TCGA.DB.A75M.01 TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.HT.7477.01 TCGA.HT.8012.01
#> "022" "021" "03" "021" "023" "022"
#> TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01 TCGA.S9.A7QZ.01
#> "021" "021" "021" "022" "021" "022"
#> TCGA.QH.A6X4.01 TCGA.P5.A77W.01 TCGA.DU.7302.01 TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.E1.5307.01
#> "022" "022" "022" "011" "021" "021"
#> TCGA.S9.A7QW.01 TCGA.DU.6402.01 TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01
#> "021" "0122" "021" "021" "011" "021"
#> TCGA.HW.7495.01 TCGA.QH.A65R.01 TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01
#> "022" "022" "022" "021" "021" "021"
#> TCGA.HT.8104.01 TCGA.FG.A70Z.01 TCGA.DU.A7TC.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01
#> "011" "011" "021" "021" "022" "021"
#> TCGA.E1.5303.01 TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01
#> "021" "0123" "022" "021" "021" "021"
#> TCGA.FG.A4MU.01 TCGA.HT.7875.01 TCGA.HT.7473.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01 TCGA.DU.7008.01
#> "0121" "022" "021" "011" "022" "021"
#> TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.FG.8189.01 TCGA.DB.A75O.01 TCGA.HT.7688.01
#> "013" "0122" "021" "03" "021" "021"
#> TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01 TCGA.P5.A5EY.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01
#> "023" "022" "014" "013" "022" "021"
#> TCGA.DU.5872.02 TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01
#> "03" "021" "021" "011" "022" "0122"
#> TCGA.DU.5874.01 TCGA.S9.A6WE.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "022" "022" "021" "021" "014" "0122"
#> 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" "022" "022" "021" "021" "022"
#> TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01 TCGA.DB.A4XF.01
#> "011" "022" "021" "014" "021" "021"
#> TCGA.HT.A74O.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01
#> "021" "021" "013" "022" "0123" "022"
#> TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.E1.A7YJ.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.S9.A6TS.01
#> "021" "022" "0121" "022" "022" "023"
#> TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01
#> "021" "021" "021" "021" "0123" "023"
#> TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01 TCGA.DU.5849.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01
#> "014" "0121" "021" "022" "021" "0122"
#> TCGA.HT.7468.01 TCGA.FG.6692.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01 TCGA.HW.7489.01
#> "022" "0121" "022" "022" "021" "021"
#> TCGA.R8.A6YH.01 TCGA.DU.7018.01 TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01
#> "021" "022" "022" "022" "022" "021"
#> TCGA.HT.7690.01 TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01
#> "021" "0121" "021" "023" "021" "011"
#> TCGA.HT.A5RA.01 TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "011" "023" "022" "022" "022" "022"
#> TCGA.HT.8013.01 TCGA.HW.7490.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01
#> "021" "021" "021" "022" "022" "0123"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.DB.A64V.01 TCGA.RY.A840.01 TCGA.E1.5302.01
#> "021" "023" "0121" "022" "022" "021"
#> TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01 TCGA.DU.5847.01
#> "022" "022" "022" "021" "011" "011"
#> TCGA.E1.A7YK.01 TCGA.HT.7874.01 TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01
#> "023" "022" "022" "0122" "011" "021"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.DU.6408.01 TCGA.DB.A4XB.01
#> "0121" "023" "021" "011" "021" "021"
#> TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01 TCGA.P5.A72U.01 TCGA.QH.A870.01
#> "03" "021" "021" "022" "011" "021"
#> TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01
#> "022" "011" "011" "022" "022" "013"
#> TCGA.DU.A7TA.01 TCGA.HW.8319.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01
#> "021" "023" "022" "021" "021" "021"
#> TCGA.DU.6400.01 TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "022" "022" "022" "021" "022" "022"
#> TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01 TCGA.E1.A7YN.01
#> "021" "022" "021" "023" "021" "011"
#> TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.QH.A6XA.01 TCGA.HT.8111.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01
#> "022" "021" "021" "021" "011" "021"
#> TCGA.VM.A8CD.01 TCGA.RY.A83Y.01 TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01
#> "0122" "022" "021" "021" "021" "021"
#> TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.DB.A64W.01 TCGA.R8.A6MO.01 TCGA.DU.A7T8.01
#> "021" "0123" "022" "022" "022" "021"
#> TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01 TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01
#> "022" "022" "022" "022" "021" "022"
#> TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01 TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01
#> "021" "013" "022" "014" "023" "022"
#> TCGA.S9.A6U9.01 TCGA.CS.6290.01 TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01
#> "021" "021" "022" "021" "021" "023"
#> TCGA.HT.7860.01 TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.S9.A7J3.01 TCGA.P5.A5F2.01
#> "011" "021" "022" "021" "022" "021"
#> TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01
#> "023" "011" "022" "03" "021" "022"
#> TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01 TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.TM.A84L.01
#> "021" "021" "022" "021" "022" "021"
#> TCGA.DU.8161.01 TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01
#> "011" "021" "022" "022" "0122" "021"
#> TCGA.TM.A7C4.01 TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.HT.8108.01 TCGA.E1.A7YD.01
#> "021" "022" "022" "022" "021" "0121"
#> TCGA.DU.7304.01 TCGA.S9.A7IY.01 TCGA.FG.7641.01 TCGA.P5.A736.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01
#> "021" "022" "022" "021" "021" "021"
#> TCGA.HT.7470.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.FG.A4MY.01 TCGA.TM.A7CF.01
#> "023" "022" "022" "03" "021" "021"
#> TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01 TCGA.DU.7010.01
#> "021" "022" "021" "013" "021" "023"
#> TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.DU.A7TD.01 TCGA.DU.6405.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "022" "022" "0121" "011" "021" "021"
#> TCGA.DU.6401.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01 TCGA.HT.A74H.01
#> "021" "023" "021" "021" "021" "0123"
#> TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01 TCGA.DB.A64L.01
#> "022" "023" "021" "011" "021" "022"
#> TCGA.VV.A829.01 TCGA.HT.A61B.01 TCGA.DH.A66B.01 TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01
#> "022" "021" "021" "021" "022" "022"
#> TCGA.HT.A4DS.01 TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01
#> "011" "021" "022" "021" "022" "0121"
#> TCGA.DB.A64P.01 TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01
#> "022" "023" "021" "021" "021" "021"
#> TCGA.HW.A5KL.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.QH.A6CZ.01 TCGA.DH.A669.02
#> "021" "011" "021" "023" "022" "022"
#> TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01 TCGA.TQ.A7RJ.01 TCGA.WY.A858.01
#> "022" "021" "021" "021" "021" "021"
#> TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01
#> "03" "022" "021" "022" "022" "021"
#> TCGA.TM.A84I.01 TCGA.CS.5394.01 TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01
#> "023" "022" "0122" "021" "021" "014"
#> TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "021" "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7885))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "022" "021" "023" "022" "023" "011"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.HT.A74L.01 TCGA.DU.A5TS.01 TCGA.DB.A4XA.01 TCGA.HT.A4DV.01
#> "022" "021" "022" "021" "022" "022"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01 TCGA.HT.8113.01
#> "013" "022" "023" "021" "021" "022"
#> TCGA.DH.A66G.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01 TCGA.HT.7689.01 TCGA.HT.8109.01
#> "021" "022" "021" "022" "023" "022"
#> TCGA.E1.A7YE.01 TCGA.S9.A7R1.01 TCGA.FG.A710.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01
#> "023" "022" "022" "023" "022" "022"
#> TCGA.QH.A6CU.01 TCGA.HW.7486.01 TCGA.FG.7634.01 TCGA.DU.8163.01 TCGA.DU.6407.02 TCGA.DU.6407.01
#> "022" "022" "022" "021" "023" "021"
#> TCGA.S9.A7IX.01 TCGA.HT.8010.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "012" "022" "021" "021" "021" "022"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.DU.7299.01 TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.DU.7011.01
#> "012" "021" "021" "011" "021" "021"
#> TCGA.TM.A84Q.01 TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.DB.5270.01
#> "021" "021" "012" "022" "022" "021"
#> TCGA.S9.A6WQ.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.E1.A7YU.01 TCGA.W9.A837.01 TCGA.TM.A7C5.01
#> "021" "021" "022" "023" "022" "022"
#> TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01 TCGA.HT.7601.01 TCGA.P5.A5ET.01
#> "022" "021" "021" "023" "021" "022"
#> TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.HT.7873.01
#> "021" "021" "021" "022" "022" "021"
#> TCGA.CS.4938.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "021" "022" "022" "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
#> "023" "012" "021" "023" "021" "012"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.DU.6403.01 TCGA.HW.7493.01
#> "014" "022" "022" "022" "011" "021"
#> TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01 TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01
#> "022" "021" "022" "021" "023" "022"
#> TCGA.DH.A7UT.01 TCGA.DU.7015.01 TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01
#> "021" "021" "021" "013" "021" "021"
#> TCGA.FG.A60K.01 TCGA.HT.7856.01 TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01
#> "022" "022" "03" "03" "021" "022"
#> TCGA.S9.A6TY.01 TCGA.CS.5395.01 TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01
#> "022" "012" "012" "011" "021" "021"
#> TCGA.TM.A84O.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.DU.5855.01 TCGA.HT.7884.01
#> "022" "021" "021" "022" "021" "021"
#> TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01 TCGA.WH.A86K.01
#> "022" "03" "012" "022" "022" "021"
#> TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01 TCGA.HT.A618.01
#> "014" "022" "013" "021" "021" "023"
#> TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01
#> "021" "022" "021" "012" "021" "022"
#> TCGA.S9.A7IZ.01 TCGA.DU.A6S7.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "021" "021" "022" "021" "022" "021"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.P5.A5F4.01 TCGA.QH.A65V.01
#> "022" "022" "012" "022" "021" "022"
#> TCGA.FG.8191.01 TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.CS.6666.01 TCGA.DU.7298.01
#> "021" "021" "022" "021" "021" "022"
#> TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01 TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01
#> "022" "011" "03" "021" "022" "022"
#> TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01 TCGA.DH.A66D.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01
#> "013" "021" "021" "021" "023" "022"
#> TCGA.DU.A76K.01 TCGA.TQ.A7RR.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.P5.A735.01
#> "012" "021" "011" "021" "022" "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" "011" "022" "013" "022" "023"
#> TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.S9.A6U5.01 TCGA.HT.7609.01 TCGA.DB.5274.01
#> "023" "022" "022" "022" "021" "022"
#> TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01 TCGA.DU.A6S2.01 TCGA.S9.A7R7.01
#> "022" "022" "014" "021" "022" "021"
#> TCGA.TM.A84R.01 TCGA.DB.A75M.01 TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.HT.7477.01 TCGA.HT.8012.01
#> "022" "021" "03" "021" "023" "022"
#> TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01 TCGA.S9.A7QZ.01
#> "021" "021" "021" "022" "021" "022"
#> TCGA.QH.A6X4.01 TCGA.P5.A77W.01 TCGA.DU.7302.01 TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.E1.5307.01
#> "022" "022" "022" "011" "021" "021"
#> TCGA.S9.A7QW.01 TCGA.DU.6402.01 TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01
#> "021" "012" "021" "021" "011" "021"
#> TCGA.HW.7495.01 TCGA.QH.A65R.01 TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01
#> "022" "022" "022" "021" "021" "021"
#> TCGA.HT.8104.01 TCGA.FG.A70Z.01 TCGA.DU.A7TC.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01
#> "011" "011" "021" "021" "022" "021"
#> TCGA.E1.5303.01 TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01
#> "021" "012" "022" "021" "021" "021"
#> TCGA.FG.A4MU.01 TCGA.HT.7875.01 TCGA.HT.7473.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01 TCGA.DU.7008.01
#> "012" "022" "021" "011" "022" "021"
#> TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.FG.8189.01 TCGA.DB.A75O.01 TCGA.HT.7688.01
#> "013" "012" "021" "03" "021" "021"
#> TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01 TCGA.P5.A5EY.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01
#> "023" "022" "014" "013" "022" "021"
#> TCGA.DU.5872.02 TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01
#> "03" "021" "021" "011" "022" "012"
#> TCGA.DU.5874.01 TCGA.S9.A6WE.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "022" "022" "021" "021" "014" "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" "022" "022" "021" "021" "022"
#> TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01 TCGA.DB.A4XF.01
#> "011" "022" "021" "014" "021" "021"
#> TCGA.HT.A74O.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01
#> "021" "021" "013" "022" "012" "022"
#> TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.E1.A7YJ.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.S9.A6TS.01
#> "021" "022" "012" "022" "022" "023"
#> TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01
#> "021" "021" "021" "021" "012" "023"
#> TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01 TCGA.DU.5849.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01
#> "014" "012" "021" "022" "021" "012"
#> TCGA.HT.7468.01 TCGA.FG.6692.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01 TCGA.HW.7489.01
#> "022" "012" "022" "022" "021" "021"
#> TCGA.R8.A6YH.01 TCGA.DU.7018.01 TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01
#> "021" "022" "022" "022" "022" "021"
#> TCGA.HT.7690.01 TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01
#> "021" "012" "021" "023" "021" "011"
#> TCGA.HT.A5RA.01 TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "011" "023" "022" "022" "022" "022"
#> TCGA.HT.8013.01 TCGA.HW.7490.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01
#> "021" "021" "021" "022" "022" "012"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.DB.A64V.01 TCGA.RY.A840.01 TCGA.E1.5302.01
#> "021" "023" "012" "022" "022" "021"
#> TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01 TCGA.DU.5847.01
#> "022" "022" "022" "021" "011" "011"
#> TCGA.E1.A7YK.01 TCGA.HT.7874.01 TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01
#> "023" "022" "022" "012" "011" "021"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.DU.6408.01 TCGA.DB.A4XB.01
#> "012" "023" "021" "011" "021" "021"
#> TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01 TCGA.P5.A72U.01 TCGA.QH.A870.01
#> "03" "021" "021" "022" "011" "021"
#> TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01
#> "022" "011" "011" "022" "022" "013"
#> TCGA.DU.A7TA.01 TCGA.HW.8319.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01
#> "021" "023" "022" "021" "021" "021"
#> TCGA.DU.6400.01 TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "022" "022" "022" "021" "022" "022"
#> TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01 TCGA.E1.A7YN.01
#> "021" "022" "021" "023" "021" "011"
#> TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.QH.A6XA.01 TCGA.HT.8111.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01
#> "022" "021" "021" "021" "011" "021"
#> TCGA.VM.A8CD.01 TCGA.RY.A83Y.01 TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01
#> "012" "022" "021" "021" "021" "021"
#> TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.DB.A64W.01 TCGA.R8.A6MO.01 TCGA.DU.A7T8.01
#> "021" "012" "022" "022" "022" "021"
#> TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01 TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01
#> "022" "022" "022" "022" "021" "022"
#> TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01 TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01
#> "021" "013" "022" "014" "023" "022"
#> TCGA.S9.A6U9.01 TCGA.CS.6290.01 TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01
#> "021" "021" "022" "021" "021" "023"
#> TCGA.HT.7860.01 TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.S9.A7J3.01 TCGA.P5.A5F2.01
#> "011" "021" "022" "021" "022" "021"
#> TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01
#> "023" "011" "022" "03" "021" "022"
#> TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01 TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.TM.A84L.01
#> "021" "021" "022" "021" "022" "021"
#> TCGA.DU.8161.01 TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01
#> "011" "021" "022" "022" "012" "021"
#> TCGA.TM.A7C4.01 TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.HT.8108.01 TCGA.E1.A7YD.01
#> "021" "022" "022" "022" "021" "012"
#> TCGA.DU.7304.01 TCGA.S9.A7IY.01 TCGA.FG.7641.01 TCGA.P5.A736.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01
#> "021" "022" "022" "021" "021" "021"
#> TCGA.HT.7470.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.FG.A4MY.01 TCGA.TM.A7CF.01
#> "023" "022" "022" "03" "021" "021"
#> TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01 TCGA.DU.7010.01
#> "021" "022" "021" "013" "021" "023"
#> TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.DU.A7TD.01 TCGA.DU.6405.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "022" "022" "012" "011" "021" "021"
#> TCGA.DU.6401.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01 TCGA.HT.A74H.01
#> "021" "023" "021" "021" "021" "012"
#> TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01 TCGA.DB.A64L.01
#> "022" "023" "021" "011" "021" "022"
#> TCGA.VV.A829.01 TCGA.HT.A61B.01 TCGA.DH.A66B.01 TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01
#> "022" "021" "021" "021" "022" "022"
#> TCGA.HT.A4DS.01 TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01
#> "011" "021" "022" "021" "022" "012"
#> TCGA.DB.A64P.01 TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01
#> "022" "023" "021" "021" "021" "021"
#> TCGA.HW.A5KL.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.QH.A6CZ.01 TCGA.DH.A669.02
#> "021" "011" "021" "023" "022" "022"
#> TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01 TCGA.TQ.A7RJ.01 TCGA.WY.A858.01
#> "022" "021" "021" "021" "021" "021"
#> TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01
#> "03" "022" "021" "022" "022" "021"
#> TCGA.TM.A84I.01 TCGA.CS.5394.01 TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01
#> "023" "022" "012" "021" "021" "014"
#> TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "021" "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8163))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "022" "021" "023" "022" "023" "011"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.HT.A74L.01 TCGA.DU.A5TS.01 TCGA.DB.A4XA.01 TCGA.HT.A4DV.01
#> "022" "021" "022" "021" "022" "022"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01 TCGA.HT.8113.01
#> "013" "022" "023" "021" "021" "022"
#> TCGA.DH.A66G.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01 TCGA.HT.7689.01 TCGA.HT.8109.01
#> "021" "022" "021" "022" "023" "022"
#> TCGA.E1.A7YE.01 TCGA.S9.A7R1.01 TCGA.FG.A710.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01
#> "023" "022" "022" "023" "022" "022"
#> TCGA.QH.A6CU.01 TCGA.HW.7486.01 TCGA.FG.7634.01 TCGA.DU.8163.01 TCGA.DU.6407.02 TCGA.DU.6407.01
#> "022" "022" "022" "021" "023" "021"
#> TCGA.S9.A7IX.01 TCGA.HT.8010.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "012" "022" "021" "021" "021" "022"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.DU.7299.01 TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.DU.7011.01
#> "012" "021" "021" "011" "021" "021"
#> TCGA.TM.A84Q.01 TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.DB.5270.01
#> "021" "021" "012" "022" "022" "021"
#> TCGA.S9.A6WQ.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.E1.A7YU.01 TCGA.W9.A837.01 TCGA.TM.A7C5.01
#> "021" "021" "022" "023" "022" "022"
#> TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01 TCGA.HT.7601.01 TCGA.P5.A5ET.01
#> "022" "021" "021" "023" "021" "022"
#> TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.HT.7873.01
#> "021" "021" "021" "022" "022" "021"
#> TCGA.CS.4938.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "021" "022" "022" "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
#> "023" "012" "021" "023" "021" "012"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.DU.6403.01 TCGA.HW.7493.01
#> "014" "022" "022" "022" "011" "021"
#> TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01 TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01
#> "022" "021" "022" "021" "023" "022"
#> TCGA.DH.A7UT.01 TCGA.DU.7015.01 TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01
#> "021" "021" "021" "013" "021" "021"
#> TCGA.FG.A60K.01 TCGA.HT.7856.01 TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01
#> "022" "022" "03" "03" "021" "022"
#> TCGA.S9.A6TY.01 TCGA.CS.5395.01 TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01
#> "022" "012" "012" "011" "021" "021"
#> TCGA.TM.A84O.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.DU.5855.01 TCGA.HT.7884.01
#> "022" "021" "021" "022" "021" "021"
#> TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01 TCGA.WH.A86K.01
#> "022" "03" "012" "022" "022" "021"
#> TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01 TCGA.HT.A618.01
#> "014" "022" "013" "021" "021" "023"
#> TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01
#> "021" "022" "021" "012" "021" "022"
#> TCGA.S9.A7IZ.01 TCGA.DU.A6S7.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "021" "021" "022" "021" "022" "021"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.P5.A5F4.01 TCGA.QH.A65V.01
#> "022" "022" "012" "022" "021" "022"
#> TCGA.FG.8191.01 TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.CS.6666.01 TCGA.DU.7298.01
#> "021" "021" "022" "021" "021" "022"
#> TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01 TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01
#> "022" "011" "03" "021" "022" "022"
#> TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01 TCGA.DH.A66D.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01
#> "013" "021" "021" "021" "023" "022"
#> TCGA.DU.A76K.01 TCGA.TQ.A7RR.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.P5.A735.01
#> "012" "021" "011" "021" "022" "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" "011" "022" "013" "022" "023"
#> TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.S9.A6U5.01 TCGA.HT.7609.01 TCGA.DB.5274.01
#> "023" "022" "022" "022" "021" "022"
#> TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01 TCGA.DU.A6S2.01 TCGA.S9.A7R7.01
#> "022" "022" "014" "021" "022" "021"
#> TCGA.TM.A84R.01 TCGA.DB.A75M.01 TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.HT.7477.01 TCGA.HT.8012.01
#> "022" "021" "03" "021" "023" "022"
#> TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01 TCGA.S9.A7QZ.01
#> "021" "021" "021" "022" "021" "022"
#> TCGA.QH.A6X4.01 TCGA.P5.A77W.01 TCGA.DU.7302.01 TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.E1.5307.01
#> "022" "022" "022" "011" "021" "021"
#> TCGA.S9.A7QW.01 TCGA.DU.6402.01 TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01
#> "021" "012" "021" "021" "011" "021"
#> TCGA.HW.7495.01 TCGA.QH.A65R.01 TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01
#> "022" "022" "022" "021" "021" "021"
#> TCGA.HT.8104.01 TCGA.FG.A70Z.01 TCGA.DU.A7TC.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01
#> "011" "011" "021" "021" "022" "021"
#> TCGA.E1.5303.01 TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01
#> "021" "012" "022" "021" "021" "021"
#> TCGA.FG.A4MU.01 TCGA.HT.7875.01 TCGA.HT.7473.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01 TCGA.DU.7008.01
#> "012" "022" "021" "011" "022" "021"
#> TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.FG.8189.01 TCGA.DB.A75O.01 TCGA.HT.7688.01
#> "013" "012" "021" "03" "021" "021"
#> TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01 TCGA.P5.A5EY.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01
#> "023" "022" "014" "013" "022" "021"
#> TCGA.DU.5872.02 TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01
#> "03" "021" "021" "011" "022" "012"
#> TCGA.DU.5874.01 TCGA.S9.A6WE.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "022" "022" "021" "021" "014" "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" "022" "022" "021" "021" "022"
#> TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01 TCGA.DB.A4XF.01
#> "011" "022" "021" "014" "021" "021"
#> TCGA.HT.A74O.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01
#> "021" "021" "013" "022" "012" "022"
#> TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.E1.A7YJ.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.S9.A6TS.01
#> "021" "022" "012" "022" "022" "023"
#> TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01
#> "021" "021" "021" "021" "012" "023"
#> TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01 TCGA.DU.5849.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01
#> "014" "012" "021" "022" "021" "012"
#> TCGA.HT.7468.01 TCGA.FG.6692.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01 TCGA.HW.7489.01
#> "022" "012" "022" "022" "021" "021"
#> TCGA.R8.A6YH.01 TCGA.DU.7018.01 TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01
#> "021" "022" "022" "022" "022" "021"
#> TCGA.HT.7690.01 TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01
#> "021" "012" "021" "023" "021" "011"
#> TCGA.HT.A5RA.01 TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "011" "023" "022" "022" "022" "022"
#> TCGA.HT.8013.01 TCGA.HW.7490.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01
#> "021" "021" "021" "022" "022" "012"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.DB.A64V.01 TCGA.RY.A840.01 TCGA.E1.5302.01
#> "021" "023" "012" "022" "022" "021"
#> TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01 TCGA.DU.5847.01
#> "022" "022" "022" "021" "011" "011"
#> TCGA.E1.A7YK.01 TCGA.HT.7874.01 TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01
#> "023" "022" "022" "012" "011" "021"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.DU.6408.01 TCGA.DB.A4XB.01
#> "012" "023" "021" "011" "021" "021"
#> TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01 TCGA.P5.A72U.01 TCGA.QH.A870.01
#> "03" "021" "021" "022" "011" "021"
#> TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01
#> "022" "011" "011" "022" "022" "013"
#> TCGA.DU.A7TA.01 TCGA.HW.8319.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01
#> "021" "023" "022" "021" "021" "021"
#> TCGA.DU.6400.01 TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "022" "022" "022" "021" "022" "022"
#> TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01 TCGA.E1.A7YN.01
#> "021" "022" "021" "023" "021" "011"
#> TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.QH.A6XA.01 TCGA.HT.8111.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01
#> "022" "021" "021" "021" "011" "021"
#> TCGA.VM.A8CD.01 TCGA.RY.A83Y.01 TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01
#> "012" "022" "021" "021" "021" "021"
#> TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.DB.A64W.01 TCGA.R8.A6MO.01 TCGA.DU.A7T8.01
#> "021" "012" "022" "022" "022" "021"
#> TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01 TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01
#> "022" "022" "022" "022" "021" "022"
#> TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01 TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01
#> "021" "013" "022" "014" "023" "022"
#> TCGA.S9.A6U9.01 TCGA.CS.6290.01 TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01
#> "021" "021" "022" "021" "021" "023"
#> TCGA.HT.7860.01 TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.S9.A7J3.01 TCGA.P5.A5F2.01
#> "011" "021" "022" "021" "022" "021"
#> TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01
#> "023" "011" "022" "03" "021" "022"
#> TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01 TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.TM.A84L.01
#> "021" "021" "022" "021" "022" "021"
#> TCGA.DU.8161.01 TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01
#> "011" "021" "022" "022" "012" "021"
#> TCGA.TM.A7C4.01 TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.HT.8108.01 TCGA.E1.A7YD.01
#> "021" "022" "022" "022" "021" "012"
#> TCGA.DU.7304.01 TCGA.S9.A7IY.01 TCGA.FG.7641.01 TCGA.P5.A736.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01
#> "021" "022" "022" "021" "021" "021"
#> TCGA.HT.7470.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.FG.A4MY.01 TCGA.TM.A7CF.01
#> "023" "022" "022" "03" "021" "021"
#> TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01 TCGA.DU.7010.01
#> "021" "022" "021" "013" "021" "023"
#> TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.DU.A7TD.01 TCGA.DU.6405.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "022" "022" "012" "011" "021" "021"
#> TCGA.DU.6401.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01 TCGA.HT.A74H.01
#> "021" "023" "021" "021" "021" "012"
#> TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01 TCGA.DB.A64L.01
#> "022" "023" "021" "011" "021" "022"
#> TCGA.VV.A829.01 TCGA.HT.A61B.01 TCGA.DH.A66B.01 TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01
#> "022" "021" "021" "021" "022" "022"
#> TCGA.HT.A4DS.01 TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01
#> "011" "021" "022" "021" "022" "012"
#> TCGA.DB.A64P.01 TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01
#> "022" "023" "021" "021" "021" "021"
#> TCGA.HW.A5KL.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.QH.A6CZ.01 TCGA.DH.A669.02
#> "021" "011" "021" "023" "022" "022"
#> TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01 TCGA.TQ.A7RJ.01 TCGA.WY.A858.01
#> "022" "021" "021" "021" "021" "021"
#> TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01
#> "03" "022" "021" "022" "022" "021"
#> TCGA.TM.A84I.01 TCGA.CS.5394.01 TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01
#> "023" "022" "012" "021" "021" "014"
#> TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "021" "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 9726))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "022" "021" "023" "022" "023" "011"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.HT.A74L.01 TCGA.DU.A5TS.01 TCGA.DB.A4XA.01 TCGA.HT.A4DV.01
#> "022" "021" "022" "021" "022" "022"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01 TCGA.HT.8113.01
#> "013" "022" "023" "021" "021" "022"
#> TCGA.DH.A66G.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01 TCGA.HT.7689.01 TCGA.HT.8109.01
#> "021" "022" "021" "022" "023" "022"
#> TCGA.E1.A7YE.01 TCGA.S9.A7R1.01 TCGA.FG.A710.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01
#> "023" "022" "022" "023" "022" "022"
#> TCGA.QH.A6CU.01 TCGA.HW.7486.01 TCGA.FG.7634.01 TCGA.DU.8163.01 TCGA.DU.6407.02 TCGA.DU.6407.01
#> "022" "022" "022" "021" "023" "021"
#> TCGA.S9.A7IX.01 TCGA.HT.8010.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "012" "022" "021" "021" "021" "022"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.DU.7299.01 TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.DU.7011.01
#> "012" "021" "021" "011" "021" "021"
#> TCGA.TM.A84Q.01 TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.DB.5270.01
#> "021" "021" "012" "022" "022" "021"
#> TCGA.S9.A6WQ.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.E1.A7YU.01 TCGA.W9.A837.01 TCGA.TM.A7C5.01
#> "021" "021" "022" "023" "022" "022"
#> TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01 TCGA.HT.7601.01 TCGA.P5.A5ET.01
#> "022" "021" "021" "023" "021" "022"
#> TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.HT.7873.01
#> "021" "021" "021" "022" "022" "021"
#> TCGA.CS.4938.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "021" "022" "022" "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
#> "023" "012" "021" "023" "021" "012"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.DU.6403.01 TCGA.HW.7493.01
#> "014" "022" "022" "022" "011" "021"
#> TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01 TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01
#> "022" "021" "022" "021" "023" "022"
#> TCGA.DH.A7UT.01 TCGA.DU.7015.01 TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01
#> "021" "021" "021" "013" "021" "021"
#> TCGA.FG.A60K.01 TCGA.HT.7856.01 TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01
#> "022" "022" "03" "03" "021" "022"
#> TCGA.S9.A6TY.01 TCGA.CS.5395.01 TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01
#> "022" "012" "012" "011" "021" "021"
#> TCGA.TM.A84O.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.DU.5855.01 TCGA.HT.7884.01
#> "022" "021" "021" "022" "021" "021"
#> TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01 TCGA.WH.A86K.01
#> "022" "03" "012" "022" "022" "021"
#> TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01 TCGA.HT.A618.01
#> "014" "022" "013" "021" "021" "023"
#> TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01
#> "021" "022" "021" "012" "021" "022"
#> TCGA.S9.A7IZ.01 TCGA.DU.A6S7.01 TCGA.P5.A72Z.01 TCGA.HT.8114.01 TCGA.DU.8168.01 TCGA.HW.8321.01
#> "021" "021" "022" "021" "022" "021"
#> TCGA.TQ.A7RN.01 TCGA.DH.5141.01 TCGA.CS.6186.01 TCGA.EZ.7264.01 TCGA.P5.A5F4.01 TCGA.QH.A65V.01
#> "022" "022" "012" "022" "021" "022"
#> TCGA.FG.8191.01 TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.CS.6666.01 TCGA.DU.7298.01
#> "021" "021" "022" "021" "021" "022"
#> TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01 TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01
#> "022" "011" "03" "021" "022" "022"
#> TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01 TCGA.DH.A66D.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01
#> "013" "021" "021" "021" "023" "022"
#> TCGA.DU.A76K.01 TCGA.TQ.A7RR.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.P5.A735.01
#> "012" "021" "011" "021" "022" "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" "011" "022" "013" "022" "023"
#> TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.S9.A6U5.01 TCGA.HT.7609.01 TCGA.DB.5274.01
#> "023" "022" "022" "022" "021" "022"
#> TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01 TCGA.DU.A6S2.01 TCGA.S9.A7R7.01
#> "022" "022" "014" "021" "022" "021"
#> TCGA.TM.A84R.01 TCGA.DB.A75M.01 TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.HT.7477.01 TCGA.HT.8012.01
#> "022" "021" "03" "021" "023" "022"
#> TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01 TCGA.S9.A7QZ.01
#> "021" "021" "021" "022" "021" "022"
#> TCGA.QH.A6X4.01 TCGA.P5.A77W.01 TCGA.DU.7302.01 TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.E1.5307.01
#> "022" "022" "022" "011" "021" "021"
#> TCGA.S9.A7QW.01 TCGA.DU.6402.01 TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01
#> "021" "012" "021" "021" "011" "021"
#> TCGA.HW.7495.01 TCGA.QH.A65R.01 TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01
#> "022" "022" "022" "021" "021" "021"
#> TCGA.HT.8104.01 TCGA.FG.A70Z.01 TCGA.DU.A7TC.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01
#> "011" "011" "021" "021" "022" "021"
#> TCGA.E1.5303.01 TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01
#> "021" "012" "022" "021" "021" "021"
#> TCGA.FG.A4MU.01 TCGA.HT.7875.01 TCGA.HT.7473.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01 TCGA.DU.7008.01
#> "012" "022" "021" "011" "022" "021"
#> TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.FG.8189.01 TCGA.DB.A75O.01 TCGA.HT.7688.01
#> "013" "012" "021" "03" "021" "021"
#> TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01 TCGA.P5.A5EY.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01
#> "023" "022" "014" "013" "022" "021"
#> TCGA.DU.5872.02 TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01
#> "03" "021" "021" "011" "022" "012"
#> TCGA.DU.5874.01 TCGA.S9.A6WE.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "022" "022" "021" "021" "014" "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" "022" "022" "021" "021" "022"
#> TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01 TCGA.DB.A4XF.01
#> "011" "022" "021" "014" "021" "021"
#> TCGA.HT.A74O.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01
#> "021" "021" "013" "022" "012" "022"
#> TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.E1.A7YJ.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.S9.A6TS.01
#> "021" "022" "012" "022" "022" "023"
#> TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01
#> "021" "021" "021" "021" "012" "023"
#> TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01 TCGA.DU.5849.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01
#> "014" "012" "021" "022" "021" "012"
#> TCGA.HT.7468.01 TCGA.FG.6692.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01 TCGA.HW.7489.01
#> "022" "012" "022" "022" "021" "021"
#> TCGA.R8.A6YH.01 TCGA.DU.7018.01 TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01
#> "021" "022" "022" "022" "022" "021"
#> TCGA.HT.7690.01 TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01
#> "021" "012" "021" "023" "021" "011"
#> TCGA.HT.A5RA.01 TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "011" "023" "022" "022" "022" "022"
#> TCGA.HT.8013.01 TCGA.HW.7490.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01
#> "021" "021" "021" "022" "022" "012"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.DB.A64V.01 TCGA.RY.A840.01 TCGA.E1.5302.01
#> "021" "023" "012" "022" "022" "021"
#> TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01 TCGA.DU.5847.01
#> "022" "022" "022" "021" "011" "011"
#> TCGA.E1.A7YK.01 TCGA.HT.7874.01 TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01
#> "023" "022" "022" "012" "011" "021"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.DU.6408.01 TCGA.DB.A4XB.01
#> "012" "023" "021" "011" "021" "021"
#> TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01 TCGA.P5.A72U.01 TCGA.QH.A870.01
#> "03" "021" "021" "022" "011" "021"
#> TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01
#> "022" "011" "011" "022" "022" "013"
#> TCGA.DU.A7TA.01 TCGA.HW.8319.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01
#> "021" "023" "022" "021" "021" "021"
#> TCGA.DU.6400.01 TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "022" "022" "022" "021" "022" "022"
#> TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01 TCGA.E1.A7YN.01
#> "021" "022" "021" "023" "021" "011"
#> TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.QH.A6XA.01 TCGA.HT.8111.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01
#> "022" "021" "021" "021" "011" "021"
#> TCGA.VM.A8CD.01 TCGA.RY.A83Y.01 TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01
#> "012" "022" "021" "021" "021" "021"
#> TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.DB.A64W.01 TCGA.R8.A6MO.01 TCGA.DU.A7T8.01
#> "021" "012" "022" "022" "022" "021"
#> TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01 TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01
#> "022" "022" "022" "022" "021" "022"
#> TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01 TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01
#> "021" "013" "022" "014" "023" "022"
#> TCGA.S9.A6U9.01 TCGA.CS.6290.01 TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01
#> "021" "021" "022" "021" "021" "023"
#> TCGA.HT.7860.01 TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.S9.A7J3.01 TCGA.P5.A5F2.01
#> "011" "021" "022" "021" "022" "021"
#> TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01
#> "023" "011" "022" "03" "021" "022"
#> TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01 TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.TM.A84L.01
#> "021" "021" "022" "021" "022" "021"
#> TCGA.DU.8161.01 TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01
#> "011" "021" "022" "022" "012" "021"
#> TCGA.TM.A7C4.01 TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.HT.8108.01 TCGA.E1.A7YD.01
#> "021" "022" "022" "022" "021" "012"
#> TCGA.DU.7304.01 TCGA.S9.A7IY.01 TCGA.FG.7641.01 TCGA.P5.A736.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01
#> "021" "022" "022" "021" "021" "021"
#> TCGA.HT.7470.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.FG.A4MY.01 TCGA.TM.A7CF.01
#> "023" "022" "022" "03" "021" "021"
#> TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01 TCGA.DU.7010.01
#> "021" "022" "021" "013" "021" "023"
#> TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.DU.A7TD.01 TCGA.DU.6405.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "022" "022" "012" "011" "021" "021"
#> TCGA.DU.6401.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01 TCGA.HT.A74H.01
#> "021" "023" "021" "021" "021" "012"
#> TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01 TCGA.DB.A64L.01
#> "022" "023" "021" "011" "021" "022"
#> TCGA.VV.A829.01 TCGA.HT.A61B.01 TCGA.DH.A66B.01 TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01
#> "022" "021" "021" "021" "022" "022"
#> TCGA.HT.A4DS.01 TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01
#> "011" "021" "022" "021" "022" "012"
#> TCGA.DB.A64P.01 TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01
#> "022" "023" "021" "021" "021" "021"
#> TCGA.HW.A5KL.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.QH.A6CZ.01 TCGA.DH.A669.02
#> "021" "011" "021" "023" "022" "022"
#> TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01 TCGA.TQ.A7RJ.01 TCGA.WY.A858.01
#> "022" "021" "021" "021" "021" "021"
#> TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01
#> "03" "022" "021" "022" "022" "021"
#> TCGA.TM.A84I.01 TCGA.CS.5394.01 TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01
#> "023" "022" "012" "021" "021" "014"
#> TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "021" "022"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 10859))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "02" "02" "02" "02" "02" "011"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.HT.A74L.01 TCGA.DU.A5TS.01 TCGA.DB.A4XA.01 TCGA.HT.A4DV.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01 TCGA.HT.8113.01
#> "013" "02" "02" "02" "02" "02"
#> TCGA.DH.A66G.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01 TCGA.HT.7689.01 TCGA.HT.8109.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.E1.A7YE.01 TCGA.S9.A7R1.01 TCGA.FG.A710.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.QH.A6CU.01 TCGA.HW.7486.01 TCGA.FG.7634.01 TCGA.DU.8163.01 TCGA.DU.6407.02 TCGA.DU.6407.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.S9.A7IX.01 TCGA.HT.8010.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "012" "02" "02" "02" "02" "02"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.DU.7299.01 TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.DU.7011.01
#> "012" "02" "02" "011" "02" "02"
#> TCGA.TM.A84Q.01 TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.DB.5270.01
#> "02" "02" "012" "02" "02" "02"
#> TCGA.S9.A6WQ.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.E1.A7YU.01 TCGA.W9.A837.01 TCGA.TM.A7C5.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01 TCGA.HT.7601.01 TCGA.P5.A5ET.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.HT.7873.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.CS.4938.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "02" "02" "02" "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
#> "02" "012" "02" "02" "02" "012"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.DU.6403.01 TCGA.HW.7493.01
#> "014" "02" "02" "02" "011" "02"
#> TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01 TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.DH.A7UT.01 TCGA.DU.7015.01 TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01
#> "02" "02" "02" "013" "02" "02"
#> TCGA.FG.A60K.01 TCGA.HT.7856.01 TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01
#> "02" "02" "03" "03" "02" "02"
#> TCGA.S9.A6TY.01 TCGA.CS.5395.01 TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01
#> "02" "012" "012" "011" "02" "02"
#> TCGA.TM.A84O.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.DU.5855.01 TCGA.HT.7884.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01 TCGA.WH.A86K.01
#> "02" "03" "012" "02" "02" "02"
#> TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01 TCGA.HT.A618.01
#> "014" "02" "013" "02" "02" "02"
#> TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01
#> "02" "02" "02" "012" "02" "02"
#> TCGA.S9.A7IZ.01 TCGA.DU.A6S7.01 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.P5.A5F4.01 TCGA.QH.A65V.01
#> "02" "02" "012" "02" "02" "02"
#> TCGA.FG.8191.01 TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.CS.6666.01 TCGA.DU.7298.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01 TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01
#> "02" "011" "03" "02" "02" "02"
#> TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01 TCGA.DH.A66D.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01
#> "013" "02" "02" "02" "02" "02"
#> TCGA.DU.A76K.01 TCGA.TQ.A7RR.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.P5.A735.01
#> "012" "02" "011" "02" "02" "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" "011" "02" "013" "02" "02"
#> TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.S9.A6U5.01 TCGA.HT.7609.01 TCGA.DB.5274.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01 TCGA.DU.A6S2.01 TCGA.S9.A7R7.01
#> "02" "02" "014" "02" "02" "02"
#> TCGA.TM.A84R.01 TCGA.DB.A75M.01 TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.HT.7477.01 TCGA.HT.8012.01
#> "02" "02" "03" "02" "02" "02"
#> TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01 TCGA.S9.A7QZ.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.QH.A6X4.01 TCGA.P5.A77W.01 TCGA.DU.7302.01 TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.E1.5307.01
#> "02" "02" "02" "011" "02" "02"
#> TCGA.S9.A7QW.01 TCGA.DU.6402.01 TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01
#> "02" "012" "02" "02" "011" "02"
#> TCGA.HW.7495.01 TCGA.QH.A65R.01 TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.8104.01 TCGA.FG.A70Z.01 TCGA.DU.A7TC.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01
#> "011" "011" "02" "02" "02" "02"
#> TCGA.E1.5303.01 TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01
#> "02" "012" "02" "02" "02" "02"
#> TCGA.FG.A4MU.01 TCGA.HT.7875.01 TCGA.HT.7473.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01 TCGA.DU.7008.01
#> "012" "02" "02" "011" "02" "02"
#> TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.FG.8189.01 TCGA.DB.A75O.01 TCGA.HT.7688.01
#> "013" "012" "02" "03" "02" "02"
#> TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01 TCGA.P5.A5EY.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01
#> "02" "02" "014" "013" "02" "02"
#> TCGA.DU.5872.02 TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01
#> "03" "02" "02" "011" "02" "012"
#> TCGA.DU.5874.01 TCGA.S9.A6WE.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "02" "02" "02" "02" "014" "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" "02" "02" "02" "02" "02"
#> TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01 TCGA.DB.A4XF.01
#> "011" "02" "02" "014" "02" "02"
#> TCGA.HT.A74O.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01
#> "02" "02" "013" "02" "012" "02"
#> TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.E1.A7YJ.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.S9.A6TS.01
#> "02" "02" "012" "02" "02" "02"
#> TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01
#> "02" "02" "02" "02" "012" "02"
#> TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01 TCGA.DU.5849.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01
#> "014" "012" "02" "02" "02" "012"
#> TCGA.HT.7468.01 TCGA.FG.6692.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01 TCGA.HW.7489.01
#> "02" "012" "02" "02" "02" "02"
#> TCGA.R8.A6YH.01 TCGA.DU.7018.01 TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.7690.01 TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01
#> "02" "012" "02" "02" "02" "011"
#> TCGA.HT.A5RA.01 TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "011" "02" "02" "02" "02" "02"
#> TCGA.HT.8013.01 TCGA.HW.7490.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01
#> "02" "02" "02" "02" "02" "012"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.DB.A64V.01 TCGA.RY.A840.01 TCGA.E1.5302.01
#> "02" "02" "012" "02" "02" "02"
#> TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01 TCGA.DU.5847.01
#> "02" "02" "02" "02" "011" "011"
#> TCGA.E1.A7YK.01 TCGA.HT.7874.01 TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01
#> "02" "02" "02" "012" "011" "02"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.DU.6408.01 TCGA.DB.A4XB.01
#> "012" "02" "02" "011" "02" "02"
#> TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01 TCGA.P5.A72U.01 TCGA.QH.A870.01
#> "03" "02" "02" "02" "011" "02"
#> TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01
#> "02" "011" "011" "02" "02" "013"
#> TCGA.DU.A7TA.01 TCGA.HW.8319.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.DU.6400.01 TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01 TCGA.E1.A7YN.01
#> "02" "02" "02" "02" "02" "011"
#> TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.QH.A6XA.01 TCGA.HT.8111.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01
#> "02" "02" "02" "02" "011" "02"
#> TCGA.VM.A8CD.01 TCGA.RY.A83Y.01 TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01
#> "012" "02" "02" "02" "02" "02"
#> TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.DB.A64W.01 TCGA.R8.A6MO.01 TCGA.DU.A7T8.01
#> "02" "012" "02" "02" "02" "02"
#> TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01 TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01 TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01
#> "02" "013" "02" "014" "02" "02"
#> TCGA.S9.A6U9.01 TCGA.CS.6290.01 TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.7860.01 TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.S9.A7J3.01 TCGA.P5.A5F2.01
#> "011" "02" "02" "02" "02" "02"
#> TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01
#> "02" "011" "02" "03" "02" "02"
#> TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01 TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.TM.A84L.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.DU.8161.01 TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01
#> "011" "02" "02" "02" "012" "02"
#> TCGA.TM.A7C4.01 TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.HT.8108.01 TCGA.E1.A7YD.01
#> "02" "02" "02" "02" "02" "012"
#> TCGA.DU.7304.01 TCGA.S9.A7IY.01 TCGA.FG.7641.01 TCGA.P5.A736.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.7470.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.FG.A4MY.01 TCGA.TM.A7CF.01
#> "02" "02" "02" "03" "02" "02"
#> TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01 TCGA.DU.7010.01
#> "02" "02" "02" "013" "02" "02"
#> TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.DU.A7TD.01 TCGA.DU.6405.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "02" "02" "012" "011" "02" "02"
#> TCGA.DU.6401.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01 TCGA.HT.A74H.01
#> "02" "02" "02" "02" "02" "012"
#> TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01 TCGA.DB.A64L.01
#> "02" "02" "02" "011" "02" "02"
#> TCGA.VV.A829.01 TCGA.HT.A61B.01 TCGA.DH.A66B.01 TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.A4DS.01 TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01
#> "011" "02" "02" "02" "02" "012"
#> TCGA.DB.A64P.01 TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HW.A5KL.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.QH.A6CZ.01 TCGA.DH.A669.02
#> "02" "011" "02" "02" "02" "02"
#> TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01 TCGA.TQ.A7RJ.01 TCGA.WY.A858.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01
#> "03" "02" "02" "02" "02" "02"
#> TCGA.TM.A84I.01 TCGA.CS.5394.01 TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01
#> "02" "02" "012" "02" "02" "014"
#> TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "02" "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 13116))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "02" "02" "02" "02" "02" "011"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.HT.A74L.01 TCGA.DU.A5TS.01 TCGA.DB.A4XA.01 TCGA.HT.A4DV.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01 TCGA.HT.8113.01
#> "013" "02" "02" "02" "02" "02"
#> TCGA.DH.A66G.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01 TCGA.HT.7689.01 TCGA.HT.8109.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.E1.A7YE.01 TCGA.S9.A7R1.01 TCGA.FG.A710.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.QH.A6CU.01 TCGA.HW.7486.01 TCGA.FG.7634.01 TCGA.DU.8163.01 TCGA.DU.6407.02 TCGA.DU.6407.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.S9.A7IX.01 TCGA.HT.8010.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "012" "02" "02" "02" "02" "02"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.DU.7299.01 TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.DU.7011.01
#> "012" "02" "02" "011" "02" "02"
#> TCGA.TM.A84Q.01 TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.DB.5270.01
#> "02" "02" "012" "02" "02" "02"
#> TCGA.S9.A6WQ.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.E1.A7YU.01 TCGA.W9.A837.01 TCGA.TM.A7C5.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01 TCGA.HT.7601.01 TCGA.P5.A5ET.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.HT.7873.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.CS.4938.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "02" "02" "02" "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
#> "02" "012" "02" "02" "02" "012"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.DU.6403.01 TCGA.HW.7493.01
#> "014" "02" "02" "02" "011" "02"
#> TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01 TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.DH.A7UT.01 TCGA.DU.7015.01 TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01
#> "02" "02" "02" "013" "02" "02"
#> TCGA.FG.A60K.01 TCGA.HT.7856.01 TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01
#> "02" "02" "03" "03" "02" "02"
#> TCGA.S9.A6TY.01 TCGA.CS.5395.01 TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01
#> "02" "012" "012" "011" "02" "02"
#> TCGA.TM.A84O.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.DU.5855.01 TCGA.HT.7884.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01 TCGA.WH.A86K.01
#> "02" "03" "012" "02" "02" "02"
#> TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01 TCGA.HT.A618.01
#> "014" "02" "013" "02" "02" "02"
#> TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01
#> "02" "02" "02" "012" "02" "02"
#> TCGA.S9.A7IZ.01 TCGA.DU.A6S7.01 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.P5.A5F4.01 TCGA.QH.A65V.01
#> "02" "02" "012" "02" "02" "02"
#> TCGA.FG.8191.01 TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.CS.6666.01 TCGA.DU.7298.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01 TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01
#> "02" "011" "03" "02" "02" "02"
#> TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01 TCGA.DH.A66D.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01
#> "013" "02" "02" "02" "02" "02"
#> TCGA.DU.A76K.01 TCGA.TQ.A7RR.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.P5.A735.01
#> "012" "02" "011" "02" "02" "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" "011" "02" "013" "02" "02"
#> TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.S9.A6U5.01 TCGA.HT.7609.01 TCGA.DB.5274.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01 TCGA.DU.A6S2.01 TCGA.S9.A7R7.01
#> "02" "02" "014" "02" "02" "02"
#> TCGA.TM.A84R.01 TCGA.DB.A75M.01 TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.HT.7477.01 TCGA.HT.8012.01
#> "02" "02" "03" "02" "02" "02"
#> TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01 TCGA.S9.A7QZ.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.QH.A6X4.01 TCGA.P5.A77W.01 TCGA.DU.7302.01 TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.E1.5307.01
#> "02" "02" "02" "011" "02" "02"
#> TCGA.S9.A7QW.01 TCGA.DU.6402.01 TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01
#> "02" "012" "02" "02" "011" "02"
#> TCGA.HW.7495.01 TCGA.QH.A65R.01 TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.8104.01 TCGA.FG.A70Z.01 TCGA.DU.A7TC.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01
#> "011" "011" "02" "02" "02" "02"
#> TCGA.E1.5303.01 TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01
#> "02" "012" "02" "02" "02" "02"
#> TCGA.FG.A4MU.01 TCGA.HT.7875.01 TCGA.HT.7473.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01 TCGA.DU.7008.01
#> "012" "02" "02" "011" "02" "02"
#> TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.FG.8189.01 TCGA.DB.A75O.01 TCGA.HT.7688.01
#> "013" "012" "02" "03" "02" "02"
#> TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01 TCGA.P5.A5EY.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01
#> "02" "02" "014" "013" "02" "02"
#> TCGA.DU.5872.02 TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01
#> "03" "02" "02" "011" "02" "012"
#> TCGA.DU.5874.01 TCGA.S9.A6WE.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "02" "02" "02" "02" "014" "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" "02" "02" "02" "02" "02"
#> TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01 TCGA.DB.A4XF.01
#> "011" "02" "02" "014" "02" "02"
#> TCGA.HT.A74O.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01
#> "02" "02" "013" "02" "012" "02"
#> TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.E1.A7YJ.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.S9.A6TS.01
#> "02" "02" "012" "02" "02" "02"
#> TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01
#> "02" "02" "02" "02" "012" "02"
#> TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01 TCGA.DU.5849.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01
#> "014" "012" "02" "02" "02" "012"
#> TCGA.HT.7468.01 TCGA.FG.6692.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01 TCGA.HW.7489.01
#> "02" "012" "02" "02" "02" "02"
#> TCGA.R8.A6YH.01 TCGA.DU.7018.01 TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.7690.01 TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01
#> "02" "012" "02" "02" "02" "011"
#> TCGA.HT.A5RA.01 TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "011" "02" "02" "02" "02" "02"
#> TCGA.HT.8013.01 TCGA.HW.7490.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01
#> "02" "02" "02" "02" "02" "012"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.DB.A64V.01 TCGA.RY.A840.01 TCGA.E1.5302.01
#> "02" "02" "012" "02" "02" "02"
#> TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01 TCGA.DU.5847.01
#> "02" "02" "02" "02" "011" "011"
#> TCGA.E1.A7YK.01 TCGA.HT.7874.01 TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01
#> "02" "02" "02" "012" "011" "02"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.DU.6408.01 TCGA.DB.A4XB.01
#> "012" "02" "02" "011" "02" "02"
#> TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01 TCGA.P5.A72U.01 TCGA.QH.A870.01
#> "03" "02" "02" "02" "011" "02"
#> TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01
#> "02" "011" "011" "02" "02" "013"
#> TCGA.DU.A7TA.01 TCGA.HW.8319.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.DU.6400.01 TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01 TCGA.E1.A7YN.01
#> "02" "02" "02" "02" "02" "011"
#> TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.QH.A6XA.01 TCGA.HT.8111.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01
#> "02" "02" "02" "02" "011" "02"
#> TCGA.VM.A8CD.01 TCGA.RY.A83Y.01 TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01
#> "012" "02" "02" "02" "02" "02"
#> TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.DB.A64W.01 TCGA.R8.A6MO.01 TCGA.DU.A7T8.01
#> "02" "012" "02" "02" "02" "02"
#> TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01 TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01 TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01
#> "02" "013" "02" "014" "02" "02"
#> TCGA.S9.A6U9.01 TCGA.CS.6290.01 TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.7860.01 TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.S9.A7J3.01 TCGA.P5.A5F2.01
#> "011" "02" "02" "02" "02" "02"
#> TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01
#> "02" "011" "02" "03" "02" "02"
#> TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01 TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.TM.A84L.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.DU.8161.01 TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01
#> "011" "02" "02" "02" "012" "02"
#> TCGA.TM.A7C4.01 TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.HT.8108.01 TCGA.E1.A7YD.01
#> "02" "02" "02" "02" "02" "012"
#> TCGA.DU.7304.01 TCGA.S9.A7IY.01 TCGA.FG.7641.01 TCGA.P5.A736.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.7470.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.FG.A4MY.01 TCGA.TM.A7CF.01
#> "02" "02" "02" "03" "02" "02"
#> TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01 TCGA.DU.7010.01
#> "02" "02" "02" "013" "02" "02"
#> TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.DU.A7TD.01 TCGA.DU.6405.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "02" "02" "012" "011" "02" "02"
#> TCGA.DU.6401.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01 TCGA.HT.A74H.01
#> "02" "02" "02" "02" "02" "012"
#> TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01 TCGA.DB.A64L.01
#> "02" "02" "02" "011" "02" "02"
#> TCGA.VV.A829.01 TCGA.HT.A61B.01 TCGA.DH.A66B.01 TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.A4DS.01 TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01
#> "011" "02" "02" "02" "02" "012"
#> TCGA.DB.A64P.01 TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HW.A5KL.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.QH.A6CZ.01 TCGA.DH.A669.02
#> "02" "011" "02" "02" "02" "02"
#> TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01 TCGA.TQ.A7RJ.01 TCGA.WY.A858.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01
#> "03" "02" "02" "02" "02" "02"
#> TCGA.TM.A84I.01 TCGA.CS.5394.01 TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01
#> "02" "02" "012" "02" "02" "014"
#> TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "02" "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 36057))
#> TCGA.E1.5319.01 TCGA.HT.7693.01 TCGA.CS.6665.01 TCGA.S9.A7J2.01 TCGA.FG.A6J3.01 TCGA.FG.6688.01
#> "02" "02" "02" "02" "02" "01"
#> TCGA.S9.A6TX.01 TCGA.VM.A8C8.01 TCGA.HT.A74L.01 TCGA.DU.A5TS.01 TCGA.DB.A4XA.01 TCGA.HT.A4DV.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.TQ.A7RP.01 TCGA.E1.5311.01 TCGA.E1.A7YI.01 TCGA.E1.5305.01 TCGA.F6.A8O4.01 TCGA.HT.8113.01
#> "01" "02" "02" "02" "02" "02"
#> TCGA.DH.A66G.01 TCGA.HT.7620.01 TCGA.P5.A731.01 TCGA.HT.7480.01 TCGA.HT.7689.01 TCGA.HT.8109.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.E1.A7YE.01 TCGA.S9.A7R1.01 TCGA.FG.A710.01 TCGA.S9.A7J0.01 TCGA.DU.A6S6.01 TCGA.HT.7877.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.QH.A6CU.01 TCGA.HW.7486.01 TCGA.FG.7634.01 TCGA.DU.8163.01 TCGA.DU.6407.02 TCGA.DU.6407.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.S9.A7IX.01 TCGA.HT.8010.01 TCGA.P5.A5F1.01 TCGA.VM.A8CF.01 TCGA.DU.6542.01 TCGA.FG.7638.01
#> "01" "02" "02" "02" "02" "02"
#> TCGA.VW.A8FI.01 TCGA.DH.5143.01 TCGA.DU.7299.01 TCGA.DU.8165.01 TCGA.CS.5393.01 TCGA.DU.7011.01
#> "01" "02" "02" "01" "02" "02"
#> TCGA.TM.A84Q.01 TCGA.DB.5281.01 TCGA.DU.A76L.01 TCGA.HT.7605.01 TCGA.FG.A6J1.01 TCGA.DB.5270.01
#> "02" "02" "01" "02" "02" "02"
#> TCGA.S9.A6WQ.01 TCGA.HT.8106.01 TCGA.HT.7608.01 TCGA.E1.A7YU.01 TCGA.W9.A837.01 TCGA.TM.A7C5.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.S9.A7QY.01 TCGA.QH.A6CW.01 TCGA.S9.A6WO.01 TCGA.IK.7675.01 TCGA.HT.7601.01 TCGA.P5.A5ET.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.7472.01 TCGA.HT.7880.01 TCGA.E1.A7Z3.01 TCGA.P5.A77X.01 TCGA.FG.A6IZ.01 TCGA.HT.7873.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.CS.4938.01 TCGA.KT.A74X.01 TCGA.P5.A5EX.01 TCGA.VM.A8CH.01 TCGA.HT.7476.01 TCGA.DB.A75L.01
#> "02" "02" "02" "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
#> "02" "01" "02" "02" "02" "01"
#> TCGA.FG.7643.01 TCGA.E1.A7YO.01 TCGA.TQ.A7RG.01 TCGA.QH.A6X5.01 TCGA.DU.6403.01 TCGA.HW.7493.01
#> "01" "02" "02" "02" "01" "02"
#> TCGA.RY.A847.01 TCGA.DU.8166.01 TCGA.VM.A8CA.01 TCGA.HT.7855.01 TCGA.S9.A89Z.01 TCGA.DB.A4XG.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.DH.A7UT.01 TCGA.DU.7015.01 TCGA.HT.A616.01 TCGA.FG.8181.01 TCGA.HT.7611.01 TCGA.HT.8018.01
#> "02" "02" "02" "01" "02" "02"
#> TCGA.FG.A60K.01 TCGA.HT.7856.01 TCGA.FG.5963.01 TCGA.FG.5963.02 TCGA.DU.5851.01 TCGA.DU.A7T6.01
#> "02" "02" "03" "03" "02" "02"
#> TCGA.S9.A6TY.01 TCGA.CS.5395.01 TCGA.DU.7292.01 TCGA.HT.A5RC.01 TCGA.WY.A85C.01 TCGA.DB.A4XC.01
#> "02" "01" "01" "01" "02" "02"
#> TCGA.TM.A84O.01 TCGA.P5.A72W.01 TCGA.S9.A6TU.01 TCGA.HT.A61A.01 TCGA.DU.5855.01 TCGA.HT.7884.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.TQ.A7RQ.01 TCGA.TM.A84C.01 TCGA.FG.A4MW.01 TCGA.IK.8125.01 TCGA.HT.A74K.01 TCGA.WH.A86K.01
#> "02" "03" "01" "02" "02" "02"
#> TCGA.DB.A75P.01 TCGA.QH.A6X8.01 TCGA.S9.A89V.01 TCGA.WY.A85E.01 TCGA.HT.A5R5.01 TCGA.HT.A618.01
#> "01" "02" "01" "02" "02" "02"
#> TCGA.FG.6691.01 TCGA.HT.7467.01 TCGA.S9.A7R3.01 TCGA.QH.A6CX.01 TCGA.FG.A4MX.01 TCGA.HT.7681.01
#> "02" "02" "02" "01" "02" "02"
#> TCGA.S9.A7IZ.01 TCGA.DU.A6S7.01 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.P5.A5F4.01 TCGA.QH.A65V.01
#> "02" "02" "01" "02" "02" "02"
#> TCGA.FG.8191.01 TCGA.DH.5142.01 TCGA.DU.A6S8.01 TCGA.E1.A7YW.01 TCGA.CS.6666.01 TCGA.DU.7298.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.DB.A64R.01 TCGA.DU.6406.01 TCGA.S9.A6UA.01 TCGA.FG.A60L.01 TCGA.CS.5390.01 TCGA.S9.A6WP.01
#> "02" "01" "03" "02" "02" "02"
#> TCGA.DU.A7TB.01 TCGA.DB.5280.01 TCGA.TM.A84T.01 TCGA.DH.A66D.01 TCGA.RY.A83Z.01 TCGA.DB.5278.01
#> "01" "02" "02" "02" "02" "02"
#> TCGA.DU.A76K.01 TCGA.TQ.A7RR.01 TCGA.DU.8162.01 TCGA.TQ.A7RH.01 TCGA.E1.A7YS.01 TCGA.P5.A735.01
#> "01" "02" "01" "02" "02" "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" "02" "01" "02" "02"
#> TCGA.DB.A64X.01 TCGA.FG.7637.01 TCGA.VM.A8CE.01 TCGA.S9.A6U5.01 TCGA.HT.7609.01 TCGA.DB.5274.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HW.7487.01 TCGA.HW.7491.01 TCGA.HT.7691.01 TCGA.CS.4944.01 TCGA.DU.A6S2.01 TCGA.S9.A7R7.01
#> "02" "02" "01" "02" "02" "02"
#> TCGA.TM.A84R.01 TCGA.DB.A75M.01 TCGA.DU.6392.01 TCGA.HW.A5KM.01 TCGA.HT.7477.01 TCGA.HT.8012.01
#> "02" "02" "03" "02" "02" "02"
#> TCGA.DU.8167.01 TCGA.S9.A6U1.01 TCGA.FG.5965.01 TCGA.FG.8187.01 TCGA.HT.A614.01 TCGA.S9.A7QZ.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.QH.A6X4.01 TCGA.P5.A77W.01 TCGA.DU.7302.01 TCGA.DU.7012.01 TCGA.DU.6399.01 TCGA.E1.5307.01
#> "02" "02" "02" "01" "02" "02"
#> TCGA.S9.A7QW.01 TCGA.DU.6402.01 TCGA.HT.7604.01 TCGA.P5.A733.01 TCGA.FG.A87Q.01 TCGA.HT.7684.01
#> "02" "01" "02" "02" "01" "02"
#> TCGA.HW.7495.01 TCGA.QH.A65R.01 TCGA.DU.A7TG.01 TCGA.DH.A7UV.01 TCGA.HT.7879.01 TCGA.TM.A84F.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.8104.01 TCGA.FG.A70Z.01 TCGA.DU.A7TC.01 TCGA.HT.7610.01 TCGA.S9.A6TW.01 TCGA.FG.A60J.01
#> "01" "01" "02" "02" "02" "02"
#> TCGA.E1.5303.01 TCGA.QH.A6XC.01 TCGA.HT.7481.01 TCGA.FN.7833.01 TCGA.E1.A7Z4.01 TCGA.DU.A5TR.01
#> "02" "01" "02" "02" "02" "02"
#> TCGA.FG.A4MU.01 TCGA.HT.7875.01 TCGA.HT.7473.01 TCGA.TM.A7C3.01 TCGA.S9.A7IQ.01 TCGA.DU.7008.01
#> "01" "02" "02" "01" "02" "02"
#> TCGA.DB.A64O.01 TCGA.DU.A5TT.01 TCGA.S9.A6WG.01 TCGA.FG.8189.01 TCGA.DB.A75O.01 TCGA.HT.7688.01
#> "01" "01" "02" "03" "02" "02"
#> TCGA.DU.7304.02 TCGA.DU.6394.01 TCGA.HT.8019.01 TCGA.P5.A5EY.01 TCGA.S9.A6WD.01 TCGA.DU.5872.01
#> "02" "02" "01" "01" "02" "02"
#> TCGA.DU.5872.02 TCGA.FG.8185.01 TCGA.HT.7902.01 TCGA.CS.5397.01 TCGA.TQ.A7RU.01 TCGA.HW.A5KK.01
#> "03" "02" "02" "01" "02" "01"
#> TCGA.DU.5874.01 TCGA.S9.A6WE.01 TCGA.FG.6690.01 TCGA.HW.8320.01 TCGA.CS.6669.01 TCGA.S9.A7R2.01
#> "02" "02" "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" "02" "02" "02" "02" "02"
#> TCGA.S9.A6WM.01 TCGA.R8.A73M.01 TCGA.CS.4942.01 TCGA.HT.7680.01 TCGA.DB.A4X9.01 TCGA.DB.A4XF.01
#> "01" "02" "02" "01" "02" "02"
#> TCGA.HT.A74O.01 TCGA.FG.8188.01 TCGA.P5.A5F6.01 TCGA.DU.A6S3.01 TCGA.HT.8110.01 TCGA.DB.A4XH.01
#> "02" "02" "01" "02" "01" "02"
#> TCGA.HT.7485.01 TCGA.VW.A7QS.01 TCGA.E1.A7YJ.01 TCGA.S9.A6WI.01 TCGA.DU.8164.01 TCGA.S9.A6TS.01
#> "02" "02" "01" "02" "02" "02"
#> TCGA.DB.A64S.01 TCGA.VV.A86M.01 TCGA.TQ.A8XE.01 TCGA.CS.6667.01 TCGA.E1.A7YL.01 TCGA.E1.A7YV.01
#> "02" "02" "02" "02" "01" "02"
#> TCGA.HT.8558.01 TCGA.HT.A61C.01 TCGA.TQ.A7RW.01 TCGA.DU.5849.01 TCGA.DU.A7TI.01 TCGA.QH.A6CV.01
#> "01" "01" "02" "02" "02" "01"
#> TCGA.HT.7468.01 TCGA.FG.6692.01 TCGA.TQ.A7RI.01 TCGA.DB.5279.01 TCGA.S9.A6U8.01 TCGA.HW.7489.01
#> "02" "01" "02" "02" "02" "02"
#> TCGA.R8.A6YH.01 TCGA.DU.7018.01 TCGA.HT.7677.01 TCGA.FG.A713.01 TCGA.DU.7300.01 TCGA.TM.A7CA.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.7690.01 TCGA.DU.7013.01 TCGA.FG.6689.01 TCGA.DU.7007.01 TCGA.TQ.A7RF.01 TCGA.KT.A7W1.01
#> "02" "01" "02" "02" "02" "01"
#> TCGA.HT.A5RA.01 TCGA.DB.5277.01 TCGA.HT.7694.01 TCGA.TM.A84M.01 TCGA.F6.A8O3.01 TCGA.QH.A86X.01
#> "01" "02" "02" "02" "02" "02"
#> TCGA.HT.8013.01 TCGA.HW.7490.01 TCGA.QH.A65S.01 TCGA.DU.A76R.01 TCGA.DH.5144.01 TCGA.CS.6188.01
#> "02" "02" "02" "02" "02" "01"
#> TCGA.P5.A780.01 TCGA.HT.7606.01 TCGA.DU.A7TJ.01 TCGA.DB.A64V.01 TCGA.RY.A840.01 TCGA.E1.5302.01
#> "02" "02" "01" "02" "02" "02"
#> TCGA.HW.A5KJ.01 TCGA.HT.A615.01 TCGA.HT.8105.01 TCGA.DU.7309.01 TCGA.DU.A5TY.01 TCGA.DU.5847.01
#> "02" "02" "02" "02" "01" "01"
#> TCGA.E1.A7YK.01 TCGA.HT.7874.01 TCGA.HT.7471.01 TCGA.HT.7882.01 TCGA.DU.5854.01 TCGA.DU.6395.01
#> "02" "02" "02" "01" "01" "02"
#> TCGA.HT.8011.01 TCGA.S9.A6TV.01 TCGA.P5.A5EW.01 TCGA.DU.5852.01 TCGA.DU.6408.01 TCGA.DB.A4XB.01
#> "01" "02" "02" "01" "02" "02"
#> TCGA.E1.A7YY.01 TCGA.FG.A4MT.01 TCGA.FG.A4MT.02 TCGA.HT.A619.01 TCGA.P5.A72U.01 TCGA.QH.A870.01
#> "03" "02" "02" "02" "01" "02"
#> TCGA.HT.A5R9.01 TCGA.DU.6404.02 TCGA.DU.6404.01 TCGA.FG.5964.01 TCGA.CS.5396.01 TCGA.HT.8107.01
#> "02" "01" "01" "02" "02" "01"
#> TCGA.DU.A7TA.01 TCGA.HW.8319.01 TCGA.DH.A7UR.01 TCGA.TM.A84H.01 TCGA.S9.A6TZ.01 TCGA.HT.7479.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.DU.6400.01 TCGA.S9.A6WL.01 TCGA.DB.A75K.01 TCGA.DB.A4XD.01 TCGA.DB.A64Q.01 TCGA.P5.A737.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.DB.5275.01 TCGA.S9.A6WH.01 TCGA.HT.7602.01 TCGA.DU.A5TU.01 TCGA.HT.A5RB.01 TCGA.E1.A7YN.01
#> "02" "02" "02" "02" "02" "01"
#> TCGA.HT.7616.01 TCGA.S9.A7R8.01 TCGA.QH.A6XA.01 TCGA.HT.8111.01 TCGA.E1.A7Z2.01 TCGA.DU.A5TP.01
#> "02" "02" "02" "02" "01" "02"
#> TCGA.VM.A8CD.01 TCGA.RY.A83Y.01 TCGA.HT.7482.01 TCGA.TQ.A7RK.02 TCGA.TQ.A7RK.01 TCGA.HT.7858.01
#> "01" "02" "02" "02" "02" "02"
#> TCGA.HT.7475.01 TCGA.HT.8564.01 TCGA.DB.A64U.01 TCGA.DB.A64W.01 TCGA.R8.A6MO.01 TCGA.DU.A7T8.01
#> "02" "01" "02" "02" "02" "02"
#> TCGA.HW.8322.01 TCGA.DU.5870.02 TCGA.CS.6668.01 TCGA.DU.5870.01 TCGA.FG.7636.01 TCGA.HT.7692.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.WY.A859.01 TCGA.HT.7854.01 TCGA.R8.A6ML.01 TCGA.VM.A8C9.01 TCGA.HT.7686.01 TCGA.DU.6410.01
#> "02" "01" "02" "01" "02" "02"
#> TCGA.S9.A6U9.01 TCGA.CS.6290.01 TCGA.TQ.A7RO.01 TCGA.DU.7019.01 TCGA.FG.A711.01 TCGA.TQ.A7RM.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.7860.01 TCGA.S9.A7R4.01 TCGA.E1.5318.01 TCGA.HT.7676.01 TCGA.S9.A7J3.01 TCGA.P5.A5F2.01
#> "01" "02" "02" "02" "02" "02"
#> TCGA.E1.5304.01 TCGA.DU.7006.01 TCGA.TM.A84S.01 TCGA.HT.7469.01 TCGA.WY.A85B.01 TCGA.TQ.A7RS.01
#> "02" "01" "02" "03" "02" "02"
#> TCGA.S9.A7QX.01 TCGA.CS.4943.01 TCGA.QH.A65Z.01 TCGA.DB.5276.01 TCGA.P5.A730.01 TCGA.TM.A84L.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.DU.8161.01 TCGA.WY.A85D.01 TCGA.RY.A83X.01 TCGA.S9.A6UB.01 TCGA.E1.A7YM.01 TCGA.DB.5273.01
#> "01" "02" "02" "02" "01" "02"
#> TCGA.TM.A7C4.01 TCGA.DH.A66F.01 TCGA.HT.7607.01 TCGA.DU.6393.01 TCGA.HT.8108.01 TCGA.E1.A7YD.01
#> "02" "02" "02" "02" "02" "01"
#> TCGA.DU.7304.01 TCGA.S9.A7IY.01 TCGA.FG.7641.01 TCGA.P5.A736.01 TCGA.P5.A5EV.01 TCGA.DU.7301.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.7470.01 TCGA.DU.7009.01 TCGA.P5.A781.01 TCGA.DH.5140.01 TCGA.FG.A4MY.01 TCGA.TM.A7CF.01
#> "02" "02" "02" "03" "02" "02"
#> TCGA.TM.A7CF.02 TCGA.FG.8186.01 TCGA.S9.A6U6.01 TCGA.HT.8015.01 TCGA.RY.A845.01 TCGA.DU.7010.01
#> "02" "02" "02" "01" "02" "02"
#> TCGA.S9.A6U2.01 TCGA.S9.A6WN.01 TCGA.DU.A7TD.01 TCGA.DU.6405.01 TCGA.FG.8182.01 TCGA.QH.A6X3.01
#> "02" "02" "01" "01" "02" "02"
#> TCGA.DU.6401.01 TCGA.DU.6396.01 TCGA.E1.A7YH.01 TCGA.DU.7306.01 TCGA.HT.A74J.01 TCGA.HT.A74H.01
#> "02" "02" "02" "02" "02" "01"
#> TCGA.DH.A7US.01 TCGA.FG.A87N.01 TCGA.HT.7478.01 TCGA.DU.7290.01 TCGA.DB.A4XE.01 TCGA.DB.A64L.01
#> "02" "02" "02" "01" "02" "02"
#> TCGA.VV.A829.01 TCGA.HT.A61B.01 TCGA.DH.A66B.01 TCGA.HT.7603.01 TCGA.DU.6397.02 TCGA.DU.6397.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HT.A4DS.01 TCGA.DU.5853.01 TCGA.CS.6670.01 TCGA.DU.7014.01 TCGA.QH.A65X.01 TCGA.TM.A84B.01
#> "01" "02" "02" "02" "02" "01"
#> TCGA.DB.A64P.01 TCGA.FG.5965.02 TCGA.FG.A70Y.01 TCGA.TQ.A7RV.01 TCGA.TQ.A7RV.02 TCGA.HT.A5R7.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.HW.A5KL.01 TCGA.DU.8158.01 TCGA.HT.7474.01 TCGA.DH.A7UU.01 TCGA.QH.A6CZ.01 TCGA.DH.A669.02
#> "02" "01" "02" "02" "02" "02"
#> TCGA.DH.A669.01 TCGA.QH.A6X9.01 TCGA.P5.A5EZ.01 TCGA.DU.5871.01 TCGA.TQ.A7RJ.01 TCGA.WY.A858.01
#> "02" "02" "02" "02" "02" "02"
#> TCGA.TM.A84J.01 TCGA.VM.A8CB.01 TCGA.HT.7483.01 TCGA.HT.7687.01 TCGA.TM.A84G.01 TCGA.E1.A7Z6.01
#> "03" "02" "02" "02" "02" "02"
#> TCGA.TM.A84I.01 TCGA.CS.5394.01 TCGA.HT.A617.01 TCGA.DU.A76O.01 TCGA.DU.A5TW.01 TCGA.HT.7857.01
#> "02" "02" "01" "02" "02" "01"
#> TCGA.WY.A85A.01 TCGA.FG.5962.01
#> "02" "02"
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 = 1373),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1373),
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 = 1386),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1386),
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 = 1614),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1614),
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 = 2070),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2070),
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 = 2422),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2422),
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 = 3007),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3007),
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 = 3040),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3040),
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 = 3432),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3432),
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 = 3536),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3536),
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 = 5170),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5170),
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 = 5644),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5644),
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 = 7885),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 7885),
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 = 8163),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 8163),
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 = 9726),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 9726),
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 = 10859),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 10859),
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 = 13116),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 13116),
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 = 36057),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 36057),
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 = 1373))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1386))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1614))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2070))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2422))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3007))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3040))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3432))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3536))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5170))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5644))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 7885))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 8163))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 9726))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 10859))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 13116))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 36057))
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-leaf .
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 375969 rows and 500 columns, randomly sampled from 530 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 '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 0.2915 0.709 0.709
#> 3 3 0.988 0.965 0.979 0.0471 0.990 0.986
#> 4 4 0.938 0.889 0.946 0.1223 0.949 0.928
#> 5 5 0.864 0.900 0.939 0.0770 0.976 0.963
#> 6 6 0.830 0.870 0.933 0.0603 0.997 0.995
#> 7 7 0.844 0.855 0.925 0.1287 0.903 0.847
#> 8 8 0.822 0.832 0.878 0.0896 0.972 0.948
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
get_classes(res, k = 2)
#> class p
#> TCGA.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.HT.A74L.01 2 0.000
#> TCGA.DU.A5TS.01 2 0.000
#> TCGA.DB.A4XA.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.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.HT.7620.01 2 0.000
#> TCGA.P5.A731.01 2 0.000
#> TCGA.HT.7480.01 2 0.000
#> TCGA.HT.7689.01 2 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.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.FG.7634.01 2 0.000
#> TCGA.DU.8163.01 2 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.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.DU.7299.01 2 0.000
#> TCGA.DU.8165.01 1 0.000
#> TCGA.CS.5393.01 2 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.DB.5270.01 2 0.000
#> TCGA.S9.A6WQ.01 2 0.000
#> TCGA.HT.8106.01 2 0.000
#> TCGA.HT.7608.01 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.E1.A7Z3.01 2 0.000
#> TCGA.P5.A77X.01 2 0.000
#> TCGA.FG.A6IZ.01 2 0.000
#> TCGA.HT.7873.01 2 0.000
#> TCGA.CS.4938.01 2 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.TQ.A7RG.01 2 0.000
#> TCGA.QH.A6X5.01 2 0.000
#> TCGA.DU.6403.01 1 0.000
#> TCGA.HW.7493.01 2 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.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.P5.A72W.01 2 0.000
#> TCGA.S9.A6TU.01 2 0.000
#> TCGA.HT.A61A.01 2 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.HT.A618.01 2 0.000
#> TCGA.FG.6691.01 2 0.000
#> TCGA.HT.7467.01 2 0.000
#> TCGA.S9.A7R3.01 2 0.000
#> TCGA.QH.A6CX.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.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.P5.A5F4.01 2 0.000
#> TCGA.QH.A65V.01 2 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.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.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.DU.8162.01 1 0.000
#> TCGA.TQ.A7RH.01 2 0.000
#> TCGA.E1.A7YS.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.DB.A64X.01 2 0.000
#> TCGA.FG.7637.01 2 0.000
#> TCGA.VM.A8CE.01 2 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.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.HT.7477.01 2 0.000
#> TCGA.HT.8012.01 2 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.S9.A7QZ.01 2 0.000
#> TCGA.QH.A6X4.01 2 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.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.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.HT.7473.01 2 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.FG.8189.01 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.S9.A6WD.01 2 0.000
#> TCGA.DU.5872.01 2 0.000
#> TCGA.DU.5872.02 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.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.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.FG.8188.01 2 0.000
#> TCGA.P5.A5F6.01 1 0.000
#> TCGA.DU.A6S3.01 2 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.E1.A7YJ.01 1 0.000
#> TCGA.S9.A6WI.01 2 0.000
#> TCGA.DU.8164.01 2 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.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.DU.A7TI.01 2 0.000
#> TCGA.QH.A6CV.01 1 0.000
#> TCGA.HT.7468.01 2 0.000
#> TCGA.FG.6692.01 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.DU.7018.01 2 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.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.TM.A84M.01 2 0.000
#> TCGA.F6.A8O3.01 2 0.000
#> TCGA.QH.A86X.01 2 0.000
#> TCGA.HT.8013.01 2 0.000
#> TCGA.HW.7490.01 2 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.P5.A780.01 2 0.000
#> TCGA.HT.7606.01 2 0.000
#> TCGA.DU.A7TJ.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.DU.5847.01 1 0.000
#> TCGA.E1.A7YK.01 2 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.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.DU.6408.01 2 0.000
#> TCGA.DB.A4XB.01 2 0.000
#> TCGA.E1.A7YY.01 2 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.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.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.DB.A64Q.01 2 0.000
#> TCGA.P5.A737.01 2 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.QH.A6XA.01 2 0.000
#> TCGA.HT.8111.01 2 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.HT.7475.01 2 0.000
#> TCGA.HT.8564.01 1 0.000
#> TCGA.DB.A64U.01 2 0.000
#> TCGA.DB.A64W.01 2 0.000
#> TCGA.R8.A6MO.01 2 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.CS.6290.01 2 0.000
#> TCGA.TQ.A7RO.01 2 0.000
#> TCGA.DU.7019.01 2 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.S9.A7J3.01 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 2 1.000
#> 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.TM.A84L.01 2 0.000
#> TCGA.DU.8161.01 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.HT.8108.01 2 0.000
#> TCGA.E1.A7YD.01 1 0.000
#> TCGA.DU.7304.01 2 0.000
#> TCGA.S9.A7IY.01 2 0.000
#> TCGA.FG.7641.01 2 0.000
#> TCGA.P5.A736.01 2 0.000
#> TCGA.P5.A5EV.01 2 0.000
#> TCGA.DU.7301.01 2 0.000
#> TCGA.HT.7470.01 2 0.000
#> TCGA.DU.7009.01 2 0.000
#> TCGA.P5.A781.01 2 0.000
#> TCGA.DH.5140.01 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.DU.A7TD.01 1 0.000
#> TCGA.DU.6405.01 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.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.HT.A61B.01 2 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.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.HW.A5KL.01 2 0.000
#> TCGA.DU.8158.01 1 0.000
#> TCGA.HT.7474.01 2 0.000
#> TCGA.DH.A7UU.01 2 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 0.498
#> TCGA.VM.A8CB.01 2 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
get_classes(res, k = 3)
#> 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.HT.A74L.01 2 0.000
#> TCGA.DU.A5TS.01 2 0.000
#> TCGA.DB.A4XA.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.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.HT.7620.01 2 0.000
#> TCGA.P5.A731.01 2 0.000
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#> 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.HT.A61B.01 2 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.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.HW.A5KL.01 2 0.000
#> TCGA.DU.8158.01 1 0.000
#> TCGA.HT.7474.01 2 0.000
#> TCGA.DH.A7UU.01 2 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 3 0.000
#> TCGA.VM.A8CB.01 2 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 1.000
#> TCGA.WY.A85A.01 2 0.000
#> TCGA.FG.5962.01 2 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 4 0.000
#> TCGA.S9.A7J2.01 2 0.000
#> TCGA.FG.A6J3.01 4 0.000
#> TCGA.FG.6688.01 1 0.000
#> TCGA.S9.A6TX.01 2 0.000
#> TCGA.VM.A8C8.01 2 0.000
#> TCGA.HT.A74L.01 2 0.000
#> TCGA.DU.A5TS.01 2 0.000
#> TCGA.DB.A4XA.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.E1.A7YI.01 4 0.000
#> TCGA.E1.5305.01 2 0.000
#> TCGA.F6.A8O4.01 2 0.000
#> TCGA.HT.8113.01 2 1.000
#> TCGA.DH.A66G.01 2 0.000
#> TCGA.HT.7620.01 2 0.000
#> TCGA.P5.A731.01 2 0.000
#> TCGA.HT.7480.01 2 0.000
#> TCGA.HT.7689.01 2 0.000
#> TCGA.HT.8109.01 2 0.000
#> TCGA.E1.A7YE.01 4 0.000
#> TCGA.S9.A7R1.01 2 0.000
#> TCGA.FG.A710.01 2 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.FG.7634.01 2 0.000
#> TCGA.DU.8163.01 2 0.000
#> TCGA.DU.6407.02 4 0.000
#> TCGA.DU.6407.01 2 0.000
#> TCGA.S9.A7IX.01 1 0.000
#> TCGA.HT.8010.01 2 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.DU.7299.01 2 0.000
#> TCGA.DU.8165.01 1 0.000
#> TCGA.CS.5393.01 2 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.DB.5270.01 2 0.000
#> TCGA.S9.A6WQ.01 2 0.000
#> TCGA.HT.8106.01 4 1.000
#> TCGA.HT.7608.01 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 1.000
#> TCGA.E1.A7Z3.01 2 0.000
#> TCGA.P5.A77X.01 2 0.000
#> TCGA.FG.A6IZ.01 2 0.000
#> TCGA.HT.7873.01 2 0.000
#> TCGA.CS.4938.01 2 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 4 0.000
#> TCGA.TQ.A8XE.02 2 0.000
#> TCGA.S9.A6U0.01 1 0.000
#> TCGA.FG.7643.01 1 0.249
#> TCGA.E1.A7YO.01 2 0.000
#> TCGA.TQ.A7RG.01 2 0.000
#> TCGA.QH.A6X5.01 2 0.000
#> TCGA.DU.6403.01 1 0.000
#> TCGA.HW.7493.01 2 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.DH.A7UT.01 2 0.000
#> TCGA.DU.7015.01 2 0.000
#> TCGA.HT.A616.01 2 0.000
#> TCGA.FG.8181.01 3 0.000
#> TCGA.HT.7611.01 2 0.000
#> TCGA.HT.8018.01 2 1.000
#> TCGA.FG.A60K.01 2 0.000
#> TCGA.HT.7856.01 2 1.000
#> TCGA.FG.5963.01 3 1.000
#> TCGA.FG.5963.02 3 0.000
#> TCGA.DU.5851.01 2 0.000
#> TCGA.DU.A7T6.01 4 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.P5.A72W.01 2 0.000
#> TCGA.S9.A6TU.01 2 0.000
#> TCGA.HT.A61A.01 2 1.000
#> 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 3 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.HT.A618.01 2 0.751
#> TCGA.FG.6691.01 2 0.000
#> TCGA.HT.7467.01 2 1.000
#> TCGA.S9.A7R3.01 2 0.000
#> TCGA.QH.A6CX.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.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.P5.A5F4.01 2 0.000
#> TCGA.QH.A65V.01 2 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.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 3 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.RY.A83Z.01 4 0.000
#> TCGA.DB.5278.01 2 0.000
#> TCGA.DU.A76K.01 1 0.000
#> TCGA.TQ.A7RR.01 2 0.000
#> TCGA.DU.8162.01 1 1.000
#> TCGA.TQ.A7RH.01 2 0.000
#> TCGA.E1.A7YS.01 2 0.000
#> TCGA.P5.A735.01 2 0.000
#> TCGA.DU.7294.01 2 0.000
#> TCGA.E1.A7YQ.01 3 0.000
#> TCGA.HT.7881.01 2 0.249
#> TCGA.QH.A6CS.01 1 0.000
#> TCGA.HT.7695.01 2 0.000
#> TCGA.P5.A5EU.01 4 0.000
#> TCGA.DB.A64X.01 2 0.000
#> TCGA.FG.7637.01 2 0.000
#> TCGA.VM.A8CE.01 2 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 1.000
#> TCGA.CS.4944.01 2 0.000
#> TCGA.DU.A6S2.01 2 0.000
#> TCGA.S9.A7R7.01 2 0.000
#> TCGA.TM.A84R.01 4 1.000
#> TCGA.DB.A75M.01 2 0.000
#> TCGA.DU.6392.01 3 0.000
#> TCGA.HW.A5KM.01 2 0.000
#> TCGA.HT.7477.01 2 0.502
#> TCGA.HT.8012.01 2 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.S9.A7QZ.01 2 0.000
#> TCGA.QH.A6X4.01 2 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.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 4 1.000
#> 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.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.HT.7473.01 2 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.FG.8189.01 3 0.000
#> TCGA.DB.A75O.01 2 0.000
#> TCGA.HT.7688.01 2 0.000
#> TCGA.DU.7304.02 2 1.000
#> TCGA.DU.6394.01 2 0.000
#> TCGA.HT.8019.01 3 0.000
#> TCGA.P5.A5EY.01 1 0.000
#> TCGA.S9.A6WD.01 2 0.000
#> TCGA.DU.5872.01 2 0.000
#> TCGA.DU.5872.02 3 0.000
#> TCGA.FG.8185.01 2 0.000
#> TCGA.HT.7902.01 4 1.000
#> 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.FG.6690.01 2 0.000
#> TCGA.HW.8320.01 2 0.000
#> TCGA.CS.6669.01 1 1.000
#> 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.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.FG.8188.01 2 0.000
#> TCGA.P5.A5F6.01 1 1.000
#> TCGA.DU.A6S3.01 2 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.E1.A7YJ.01 1 0.000
#> TCGA.S9.A6WI.01 2 1.000
#> TCGA.DU.8164.01 2 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.E1.A7YL.01 1 0.000
#> TCGA.E1.A7YV.01 4 0.000
#> TCGA.HT.8558.01 3 0.000
#> TCGA.HT.A61C.01 1 0.000
#> TCGA.TQ.A7RW.01 2 0.000
#> TCGA.DU.5849.01 2 0.000
#> TCGA.DU.A7TI.01 2 0.000
#> TCGA.QH.A6CV.01 1 0.000
#> TCGA.HT.7468.01 2 0.000
#> TCGA.FG.6692.01 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.DU.7018.01 2 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.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.TM.A84M.01 2 0.000
#> TCGA.F6.A8O3.01 2 0.000
#> TCGA.QH.A86X.01 2 0.000
#> TCGA.HT.8013.01 2 0.000
#> TCGA.HW.7490.01 2 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.P5.A780.01 2 0.000
#> TCGA.HT.7606.01 2 0.000
#> TCGA.DU.A7TJ.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.DU.5847.01 1 0.000
#> TCGA.E1.A7YK.01 2 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.HT.8011.01 1 0.249
#> TCGA.S9.A6TV.01 2 0.000
#> TCGA.P5.A5EW.01 2 0.000
#> TCGA.DU.5852.01 1 0.000
#> TCGA.DU.6408.01 2 0.000
#> TCGA.DB.A4XB.01 2 0.000
#> TCGA.E1.A7YY.01 3 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 0.498
#> TCGA.DU.6404.01 1 0.747
#> TCGA.FG.5964.01 2 0.000
#> TCGA.CS.5396.01 2 0.000
#> TCGA.HT.8107.01 3 0.249
#> TCGA.DU.A7TA.01 2 0.000
#> TCGA.HW.8319.01 2 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.DB.A64Q.01 2 0.000
#> TCGA.P5.A737.01 2 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.QH.A6XA.01 2 0.000
#> TCGA.HT.8111.01 2 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.HT.7475.01 2 0.000
#> TCGA.HT.8564.01 1 0.751
#> TCGA.DB.A64U.01 2 0.000
#> TCGA.DB.A64W.01 2 0.000
#> TCGA.R8.A6MO.01 2 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.CS.6290.01 2 0.000
#> TCGA.TQ.A7RO.01 2 0.000
#> TCGA.DU.7019.01 2 0.000
#> TCGA.FG.A711.01 2 0.000
#> TCGA.TQ.A7RM.01 2 0.502
#> 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.S9.A7J3.01 2 0.000
#> TCGA.P5.A5F2.01 2 0.000
#> TCGA.E1.5304.01 4 1.000
#> TCGA.DU.7006.01 1 0.000
#> TCGA.TM.A84S.01 2 0.000
#> TCGA.HT.7469.01 3 0.751
#> 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 0.498
#> TCGA.P5.A730.01 2 0.000
#> TCGA.TM.A84L.01 2 0.000
#> TCGA.DU.8161.01 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 1.000
#> TCGA.DU.6393.01 2 0.000
#> TCGA.HT.8108.01 2 0.000
#> TCGA.E1.A7YD.01 1 0.000
#> TCGA.DU.7304.01 2 0.000
#> TCGA.S9.A7IY.01 2 0.000
#> TCGA.FG.7641.01 2 0.000
#> TCGA.P5.A736.01 2 0.000
#> TCGA.P5.A5EV.01 2 0.000
#> TCGA.DU.7301.01 2 0.000
#> TCGA.HT.7470.01 2 0.000
#> TCGA.DU.7009.01 2 0.000
#> TCGA.P5.A781.01 2 0.000
#> TCGA.DH.5140.01 3 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 4 0.000
#> TCGA.S9.A6U2.01 2 0.000
#> TCGA.S9.A6WN.01 4 1.000
#> TCGA.DU.A7TD.01 1 0.000
#> TCGA.DU.6405.01 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.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 4 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.HT.A61B.01 2 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.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 4 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 4 0.498
#> TCGA.HW.A5KL.01 2 0.000
#> TCGA.DU.8158.01 1 0.000
#> TCGA.HT.7474.01 2 0.000
#> TCGA.DH.A7UU.01 2 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 3 0.000
#> TCGA.VM.A8CB.01 2 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 4 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 3 1.000
#> TCGA.WY.A85A.01 2 0.000
#> TCGA.FG.5962.01 2 0.000
get_classes(res, k = 5)
#> class p
#> TCGA.E1.5319.01 2 0.000
#> TCGA.HT.7693.01 2 0.000
#> TCGA.CS.6665.01 4 0.000
#> TCGA.S9.A7J2.01 2 0.000
#> TCGA.FG.A6J3.01 4 0.000
#> TCGA.FG.6688.01 5 1.000
#> TCGA.S9.A6TX.01 2 0.000
#> TCGA.VM.A8C8.01 2 0.000
#> TCGA.HT.A74L.01 2 0.000
#> TCGA.DU.A5TS.01 2 0.000
#> TCGA.DB.A4XA.01 2 0.000
#> TCGA.HT.A4DV.01 2 1.000
#> TCGA.TQ.A7RP.01 5 0.498
#> TCGA.E1.5311.01 2 0.000
#> TCGA.E1.A7YI.01 4 0.000
#> TCGA.E1.5305.01 2 0.000
#> TCGA.F6.A8O4.01 2 0.000
#> TCGA.HT.8113.01 4 1.000
#> TCGA.DH.A66G.01 2 0.000
#> TCGA.HT.7620.01 2 1.000
#> TCGA.P5.A731.01 2 0.000
#> TCGA.HT.7480.01 2 0.000
#> TCGA.HT.7689.01 2 0.000
#> TCGA.HT.8109.01 2 0.000
#> TCGA.E1.A7YE.01 4 0.000
#> TCGA.S9.A7R1.01 2 0.000
#> TCGA.FG.A710.01 2 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.FG.7634.01 2 0.000
#> TCGA.DU.8163.01 2 0.000
#> TCGA.DU.6407.02 4 0.000
#> TCGA.DU.6407.01 2 0.000
#> TCGA.S9.A7IX.01 1 0.000
#> TCGA.HT.8010.01 2 0.747
#> 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.DU.7299.01 2 0.000
#> TCGA.DU.8165.01 1 0.000
#> TCGA.CS.5393.01 2 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.DB.5270.01 2 0.000
#> TCGA.S9.A6WQ.01 2 0.000
#> TCGA.HT.8106.01 4 0.747
#> TCGA.HT.7608.01 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 4 1.000
#> TCGA.E1.A7Z3.01 2 0.000
#> TCGA.P5.A77X.01 2 0.000
#> TCGA.FG.A6IZ.01 2 0.000
#> TCGA.HT.7873.01 2 0.000
#> TCGA.CS.4938.01 2 0.000
#> TCGA.KT.A74X.01 2 0.000
#> TCGA.P5.A5EX.01 2 1.000
#> 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 4 1.000
#> TCGA.CS.4941.01 1 0.000
#> TCGA.RY.A843.01 2 0.000
#> TCGA.S9.A7IS.01 4 0.000
#> TCGA.TQ.A8XE.02 2 0.000
#> TCGA.S9.A6U0.01 1 0.000
#> TCGA.FG.7643.01 5 0.000
#> TCGA.E1.A7YO.01 2 0.000
#> TCGA.TQ.A7RG.01 2 0.000
#> TCGA.QH.A6X5.01 2 0.000
#> TCGA.DU.6403.01 1 0.000
#> TCGA.HW.7493.01 2 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.DH.A7UT.01 2 0.000
#> TCGA.DU.7015.01 2 0.000
#> TCGA.HT.A616.01 2 0.000
#> TCGA.FG.8181.01 5 0.000
#> TCGA.HT.7611.01 2 0.000
#> TCGA.HT.8018.01 4 1.000
#> TCGA.FG.A60K.01 2 0.000
#> TCGA.HT.7856.01 4 1.000
#> TCGA.FG.5963.01 3 1.000
#> TCGA.FG.5963.02 3 0.000
#> TCGA.DU.5851.01 2 1.000
#> TCGA.DU.A7T6.01 4 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.P5.A72W.01 2 0.000
#> TCGA.S9.A6TU.01 2 0.000
#> TCGA.HT.A61A.01 4 1.000
#> 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 3 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 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 2 0.000
#> TCGA.HT.A618.01 4 0.000
#> TCGA.FG.6691.01 2 0.000
#> TCGA.HT.7467.01 4 1.000
#> TCGA.S9.A7R3.01 2 0.000
#> TCGA.QH.A6CX.01 1 1.000
#> 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.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.P5.A5F4.01 2 0.000
#> TCGA.QH.A65V.01 2 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.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 5 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 5 1.000
#> TCGA.DB.5280.01 2 0.000
#> TCGA.TM.A84T.01 2 0.000
#> TCGA.DH.A66D.01 2 0.000
#> TCGA.RY.A83Z.01 4 0.000
#> TCGA.DB.5278.01 2 0.000
#> TCGA.DU.A76K.01 1 0.000
#> TCGA.TQ.A7RR.01 2 0.000
#> TCGA.DU.8162.01 5 0.000
#> TCGA.TQ.A7RH.01 2 0.000
#> TCGA.E1.A7YS.01 2 0.000
#> TCGA.P5.A735.01 2 0.000
#> TCGA.DU.7294.01 2 0.000
#> TCGA.E1.A7YQ.01 5 0.751
#> TCGA.HT.7881.01 4 1.000
#> TCGA.QH.A6CS.01 5 0.000
#> TCGA.HT.7695.01 2 0.000
#> TCGA.P5.A5EU.01 4 0.000
#> TCGA.DB.A64X.01 2 0.000
#> TCGA.FG.7637.01 2 0.000
#> TCGA.VM.A8CE.01 2 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 5 0.000
#> TCGA.CS.4944.01 2 0.000
#> TCGA.DU.A6S2.01 2 0.000
#> TCGA.S9.A7R7.01 2 0.249
#> TCGA.TM.A84R.01 4 1.000
#> TCGA.DB.A75M.01 2 0.000
#> TCGA.DU.6392.01 3 0.000
#> TCGA.HW.A5KM.01 2 0.000
#> TCGA.HT.7477.01 4 1.000
#> TCGA.HT.8012.01 2 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.S9.A7QZ.01 2 0.000
#> TCGA.QH.A6X4.01 2 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.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 4 1.000
#> TCGA.DH.A7UV.01 2 0.000
#> TCGA.HT.7879.01 2 0.000
#> TCGA.TM.A84F.01 4 1.000
#> TCGA.HT.8104.01 1 0.000
#> TCGA.FG.A70Z.01 1 0.000
#> TCGA.DU.A7TC.01 2 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.HT.7473.01 2 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 1.000
#> TCGA.DU.A5TT.01 1 0.000
#> TCGA.S9.A6WG.01 2 1.000
#> TCGA.FG.8189.01 3 1.000
#> TCGA.DB.A75O.01 2 0.000
#> TCGA.HT.7688.01 2 0.000
#> TCGA.DU.7304.02 4 1.000
#> TCGA.DU.6394.01 2 0.000
#> TCGA.HT.8019.01 5 0.000
#> TCGA.P5.A5EY.01 5 0.000
#> TCGA.S9.A6WD.01 2 0.000
#> TCGA.DU.5872.01 2 0.000
#> TCGA.DU.5872.02 5 1.000
#> TCGA.FG.8185.01 2 0.000
#> TCGA.HT.7902.01 4 0.000
#> TCGA.CS.5397.01 1 0.000
#> 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.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 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.S9.A6WM.01 1 0.000
#> TCGA.R8.A73M.01 2 0.000
#> TCGA.CS.4942.01 2 0.000
#> TCGA.HT.7680.01 5 0.000
#> TCGA.DB.A4X9.01 2 0.000
#> TCGA.DB.A4XF.01 2 0.000
#> TCGA.HT.A74O.01 2 0.000
#> TCGA.FG.8188.01 2 0.000
#> TCGA.P5.A5F6.01 5 0.000
#> TCGA.DU.A6S3.01 2 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.E1.A7YJ.01 1 0.000
#> TCGA.S9.A6WI.01 4 1.000
#> TCGA.DU.8164.01 2 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.E1.A7YL.01 1 0.000
#> TCGA.E1.A7YV.01 4 0.000
#> TCGA.HT.8558.01 5 0.000
#> TCGA.HT.A61C.01 1 0.000
#> TCGA.TQ.A7RW.01 2 0.000
#> TCGA.DU.5849.01 2 0.000
#> TCGA.DU.A7TI.01 2 0.000
#> TCGA.QH.A6CV.01 1 0.000
#> TCGA.HT.7468.01 2 0.000
#> TCGA.FG.6692.01 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.DU.7018.01 2 0.000
#> TCGA.HT.7677.01 2 0.000
#> TCGA.FG.A713.01 2 1.000
#> TCGA.DU.7300.01 2 0.000
#> TCGA.TM.A7CA.01 2 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 0.498
#> TCGA.TM.A84M.01 2 0.000
#> TCGA.F6.A8O3.01 2 0.000
#> TCGA.QH.A86X.01 2 0.000
#> TCGA.HT.8013.01 2 0.000
#> TCGA.HW.7490.01 2 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.P5.A780.01 2 0.000
#> TCGA.HT.7606.01 2 0.000
#> TCGA.DU.A7TJ.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.DU.5847.01 1 0.000
#> TCGA.E1.A7YK.01 4 1.000
#> TCGA.HT.7874.01 4 1.000
#> TCGA.HT.7471.01 2 0.000
#> TCGA.HT.7882.01 1 1.000
#> TCGA.DU.5854.01 1 0.000
#> TCGA.DU.6395.01 2 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.DU.6408.01 2 0.000
#> TCGA.DB.A4XB.01 2 0.000
#> TCGA.E1.A7YY.01 3 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 5 1.000
#> TCGA.DU.6404.01 5 1.000
#> TCGA.FG.5964.01 2 0.000
#> TCGA.CS.5396.01 2 0.000
#> TCGA.HT.8107.01 5 0.000
#> TCGA.DU.A7TA.01 2 0.000
#> TCGA.HW.8319.01 2 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.DB.A64Q.01 2 0.000
#> TCGA.P5.A737.01 2 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 1.000
#> TCGA.HT.7616.01 2 0.000
#> TCGA.S9.A7R8.01 2 0.000
#> TCGA.QH.A6XA.01 2 0.000
#> TCGA.HT.8111.01 2 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.HT.7475.01 2 0.000
#> TCGA.HT.8564.01 1 1.000
#> TCGA.DB.A64U.01 2 0.000
#> TCGA.DB.A64W.01 2 0.000
#> TCGA.R8.A6MO.01 2 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 5 1.000
#> TCGA.R8.A6ML.01 2 0.000
#> TCGA.VM.A8C9.01 5 0.000
#> TCGA.HT.7686.01 2 0.000
#> TCGA.DU.6410.01 2 0.000
#> TCGA.S9.A6U9.01 2 0.000
#> TCGA.CS.6290.01 2 0.000
#> TCGA.TQ.A7RO.01 2 0.000
#> TCGA.DU.7019.01 2 0.000
#> TCGA.FG.A711.01 2 0.000
#> TCGA.TQ.A7RM.01 2 1.000
#> 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.S9.A7J3.01 2 0.000
#> TCGA.P5.A5F2.01 2 0.000
#> TCGA.E1.5304.01 4 1.000
#> TCGA.DU.7006.01 1 0.000
#> TCGA.TM.A84S.01 2 0.000
#> TCGA.HT.7469.01 3 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 1.000
#> TCGA.P5.A730.01 2 0.000
#> TCGA.TM.A84L.01 2 0.000
#> TCGA.DU.8161.01 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 4 1.000
#> TCGA.DU.6393.01 2 0.000
#> TCGA.HT.8108.01 2 0.000
#> TCGA.E1.A7YD.01 1 0.000
#> TCGA.DU.7304.01 2 0.000
#> TCGA.S9.A7IY.01 2 0.000
#> TCGA.FG.7641.01 2 0.000
#> TCGA.P5.A736.01 2 0.000
#> TCGA.P5.A5EV.01 2 0.000
#> TCGA.DU.7301.01 2 0.000
#> TCGA.HT.7470.01 2 0.000
#> TCGA.DU.7009.01 2 0.000
#> TCGA.P5.A781.01 2 0.000
#> TCGA.DH.5140.01 3 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 5 0.000
#> TCGA.RY.A845.01 2 0.000
#> TCGA.DU.7010.01 4 0.000
#> TCGA.S9.A6U2.01 2 0.000
#> TCGA.S9.A6WN.01 4 0.000
#> TCGA.DU.A7TD.01 1 0.000
#> TCGA.DU.6405.01 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.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 1.000
#> TCGA.DH.A7US.01 2 0.000
#> TCGA.FG.A87N.01 4 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.HT.A61B.01 2 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.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 4 0.000
#> TCGA.FG.A70Y.01 2 0.000
#> TCGA.TQ.A7RV.01 2 0.000
#> TCGA.TQ.A7RV.02 2 0.498
#> TCGA.HT.A5R7.01 4 0.000
#> TCGA.HW.A5KL.01 2 0.000
#> TCGA.DU.8158.01 1 1.000
#> TCGA.HT.7474.01 2 0.000
#> TCGA.DH.A7UU.01 2 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 3 0.000
#> TCGA.VM.A8CB.01 2 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 4 0.000
#> TCGA.CS.5394.01 2 0.000
#> TCGA.HT.A617.01 1 1.000
#> TCGA.DU.A76O.01 2 0.000
#> TCGA.DU.A5TW.01 2 0.000
#> TCGA.HT.7857.01 5 0.000
#> TCGA.WY.A85A.01 2 0.000
#> TCGA.FG.5962.01 2 0.000
get_classes(res, k = 6)
#> class p
#> TCGA.E1.5319.01 2 0.000
#> TCGA.HT.7693.01 2 0.000
#> TCGA.CS.6665.01 4 0.000
#> TCGA.S9.A7J2.01 2 0.000
#> TCGA.FG.A6J3.01 4 0.000
#> TCGA.FG.6688.01 1 1.000
#> TCGA.S9.A6TX.01 2 0.000
#> TCGA.VM.A8C8.01 2 0.000
#> TCGA.HT.A74L.01 2 0.000
#> TCGA.DU.A5TS.01 2 0.000
#> TCGA.DB.A4XA.01 2 0.000
#> TCGA.HT.A4DV.01 2 1.000
#> TCGA.TQ.A7RP.01 5 1.000
#> TCGA.E1.5311.01 2 0.000
#> TCGA.E1.A7YI.01 4 0.000
#> TCGA.E1.5305.01 2 0.000
#> TCGA.F6.A8O4.01 2 0.000
#> TCGA.HT.8113.01 2 1.000
#> TCGA.DH.A66G.01 2 0.000
#> TCGA.HT.7620.01 2 1.000
#> TCGA.P5.A731.01 2 0.000
#> TCGA.HT.7480.01 2 0.000
#> TCGA.HT.7689.01 2 0.000
#> TCGA.HT.8109.01 2 0.000
#> TCGA.E1.A7YE.01 4 0.000
#> TCGA.S9.A7R1.01 2 0.000
#> TCGA.FG.A710.01 2 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.FG.7634.01 2 0.000
#> TCGA.DU.8163.01 2 0.000
#> TCGA.DU.6407.02 4 0.000
#> TCGA.DU.6407.01 2 0.000
#> TCGA.S9.A7IX.01 1 0.000
#> TCGA.HT.8010.01 2 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.DU.7299.01 2 0.000
#> TCGA.DU.8165.01 1 0.000
#> TCGA.CS.5393.01 2 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.DB.5270.01 2 0.000
#> TCGA.S9.A6WQ.01 2 0.000
#> TCGA.HT.8106.01 4 1.000
#> TCGA.HT.7608.01 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 1.000
#> TCGA.E1.A7Z3.01 2 0.000
#> TCGA.P5.A77X.01 2 0.000
#> TCGA.FG.A6IZ.01 2 0.000
#> TCGA.HT.7873.01 2 0.000
#> TCGA.CS.4938.01 2 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 1.000
#> TCGA.CS.4941.01 1 0.000
#> TCGA.RY.A843.01 2 0.000
#> TCGA.S9.A7IS.01 4 0.000
#> TCGA.TQ.A8XE.02 2 0.000
#> TCGA.S9.A6U0.01 1 0.000
#> TCGA.FG.7643.01 5 0.000
#> TCGA.E1.A7YO.01 2 0.000
#> TCGA.TQ.A7RG.01 2 0.000
#> TCGA.QH.A6X5.01 2 0.000
#> TCGA.DU.6403.01 1 0.000
#> TCGA.HW.7493.01 2 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.DH.A7UT.01 2 0.000
#> TCGA.DU.7015.01 2 0.000
#> TCGA.HT.A616.01 2 0.000
#> TCGA.FG.8181.01 5 0.000
#> TCGA.HT.7611.01 2 0.000
#> TCGA.HT.8018.01 4 1.000
#> TCGA.FG.A60K.01 2 0.000
#> TCGA.HT.7856.01 4 1.000
#> TCGA.FG.5963.01 3 0.000
#> TCGA.FG.5963.02 3 0.000
#> TCGA.DU.5851.01 2 0.000
#> TCGA.DU.A7T6.01 4 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.P5.A72W.01 2 0.000
#> TCGA.S9.A6TU.01 2 0.000
#> TCGA.HT.A61A.01 4 1.000
#> 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 5 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 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 2 0.000
#> TCGA.HT.A618.01 4 0.502
#> TCGA.FG.6691.01 2 0.000
#> TCGA.HT.7467.01 2 1.000
#> TCGA.S9.A7R3.01 2 0.000
#> TCGA.QH.A6CX.01 1 1.000
#> 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.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.P5.A5F4.01 2 0.000
#> TCGA.QH.A65V.01 2 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.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 5 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 5 1.000
#> TCGA.DB.5280.01 2 0.000
#> TCGA.TM.A84T.01 2 0.000
#> TCGA.DH.A66D.01 2 0.000
#> TCGA.RY.A83Z.01 4 0.000
#> TCGA.DB.5278.01 2 0.000
#> TCGA.DU.A76K.01 1 0.000
#> TCGA.TQ.A7RR.01 2 0.000
#> TCGA.DU.8162.01 5 0.000
#> TCGA.TQ.A7RH.01 2 0.000
#> TCGA.E1.A7YS.01 2 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 2 1.000
#> TCGA.QH.A6CS.01 5 1.000
#> TCGA.HT.7695.01 2 0.000
#> TCGA.P5.A5EU.01 4 0.000
#> TCGA.DB.A64X.01 2 0.000
#> TCGA.FG.7637.01 2 0.000
#> TCGA.VM.A8CE.01 2 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 5 0.000
#> TCGA.CS.4944.01 2 0.000
#> TCGA.DU.A6S2.01 2 0.000
#> TCGA.S9.A7R7.01 2 0.000
#> TCGA.TM.A84R.01 4 1.000
#> TCGA.DB.A75M.01 2 0.000
#> TCGA.DU.6392.01 5 0.000
#> TCGA.HW.A5KM.01 2 0.000
#> TCGA.HT.7477.01 4 0.751
#> TCGA.HT.8012.01 2 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.S9.A7QZ.01 2 0.000
#> TCGA.QH.A6X4.01 2 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.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 4 1.000
#> TCGA.DH.A7UV.01 2 0.000
#> TCGA.HT.7879.01 2 0.000
#> TCGA.TM.A84F.01 2 1.000
#> TCGA.HT.8104.01 1 0.000
#> TCGA.FG.A70Z.01 1 0.000
#> TCGA.DU.A7TC.01 2 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.HT.7473.01 2 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 1.000
#> TCGA.DU.A5TT.01 1 0.000
#> TCGA.S9.A6WG.01 2 0.000
#> TCGA.FG.8189.01 5 0.000
#> TCGA.DB.A75O.01 2 0.000
#> TCGA.HT.7688.01 2 0.000
#> TCGA.DU.7304.02 2 1.000
#> TCGA.DU.6394.01 2 0.000
#> TCGA.HT.8019.01 5 0.000
#> TCGA.P5.A5EY.01 5 0.000
#> TCGA.S9.A6WD.01 2 0.000
#> TCGA.DU.5872.01 2 0.000
#> TCGA.DU.5872.02 5 0.000
#> TCGA.FG.8185.01 2 0.000
#> TCGA.HT.7902.01 4 0.498
#> TCGA.CS.5397.01 1 0.000
#> TCGA.TQ.A7RU.01 2 0.000
#> TCGA.HW.A5KK.01 1 1.000
#> TCGA.DU.5874.01 2 0.000
#> TCGA.S9.A6WE.01 2 0.000
#> 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 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.S9.A6WM.01 1 0.000
#> TCGA.R8.A73M.01 2 0.000
#> TCGA.CS.4942.01 2 0.000
#> TCGA.HT.7680.01 5 0.000
#> TCGA.DB.A4X9.01 2 0.000
#> TCGA.DB.A4XF.01 2 0.000
#> TCGA.HT.A74O.01 2 0.000
#> TCGA.FG.8188.01 2 0.000
#> TCGA.P5.A5F6.01 5 0.000
#> TCGA.DU.A6S3.01 2 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.E1.A7YJ.01 1 0.000
#> TCGA.S9.A6WI.01 4 1.000
#> TCGA.DU.8164.01 2 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.E1.A7YL.01 1 0.000
#> TCGA.E1.A7YV.01 4 0.000
#> TCGA.HT.8558.01 5 0.000
#> TCGA.HT.A61C.01 1 0.000
#> TCGA.TQ.A7RW.01 2 0.000
#> TCGA.DU.5849.01 2 0.000
#> TCGA.DU.A7TI.01 2 0.000
#> TCGA.QH.A6CV.01 1 0.000
#> TCGA.HT.7468.01 2 0.000
#> TCGA.FG.6692.01 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.DU.7018.01 2 0.000
#> TCGA.HT.7677.01 2 0.000
#> TCGA.FG.A713.01 2 1.000
#> TCGA.DU.7300.01 2 0.000
#> TCGA.TM.A7CA.01 2 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.TM.A84M.01 2 0.000
#> TCGA.F6.A8O3.01 2 0.000
#> TCGA.QH.A86X.01 2 0.000
#> TCGA.HT.8013.01 2 0.000
#> TCGA.HW.7490.01 2 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.P5.A780.01 2 0.000
#> TCGA.HT.7606.01 2 0.000
#> TCGA.DU.A7TJ.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.DU.5847.01 1 0.000
#> TCGA.E1.A7YK.01 2 1.000
#> TCGA.HT.7874.01 2 1.000
#> TCGA.HT.7471.01 2 0.000
#> TCGA.HT.7882.01 1 1.000
#> TCGA.DU.5854.01 1 0.000
#> TCGA.DU.6395.01 2 0.000
#> TCGA.HT.8011.01 1 1.000
#> TCGA.S9.A6TV.01 2 0.000
#> TCGA.P5.A5EW.01 2 0.000
#> TCGA.DU.5852.01 1 0.000
#> TCGA.DU.6408.01 2 0.000
#> TCGA.DB.A4XB.01 2 0.000
#> TCGA.E1.A7YY.01 4 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 6 0.000
#> TCGA.DU.6404.01 6 0.000
#> TCGA.FG.5964.01 2 0.000
#> TCGA.CS.5396.01 2 0.000
#> TCGA.HT.8107.01 5 0.000
#> TCGA.DU.A7TA.01 2 0.000
#> TCGA.HW.8319.01 2 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.DB.A64Q.01 2 0.000
#> TCGA.P5.A737.01 2 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 1.000
#> TCGA.HT.7616.01 2 0.000
#> TCGA.S9.A7R8.01 2 0.000
#> TCGA.QH.A6XA.01 2 0.000
#> TCGA.HT.8111.01 2 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.HT.7475.01 2 0.000
#> TCGA.HT.8564.01 1 1.000
#> TCGA.DB.A64U.01 2 0.000
#> TCGA.DB.A64W.01 2 0.000
#> TCGA.R8.A6MO.01 2 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 5 1.000
#> TCGA.R8.A6ML.01 2 0.000
#> TCGA.VM.A8C9.01 5 0.000
#> TCGA.HT.7686.01 2 0.000
#> TCGA.DU.6410.01 2 0.000
#> TCGA.S9.A6U9.01 2 0.000
#> TCGA.CS.6290.01 2 0.000
#> TCGA.TQ.A7RO.01 2 0.000
#> TCGA.DU.7019.01 2 0.000
#> TCGA.FG.A711.01 2 0.000
#> TCGA.TQ.A7RM.01 2 0.249
#> 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.S9.A7J3.01 2 0.000
#> TCGA.P5.A5F2.01 2 0.000
#> TCGA.E1.5304.01 4 0.249
#> TCGA.DU.7006.01 1 0.249
#> TCGA.TM.A84S.01 2 0.000
#> TCGA.HT.7469.01 6 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 1.000
#> TCGA.P5.A730.01 2 0.000
#> TCGA.TM.A84L.01 2 0.000
#> TCGA.DU.8161.01 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 4 1.000
#> TCGA.DU.6393.01 2 0.000
#> TCGA.HT.8108.01 2 0.000
#> TCGA.E1.A7YD.01 1 0.000
#> TCGA.DU.7304.01 2 0.000
#> TCGA.S9.A7IY.01 2 0.000
#> TCGA.FG.7641.01 2 0.000
#> TCGA.P5.A736.01 2 0.000
#> TCGA.P5.A5EV.01 2 0.000
#> TCGA.DU.7301.01 2 0.000
#> TCGA.HT.7470.01 2 0.000
#> TCGA.DU.7009.01 2 0.000
#> TCGA.P5.A781.01 2 0.000
#> TCGA.DH.5140.01 5 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 5 0.000
#> TCGA.RY.A845.01 2 0.000
#> TCGA.DU.7010.01 4 0.000
#> TCGA.S9.A6U2.01 2 0.000
#> TCGA.S9.A6WN.01 4 1.000
#> TCGA.DU.A7TD.01 1 0.000
#> TCGA.DU.6405.01 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.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 1.000
#> TCGA.DH.A7US.01 2 0.000
#> TCGA.FG.A87N.01 4 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.HT.A61B.01 2 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.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 4 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 4 1.000
#> TCGA.HW.A5KL.01 2 0.000
#> TCGA.DU.8158.01 1 1.000
#> TCGA.HT.7474.01 2 0.000
#> TCGA.DH.A7UU.01 2 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 3 0.000
#> TCGA.VM.A8CB.01 2 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 4 0.000
#> TCGA.CS.5394.01 2 0.000
#> TCGA.HT.A617.01 1 1.000
#> TCGA.DU.A76O.01 2 0.000
#> TCGA.DU.A5TW.01 2 0.000
#> TCGA.HT.7857.01 5 0.000
#> TCGA.WY.A85A.01 2 0.000
#> TCGA.FG.5962.01 2 0.000
get_classes(res, k = 7)
#> class p
#> TCGA.E1.5319.01 2 0.000
#> TCGA.HT.7693.01 2 0.000
#> TCGA.CS.6665.01 4 0.000
#> TCGA.S9.A7J2.01 2 0.000
#> TCGA.FG.A6J3.01 4 0.000
#> TCGA.FG.6688.01 5 0.502
#> TCGA.S9.A6TX.01 2 0.000
#> TCGA.VM.A8C8.01 2 0.000
#> TCGA.HT.A74L.01 2 0.000
#> TCGA.DU.A5TS.01 2 0.000
#> TCGA.DB.A4XA.01 2 0.000
#> TCGA.HT.A4DV.01 6 0.000
#> TCGA.TQ.A7RP.01 5 0.000
#> TCGA.E1.5311.01 2 0.000
#> TCGA.E1.A7YI.01 4 0.000
#> TCGA.E1.5305.01 2 0.000
#> TCGA.F6.A8O4.01 2 0.000
#> TCGA.HT.8113.01 6 0.000
#> TCGA.DH.A66G.01 2 0.000
#> TCGA.HT.7620.01 6 0.000
#> TCGA.P5.A731.01 2 0.000
#> TCGA.HT.7480.01 2 0.000
#> TCGA.HT.7689.01 2 0.000
#> TCGA.HT.8109.01 2 0.000
#> TCGA.E1.A7YE.01 4 0.000
#> TCGA.S9.A7R1.01 2 0.000
#> TCGA.FG.A710.01 2 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 6 0.000
#> TCGA.FG.7634.01 2 0.000
#> TCGA.DU.8163.01 2 0.000
#> TCGA.DU.6407.02 4 0.000
#> TCGA.DU.6407.01 2 0.000
#> TCGA.S9.A7IX.01 1 0.249
#> TCGA.HT.8010.01 6 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.DU.7299.01 2 0.000
#> TCGA.DU.8165.01 1 0.000
#> TCGA.CS.5393.01 2 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.DB.5270.01 6 0.000
#> TCGA.S9.A6WQ.01 2 0.000
#> TCGA.HT.8106.01 6 0.000
#> TCGA.HT.7608.01 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 1.000
#> TCGA.P5.A5ET.01 2 0.000
#> TCGA.HT.7472.01 2 0.000
#> TCGA.HT.7880.01 6 0.000
#> TCGA.E1.A7Z3.01 6 0.000
#> TCGA.P5.A77X.01 2 0.000
#> TCGA.FG.A6IZ.01 2 0.000
#> TCGA.HT.7873.01 2 0.000
#> TCGA.CS.4938.01 2 0.000
#> TCGA.KT.A74X.01 2 0.000
#> TCGA.P5.A5EX.01 6 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 6 0.000
#> TCGA.CS.4941.01 1 0.249
#> TCGA.RY.A843.01 2 0.000
#> TCGA.S9.A7IS.01 4 0.000
#> TCGA.TQ.A8XE.02 2 0.000
#> TCGA.S9.A6U0.01 5 1.000
#> TCGA.FG.7643.01 5 0.000
#> TCGA.E1.A7YO.01 2 0.000
#> TCGA.TQ.A7RG.01 2 0.000
#> TCGA.QH.A6X5.01 2 0.000
#> TCGA.DU.6403.01 1 0.000
#> TCGA.HW.7493.01 2 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.DH.A7UT.01 2 0.000
#> TCGA.DU.7015.01 2 0.000
#> TCGA.HT.A616.01 2 0.000
#> TCGA.FG.8181.01 5 0.000
#> TCGA.HT.7611.01 2 0.000
#> TCGA.HT.8018.01 6 0.000
#> TCGA.FG.A60K.01 2 0.000
#> TCGA.HT.7856.01 6 0.000
#> TCGA.FG.5963.01 3 0.000
#> TCGA.FG.5963.02 3 0.000
#> TCGA.DU.5851.01 6 0.000
#> TCGA.DU.A7T6.01 4 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.P5.A72W.01 2 0.000
#> TCGA.S9.A6TU.01 2 0.000
#> TCGA.HT.A61A.01 6 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 5 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 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 2 0.000
#> TCGA.HT.A618.01 4 0.000
#> TCGA.FG.6691.01 2 0.000
#> TCGA.HT.7467.01 6 0.000
#> TCGA.S9.A7R3.01 2 0.000
#> TCGA.QH.A6CX.01 5 0.747
#> 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.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 0.751
#> TCGA.EZ.7264.01 2 0.000
#> TCGA.P5.A5F4.01 2 0.000
#> TCGA.QH.A65V.01 2 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.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 5 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 5 1.000
#> TCGA.DB.5280.01 2 0.000
#> TCGA.TM.A84T.01 2 0.000
#> TCGA.DH.A66D.01 2 0.000
#> TCGA.RY.A83Z.01 4 1.000
#> TCGA.DB.5278.01 2 0.000
#> TCGA.DU.A76K.01 1 0.000
#> TCGA.TQ.A7RR.01 2 0.000
#> TCGA.DU.8162.01 5 0.000
#> TCGA.TQ.A7RH.01 2 0.000
#> TCGA.E1.A7YS.01 2 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 6 0.000
#> TCGA.QH.A6CS.01 5 0.000
#> TCGA.HT.7695.01 2 0.000
#> TCGA.P5.A5EU.01 4 0.000
#> TCGA.DB.A64X.01 2 0.000
#> TCGA.FG.7637.01 2 0.000
#> TCGA.VM.A8CE.01 2 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 5 0.000
#> TCGA.CS.4944.01 2 0.000
#> TCGA.DU.A6S2.01 2 0.000
#> TCGA.S9.A7R7.01 2 1.000
#> TCGA.TM.A84R.01 6 0.000
#> TCGA.DB.A75M.01 2 0.000
#> TCGA.DU.6392.01 5 0.000
#> TCGA.HW.A5KM.01 2 0.000
#> TCGA.HT.7477.01 2 1.000
#> TCGA.HT.8012.01 2 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.S9.A7QZ.01 2 0.000
#> TCGA.QH.A6X4.01 2 0.000
#> TCGA.P5.A77W.01 2 0.000
#> TCGA.DU.7302.01 2 0.000
#> TCGA.DU.7012.01 5 1.000
#> TCGA.DU.6399.01 2 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 0.751
#> 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 6 0.000
#> TCGA.DH.A7UV.01 2 0.000
#> TCGA.HT.7879.01 2 0.000
#> TCGA.TM.A84F.01 6 0.000
#> TCGA.HT.8104.01 1 0.000
#> TCGA.FG.A70Z.01 1 0.000
#> TCGA.DU.A7TC.01 2 0.000
#> TCGA.HT.7610.01 2 0.000
#> TCGA.S9.A6TW.01 6 0.249
#> 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 6 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.HT.7473.01 2 0.000
#> TCGA.TM.A7C3.01 1 0.000
#> TCGA.S9.A7IQ.01 6 0.000
#> TCGA.DU.7008.01 2 0.000
#> TCGA.DB.A64O.01 5 1.000
#> TCGA.DU.A5TT.01 1 0.751
#> TCGA.S9.A6WG.01 6 0.000
#> TCGA.FG.8189.01 5 0.000
#> TCGA.DB.A75O.01 2 0.000
#> TCGA.HT.7688.01 2 0.000
#> TCGA.DU.7304.02 2 0.747
#> TCGA.DU.6394.01 2 0.000
#> TCGA.HT.8019.01 5 0.000
#> TCGA.P5.A5EY.01 5 0.000
#> TCGA.S9.A6WD.01 2 0.000
#> TCGA.DU.5872.01 2 0.000
#> TCGA.DU.5872.02 5 0.000
#> TCGA.FG.8185.01 2 0.000
#> TCGA.HT.7902.01 6 0.000
#> TCGA.CS.5397.01 1 1.000
#> TCGA.TQ.A7RU.01 2 0.000
#> TCGA.HW.A5KK.01 5 0.000
#> TCGA.DU.5874.01 2 0.000
#> TCGA.S9.A6WE.01 2 0.000
#> 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 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.S9.A6WM.01 1 0.000
#> TCGA.R8.A73M.01 2 0.000
#> TCGA.CS.4942.01 2 0.000
#> TCGA.HT.7680.01 5 0.000
#> TCGA.DB.A4X9.01 2 0.000
#> TCGA.DB.A4XF.01 2 0.000
#> TCGA.HT.A74O.01 2 0.000
#> TCGA.FG.8188.01 2 0.000
#> TCGA.P5.A5F6.01 5 0.000
#> TCGA.DU.A6S3.01 2 0.000
#> TCGA.HT.8110.01 1 1.000
#> TCGA.DB.A4XH.01 2 0.000
#> TCGA.HT.7485.01 2 0.000
#> TCGA.VW.A7QS.01 2 0.000
#> TCGA.E1.A7YJ.01 1 0.000
#> TCGA.S9.A6WI.01 6 0.000
#> TCGA.DU.8164.01 2 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.E1.A7YL.01 1 0.000
#> TCGA.E1.A7YV.01 4 0.000
#> TCGA.HT.8558.01 5 0.000
#> TCGA.HT.A61C.01 1 1.000
#> TCGA.TQ.A7RW.01 2 0.000
#> TCGA.DU.5849.01 6 1.000
#> TCGA.DU.A7TI.01 2 0.000
#> TCGA.QH.A6CV.01 1 0.000
#> TCGA.HT.7468.01 2 0.000
#> TCGA.FG.6692.01 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.DU.7018.01 2 0.000
#> TCGA.HT.7677.01 2 0.000
#> TCGA.FG.A713.01 6 0.000
#> TCGA.DU.7300.01 2 0.000
#> TCGA.TM.A7CA.01 2 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 6 0.000
#> TCGA.TM.A84M.01 2 0.000
#> TCGA.F6.A8O3.01 2 0.000
#> TCGA.QH.A86X.01 2 0.000
#> TCGA.HT.8013.01 2 0.000
#> TCGA.HW.7490.01 2 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.P5.A780.01 2 0.000
#> TCGA.HT.7606.01 2 0.000
#> TCGA.DU.A7TJ.01 1 0.000
#> TCGA.DB.A64V.01 6 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 0.253
#> TCGA.DU.5847.01 1 0.000
#> TCGA.E1.A7YK.01 6 0.000
#> TCGA.HT.7874.01 6 0.000
#> TCGA.HT.7471.01 2 0.000
#> TCGA.HT.7882.01 5 0.000
#> TCGA.DU.5854.01 1 1.000
#> TCGA.DU.6395.01 2 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.DU.6408.01 2 0.000
#> TCGA.DB.A4XB.01 2 0.000
#> TCGA.E1.A7YY.01 6 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 5 1.000
#> TCGA.QH.A870.01 2 0.000
#> TCGA.HT.A5R9.01 2 0.000
#> TCGA.DU.6404.02 5 0.000
#> TCGA.DU.6404.01 5 0.000
#> TCGA.FG.5964.01 6 0.000
#> TCGA.CS.5396.01 2 0.000
#> TCGA.HT.8107.01 5 0.000
#> TCGA.DU.A7TA.01 2 0.000
#> TCGA.HW.8319.01 2 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.DB.A64Q.01 2 0.000
#> TCGA.P5.A737.01 2 0.000
#> TCGA.DB.5275.01 2 0.000
#> TCGA.S9.A6WH.01 2 0.000
#> TCGA.HT.7602.01 6 0.000
#> TCGA.DU.A5TU.01 2 0.000
#> TCGA.HT.A5RB.01 2 0.000
#> TCGA.E1.A7YN.01 5 0.000
#> TCGA.HT.7616.01 2 0.000
#> TCGA.S9.A7R8.01 2 0.000
#> TCGA.QH.A6XA.01 2 0.000
#> TCGA.HT.8111.01 2 0.000
#> TCGA.E1.A7Z2.01 1 1.000
#> TCGA.DU.A5TP.01 2 0.000
#> TCGA.VM.A8CD.01 1 1.000
#> 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.HT.7475.01 2 0.000
#> TCGA.HT.8564.01 5 0.502
#> TCGA.DB.A64U.01 2 0.000
#> TCGA.DB.A64W.01 2 0.000
#> TCGA.R8.A6MO.01 2 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 5 0.000
#> TCGA.R8.A6ML.01 2 0.000
#> TCGA.VM.A8C9.01 5 0.000
#> TCGA.HT.7686.01 2 0.000
#> TCGA.DU.6410.01 2 0.000
#> TCGA.S9.A6U9.01 2 0.000
#> TCGA.CS.6290.01 2 1.000
#> TCGA.TQ.A7RO.01 2 0.000
#> TCGA.DU.7019.01 2 0.000
#> TCGA.FG.A711.01 2 0.000
#> TCGA.TQ.A7RM.01 2 0.502
#> 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.S9.A7J3.01 2 0.000
#> TCGA.P5.A5F2.01 2 0.000
#> TCGA.E1.5304.01 2 1.000
#> TCGA.DU.7006.01 5 1.000
#> TCGA.TM.A84S.01 2 0.000
#> TCGA.HT.7469.01 6 1.000
#> 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 6 0.000
#> TCGA.P5.A730.01 2 0.000
#> TCGA.TM.A84L.01 2 0.000
#> TCGA.DU.8161.01 1 1.000
#> 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 1.000
#> 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 6 0.000
#> TCGA.DU.6393.01 2 0.000
#> TCGA.HT.8108.01 2 0.000
#> TCGA.E1.A7YD.01 1 0.000
#> TCGA.DU.7304.01 2 0.000
#> TCGA.S9.A7IY.01 2 0.000
#> TCGA.FG.7641.01 2 0.000
#> TCGA.P5.A736.01 2 0.000
#> TCGA.P5.A5EV.01 2 0.000
#> TCGA.DU.7301.01 2 0.000
#> TCGA.HT.7470.01 2 0.000
#> TCGA.DU.7009.01 2 0.000
#> TCGA.P5.A781.01 2 0.000
#> TCGA.DH.5140.01 5 0.000
#> TCGA.FG.A4MY.01 2 0.000
#> TCGA.TM.A7CF.01 2 0.000
#> TCGA.TM.A7CF.02 6 0.000
#> TCGA.FG.8186.01 2 0.000
#> TCGA.S9.A6U6.01 2 0.000
#> TCGA.HT.8015.01 5 0.000
#> TCGA.RY.A845.01 2 0.000
#> TCGA.DU.7010.01 4 0.000
#> TCGA.S9.A6U2.01 2 0.000
#> TCGA.S9.A6WN.01 6 0.000
#> TCGA.DU.A7TD.01 1 0.000
#> TCGA.DU.6405.01 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.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 5 1.000
#> TCGA.DH.A7US.01 2 0.000
#> TCGA.FG.A87N.01 4 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.HT.A61B.01 2 0.000
#> TCGA.DH.A66B.01 2 0.000
#> TCGA.HT.7603.01 6 0.000
#> TCGA.DU.6397.02 2 0.000
#> TCGA.DU.6397.01 2 0.000
#> TCGA.HT.A4DS.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 6 1.000
#> TCGA.FG.A70Y.01 2 0.000
#> TCGA.TQ.A7RV.01 2 0.000
#> TCGA.TQ.A7RV.02 6 0.000
#> TCGA.HT.A5R7.01 6 0.000
#> TCGA.HW.A5KL.01 2 0.000
#> TCGA.DU.8158.01 5 0.000
#> TCGA.HT.7474.01 6 1.000
#> TCGA.DH.A7UU.01 2 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 6 1.000
#> TCGA.VM.A8CB.01 2 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 4 1.000
#> TCGA.CS.5394.01 2 0.000
#> TCGA.HT.A617.01 5 0.498
#> TCGA.DU.A76O.01 2 0.000
#> TCGA.DU.A5TW.01 2 0.000
#> TCGA.HT.7857.01 5 0.000
#> TCGA.WY.A85A.01 2 0.000
#> TCGA.FG.5962.01 2 0.000
get_classes(res, k = 8)
#> class p
#> TCGA.E1.5319.01 2 0.000
#> TCGA.HT.7693.01 2 0.000
#> TCGA.CS.6665.01 4 0.000
#> TCGA.S9.A7J2.01 2 0.000
#> TCGA.FG.A6J3.01 4 0.000
#> TCGA.FG.6688.01 5 0.000
#> TCGA.S9.A6TX.01 2 0.000
#> TCGA.VM.A8C8.01 2 0.000
#> TCGA.HT.A74L.01 2 0.000
#> TCGA.DU.A5TS.01 2 0.000
#> TCGA.DB.A4XA.01 2 0.000
#> TCGA.HT.A4DV.01 6 0.000
#> TCGA.TQ.A7RP.01 5 0.000
#> TCGA.E1.5311.01 2 0.000
#> TCGA.E1.A7YI.01 4 0.000
#> TCGA.E1.5305.01 2 0.000
#> TCGA.F6.A8O4.01 2 0.000
#> TCGA.HT.8113.01 6 0.000
#> TCGA.DH.A66G.01 2 0.000
#> TCGA.HT.7620.01 6 0.000
#> TCGA.P5.A731.01 2 0.000
#> TCGA.HT.7480.01 2 0.000
#> TCGA.HT.7689.01 2 0.000
#> TCGA.HT.8109.01 2 0.000
#> TCGA.E1.A7YE.01 4 0.000
#> TCGA.S9.A7R1.01 2 0.000
#> TCGA.FG.A710.01 2 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 6 0.000
#> TCGA.FG.7634.01 2 0.000
#> TCGA.DU.8163.01 2 0.000
#> TCGA.DU.6407.02 4 0.000
#> TCGA.DU.6407.01 2 0.000
#> TCGA.S9.A7IX.01 5 1.000
#> TCGA.HT.8010.01 6 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.DU.7299.01 2 0.000
#> TCGA.DU.8165.01 5 1.000
#> TCGA.CS.5393.01 2 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 5 1.000
#> TCGA.HT.7605.01 2 0.000
#> TCGA.FG.A6J1.01 2 0.000
#> TCGA.DB.5270.01 6 0.000
#> TCGA.S9.A6WQ.01 2 0.000
#> TCGA.HT.8106.01 6 0.000
#> TCGA.HT.7608.01 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 6 0.498
#> TCGA.P5.A5ET.01 2 0.000
#> TCGA.HT.7472.01 2 0.000
#> TCGA.HT.7880.01 6 0.000
#> TCGA.E1.A7Z3.01 6 0.000
#> TCGA.P5.A77X.01 2 0.000
#> TCGA.FG.A6IZ.01 2 0.000
#> TCGA.HT.7873.01 2 0.000
#> TCGA.CS.4938.01 2 0.000
#> TCGA.KT.A74X.01 2 0.000
#> TCGA.P5.A5EX.01 6 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 6 0.000
#> TCGA.CS.4941.01 5 0.000
#> TCGA.RY.A843.01 2 0.000
#> TCGA.S9.A7IS.01 4 0.000
#> TCGA.TQ.A8XE.02 2 0.000
#> TCGA.S9.A6U0.01 5 0.000
#> TCGA.FG.7643.01 5 0.000
#> TCGA.E1.A7YO.01 2 0.000
#> TCGA.TQ.A7RG.01 2 0.000
#> TCGA.QH.A6X5.01 2 0.000
#> TCGA.DU.6403.01 1 1.000
#> TCGA.HW.7493.01 2 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.DH.A7UT.01 2 0.000
#> TCGA.DU.7015.01 2 0.000
#> TCGA.HT.A616.01 2 0.000
#> TCGA.FG.8181.01 5 0.000
#> TCGA.HT.7611.01 2 0.000
#> TCGA.HT.8018.01 6 0.000
#> TCGA.FG.A60K.01 2 0.000
#> TCGA.HT.7856.01 6 0.000
#> TCGA.FG.5963.01 3 0.000
#> TCGA.FG.5963.02 3 0.000
#> TCGA.DU.5851.01 6 0.000
#> TCGA.DU.A7T6.01 4 0.000
#> TCGA.S9.A6TY.01 2 0.000
#> TCGA.CS.5395.01 1 1.000
#> 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.P5.A72W.01 2 0.000
#> TCGA.S9.A6TU.01 2 0.000
#> TCGA.HT.A61A.01 6 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 6 1.000
#> 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 5 0.000
#> TCGA.QH.A6X8.01 2 0.000
#> TCGA.S9.A89V.01 5 0.000
#> TCGA.WY.A85E.01 2 0.000
#> TCGA.HT.A5R5.01 2 0.498
#> TCGA.HT.A618.01 4 0.000
#> TCGA.FG.6691.01 2 0.000
#> TCGA.HT.7467.01 6 0.000
#> TCGA.S9.A7R3.01 2 0.000
#> TCGA.QH.A6CX.01 5 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.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 5 1.000
#> TCGA.EZ.7264.01 2 0.000
#> TCGA.P5.A5F4.01 2 0.000
#> TCGA.QH.A65V.01 2 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.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 5 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 5 0.000
#> TCGA.DB.5280.01 2 0.000
#> TCGA.TM.A84T.01 2 0.000
#> TCGA.DH.A66D.01 2 0.000
#> TCGA.RY.A83Z.01 4 0.000
#> TCGA.DB.5278.01 2 0.000
#> TCGA.DU.A76K.01 5 1.000
#> TCGA.TQ.A7RR.01 2 0.000
#> TCGA.DU.8162.01 5 0.000
#> TCGA.TQ.A7RH.01 2 0.000
#> TCGA.E1.A7YS.01 2 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 6 0.000
#> TCGA.QH.A6CS.01 5 0.000
#> TCGA.HT.7695.01 2 0.000
#> TCGA.P5.A5EU.01 4 0.000
#> TCGA.DB.A64X.01 2 0.000
#> TCGA.FG.7637.01 2 0.000
#> TCGA.VM.A8CE.01 2 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 5 0.000
#> TCGA.CS.4944.01 2 0.000
#> TCGA.DU.A6S2.01 2 0.000
#> TCGA.S9.A7R7.01 6 0.249
#> TCGA.TM.A84R.01 6 0.000
#> TCGA.DB.A75M.01 2 0.000
#> TCGA.DU.6392.01 5 0.751
#> TCGA.HW.A5KM.01 2 0.000
#> TCGA.HT.7477.01 2 1.000
#> TCGA.HT.8012.01 2 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.S9.A7QZ.01 2 0.000
#> TCGA.QH.A6X4.01 2 0.000
#> TCGA.P5.A77W.01 2 0.000
#> TCGA.DU.7302.01 2 0.000
#> TCGA.DU.7012.01 5 0.000
#> TCGA.DU.6399.01 2 0.000
#> TCGA.E1.5307.01 2 0.000
#> TCGA.S9.A7QW.01 2 0.000
#> TCGA.DU.6402.01 1 1.000
#> TCGA.HT.7604.01 2 0.000
#> TCGA.P5.A733.01 2 0.000
#> TCGA.FG.A87Q.01 5 1.000
#> 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 6 0.000
#> TCGA.DH.A7UV.01 2 0.000
#> TCGA.HT.7879.01 2 0.000
#> TCGA.TM.A84F.01 6 0.000
#> TCGA.HT.8104.01 1 0.000
#> TCGA.FG.A70Z.01 1 1.000
#> TCGA.DU.A7TC.01 2 0.000
#> TCGA.HT.7610.01 2 0.000
#> TCGA.S9.A6TW.01 6 0.000
#> TCGA.FG.A60J.01 2 0.000
#> TCGA.E1.5303.01 2 0.000
#> TCGA.QH.A6XC.01 1 0.249
#> TCGA.HT.7481.01 6 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.HT.7473.01 2 0.000
#> TCGA.TM.A7C3.01 1 0.000
#> TCGA.S9.A7IQ.01 6 0.000
#> TCGA.DU.7008.01 2 0.000
#> TCGA.DB.A64O.01 5 0.000
#> TCGA.DU.A5TT.01 5 1.000
#> TCGA.S9.A6WG.01 6 0.000
#> TCGA.FG.8189.01 6 0.000
#> TCGA.DB.A75O.01 2 0.000
#> TCGA.HT.7688.01 2 0.000
#> TCGA.DU.7304.02 2 1.000
#> TCGA.DU.6394.01 2 0.000
#> TCGA.HT.8019.01 5 0.000
#> TCGA.P5.A5EY.01 5 0.000
#> TCGA.S9.A6WD.01 2 0.000
#> TCGA.DU.5872.01 2 0.000
#> TCGA.DU.5872.02 5 0.000
#> TCGA.FG.8185.01 2 0.000
#> TCGA.HT.7902.01 6 0.000
#> TCGA.CS.5397.01 5 1.000
#> TCGA.TQ.A7RU.01 2 0.000
#> TCGA.HW.A5KK.01 5 0.000
#> TCGA.DU.5874.01 2 0.000
#> TCGA.S9.A6WE.01 2 0.000
#> 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 5 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.S9.A6WM.01 1 1.000
#> TCGA.R8.A73M.01 2 0.000
#> TCGA.CS.4942.01 2 0.000
#> TCGA.HT.7680.01 5 0.000
#> TCGA.DB.A4X9.01 2 0.000
#> TCGA.DB.A4XF.01 2 0.000
#> TCGA.HT.A74O.01 2 0.000
#> TCGA.FG.8188.01 2 0.000
#> TCGA.P5.A5F6.01 5 0.000
#> TCGA.DU.A6S3.01 2 0.000
#> TCGA.HT.8110.01 5 0.000
#> TCGA.DB.A4XH.01 2 0.000
#> TCGA.HT.7485.01 2 0.000
#> TCGA.VW.A7QS.01 2 0.000
#> TCGA.E1.A7YJ.01 1 0.000
#> TCGA.S9.A6WI.01 6 0.000
#> TCGA.DU.8164.01 2 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.E1.A7YL.01 5 1.000
#> TCGA.E1.A7YV.01 4 0.000
#> TCGA.HT.8558.01 5 0.000
#> TCGA.HT.A61C.01 5 1.000
#> TCGA.TQ.A7RW.01 2 0.000
#> TCGA.DU.5849.01 6 0.249
#> TCGA.DU.A7TI.01 2 0.000
#> TCGA.QH.A6CV.01 1 0.000
#> TCGA.HT.7468.01 2 0.000
#> TCGA.FG.6692.01 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 0.498
#> TCGA.R8.A6YH.01 2 0.000
#> TCGA.DU.7018.01 2 0.000
#> TCGA.HT.7677.01 2 0.000
#> TCGA.FG.A713.01 6 0.000
#> TCGA.DU.7300.01 2 0.000
#> TCGA.TM.A7CA.01 2 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 0.249
#> TCGA.DB.5277.01 2 0.000
#> TCGA.HT.7694.01 6 0.000
#> TCGA.TM.A84M.01 2 0.000
#> TCGA.F6.A8O3.01 2 0.000
#> TCGA.QH.A86X.01 2 0.000
#> TCGA.HT.8013.01 2 0.000
#> TCGA.HW.7490.01 2 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 1.000
#> TCGA.P5.A780.01 2 0.000
#> TCGA.HT.7606.01 2 0.000
#> TCGA.DU.A7TJ.01 1 0.000
#> TCGA.DB.A64V.01 6 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 5 1.000
#> TCGA.DU.5847.01 1 1.000
#> TCGA.E1.A7YK.01 6 0.000
#> TCGA.HT.7874.01 6 0.000
#> TCGA.HT.7471.01 2 0.000
#> TCGA.HT.7882.01 5 0.000
#> TCGA.DU.5854.01 5 1.000
#> TCGA.DU.6395.01 2 0.000
#> TCGA.HT.8011.01 1 0.249
#> TCGA.S9.A6TV.01 2 0.000
#> TCGA.P5.A5EW.01 2 0.000
#> TCGA.DU.5852.01 1 0.498
#> TCGA.DU.6408.01 2 0.000
#> TCGA.DB.A4XB.01 2 0.000
#> TCGA.E1.A7YY.01 6 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 5 0.000
#> TCGA.QH.A870.01 2 0.000
#> TCGA.HT.A5R9.01 2 0.000
#> TCGA.DU.6404.02 5 0.000
#> TCGA.DU.6404.01 5 0.253
#> TCGA.FG.5964.01 6 0.000
#> TCGA.CS.5396.01 2 0.000
#> TCGA.HT.8107.01 5 0.000
#> TCGA.DU.A7TA.01 2 0.000
#> TCGA.HW.8319.01 2 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.DB.A64Q.01 2 0.000
#> TCGA.P5.A737.01 2 0.000
#> TCGA.DB.5275.01 2 0.000
#> TCGA.S9.A6WH.01 2 0.000
#> TCGA.HT.7602.01 6 0.000
#> TCGA.DU.A5TU.01 2 0.000
#> TCGA.HT.A5RB.01 2 0.000
#> TCGA.E1.A7YN.01 5 0.000
#> TCGA.HT.7616.01 2 0.000
#> TCGA.S9.A7R8.01 2 0.000
#> TCGA.QH.A6XA.01 2 0.000
#> TCGA.HT.8111.01 2 0.000
#> TCGA.E1.A7Z2.01 5 1.000
#> TCGA.DU.A5TP.01 2 0.000
#> TCGA.VM.A8CD.01 5 0.249
#> 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.HT.7475.01 2 0.000
#> TCGA.HT.8564.01 5 0.498
#> TCGA.DB.A64U.01 2 0.000
#> TCGA.DB.A64W.01 2 0.000
#> TCGA.R8.A6MO.01 2 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 5 0.000
#> TCGA.R8.A6ML.01 2 0.000
#> TCGA.VM.A8C9.01 5 0.000
#> TCGA.HT.7686.01 2 0.000
#> TCGA.DU.6410.01 2 0.000
#> TCGA.S9.A6U9.01 2 0.000
#> TCGA.CS.6290.01 6 0.000
#> TCGA.TQ.A7RO.01 2 0.000
#> TCGA.DU.7019.01 2 0.000
#> TCGA.FG.A711.01 2 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.S9.A7J3.01 2 0.000
#> TCGA.P5.A5F2.01 2 0.000
#> TCGA.E1.5304.01 4 1.000
#> TCGA.DU.7006.01 5 1.000
#> TCGA.TM.A84S.01 2 0.000
#> TCGA.HT.7469.01 6 1.000
#> 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 6 0.000
#> TCGA.P5.A730.01 2 0.000
#> TCGA.TM.A84L.01 2 0.747
#> TCGA.DU.8161.01 5 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 5 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 6 0.000
#> TCGA.DU.6393.01 2 0.000
#> TCGA.HT.8108.01 2 0.000
#> TCGA.E1.A7YD.01 1 1.000
#> TCGA.DU.7304.01 2 0.000
#> TCGA.S9.A7IY.01 2 0.000
#> TCGA.FG.7641.01 2 0.000
#> TCGA.P5.A736.01 2 0.000
#> TCGA.P5.A5EV.01 2 0.000
#> TCGA.DU.7301.01 2 0.000
#> TCGA.HT.7470.01 2 0.000
#> TCGA.DU.7009.01 2 0.000
#> TCGA.P5.A781.01 2 0.000
#> TCGA.DH.5140.01 3 0.000
#> TCGA.FG.A4MY.01 2 0.000
#> TCGA.TM.A7CF.01 2 0.000
#> TCGA.TM.A7CF.02 6 0.000
#> TCGA.FG.8186.01 2 0.000
#> TCGA.S9.A6U6.01 2 0.000
#> TCGA.HT.8015.01 5 0.000
#> TCGA.RY.A845.01 2 0.000
#> TCGA.DU.7010.01 4 0.000
#> TCGA.S9.A6U2.01 2 0.000
#> TCGA.S9.A6WN.01 6 0.000
#> TCGA.DU.A7TD.01 1 0.000
#> TCGA.DU.6405.01 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.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 5 0.000
#> TCGA.DH.A7US.01 2 0.000
#> TCGA.FG.A87N.01 4 0.000
#> TCGA.HT.7478.01 2 0.000
#> TCGA.DU.7290.01 1 1.000
#> TCGA.DB.A4XE.01 2 0.000
#> TCGA.DB.A64L.01 2 0.000
#> TCGA.VV.A829.01 2 0.000
#> TCGA.HT.A61B.01 2 0.000
#> TCGA.DH.A66B.01 2 0.000
#> TCGA.HT.7603.01 6 0.000
#> TCGA.DU.6397.02 2 0.000
#> TCGA.DU.6397.01 2 0.000
#> TCGA.HT.A4DS.01 5 1.000
#> 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 1.000
#> TCGA.DB.A64P.01 2 0.000
#> TCGA.FG.5965.02 6 1.000
#> TCGA.FG.A70Y.01 2 0.000
#> TCGA.TQ.A7RV.01 2 0.000
#> TCGA.TQ.A7RV.02 6 0.000
#> TCGA.HT.A5R7.01 6 0.000
#> TCGA.HW.A5KL.01 2 0.000
#> TCGA.DU.8158.01 5 0.000
#> TCGA.HT.7474.01 6 0.747
#> TCGA.DH.A7UU.01 2 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 6 1.000
#> TCGA.VM.A8CB.01 2 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 4 0.747
#> TCGA.CS.5394.01 2 0.000
#> TCGA.HT.A617.01 5 0.000
#> TCGA.DU.A76O.01 2 0.000
#> TCGA.DU.A5TW.01 2 0.000
#> TCGA.HT.7857.01 5 0.000
#> TCGA.WY.A85A.01 2 0.000
#> TCGA.FG.5962.01 2 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-leaf , Node012 , Node013-leaf , Node014-leaf , Node021 , Node022 , Node023 .
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 88 columns.
#> Top rows (1000) are extracted by 'SD' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.5039 0.497 0.497
#> 3 3 1.000 0.984 0.992 0.2034 0.897 0.792
#> 4 4 1.000 0.968 0.985 0.1207 0.925 0.809
#> 5 5 0.793 0.871 0.912 0.1087 0.894 0.683
#> 6 6 0.768 0.803 0.863 0.0634 0.927 0.703
#> 7 7 0.763 0.743 0.839 0.0170 0.974 0.863
#> 8 8 0.775 0.726 0.847 0.0186 0.951 0.747
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.FG.6688.01 1 0 1 1 0
#> TCGA.TQ.A7RP.01 2 0 1 0 1
#> TCGA.S9.A7IX.01 2 0 1 0 1
#> TCGA.VW.A8FI.01 2 0 1 0 1
#> TCGA.DU.8165.01 1 0 1 1 0
#> TCGA.DU.A76L.01 2 0 1 0 1
#> TCGA.CS.4941.01 2 0 1 0 1
#> TCGA.S9.A6U0.01 2 0 1 0 1
#> TCGA.FG.7643.01 1 0 1 1 0
#> TCGA.DU.6403.01 1 0 1 1 0
#> TCGA.FG.8181.01 2 0 1 0 1
#> TCGA.CS.5395.01 2 0 1 0 1
#> TCGA.DU.7292.01 2 0 1 0 1
#> TCGA.HT.A5RC.01 1 0 1 1 0
#> TCGA.FG.A4MW.01 2 0 1 0 1
#> TCGA.DB.A75P.01 1 0 1 1 0
#> TCGA.S9.A89V.01 2 0 1 0 1
#> TCGA.QH.A6CX.01 2 0 1 0 1
#> TCGA.CS.6186.01 2 0 1 0 1
#> TCGA.DU.6406.01 1 0 1 1 0
#> TCGA.DU.A7TB.01 2 0 1 0 1
#> TCGA.DU.A76K.01 2 0 1 0 1
#> TCGA.DU.8162.01 1 0 1 1 0
#> TCGA.E1.A7YQ.01 1 0 1 1 0
#> TCGA.QH.A6CS.01 2 0 1 0 1
#> TCGA.HT.7691.01 1 0 1 1 0
#> TCGA.DU.7012.01 1 0 1 1 0
#> TCGA.DU.6402.01 2 0 1 0 1
#> TCGA.FG.A87Q.01 1 0 1 1 0
#> TCGA.HT.8104.01 1 0 1 1 0
#> TCGA.FG.A70Z.01 1 0 1 1 0
#> TCGA.QH.A6XC.01 2 0 1 0 1
#> TCGA.FG.A4MU.01 2 0 1 0 1
#> TCGA.TM.A7C3.01 1 0 1 1 0
#> TCGA.DB.A64O.01 2 0 1 0 1
#> TCGA.DU.A5TT.01 2 0 1 0 1
#> TCGA.HT.8019.01 1 0 1 1 0
#> TCGA.P5.A5EY.01 2 0 1 0 1
#> TCGA.CS.5397.01 1 0 1 1 0
#> TCGA.HW.A5KK.01 2 0 1 0 1
#> TCGA.CS.6669.01 1 0 1 1 0
#> TCGA.S9.A7R2.01 2 0 1 0 1
#> TCGA.S9.A6WM.01 1 0 1 1 0
#> TCGA.HT.7680.01 1 0 1 1 0
#> TCGA.P5.A5F6.01 2 0 1 0 1
#> TCGA.HT.8110.01 2 0 1 0 1
#> TCGA.E1.A7YJ.01 2 0 1 0 1
#> TCGA.E1.A7YL.01 2 0 1 0 1
#> TCGA.HT.8558.01 1 0 1 1 0
#> TCGA.HT.A61C.01 2 0 1 0 1
#> TCGA.QH.A6CV.01 2 0 1 0 1
#> TCGA.FG.6692.01 2 0 1 0 1
#> TCGA.DU.7013.01 2 0 1 0 1
#> TCGA.KT.A7W1.01 1 0 1 1 0
#> TCGA.HT.A5RA.01 1 0 1 1 0
#> TCGA.CS.6188.01 2 0 1 0 1
#> TCGA.DU.A7TJ.01 2 0 1 0 1
#> TCGA.DU.A5TY.01 1 0 1 1 0
#> TCGA.DU.5847.01 1 0 1 1 0
#> TCGA.HT.7882.01 2 0 1 0 1
#> TCGA.DU.5854.01 1 0 1 1 0
#> TCGA.HT.8011.01 2 0 1 0 1
#> TCGA.DU.5852.01 1 0 1 1 0
#> TCGA.P5.A72U.01 1 0 1 1 0
#> TCGA.DU.6404.02 1 0 1 1 0
#> TCGA.DU.6404.01 1 0 1 1 0
#> TCGA.HT.8107.01 2 0 1 0 1
#> TCGA.E1.A7YN.01 1 0 1 1 0
#> TCGA.E1.A7Z2.01 1 0 1 1 0
#> TCGA.VM.A8CD.01 2 0 1 0 1
#> TCGA.HT.8564.01 2 0 1 0 1
#> TCGA.HT.7854.01 2 0 1 0 1
#> TCGA.VM.A8C9.01 1 0 1 1 0
#> TCGA.HT.7860.01 1 0 1 1 0
#> TCGA.DU.7006.01 1 0 1 1 0
#> TCGA.DU.8161.01 1 0 1 1 0
#> TCGA.E1.A7YM.01 2 0 1 0 1
#> TCGA.E1.A7YD.01 2 0 1 0 1
#> TCGA.HT.8015.01 2 0 1 0 1
#> TCGA.DU.A7TD.01 2 0 1 0 1
#> TCGA.DU.6405.01 1 0 1 1 0
#> TCGA.HT.A74H.01 2 0 1 0 1
#> TCGA.DU.7290.01 1 0 1 1 0
#> TCGA.HT.A4DS.01 1 0 1 1 0
#> TCGA.TM.A84B.01 2 0 1 0 1
#> TCGA.DU.8158.01 1 0 1 1 0
#> 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.FG.6688.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.TQ.A7RP.01 3 0.556 0.593 0.00 0.30 0.70
#> TCGA.S9.A7IX.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.VW.A8FI.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.DU.8165.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.DU.A76L.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.CS.4941.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.S9.A6U0.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.FG.7643.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.DU.6403.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.FG.8181.01 3 0.000 0.957 0.00 0.00 1.00
#> TCGA.CS.5395.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.DU.7292.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.HT.A5RC.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.FG.A4MW.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.DB.A75P.01 1 0.153 0.967 0.96 0.00 0.04
#> TCGA.S9.A89V.01 3 0.000 0.957 0.00 0.00 1.00
#> TCGA.QH.A6CX.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.CS.6186.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.DU.6406.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.DU.A7TB.01 3 0.153 0.941 0.00 0.04 0.96
#> TCGA.DU.A76K.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.DU.8162.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.E1.A7YQ.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.QH.A6CS.01 3 0.000 0.957 0.00 0.00 1.00
#> TCGA.HT.7691.01 1 0.153 0.967 0.96 0.00 0.04
#> TCGA.DU.7012.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.DU.6402.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.FG.A87Q.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.HT.8104.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.FG.A70Z.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.QH.A6XC.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.FG.A4MU.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.TM.A7C3.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.DB.A64O.01 3 0.153 0.941 0.00 0.04 0.96
#> TCGA.DU.A5TT.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.HT.8019.01 1 0.153 0.967 0.96 0.00 0.04
#> TCGA.P5.A5EY.01 3 0.000 0.957 0.00 0.00 1.00
#> TCGA.CS.5397.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.HW.A5KK.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.CS.6669.01 1 0.153 0.967 0.96 0.00 0.04
#> TCGA.S9.A7R2.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.S9.A6WM.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.HT.7680.01 1 0.153 0.967 0.96 0.00 0.04
#> TCGA.P5.A5F6.01 3 0.000 0.957 0.00 0.00 1.00
#> TCGA.HT.8110.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.E1.A7YJ.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.E1.A7YL.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.HT.8558.01 1 0.153 0.967 0.96 0.00 0.04
#> TCGA.HT.A61C.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.QH.A6CV.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.FG.6692.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.DU.7013.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.KT.A7W1.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.HT.A5RA.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.CS.6188.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.DU.A7TJ.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.DU.A5TY.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.DU.5847.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.HT.7882.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.DU.5854.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.HT.8011.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.DU.5852.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.P5.A72U.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.DU.6404.02 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.DU.6404.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.HT.8107.01 3 0.000 0.957 0.00 0.00 1.00
#> TCGA.E1.A7YN.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.E1.A7Z2.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.VM.A8CD.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.HT.8564.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.HT.7854.01 3 0.153 0.941 0.00 0.04 0.96
#> TCGA.VM.A8C9.01 1 0.153 0.967 0.96 0.00 0.04
#> TCGA.HT.7860.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.DU.7006.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.DU.8161.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.E1.A7YM.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.E1.A7YD.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.HT.8015.01 3 0.000 0.957 0.00 0.00 1.00
#> TCGA.DU.A7TD.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.DU.6405.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.HT.A74H.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.DU.7290.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.HT.A4DS.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.TM.A84B.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.DU.8158.01 1 0.000 0.992 1.00 0.00 0.00
#> TCGA.HT.A617.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.HT.7857.01 1 0.153 0.967 0.96 0.00 0.04
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.FG.6688.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RP.01 3 0.2706 0.8619 0.00 0.08 0.90 0.02
#> TCGA.S9.A7IX.01 2 0.0707 0.9881 0.00 0.98 0.00 0.02
#> TCGA.VW.A8FI.01 2 0.0000 0.9915 0.00 1.00 0.00 0.00
#> TCGA.DU.8165.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.DU.A76L.01 2 0.0000 0.9915 0.00 1.00 0.00 0.00
#> TCGA.CS.4941.01 2 0.0707 0.9881 0.00 0.98 0.00 0.02
#> TCGA.S9.A6U0.01 2 0.0707 0.9881 0.00 0.98 0.00 0.02
#> TCGA.FG.7643.01 4 0.5000 0.0238 0.50 0.00 0.00 0.50
#> TCGA.DU.6403.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.FG.8181.01 3 0.0000 0.9787 0.00 0.00 1.00 0.00
#> TCGA.CS.5395.01 2 0.0000 0.9915 0.00 1.00 0.00 0.00
#> TCGA.DU.7292.01 2 0.0000 0.9915 0.00 1.00 0.00 0.00
#> TCGA.HT.A5RC.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.FG.A4MW.01 2 0.0000 0.9915 0.00 1.00 0.00 0.00
#> TCGA.DB.A75P.01 4 0.0707 0.9114 0.02 0.00 0.00 0.98
#> TCGA.S9.A89V.01 3 0.0000 0.9787 0.00 0.00 1.00 0.00
#> TCGA.QH.A6CX.01 2 0.0707 0.9881 0.00 0.98 0.00 0.02
#> TCGA.CS.6186.01 2 0.0707 0.9881 0.00 0.98 0.00 0.02
#> TCGA.DU.6406.01 1 0.0707 0.9741 0.98 0.02 0.00 0.00
#> TCGA.DU.A7TB.01 3 0.0000 0.9787 0.00 0.00 1.00 0.00
#> TCGA.DU.A76K.01 2 0.0000 0.9915 0.00 1.00 0.00 0.00
#> TCGA.DU.8162.01 1 0.1211 0.9563 0.96 0.00 0.00 0.04
#> TCGA.E1.A7YQ.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.QH.A6CS.01 3 0.0000 0.9787 0.00 0.00 1.00 0.00
#> TCGA.HT.7691.01 4 0.0707 0.9114 0.02 0.00 0.00 0.98
#> TCGA.DU.7012.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.DU.6402.01 2 0.0707 0.9881 0.00 0.98 0.00 0.02
#> TCGA.FG.A87Q.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.HT.8104.01 1 0.0707 0.9741 0.98 0.02 0.00 0.00
#> TCGA.FG.A70Z.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.QH.A6XC.01 2 0.0000 0.9915 0.00 1.00 0.00 0.00
#> TCGA.FG.A4MU.01 2 0.0000 0.9915 0.00 1.00 0.00 0.00
#> TCGA.TM.A7C3.01 1 0.0707 0.9741 0.98 0.02 0.00 0.00
#> TCGA.DB.A64O.01 3 0.0707 0.9657 0.00 0.00 0.98 0.02
#> TCGA.DU.A5TT.01 2 0.0707 0.9881 0.00 0.98 0.00 0.02
#> TCGA.HT.8019.01 4 0.0707 0.9114 0.02 0.00 0.00 0.98
#> TCGA.P5.A5EY.01 3 0.0000 0.9787 0.00 0.00 1.00 0.00
#> TCGA.CS.5397.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.HW.A5KK.01 2 0.0707 0.9881 0.00 0.98 0.00 0.02
#> TCGA.CS.6669.01 4 0.0707 0.9114 0.02 0.00 0.00 0.98
#> TCGA.S9.A7R2.01 2 0.0707 0.9881 0.00 0.98 0.00 0.02
#> TCGA.S9.A6WM.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.HT.7680.01 4 0.0707 0.9114 0.02 0.00 0.00 0.98
#> TCGA.P5.A5F6.01 3 0.0000 0.9787 0.00 0.00 1.00 0.00
#> TCGA.HT.8110.01 2 0.0707 0.9881 0.00 0.98 0.00 0.02
#> TCGA.E1.A7YJ.01 2 0.0000 0.9915 0.00 1.00 0.00 0.00
#> TCGA.E1.A7YL.01 2 0.0000 0.9915 0.00 1.00 0.00 0.00
#> TCGA.HT.8558.01 4 0.0707 0.9114 0.02 0.00 0.00 0.98
#> TCGA.HT.A61C.01 2 0.0000 0.9915 0.00 1.00 0.00 0.00
#> TCGA.QH.A6CV.01 2 0.0000 0.9915 0.00 1.00 0.00 0.00
#> TCGA.FG.6692.01 2 0.0000 0.9915 0.00 1.00 0.00 0.00
#> TCGA.DU.7013.01 2 0.0000 0.9915 0.00 1.00 0.00 0.00
#> TCGA.KT.A7W1.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.HT.A5RA.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.CS.6188.01 2 0.0000 0.9915 0.00 1.00 0.00 0.00
#> TCGA.DU.A7TJ.01 2 0.0000 0.9915 0.00 1.00 0.00 0.00
#> TCGA.DU.A5TY.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.DU.5847.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.HT.7882.01 2 0.0707 0.9881 0.00 0.98 0.00 0.02
#> TCGA.DU.5854.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.HT.8011.01 2 0.0000 0.9915 0.00 1.00 0.00 0.00
#> TCGA.DU.5852.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.P5.A72U.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.DU.6404.02 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.DU.6404.01 1 0.0707 0.9763 0.98 0.00 0.00 0.02
#> TCGA.HT.8107.01 3 0.0000 0.9787 0.00 0.00 1.00 0.00
#> TCGA.E1.A7YN.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.E1.A7Z2.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.VM.A8CD.01 2 0.0707 0.9881 0.00 0.98 0.00 0.02
#> TCGA.HT.8564.01 2 0.0000 0.9915 0.00 1.00 0.00 0.00
#> TCGA.HT.7854.01 3 0.1411 0.9468 0.00 0.02 0.96 0.02
#> TCGA.VM.A8C9.01 4 0.0707 0.9114 0.02 0.00 0.00 0.98
#> TCGA.HT.7860.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.DU.7006.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.DU.8161.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YM.01 2 0.0707 0.9881 0.00 0.98 0.00 0.02
#> TCGA.E1.A7YD.01 2 0.0000 0.9915 0.00 1.00 0.00 0.00
#> TCGA.HT.8015.01 3 0.0000 0.9787 0.00 0.00 1.00 0.00
#> TCGA.DU.A7TD.01 2 0.0000 0.9915 0.00 1.00 0.00 0.00
#> TCGA.DU.6405.01 1 0.0707 0.9741 0.98 0.02 0.00 0.00
#> TCGA.HT.A74H.01 2 0.0707 0.9881 0.00 0.98 0.00 0.02
#> TCGA.DU.7290.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.HT.A4DS.01 1 0.1211 0.9563 0.96 0.00 0.00 0.04
#> TCGA.TM.A84B.01 2 0.0000 0.9915 0.00 1.00 0.00 0.00
#> TCGA.DU.8158.01 1 0.0000 0.9930 1.00 0.00 0.00 0.00
#> TCGA.HT.A617.01 2 0.0707 0.9881 0.00 0.98 0.00 0.02
#> TCGA.HT.7857.01 4 0.0707 0.9114 0.02 0.00 0.00 0.98
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.FG.6688.01 1 0.1732 0.938 0.92 0.08 0.00 0.00 0.00
#> TCGA.TQ.A7RP.01 2 0.2873 0.764 0.00 0.86 0.12 0.00 0.02
#> TCGA.S9.A7IX.01 2 0.2020 0.868 0.00 0.90 0.00 0.00 0.10
#> TCGA.VW.A8FI.01 5 0.2020 0.878 0.00 0.10 0.00 0.00 0.90
#> TCGA.DU.8165.01 1 0.0000 0.947 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A76L.01 2 0.3895 0.656 0.00 0.68 0.00 0.00 0.32
#> TCGA.CS.4941.01 2 0.2280 0.863 0.00 0.88 0.00 0.00 0.12
#> TCGA.S9.A6U0.01 2 0.2020 0.868 0.00 0.90 0.00 0.00 0.10
#> TCGA.FG.7643.01 4 0.4876 0.568 0.22 0.08 0.00 0.70 0.00
#> TCGA.DU.6403.01 1 0.0609 0.947 0.98 0.02 0.00 0.00 0.00
#> TCGA.FG.8181.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00
#> TCGA.CS.5395.01 2 0.3424 0.771 0.00 0.76 0.00 0.00 0.24
#> TCGA.DU.7292.01 5 0.2020 0.878 0.00 0.10 0.00 0.00 0.90
#> TCGA.HT.A5RC.01 1 0.0609 0.947 0.98 0.02 0.00 0.00 0.00
#> TCGA.FG.A4MW.01 5 0.2020 0.878 0.00 0.10 0.00 0.00 0.90
#> TCGA.DB.A75P.01 4 0.0000 0.948 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A89V.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00
#> TCGA.QH.A6CX.01 2 0.2020 0.868 0.00 0.90 0.00 0.00 0.10
#> TCGA.CS.6186.01 2 0.3274 0.798 0.00 0.78 0.00 0.00 0.22
#> TCGA.DU.6406.01 1 0.0609 0.947 0.98 0.02 0.00 0.00 0.00
#> TCGA.DU.A7TB.01 3 0.0609 0.981 0.00 0.00 0.98 0.00 0.02
#> TCGA.DU.A76K.01 2 0.4060 0.564 0.00 0.64 0.00 0.00 0.36
#> TCGA.DU.8162.01 1 0.3946 0.835 0.80 0.08 0.00 0.12 0.00
#> TCGA.E1.A7YQ.01 1 0.0609 0.947 0.98 0.02 0.00 0.00 0.00
#> TCGA.QH.A6CS.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7691.01 4 0.0000 0.948 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.7012.01 1 0.1732 0.938 0.92 0.08 0.00 0.00 0.00
#> TCGA.DU.6402.01 2 0.3109 0.818 0.00 0.80 0.00 0.00 0.20
#> TCGA.FG.A87Q.01 1 0.0609 0.947 0.98 0.02 0.00 0.00 0.00
#> TCGA.HT.8104.01 1 0.0609 0.947 0.98 0.02 0.00 0.00 0.00
#> TCGA.FG.A70Z.01 1 0.1043 0.945 0.96 0.04 0.00 0.00 0.00
#> TCGA.QH.A6XC.01 5 0.3684 0.629 0.00 0.28 0.00 0.00 0.72
#> TCGA.FG.A4MU.01 5 0.2020 0.878 0.00 0.10 0.00 0.00 0.90
#> TCGA.TM.A7C3.01 1 0.0609 0.947 0.98 0.02 0.00 0.00 0.00
#> TCGA.DB.A64O.01 2 0.3796 0.512 0.00 0.70 0.30 0.00 0.00
#> TCGA.DU.A5TT.01 2 0.2732 0.845 0.00 0.84 0.00 0.00 0.16
#> TCGA.HT.8019.01 4 0.0000 0.948 0.00 0.00 0.00 1.00 0.00
#> TCGA.P5.A5EY.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00
#> TCGA.CS.5397.01 1 0.1732 0.938 0.92 0.08 0.00 0.00 0.00
#> TCGA.HW.A5KK.01 2 0.2020 0.868 0.00 0.90 0.00 0.00 0.10
#> TCGA.CS.6669.01 4 0.0000 0.948 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A7R2.01 2 0.2020 0.868 0.00 0.90 0.00 0.00 0.10
#> TCGA.S9.A6WM.01 1 0.0609 0.947 0.98 0.02 0.00 0.00 0.00
#> TCGA.HT.7680.01 4 0.0000 0.948 0.00 0.00 0.00 1.00 0.00
#> TCGA.P5.A5F6.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.8110.01 2 0.3109 0.820 0.00 0.80 0.00 0.00 0.20
#> TCGA.E1.A7YJ.01 5 0.2020 0.878 0.00 0.10 0.00 0.00 0.90
#> TCGA.E1.A7YL.01 5 0.4182 0.316 0.00 0.40 0.00 0.00 0.60
#> TCGA.HT.8558.01 4 0.0000 0.948 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.A61C.01 5 0.0000 0.853 0.00 0.00 0.00 0.00 1.00
#> TCGA.QH.A6CV.01 5 0.4182 0.308 0.00 0.40 0.00 0.00 0.60
#> TCGA.FG.6692.01 5 0.2020 0.878 0.00 0.10 0.00 0.00 0.90
#> TCGA.DU.7013.01 5 0.0609 0.863 0.00 0.02 0.00 0.00 0.98
#> TCGA.KT.A7W1.01 1 0.0609 0.947 0.98 0.02 0.00 0.00 0.00
#> TCGA.HT.A5RA.01 1 0.0609 0.947 0.98 0.02 0.00 0.00 0.00
#> TCGA.CS.6188.01 2 0.3895 0.651 0.00 0.68 0.00 0.00 0.32
#> TCGA.DU.A7TJ.01 5 0.1732 0.877 0.00 0.08 0.00 0.00 0.92
#> TCGA.DU.A5TY.01 1 0.1732 0.938 0.92 0.08 0.00 0.00 0.00
#> TCGA.DU.5847.01 1 0.0609 0.947 0.98 0.02 0.00 0.00 0.00
#> TCGA.HT.7882.01 2 0.2020 0.868 0.00 0.90 0.00 0.00 0.10
#> TCGA.DU.5854.01 1 0.1732 0.938 0.92 0.08 0.00 0.00 0.00
#> TCGA.HT.8011.01 5 0.0000 0.853 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.5852.01 1 0.0609 0.947 0.98 0.02 0.00 0.00 0.00
#> TCGA.P5.A72U.01 1 0.1410 0.942 0.94 0.06 0.00 0.00 0.00
#> TCGA.DU.6404.02 1 0.1732 0.938 0.92 0.08 0.00 0.00 0.00
#> TCGA.DU.6404.01 1 0.3697 0.858 0.82 0.08 0.00 0.10 0.00
#> TCGA.HT.8107.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00
#> TCGA.E1.A7YN.01 1 0.1732 0.938 0.92 0.08 0.00 0.00 0.00
#> TCGA.E1.A7Z2.01 1 0.1732 0.938 0.92 0.08 0.00 0.00 0.00
#> TCGA.VM.A8CD.01 2 0.2020 0.868 0.00 0.90 0.00 0.00 0.10
#> TCGA.HT.8564.01 5 0.0000 0.853 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.7854.01 2 0.3895 0.471 0.00 0.68 0.32 0.00 0.00
#> TCGA.VM.A8C9.01 4 0.0000 0.948 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7860.01 1 0.0609 0.947 0.98 0.02 0.00 0.00 0.00
#> TCGA.DU.7006.01 1 0.1732 0.938 0.92 0.08 0.00 0.00 0.00
#> TCGA.DU.8161.01 1 0.2331 0.928 0.90 0.08 0.00 0.02 0.00
#> TCGA.E1.A7YM.01 2 0.2020 0.868 0.00 0.90 0.00 0.00 0.10
#> TCGA.E1.A7YD.01 5 0.0000 0.853 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.8015.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.A7TD.01 5 0.0609 0.863 0.00 0.02 0.00 0.00 0.98
#> TCGA.DU.6405.01 1 0.0609 0.947 0.98 0.02 0.00 0.00 0.00
#> TCGA.HT.A74H.01 2 0.2929 0.844 0.00 0.82 0.00 0.00 0.18
#> TCGA.DU.7290.01 1 0.1410 0.942 0.94 0.06 0.00 0.00 0.00
#> TCGA.HT.A4DS.01 1 0.3421 0.880 0.84 0.08 0.00 0.08 0.00
#> TCGA.TM.A84B.01 5 0.1732 0.878 0.00 0.08 0.00 0.00 0.92
#> TCGA.DU.8158.01 1 0.0609 0.947 0.98 0.02 0.00 0.00 0.00
#> TCGA.HT.A617.01 2 0.2020 0.868 0.00 0.90 0.00 0.00 0.10
#> TCGA.HT.7857.01 4 0.0000 0.948 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 1 0.0000 0.875 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RP.01 2 0.1267 0.771 0.00 0.94 0.06 0.00 0.00 0.00
#> TCGA.S9.A7IX.01 2 0.1267 0.799 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.VW.A8FI.01 5 0.2793 0.796 0.00 0.20 0.00 0.00 0.80 0.00
#> TCGA.DU.8165.01 6 0.3756 0.745 0.40 0.00 0.00 0.00 0.00 0.60
#> TCGA.DU.A76L.01 2 0.3309 0.559 0.00 0.72 0.00 0.00 0.28 0.00
#> TCGA.CS.4941.01 2 0.0937 0.806 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.S9.A6U0.01 2 0.0000 0.814 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7643.01 1 0.2793 0.642 0.80 0.00 0.00 0.20 0.00 0.00
#> TCGA.DU.6403.01 6 0.3076 0.952 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.FG.8181.01 3 0.0000 0.984 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CS.5395.01 2 0.3409 0.527 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.DU.7292.01 5 0.3076 0.774 0.00 0.24 0.00 0.00 0.76 0.00
#> TCGA.HT.A5RC.01 6 0.3076 0.952 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.FG.A4MW.01 5 0.3076 0.774 0.00 0.24 0.00 0.00 0.76 0.00
#> TCGA.DB.A75P.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A89V.01 3 0.0547 0.972 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.QH.A6CX.01 2 0.0000 0.814 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6186.01 2 0.3198 0.605 0.00 0.74 0.00 0.00 0.26 0.00
#> TCGA.DU.6406.01 6 0.3076 0.952 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.DU.A7TB.01 3 0.2190 0.927 0.00 0.04 0.90 0.00 0.00 0.06
#> TCGA.DU.A76K.01 2 0.3756 0.228 0.00 0.60 0.00 0.00 0.40 0.00
#> TCGA.DU.8162.01 1 0.0547 0.862 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.E1.A7YQ.01 6 0.3076 0.952 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.QH.A6CS.01 3 0.0000 0.984 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7691.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.7012.01 1 0.0000 0.875 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6402.01 2 0.3198 0.604 0.00 0.74 0.00 0.00 0.26 0.00
#> TCGA.FG.A87Q.01 6 0.3647 0.822 0.36 0.00 0.00 0.00 0.00 0.64
#> TCGA.HT.8104.01 6 0.3076 0.952 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.FG.A70Z.01 1 0.3309 0.413 0.72 0.00 0.00 0.00 0.00 0.28
#> TCGA.QH.A6XC.01 5 0.3578 0.629 0.00 0.34 0.00 0.00 0.66 0.00
#> TCGA.FG.A4MU.01 5 0.2793 0.796 0.00 0.20 0.00 0.00 0.80 0.00
#> TCGA.TM.A7C3.01 6 0.3076 0.952 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.DB.A64O.01 2 0.3499 0.420 0.00 0.68 0.32 0.00 0.00 0.00
#> TCGA.DU.A5TT.01 2 0.1267 0.798 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.HT.8019.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.P5.A5EY.01 3 0.0000 0.984 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CS.5397.01 1 0.0000 0.875 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HW.A5KK.01 2 0.0000 0.814 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6669.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A7R2.01 2 0.0000 0.814 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WM.01 6 0.3076 0.952 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.HT.7680.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.P5.A5F6.01 3 0.0547 0.976 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.HT.8110.01 2 0.1814 0.766 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.E1.A7YJ.01 5 0.3076 0.774 0.00 0.24 0.00 0.00 0.76 0.00
#> TCGA.E1.A7YL.01 5 0.3797 0.443 0.00 0.42 0.00 0.00 0.58 0.00
#> TCGA.HT.8558.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.A61C.01 5 0.3045 0.745 0.00 0.06 0.00 0.00 0.84 0.10
#> TCGA.QH.A6CV.01 5 0.3864 0.237 0.00 0.48 0.00 0.00 0.52 0.00
#> TCGA.FG.6692.01 5 0.2793 0.794 0.00 0.20 0.00 0.00 0.80 0.00
#> TCGA.DU.7013.01 5 0.2190 0.766 0.00 0.06 0.00 0.00 0.90 0.04
#> TCGA.KT.A7W1.01 6 0.3076 0.952 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.HT.A5RA.01 6 0.3076 0.952 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.CS.6188.01 2 0.3499 0.480 0.00 0.68 0.00 0.00 0.32 0.00
#> TCGA.DU.A7TJ.01 5 0.2793 0.796 0.00 0.20 0.00 0.00 0.80 0.00
#> TCGA.DU.A5TY.01 1 0.0000 0.875 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5847.01 6 0.3578 0.852 0.34 0.00 0.00 0.00 0.00 0.66
#> TCGA.HT.7882.01 2 0.0000 0.814 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5854.01 1 0.0000 0.875 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8011.01 5 0.2350 0.716 0.00 0.02 0.00 0.00 0.88 0.10
#> TCGA.DU.5852.01 6 0.3076 0.952 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.P5.A72U.01 1 0.2631 0.648 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.DU.6404.02 1 0.4067 0.649 0.70 0.00 0.00 0.00 0.04 0.26
#> TCGA.DU.6404.01 1 0.3351 0.755 0.80 0.00 0.00 0.00 0.04 0.16
#> TCGA.HT.8107.01 3 0.0000 0.984 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YN.01 1 0.0000 0.875 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7Z2.01 1 0.0000 0.875 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8CD.01 2 0.0000 0.814 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8564.01 5 0.2350 0.716 0.00 0.02 0.00 0.00 0.88 0.10
#> TCGA.HT.7854.01 2 0.3711 0.503 0.00 0.72 0.26 0.00 0.00 0.02
#> TCGA.VM.A8C9.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7860.01 6 0.3578 0.852 0.34 0.00 0.00 0.00 0.00 0.66
#> TCGA.DU.7006.01 1 0.0000 0.875 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.8161.01 1 0.0000 0.875 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YM.01 2 0.0000 0.814 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YD.01 5 0.2190 0.751 0.00 0.04 0.00 0.00 0.90 0.06
#> TCGA.HT.8015.01 3 0.0000 0.984 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.A7TD.01 5 0.2190 0.751 0.00 0.04 0.00 0.00 0.90 0.06
#> TCGA.DU.6405.01 6 0.3076 0.952 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.HT.A74H.01 2 0.2260 0.734 0.00 0.86 0.00 0.00 0.14 0.00
#> TCGA.DU.7290.01 1 0.3409 0.332 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.HT.A4DS.01 1 0.0937 0.846 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.TM.A84B.01 5 0.2981 0.793 0.00 0.16 0.00 0.00 0.82 0.02
#> TCGA.DU.8158.01 6 0.3076 0.952 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.HT.A617.01 2 0.0000 0.814 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7857.01 4 0.0000 1.000 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 1 0.2832 0.834 0.76 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.TQ.A7RP.01 2 0.1664 0.757 0.00 0.92 0.02 0.00 0.00 0.00 0.06
#> TCGA.S9.A7IX.01 2 0.1664 0.781 0.00 0.92 0.02 0.00 0.06 0.00 0.00
#> TCGA.VW.A8FI.01 5 0.1886 0.779 0.00 0.12 0.00 0.00 0.88 0.00 0.00
#> TCGA.DU.8165.01 6 0.2376 0.789 0.12 0.00 0.02 0.00 0.00 0.86 0.00
#> TCGA.DU.A76L.01 2 0.3815 0.377 0.00 0.62 0.02 0.00 0.36 0.00 0.00
#> TCGA.CS.4941.01 2 0.2163 0.760 0.00 0.88 0.02 0.00 0.10 0.00 0.00
#> TCGA.S9.A6U0.01 2 0.0504 0.797 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.FG.7643.01 1 0.4092 0.684 0.74 0.00 0.02 0.16 0.00 0.08 0.00
#> TCGA.DU.6403.01 6 0.0000 0.889 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FG.8181.01 7 0.0000 0.942 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CS.5395.01 2 0.5083 0.316 0.04 0.56 0.06 0.00 0.34 0.00 0.00
#> TCGA.DU.7292.01 5 0.3052 0.716 0.00 0.20 0.02 0.00 0.78 0.00 0.00
#> TCGA.HT.A5RC.01 6 0.0504 0.883 0.00 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.FG.A4MW.01 5 0.2081 0.774 0.00 0.14 0.00 0.00 0.86 0.00 0.00
#> TCGA.DB.A75P.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A89V.01 7 0.2159 0.904 0.02 0.02 0.06 0.00 0.00 0.00 0.90
#> TCGA.QH.A6CX.01 2 0.0504 0.797 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.CS.6186.01 2 0.3815 0.375 0.00 0.62 0.02 0.00 0.36 0.00 0.00
#> TCGA.DU.6406.01 6 0.0000 0.889 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.A7TB.01 7 0.4666 0.709 0.02 0.02 0.34 0.00 0.02 0.00 0.60
#> TCGA.DU.A76K.01 5 0.3985 0.124 0.00 0.46 0.02 0.00 0.52 0.00 0.00
#> TCGA.DU.8162.01 1 0.3863 0.808 0.74 0.00 0.02 0.04 0.00 0.20 0.00
#> TCGA.E1.A7YQ.01 6 0.0504 0.883 0.00 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.QH.A6CS.01 7 0.0000 0.942 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.7691.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7012.01 1 0.2945 0.830 0.74 0.00 0.00 0.00 0.00 0.26 0.00
#> TCGA.DU.6402.01 2 0.3755 0.432 0.00 0.64 0.02 0.00 0.34 0.00 0.00
#> TCGA.FG.A87Q.01 6 0.2745 0.734 0.16 0.00 0.02 0.00 0.00 0.82 0.00
#> TCGA.HT.8104.01 6 0.0000 0.889 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FG.A70Z.01 6 0.3221 0.358 0.32 0.00 0.00 0.00 0.00 0.68 0.00
#> TCGA.QH.A6XC.01 5 0.3307 0.669 0.00 0.24 0.02 0.00 0.74 0.00 0.00
#> TCGA.FG.A4MU.01 5 0.2081 0.774 0.00 0.14 0.00 0.00 0.86 0.00 0.00
#> TCGA.TM.A7C3.01 6 0.0000 0.889 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DB.A64O.01 2 0.3908 0.534 0.00 0.72 0.08 0.00 0.00 0.00 0.20
#> TCGA.DU.A5TT.01 2 0.1928 0.773 0.00 0.90 0.02 0.00 0.08 0.00 0.00
#> TCGA.HT.8019.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A5EY.01 7 0.0000 0.942 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CS.5397.01 1 0.3307 0.833 0.74 0.00 0.02 0.00 0.00 0.24 0.00
#> TCGA.HW.A5KK.01 2 0.0000 0.798 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6669.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A7R2.01 2 0.0504 0.796 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WM.01 6 0.0000 0.889 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7680.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A5F6.01 7 0.1664 0.912 0.00 0.00 0.06 0.00 0.02 0.00 0.92
#> TCGA.HT.8110.01 2 0.1664 0.782 0.00 0.92 0.02 0.00 0.06 0.00 0.00
#> TCGA.E1.A7YJ.01 5 0.2081 0.774 0.00 0.14 0.00 0.00 0.86 0.00 0.00
#> TCGA.E1.A7YL.01 5 0.3755 0.501 0.00 0.34 0.02 0.00 0.64 0.00 0.00
#> TCGA.HT.8558.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.A61C.01 5 0.3055 0.690 0.02 0.02 0.14 0.00 0.82 0.00 0.00
#> TCGA.QH.A6CV.01 5 0.3755 0.497 0.00 0.34 0.02 0.00 0.64 0.00 0.00
#> TCGA.FG.6692.01 5 0.1886 0.779 0.00 0.12 0.00 0.00 0.88 0.00 0.00
#> TCGA.DU.7013.01 5 0.1006 0.749 0.00 0.02 0.02 0.00 0.96 0.00 0.00
#> TCGA.KT.A7W1.01 6 0.0000 0.889 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.A5RA.01 6 0.0000 0.889 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CS.6188.01 2 0.3968 0.132 0.00 0.54 0.02 0.00 0.44 0.00 0.00
#> TCGA.DU.A7TJ.01 5 0.1886 0.779 0.00 0.12 0.00 0.00 0.88 0.00 0.00
#> TCGA.DU.A5TY.01 1 0.2945 0.830 0.74 0.00 0.00 0.00 0.00 0.26 0.00
#> TCGA.DU.5847.01 6 0.2569 0.763 0.14 0.00 0.02 0.00 0.00 0.84 0.00
#> TCGA.HT.7882.01 2 0.0000 0.798 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5854.01 1 0.3047 0.810 0.72 0.00 0.00 0.00 0.00 0.28 0.00
#> TCGA.HT.8011.01 5 0.4317 0.463 0.02 0.02 0.38 0.00 0.58 0.00 0.00
#> TCGA.DU.5852.01 6 0.0000 0.889 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.P5.A72U.01 1 0.3943 0.505 0.56 0.00 0.02 0.00 0.00 0.42 0.00
#> TCGA.DU.6404.02 1 0.5341 0.275 0.50 0.00 0.26 0.00 0.00 0.24 0.00
#> TCGA.DU.6404.01 1 0.5259 0.313 0.52 0.00 0.26 0.00 0.00 0.22 0.00
#> TCGA.HT.8107.01 7 0.0000 0.942 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.E1.A7YN.01 1 0.2945 0.830 0.74 0.00 0.00 0.00 0.00 0.26 0.00
#> TCGA.E1.A7Z2.01 1 0.3307 0.833 0.74 0.00 0.02 0.00 0.00 0.24 0.00
#> TCGA.VM.A8CD.01 2 0.0504 0.796 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.HT.8564.01 5 0.3867 0.486 0.00 0.02 0.38 0.00 0.60 0.00 0.00
#> TCGA.HT.7854.01 2 0.4146 0.483 0.00 0.68 0.08 0.00 0.00 0.00 0.24
#> TCGA.VM.A8C9.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7860.01 6 0.1928 0.828 0.08 0.00 0.02 0.00 0.00 0.90 0.00
#> TCGA.DU.7006.01 1 0.2945 0.830 0.74 0.00 0.00 0.00 0.00 0.26 0.00
#> TCGA.DU.8161.01 1 0.3307 0.833 0.74 0.00 0.02 0.00 0.00 0.24 0.00
#> TCGA.E1.A7YM.01 2 0.0863 0.798 0.00 0.96 0.04 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YD.01 5 0.2376 0.714 0.00 0.02 0.12 0.00 0.86 0.00 0.00
#> TCGA.HT.8015.01 7 0.0000 0.942 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.A7TD.01 5 0.2376 0.713 0.00 0.02 0.12 0.00 0.86 0.00 0.00
#> TCGA.DU.6405.01 6 0.0000 0.889 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.A74H.01 2 0.2376 0.743 0.00 0.86 0.02 0.00 0.12 0.00 0.00
#> TCGA.DU.7290.01 6 0.3968 -0.183 0.44 0.00 0.02 0.00 0.00 0.54 0.00
#> TCGA.HT.A4DS.01 1 0.3661 0.824 0.74 0.00 0.02 0.02 0.00 0.22 0.00
#> TCGA.TM.A84B.01 5 0.1928 0.770 0.00 0.08 0.02 0.00 0.90 0.00 0.00
#> TCGA.DU.8158.01 6 0.0504 0.883 0.00 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.HT.A617.01 2 0.0504 0.796 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.HT.7857.01 4 0.0000 1.000 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 1 0.2224 0.8417 0.86 0.00 0.02 0.00 0.00 0.12 0.00 0.00
#> TCGA.TQ.A7RP.01 2 0.1557 0.7391 0.00 0.92 0.02 0.00 0.00 0.00 0.00 0.06
#> TCGA.S9.A7IX.01 2 0.2025 0.7831 0.00 0.88 0.00 0.00 0.10 0.00 0.00 0.02
#> TCGA.VW.A8FI.01 5 0.0471 0.6750 0.00 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.DU.8165.01 6 0.2719 0.7109 0.18 0.00 0.02 0.00 0.00 0.80 0.00 0.00
#> TCGA.DU.A76L.01 2 0.4533 0.1318 0.02 0.50 0.02 0.00 0.44 0.00 0.00 0.02
#> TCGA.CS.4941.01 2 0.2569 0.7480 0.00 0.82 0.00 0.00 0.16 0.00 0.00 0.02
#> TCGA.S9.A6U0.01 2 0.2348 0.7896 0.00 0.88 0.02 0.00 0.06 0.00 0.00 0.04
#> TCGA.FG.7643.01 1 0.2591 0.7033 0.86 0.00 0.00 0.08 0.00 0.04 0.00 0.02
#> TCGA.DU.6403.01 6 0.0000 0.9235 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FG.8181.01 7 0.0000 0.8574 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CS.5395.01 2 0.5322 0.1903 0.02 0.48 0.02 0.00 0.38 0.00 0.00 0.10
#> TCGA.DU.7292.01 5 0.0808 0.6965 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.HT.A5RC.01 6 0.0000 0.9235 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FG.A4MW.01 5 0.0808 0.6965 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.DB.A75P.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A89V.01 7 0.5130 0.6457 0.04 0.02 0.22 0.00 0.00 0.00 0.62 0.10
#> TCGA.QH.A6CX.01 2 0.1275 0.7816 0.00 0.94 0.00 0.00 0.02 0.00 0.00 0.04
#> TCGA.CS.6186.01 5 0.3318 0.0721 0.00 0.46 0.00 0.00 0.54 0.00 0.00 0.00
#> TCGA.DU.6406.01 6 0.0000 0.9235 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.A7TB.01 7 0.6175 0.3518 0.04 0.02 0.24 0.00 0.00 0.00 0.36 0.34
#> TCGA.DU.A76K.01 5 0.3015 0.4732 0.00 0.32 0.00 0.00 0.68 0.00 0.00 0.00
#> TCGA.DU.8162.01 1 0.2224 0.8418 0.86 0.00 0.00 0.00 0.00 0.12 0.00 0.02
#> TCGA.E1.A7YQ.01 6 0.0000 0.9235 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.QH.A6CS.01 7 0.0471 0.8509 0.00 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.HT.7691.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7012.01 1 0.2224 0.8417 0.86 0.00 0.02 0.00 0.00 0.12 0.00 0.00
#> TCGA.DU.6402.01 2 0.3329 0.0738 0.00 0.52 0.00 0.00 0.48 0.00 0.00 0.00
#> TCGA.FG.A87Q.01 6 0.2856 0.6720 0.20 0.00 0.02 0.00 0.00 0.78 0.00 0.00
#> TCGA.HT.8104.01 6 0.0000 0.9235 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FG.A70Z.01 1 0.3318 0.3082 0.54 0.00 0.00 0.00 0.00 0.46 0.00 0.00
#> TCGA.QH.A6XC.01 5 0.1563 0.6676 0.00 0.10 0.00 0.00 0.90 0.00 0.00 0.00
#> TCGA.FG.A4MU.01 5 0.0808 0.6965 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.TM.A7C3.01 6 0.0000 0.9235 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DB.A64O.01 2 0.3817 0.5823 0.00 0.76 0.04 0.00 0.00 0.00 0.12 0.08
#> TCGA.DU.A5TT.01 2 0.2981 0.6719 0.02 0.76 0.00 0.00 0.22 0.00 0.00 0.00
#> TCGA.HT.8019.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A5EY.01 7 0.0000 0.8574 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CS.5397.01 1 0.2224 0.8418 0.86 0.00 0.00 0.00 0.00 0.12 0.00 0.02
#> TCGA.HW.A5KK.01 2 0.0471 0.7900 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.CS.6669.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7R2.01 2 0.0941 0.7885 0.00 0.96 0.00 0.00 0.02 0.00 0.00 0.02
#> TCGA.S9.A6WM.01 6 0.0000 0.9235 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7680.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A5F6.01 7 0.2864 0.7959 0.00 0.02 0.08 0.00 0.00 0.00 0.84 0.06
#> TCGA.HT.8110.01 2 0.2818 0.7647 0.00 0.82 0.00 0.00 0.12 0.00 0.00 0.06
#> TCGA.E1.A7YJ.01 5 0.0808 0.6965 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.E1.A7YL.01 5 0.2534 0.5774 0.00 0.22 0.00 0.00 0.78 0.00 0.00 0.00
#> TCGA.HT.8558.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A61C.01 5 0.2852 -0.1890 0.00 0.00 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.QH.A6CV.01 5 0.2534 0.5764 0.00 0.22 0.00 0.00 0.78 0.00 0.00 0.00
#> TCGA.FG.6692.01 5 0.0808 0.6965 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.DU.7013.01 5 0.0808 0.5898 0.00 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.KT.A7W1.01 6 0.0000 0.9235 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.A5RA.01 6 0.0000 0.9235 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CS.6188.01 5 0.3299 0.1575 0.00 0.44 0.00 0.00 0.56 0.00 0.00 0.00
#> TCGA.DU.A7TJ.01 5 0.0808 0.6965 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.DU.A5TY.01 1 0.1765 0.8453 0.88 0.00 0.00 0.00 0.00 0.12 0.00 0.00
#> TCGA.DU.5847.01 6 0.3095 0.6004 0.24 0.00 0.02 0.00 0.00 0.74 0.00 0.00
#> TCGA.HT.7882.01 2 0.1341 0.7917 0.00 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.DU.5854.01 1 0.2224 0.8417 0.86 0.00 0.02 0.00 0.00 0.12 0.00 0.00
#> TCGA.HT.8011.01 8 0.3714 0.9179 0.00 0.00 0.02 0.00 0.44 0.00 0.00 0.54
#> TCGA.DU.5852.01 6 0.0000 0.9235 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.P5.A72U.01 1 0.3449 0.5579 0.66 0.00 0.02 0.00 0.00 0.32 0.00 0.00
#> TCGA.DU.6404.02 3 0.4614 0.8966 0.26 0.00 0.58 0.00 0.00 0.16 0.00 0.00
#> TCGA.DU.6404.01 3 0.4960 0.8952 0.28 0.00 0.58 0.04 0.00 0.10 0.00 0.00
#> TCGA.HT.8107.01 7 0.0000 0.8574 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.E1.A7YN.01 1 0.2224 0.8417 0.86 0.00 0.02 0.00 0.00 0.12 0.00 0.00
#> TCGA.E1.A7Z2.01 1 0.2025 0.8222 0.88 0.00 0.00 0.00 0.00 0.10 0.00 0.02
#> TCGA.VM.A8CD.01 2 0.0808 0.7945 0.00 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.HT.8564.01 8 0.3237 0.9218 0.00 0.00 0.00 0.00 0.40 0.00 0.00 0.60
#> TCGA.HT.7854.01 2 0.5266 0.4197 0.00 0.60 0.08 0.00 0.00 0.00 0.16 0.16
#> TCGA.VM.A8C9.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7860.01 6 0.2025 0.8092 0.10 0.00 0.02 0.00 0.00 0.88 0.00 0.00
#> TCGA.DU.7006.01 1 0.1765 0.8453 0.88 0.00 0.00 0.00 0.00 0.12 0.00 0.00
#> TCGA.DU.8161.01 1 0.2224 0.8418 0.86 0.00 0.00 0.00 0.00 0.12 0.00 0.02
#> TCGA.E1.A7YM.01 2 0.0941 0.7885 0.00 0.96 0.00 0.00 0.02 0.00 0.00 0.02
#> TCGA.E1.A7YD.01 5 0.2569 0.3256 0.02 0.00 0.00 0.00 0.82 0.00 0.00 0.16
#> TCGA.HT.8015.01 7 0.0000 0.8574 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.A7TD.01 5 0.2114 0.3613 0.00 0.00 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.DU.6405.01 6 0.0000 0.9235 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.A74H.01 2 0.3198 0.6294 0.00 0.72 0.00 0.00 0.26 0.00 0.00 0.02
#> TCGA.DU.7290.01 1 0.3714 0.3389 0.54 0.00 0.02 0.00 0.00 0.44 0.00 0.00
#> TCGA.HT.A4DS.01 1 0.2484 0.8209 0.86 0.00 0.00 0.02 0.00 0.10 0.00 0.02
#> TCGA.TM.A84B.01 5 0.0941 0.6556 0.00 0.02 0.00 0.00 0.96 0.00 0.00 0.02
#> TCGA.DU.8158.01 6 0.0000 0.9235 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.A617.01 2 0.0808 0.7945 0.00 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.HT.7857.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 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: Node01. Child nodes: Node0121 , Node0122-leaf , Node0123-leaf , Node0211-leaf , Node0212-leaf , Node0213-leaf , Node0221 , Node0222 , Node0231 , Node0232 .
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 36 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 0.744 0.889 0.955 0.5035 0.487 0.487
#> 3 3 1.000 1.000 1.000 0.3594 0.733 0.501
#> 4 4 0.845 0.883 0.894 0.0707 1.000 1.000
#> 5 5 0.797 0.539 0.789 0.0494 0.933 0.789
#> 6 6 0.772 0.670 0.796 0.0368 0.902 0.629
#> 7 7 0.747 0.787 0.843 0.0297 0.956 0.772
#> 8 8 0.774 0.742 0.864 0.0311 0.986 0.913
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.S9.A7IX.01 2 0.000 0.974 0.00 1.00
#> TCGA.VW.A8FI.01 1 0.000 0.918 1.00 0.00
#> TCGA.DU.A76L.01 1 0.971 0.378 0.60 0.40
#> TCGA.CS.4941.01 2 0.000 0.974 0.00 1.00
#> TCGA.S9.A6U0.01 2 0.469 0.877 0.10 0.90
#> TCGA.CS.5395.01 1 0.000 0.918 1.00 0.00
#> TCGA.DU.7292.01 1 0.000 0.918 1.00 0.00
#> TCGA.FG.A4MW.01 1 0.000 0.918 1.00 0.00
#> TCGA.QH.A6CX.01 2 0.000 0.974 0.00 1.00
#> TCGA.CS.6186.01 2 0.000 0.974 0.00 1.00
#> TCGA.DU.A76K.01 2 0.000 0.974 0.00 1.00
#> TCGA.DU.6402.01 2 0.000 0.974 0.00 1.00
#> TCGA.QH.A6XC.01 2 0.795 0.662 0.24 0.76
#> TCGA.FG.A4MU.01 1 0.000 0.918 1.00 0.00
#> TCGA.DU.A5TT.01 2 0.000 0.974 0.00 1.00
#> TCGA.HW.A5KK.01 2 0.000 0.974 0.00 1.00
#> TCGA.S9.A7R2.01 2 0.000 0.974 0.00 1.00
#> TCGA.HT.8110.01 1 0.971 0.378 0.60 0.40
#> TCGA.E1.A7YJ.01 1 0.000 0.918 1.00 0.00
#> TCGA.E1.A7YL.01 1 0.971 0.378 0.60 0.40
#> TCGA.HT.A61C.01 1 0.000 0.918 1.00 0.00
#> TCGA.QH.A6CV.01 2 0.000 0.974 0.00 1.00
#> TCGA.FG.6692.01 1 0.000 0.918 1.00 0.00
#> TCGA.DU.7013.01 1 0.000 0.918 1.00 0.00
#> TCGA.CS.6188.01 2 0.000 0.974 0.00 1.00
#> TCGA.DU.A7TJ.01 1 0.000 0.918 1.00 0.00
#> TCGA.HT.7882.01 2 0.000 0.974 0.00 1.00
#> TCGA.HT.8011.01 1 0.000 0.918 1.00 0.00
#> TCGA.VM.A8CD.01 2 0.000 0.974 0.00 1.00
#> TCGA.HT.8564.01 2 0.402 0.900 0.08 0.92
#> TCGA.E1.A7YM.01 2 0.000 0.974 0.00 1.00
#> TCGA.E1.A7YD.01 1 0.000 0.918 1.00 0.00
#> TCGA.DU.A7TD.01 1 0.000 0.918 1.00 0.00
#> TCGA.HT.A74H.01 2 0.000 0.974 0.00 1.00
#> TCGA.TM.A84B.01 1 0.000 0.918 1.00 0.00
#> TCGA.HT.A617.01 2 0.000 0.974 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.S9.A7IX.01 2 0 1 0 1 0
#> TCGA.VW.A8FI.01 1 0 1 1 0 0
#> TCGA.DU.A76L.01 3 0 1 0 0 1
#> TCGA.CS.4941.01 3 0 1 0 0 1
#> TCGA.S9.A6U0.01 3 0 1 0 0 1
#> TCGA.CS.5395.01 3 0 1 0 0 1
#> TCGA.DU.7292.01 3 0 1 0 0 1
#> TCGA.FG.A4MW.01 1 0 1 1 0 0
#> TCGA.QH.A6CX.01 2 0 1 0 1 0
#> TCGA.CS.6186.01 2 0 1 0 1 0
#> TCGA.DU.A76K.01 2 0 1 0 1 0
#> TCGA.DU.6402.01 2 0 1 0 1 0
#> TCGA.QH.A6XC.01 3 0 1 0 0 1
#> TCGA.FG.A4MU.01 1 0 1 1 0 0
#> TCGA.DU.A5TT.01 2 0 1 0 1 0
#> TCGA.HW.A5KK.01 2 0 1 0 1 0
#> TCGA.S9.A7R2.01 2 0 1 0 1 0
#> TCGA.HT.8110.01 3 0 1 0 0 1
#> TCGA.E1.A7YJ.01 1 0 1 1 0 0
#> TCGA.E1.A7YL.01 3 0 1 0 0 1
#> TCGA.HT.A61C.01 1 0 1 1 0 0
#> TCGA.QH.A6CV.01 2 0 1 0 1 0
#> TCGA.FG.6692.01 1 0 1 1 0 0
#> TCGA.DU.7013.01 1 0 1 1 0 0
#> TCGA.CS.6188.01 3 0 1 0 0 1
#> TCGA.DU.A7TJ.01 1 0 1 1 0 0
#> TCGA.HT.7882.01 2 0 1 0 1 0
#> TCGA.HT.8011.01 1 0 1 1 0 0
#> TCGA.VM.A8CD.01 2 0 1 0 1 0
#> TCGA.HT.8564.01 3 0 1 0 0 1
#> TCGA.E1.A7YM.01 2 0 1 0 1 0
#> TCGA.E1.A7YD.01 1 0 1 1 0 0
#> TCGA.DU.A7TD.01 1 0 1 1 0 0
#> TCGA.HT.A74H.01 3 0 1 0 0 1
#> TCGA.TM.A84B.01 1 0 1 1 0 0
#> TCGA.HT.A617.01 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.S9.A7IX.01 2 0.1637 0.895 0.06 0.94 0.00 0.00
#> TCGA.VW.A8FI.01 4 0.0000 0.875 0.00 0.00 0.00 1.00
#> TCGA.DU.A76L.01 3 0.0000 0.965 0.00 0.00 1.00 0.00
#> TCGA.CS.4941.01 3 0.0707 0.960 0.00 0.02 0.98 0.00
#> TCGA.S9.A6U0.01 3 0.0000 0.965 0.00 0.00 1.00 0.00
#> TCGA.CS.5395.01 3 0.0000 0.965 0.00 0.00 1.00 0.00
#> TCGA.DU.7292.01 3 0.3335 0.903 0.12 0.00 0.86 0.02
#> TCGA.FG.A4MW.01 4 0.0000 0.875 0.00 0.00 0.00 1.00
#> TCGA.QH.A6CX.01 2 0.0000 0.897 0.00 1.00 0.00 0.00
#> TCGA.CS.6186.01 2 0.4977 0.713 0.46 0.54 0.00 0.00
#> TCGA.DU.A76K.01 2 0.1637 0.895 0.06 0.94 0.00 0.00
#> TCGA.DU.6402.01 2 0.2921 0.883 0.14 0.86 0.00 0.00
#> TCGA.QH.A6XC.01 3 0.2647 0.916 0.12 0.00 0.88 0.00
#> TCGA.FG.A4MU.01 4 0.0000 0.875 0.00 0.00 0.00 1.00
#> TCGA.DU.A5TT.01 2 0.1637 0.895 0.06 0.94 0.00 0.00
#> TCGA.HW.A5KK.01 2 0.0707 0.897 0.02 0.98 0.00 0.00
#> TCGA.S9.A7R2.01 2 0.0000 0.897 0.00 1.00 0.00 0.00
#> TCGA.HT.8110.01 3 0.0000 0.965 0.00 0.00 1.00 0.00
#> TCGA.E1.A7YJ.01 4 0.2011 0.833 0.08 0.00 0.00 0.92
#> TCGA.E1.A7YL.01 3 0.0000 0.965 0.00 0.00 1.00 0.00
#> TCGA.HT.A61C.01 4 0.4522 0.835 0.32 0.00 0.00 0.68
#> TCGA.QH.A6CV.01 2 0.3172 0.876 0.16 0.84 0.00 0.00
#> TCGA.FG.6692.01 4 0.0707 0.876 0.02 0.00 0.00 0.98
#> TCGA.DU.7013.01 4 0.4522 0.835 0.32 0.00 0.00 0.68
#> TCGA.CS.6188.01 3 0.1913 0.951 0.04 0.02 0.94 0.00
#> TCGA.DU.A7TJ.01 4 0.0000 0.875 0.00 0.00 0.00 1.00
#> TCGA.HT.7882.01 2 0.0000 0.897 0.00 1.00 0.00 0.00
#> TCGA.HT.8011.01 4 0.4522 0.835 0.32 0.00 0.00 0.68
#> TCGA.VM.A8CD.01 2 0.4624 0.745 0.34 0.66 0.00 0.00
#> TCGA.HT.8564.01 3 0.2345 0.917 0.10 0.00 0.90 0.00
#> TCGA.E1.A7YM.01 2 0.0707 0.897 0.02 0.98 0.00 0.00
#> TCGA.E1.A7YD.01 4 0.4522 0.835 0.32 0.00 0.00 0.68
#> TCGA.DU.A7TD.01 4 0.4522 0.835 0.32 0.00 0.00 0.68
#> TCGA.HT.A74H.01 3 0.0707 0.960 0.00 0.02 0.98 0.00
#> TCGA.TM.A84B.01 4 0.0707 0.876 0.02 0.00 0.00 0.98
#> TCGA.HT.A617.01 2 0.4790 0.729 0.38 0.62 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.A7IX.01 2 0.0609 0.784 0.00 0.98 0.00 0.00 0.02
#> TCGA.VW.A8FI.01 4 0.0000 0.613 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.A76L.01 3 0.0000 0.882 0.00 0.00 1.00 0.00 0.00
#> TCGA.CS.4941.01 3 0.1410 0.876 0.00 0.00 0.94 0.00 0.06
#> TCGA.S9.A6U0.01 3 0.1043 0.879 0.00 0.00 0.96 0.00 0.04
#> TCGA.CS.5395.01 3 0.0000 0.882 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.7292.01 3 0.5818 0.729 0.14 0.00 0.66 0.02 0.18
#> TCGA.FG.A4MW.01 4 0.0000 0.613 0.00 0.00 0.00 1.00 0.00
#> TCGA.QH.A6CX.01 2 0.0000 0.787 0.00 1.00 0.00 0.00 0.00
#> TCGA.CS.6186.01 5 0.3796 0.785 0.00 0.30 0.00 0.00 0.70
#> TCGA.DU.A76K.01 2 0.0609 0.784 0.00 0.98 0.00 0.00 0.02
#> TCGA.DU.6402.01 2 0.3684 0.306 0.00 0.72 0.00 0.00 0.28
#> TCGA.QH.A6XC.01 3 0.5258 0.745 0.14 0.00 0.68 0.00 0.18
#> TCGA.FG.A4MU.01 4 0.0000 0.613 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.A5TT.01 2 0.0609 0.784 0.00 0.98 0.00 0.00 0.02
#> TCGA.HW.A5KK.01 2 0.0609 0.776 0.00 0.98 0.00 0.00 0.02
#> TCGA.S9.A7R2.01 2 0.0000 0.787 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.8110.01 3 0.0000 0.882 0.00 0.00 1.00 0.00 0.00
#> TCGA.E1.A7YJ.01 4 0.3037 0.466 0.10 0.00 0.00 0.86 0.04
#> TCGA.E1.A7YL.01 3 0.0000 0.882 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.A61C.01 1 0.4307 1.000 0.50 0.00 0.00 0.50 0.00
#> TCGA.QH.A6CV.01 2 0.5558 -0.188 0.08 0.56 0.00 0.00 0.36
#> TCGA.FG.6692.01 4 0.0609 0.598 0.02 0.00 0.00 0.98 0.00
#> TCGA.DU.7013.01 4 0.4307 -1.000 0.50 0.00 0.00 0.50 0.00
#> TCGA.CS.6188.01 3 0.3521 0.829 0.04 0.00 0.82 0.00 0.14
#> TCGA.DU.A7TJ.01 4 0.0000 0.613 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7882.01 2 0.0000 0.787 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.8011.01 1 0.4307 1.000 0.50 0.00 0.00 0.50 0.00
#> TCGA.VM.A8CD.01 2 0.4302 -0.637 0.00 0.52 0.00 0.00 0.48
#> TCGA.HT.8564.01 3 0.5245 0.603 0.28 0.00 0.64 0.00 0.08
#> TCGA.E1.A7YM.01 2 0.0609 0.776 0.00 0.98 0.00 0.00 0.02
#> TCGA.E1.A7YD.01 4 0.4307 -1.000 0.50 0.00 0.00 0.50 0.00
#> TCGA.DU.A7TD.01 4 0.4307 -1.000 0.50 0.00 0.00 0.50 0.00
#> TCGA.HT.A74H.01 3 0.1410 0.849 0.00 0.06 0.94 0.00 0.00
#> TCGA.TM.A84B.01 4 0.2077 0.549 0.04 0.00 0.00 0.92 0.04
#> TCGA.HT.A617.01 5 0.4227 0.752 0.00 0.42 0.00 0.00 0.58
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.S9.A7IX.01 2 0.1092 0.8318 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.VW.A8FI.01 4 0.3797 0.9127 0.42 0.00 0.00 0.58 0.00 0.00
#> TCGA.DU.A76L.01 3 0.0000 0.7570 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CS.4941.01 3 0.2094 0.6812 0.00 0.00 0.90 0.00 0.02 0.08
#> TCGA.S9.A6U0.01 3 0.0937 0.7342 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.CS.5395.01 3 0.0547 0.7493 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.DU.7292.01 6 0.4552 0.8669 0.00 0.00 0.30 0.06 0.00 0.64
#> TCGA.FG.A4MW.01 4 0.3797 0.9127 0.42 0.00 0.00 0.58 0.00 0.00
#> TCGA.QH.A6CX.01 2 0.0000 0.8305 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6186.01 5 0.4094 0.6331 0.00 0.18 0.00 0.00 0.74 0.08
#> TCGA.DU.A76K.01 2 0.1092 0.8318 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.DU.6402.01 2 0.4066 0.6220 0.00 0.78 0.00 0.02 0.12 0.08
#> TCGA.QH.A6XC.01 6 0.3647 0.8558 0.00 0.00 0.36 0.00 0.00 0.64
#> TCGA.FG.A4MU.01 4 0.3797 0.9127 0.42 0.00 0.00 0.58 0.00 0.00
#> TCGA.DU.A5TT.01 2 0.1092 0.8318 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.HW.A5KK.01 2 0.1556 0.7883 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.S9.A7R2.01 2 0.0547 0.8263 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.HT.8110.01 3 0.0000 0.7570 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YJ.01 4 0.5289 0.6974 0.28 0.00 0.00 0.58 0.00 0.14
#> TCGA.E1.A7YL.01 3 0.0000 0.7570 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.A61C.01 1 0.0000 0.8352 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CV.01 2 0.6956 -0.0793 0.00 0.46 0.00 0.10 0.26 0.18
#> TCGA.FG.6692.01 4 0.3864 0.8072 0.48 0.00 0.00 0.52 0.00 0.00
#> TCGA.DU.7013.01 1 0.0000 0.8352 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6188.01 3 0.4806 -0.5980 0.00 0.02 0.48 0.00 0.02 0.48
#> TCGA.DU.A7TJ.01 4 0.3797 0.9127 0.42 0.00 0.00 0.58 0.00 0.00
#> TCGA.HT.7882.01 2 0.0547 0.8210 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.HT.8011.01 1 0.0000 0.8352 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8CD.01 5 0.3797 0.6432 0.00 0.42 0.00 0.00 0.58 0.00
#> TCGA.HT.8564.01 3 0.6549 0.1079 0.00 0.00 0.48 0.32 0.12 0.08
#> TCGA.E1.A7YM.01 2 0.1556 0.7883 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.E1.A7YD.01 1 0.0000 0.8352 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A7TD.01 1 0.0000 0.8352 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A74H.01 3 0.2094 0.6760 0.00 0.08 0.90 0.00 0.02 0.00
#> TCGA.TM.A84B.01 1 0.6022 -0.6627 0.48 0.00 0.00 0.38 0.04 0.10
#> TCGA.HT.A617.01 5 0.3578 0.7337 0.00 0.34 0.00 0.00 0.66 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.A7IX.01 2 0.1664 0.8174 0.02 0.92 0.00 0.00 0.00 0.06 0.00
#> TCGA.VW.A8FI.01 4 0.0000 0.9292 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.A76L.01 3 0.0504 0.8450 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CS.4941.01 3 0.3876 0.6997 0.02 0.02 0.78 0.00 0.04 0.14 0.00
#> TCGA.S9.A6U0.01 3 0.2213 0.8148 0.02 0.00 0.90 0.00 0.04 0.04 0.00
#> TCGA.CS.5395.01 3 0.3257 0.7038 0.04 0.00 0.84 0.00 0.02 0.08 0.02
#> TCGA.DU.7292.01 6 0.4055 0.7699 0.04 0.00 0.18 0.00 0.04 0.74 0.00
#> TCGA.FG.A4MW.01 4 0.0000 0.9292 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.QH.A6CX.01 2 0.0000 0.8167 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6186.01 5 0.4139 0.6999 0.06 0.20 0.00 0.00 0.72 0.00 0.02
#> TCGA.DU.A76K.01 2 0.1664 0.8174 0.02 0.92 0.00 0.00 0.00 0.06 0.00
#> TCGA.DU.6402.01 2 0.3887 0.7155 0.02 0.80 0.00 0.00 0.06 0.08 0.04
#> TCGA.QH.A6XC.01 6 0.2422 0.8003 0.00 0.00 0.18 0.00 0.00 0.82 0.00
#> TCGA.FG.A4MU.01 4 0.0000 0.9292 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.A5TT.01 2 0.1664 0.8174 0.02 0.92 0.00 0.00 0.00 0.06 0.00
#> TCGA.HW.A5KK.01 2 0.1166 0.7978 0.00 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.S9.A7R2.01 2 0.0863 0.8082 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.HT.8110.01 3 0.0000 0.8478 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YJ.01 4 0.3343 0.7509 0.04 0.00 0.00 0.82 0.04 0.10 0.00
#> TCGA.E1.A7YL.01 3 0.0504 0.8450 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.HT.A61C.01 1 0.3517 0.9812 0.70 0.00 0.00 0.28 0.00 0.00 0.02
#> TCGA.QH.A6CV.01 2 0.7324 -0.0186 0.16 0.44 0.00 0.00 0.16 0.06 0.18
#> TCGA.FG.6692.01 4 0.0000 0.9292 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7013.01 1 0.3047 0.9953 0.72 0.00 0.00 0.28 0.00 0.00 0.00
#> TCGA.CS.6188.01 6 0.4765 0.6571 0.02 0.02 0.28 0.00 0.04 0.64 0.00
#> TCGA.DU.A7TJ.01 4 0.0000 0.9292 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7882.01 2 0.1860 0.7585 0.00 0.92 0.02 0.00 0.04 0.02 0.00
#> TCGA.HT.8011.01 1 0.3047 0.9953 0.72 0.00 0.00 0.28 0.00 0.00 0.00
#> TCGA.VM.A8CD.01 5 0.3358 0.8001 0.00 0.36 0.00 0.00 0.64 0.00 0.00
#> TCGA.HT.8564.01 7 0.3186 0.0000 0.00 0.00 0.22 0.00 0.00 0.02 0.76
#> TCGA.E1.A7YM.01 2 0.1166 0.7978 0.00 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.E1.A7YD.01 1 0.3047 0.9953 0.72 0.00 0.00 0.28 0.00 0.00 0.00
#> TCGA.DU.A7TD.01 1 0.3047 0.9953 0.72 0.00 0.00 0.28 0.00 0.00 0.00
#> TCGA.HT.A74H.01 3 0.3257 0.7454 0.02 0.08 0.84 0.00 0.04 0.02 0.00
#> TCGA.TM.A84B.01 4 0.3000 0.7883 0.02 0.00 0.00 0.84 0.10 0.00 0.04
#> TCGA.HT.A617.01 5 0.3221 0.8283 0.00 0.32 0.00 0.00 0.68 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.A7IX.01 2 0.2020 0.716 0.00 0.90 0.00 0.02 0.00 0.02 0.00 0.06
#> TCGA.VW.A8FI.01 4 0.1765 0.898 0.12 0.00 0.00 0.88 0.00 0.00 0.00 0.00
#> TCGA.DU.A76L.01 3 0.1563 0.883 0.00 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.CS.4941.01 3 0.1804 0.791 0.00 0.00 0.90 0.00 0.00 0.08 0.00 0.02
#> TCGA.S9.A6U0.01 3 0.0000 0.862 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.5395.01 3 0.3293 0.745 0.00 0.00 0.74 0.04 0.00 0.00 0.00 0.22
#> TCGA.DU.7292.01 6 0.3688 0.706 0.00 0.00 0.08 0.04 0.00 0.80 0.04 0.04
#> TCGA.FG.A4MW.01 4 0.1765 0.898 0.12 0.00 0.00 0.88 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CX.01 2 0.0471 0.751 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.CS.6186.01 5 0.3980 0.713 0.02 0.10 0.00 0.00 0.78 0.02 0.02 0.06
#> TCGA.DU.A76K.01 2 0.3311 0.625 0.00 0.80 0.00 0.02 0.00 0.02 0.02 0.14
#> TCGA.DU.6402.01 2 0.4967 0.225 0.00 0.66 0.00 0.02 0.08 0.02 0.02 0.20
#> TCGA.QH.A6XC.01 6 0.1341 0.748 0.00 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.FG.A4MU.01 4 0.1765 0.898 0.12 0.00 0.00 0.88 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TT.01 2 0.3311 0.625 0.00 0.80 0.00 0.02 0.00 0.02 0.02 0.14
#> TCGA.HW.A5KK.01 2 0.1557 0.738 0.00 0.92 0.00 0.02 0.06 0.00 0.00 0.00
#> TCGA.S9.A7R2.01 2 0.1557 0.738 0.00 0.92 0.00 0.02 0.06 0.00 0.00 0.00
#> TCGA.HT.8110.01 3 0.1563 0.883 0.00 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.E1.A7YJ.01 4 0.2914 0.706 0.00 0.00 0.00 0.84 0.00 0.08 0.04 0.04
#> TCGA.E1.A7YL.01 3 0.1563 0.883 0.00 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.HT.A61C.01 1 0.0941 0.982 0.96 0.00 0.00 0.02 0.02 0.00 0.00 0.00
#> TCGA.QH.A6CV.01 8 0.4588 0.000 0.00 0.34 0.00 0.00 0.12 0.00 0.00 0.54
#> TCGA.FG.6692.01 4 0.1765 0.898 0.12 0.00 0.00 0.88 0.00 0.00 0.00 0.00
#> TCGA.DU.7013.01 1 0.0471 0.996 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.CS.6188.01 6 0.3808 0.588 0.00 0.02 0.30 0.00 0.00 0.66 0.00 0.02
#> TCGA.DU.A7TJ.01 4 0.1765 0.898 0.12 0.00 0.00 0.88 0.00 0.00 0.00 0.00
#> TCGA.HT.7882.01 2 0.0808 0.720 0.00 0.96 0.04 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8011.01 1 0.0471 0.996 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.VM.A8CD.01 5 0.2981 0.728 0.00 0.22 0.00 0.02 0.76 0.00 0.00 0.00
#> TCGA.HT.8564.01 7 0.2224 0.000 0.00 0.00 0.12 0.00 0.00 0.02 0.86 0.00
#> TCGA.E1.A7YM.01 2 0.1557 0.738 0.00 0.92 0.00 0.02 0.06 0.00 0.00 0.00
#> TCGA.E1.A7YD.01 1 0.0471 0.996 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.DU.A7TD.01 1 0.0471 0.996 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.HT.A74H.01 3 0.1275 0.830 0.00 0.04 0.94 0.00 0.00 0.00 0.00 0.02
#> TCGA.TM.A84B.01 4 0.6877 0.517 0.14 0.00 0.00 0.50 0.08 0.04 0.06 0.18
#> TCGA.HT.A617.01 5 0.1947 0.804 0.00 0.14 0.00 0.00 0.86 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node012. Child nodes: Node01211-leaf , Node01212-leaf , Node01213-leaf , Node02211 , Node02212 , Node02221 , Node02222-leaf , Node02223 , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02321-leaf , Node02322-leaf , Node02323-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 12 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.5308 0.470 0.470
#> 3 3 1.000 1.000 1.000 0.3422 0.758 0.515
#> 4 4 1.000 0.902 0.990 0.0842 0.818 0.478
#> 5 5 0.894 0.848 0.912 0.0710 0.939 0.733
#> 6 6 0.803 0.741 0.910 0.0471 0.955 0.727
#> 7 7 0.848 0.618 0.868 0.0350 1.000 1.000
#> 8 8 0.879 0.223 0.773 0.0304 0.955 0.625
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.VW.A8FI.01 1 0 1 1 0
#> TCGA.FG.A4MW.01 1 0 1 1 0
#> TCGA.FG.A4MU.01 1 0 1 1 0
#> TCGA.E1.A7YJ.01 1 0 1 1 0
#> TCGA.HT.A61C.01 2 0 1 0 1
#> TCGA.FG.6692.01 1 0 1 1 0
#> TCGA.DU.7013.01 1 0 1 1 0
#> TCGA.DU.A7TJ.01 1 0 1 1 0
#> TCGA.HT.8011.01 2 0 1 0 1
#> TCGA.E1.A7YD.01 2 0 1 0 1
#> TCGA.DU.A7TD.01 2 0 1 0 1
#> TCGA.TM.A84B.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.VW.A8FI.01 3 0 1 0 0 1
#> TCGA.FG.A4MW.01 1 0 1 1 0 0
#> TCGA.FG.A4MU.01 1 0 1 1 0 0
#> TCGA.E1.A7YJ.01 1 0 1 1 0 0
#> TCGA.HT.A61C.01 2 0 1 0 1 0
#> TCGA.FG.6692.01 1 0 1 1 0 0
#> TCGA.DU.7013.01 3 0 1 0 0 1
#> TCGA.DU.A7TJ.01 1 0 1 1 0 0
#> TCGA.HT.8011.01 2 0 1 0 1 0
#> TCGA.E1.A7YD.01 2 0 1 0 1 0
#> TCGA.DU.A7TD.01 2 0 1 0 1 0
#> TCGA.TM.A84B.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.VW.A8FI.01 3 0.0707 0.957 0.00 0 0.98 0.02
#> TCGA.FG.A4MW.01 1 0.0000 1.000 1.00 0 0.00 0.00
#> TCGA.FG.A4MU.01 3 0.1211 0.957 0.04 0 0.96 0.00
#> TCGA.E1.A7YJ.01 1 0.0000 1.000 1.00 0 0.00 0.00
#> TCGA.HT.A61C.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.FG.6692.01 1 0.0000 1.000 1.00 0 0.00 0.00
#> TCGA.DU.7013.01 3 0.0707 0.957 0.00 0 0.98 0.02
#> TCGA.DU.A7TJ.01 3 0.1211 0.957 0.04 0 0.96 0.00
#> TCGA.HT.8011.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.E1.A7YD.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.DU.A7TD.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.TM.A84B.01 4 0.0000 0.000 0.00 0 0.00 1.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.VW.A8FI.01 3 0.104 0.938 0.00 0.00 0.96 0 0.04
#> TCGA.FG.A4MW.01 1 0.000 1.000 1.00 0.00 0.00 0 0.00
#> TCGA.FG.A4MU.01 5 0.446 1.000 0.02 0.00 0.32 0 0.66
#> TCGA.E1.A7YJ.01 1 0.000 1.000 1.00 0.00 0.00 0 0.00
#> TCGA.HT.A61C.01 2 0.000 0.892 0.00 1.00 0.00 0 0.00
#> TCGA.FG.6692.01 1 0.000 1.000 1.00 0.00 0.00 0 0.00
#> TCGA.DU.7013.01 3 0.000 0.939 0.00 0.00 1.00 0 0.00
#> TCGA.DU.A7TJ.01 5 0.446 1.000 0.02 0.00 0.32 0 0.66
#> TCGA.HT.8011.01 2 0.000 0.892 0.00 1.00 0.00 0 0.00
#> TCGA.E1.A7YD.01 2 0.000 0.892 0.00 1.00 0.00 0 0.00
#> TCGA.DU.A7TD.01 2 0.398 0.626 0.00 0.66 0.00 0 0.34
#> TCGA.TM.A84B.01 4 0.000 0.000 0.00 0.00 0.00 1 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.VW.A8FI.01 3 0.209 0.880 0.00 0.02 0.90 0 0.08 0.00
#> TCGA.FG.A4MW.01 1 0.000 0.947 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.FG.A4MU.01 5 0.454 0.836 0.00 0.18 0.12 0 0.70 0.00
#> TCGA.E1.A7YJ.01 1 0.205 0.890 0.88 0.12 0.00 0 0.00 0.00
#> TCGA.HT.A61C.01 2 0.350 0.920 0.00 0.68 0.00 0 0.00 0.32
#> TCGA.FG.6692.01 1 0.000 0.947 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.DU.7013.01 3 0.000 0.886 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.DU.A7TJ.01 5 0.205 0.836 0.00 0.00 0.12 0 0.88 0.00
#> TCGA.HT.8011.01 2 0.527 0.833 0.00 0.56 0.00 0 0.12 0.32
#> TCGA.E1.A7YD.01 2 0.350 0.920 0.00 0.68 0.00 0 0.00 0.32
#> TCGA.DU.A7TD.01 6 0.000 0.000 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.TM.A84B.01 4 0.000 0.000 0.00 0.00 0.00 1 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.VW.A8FI.01 3 0.0863 0.869 0.00 0.00 0.96 0 0.04 0.00 0.00
#> TCGA.FG.A4MW.01 1 0.0000 0.811 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.FG.A4MU.01 5 0.5643 0.632 0.00 0.00 0.06 0 0.56 0.12 0.26
#> TCGA.E1.A7YJ.01 1 0.3413 0.599 0.62 0.00 0.00 0 0.00 0.00 0.38
#> TCGA.HT.A61C.01 2 0.3221 0.796 0.00 0.68 0.00 0 0.00 0.00 0.32
#> TCGA.FG.6692.01 1 0.0504 0.807 0.98 0.00 0.00 0 0.00 0.02 0.00
#> TCGA.DU.7013.01 3 0.2016 0.873 0.00 0.00 0.90 0 0.00 0.06 0.04
#> TCGA.DU.A7TJ.01 5 0.0863 0.632 0.00 0.00 0.04 0 0.96 0.00 0.00
#> TCGA.HT.8011.01 2 0.0000 0.597 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.E1.A7YD.01 2 0.3841 0.796 0.00 0.68 0.00 0 0.04 0.00 0.28
#> TCGA.DU.A7TD.01 6 0.2572 0.000 0.00 0.20 0.00 0 0.00 0.80 0.00
#> TCGA.TM.A84B.01 4 0.0000 0.000 0.00 0.00 0.00 1 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.VW.A8FI.01 3 0.331 0.810 0.00 0.00 0.8 0 0.08 0.02 0.00 0.10
#> TCGA.FG.A4MW.01 1 0.000 0.714 1.00 0.00 0.0 0 0.00 0.00 0.00 0.00
#> TCGA.FG.A4MU.01 5 0.000 0.000 0.00 0.00 0.0 0 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YJ.01 1 0.480 0.445 0.52 0.00 0.0 0 0.00 0.00 0.16 0.32
#> TCGA.HT.A61C.01 2 0.468 -0.797 0.00 0.48 0.0 0 0.00 0.00 0.12 0.40
#> TCGA.FG.6692.01 1 0.189 0.688 0.90 0.00 0.0 0 0.00 0.04 0.00 0.06
#> TCGA.DU.7013.01 3 0.000 0.817 0.00 0.00 1.0 0 0.00 0.00 0.00 0.00
#> TCGA.DU.A7TJ.01 7 0.285 0.000 0.00 0.00 0.0 0 0.28 0.00 0.72 0.00
#> TCGA.HT.8011.01 2 0.000 0.000 0.00 1.00 0.0 0 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YD.01 8 0.333 0.000 0.00 0.48 0.0 0 0.00 0.00 0.00 0.52
#> TCGA.DU.A7TD.01 6 0.109 0.000 0.00 0.06 0.0 0 0.00 0.94 0.00 0.00
#> TCGA.TM.A84B.01 4 0.000 0.000 0.00 0.00 0.0 1 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011-leaf , Node012 , Node013-leaf , Node014-leaf , Node021 , Node022 , Node023 .
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 431 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 0.995 0.4932 0.507 0.507
#> 3 3 1.000 0.975 0.990 0.1581 0.915 0.833
#> 4 4 0.948 0.907 0.965 0.1983 0.855 0.674
#> 5 5 0.929 0.898 0.961 0.1244 0.900 0.690
#> 6 6 0.850 0.792 0.906 0.0322 0.967 0.860
#> 7 7 0.809 0.710 0.852 0.0266 0.956 0.804
#> 8 8 0.755 0.600 0.798 0.0174 0.976 0.884
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.E1.5319.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.7693.01 1 0.000 0.997 1.00 0.00
#> TCGA.CS.6665.01 1 0.242 0.955 0.96 0.04
#> TCGA.S9.A7J2.01 2 0.971 0.336 0.40 0.60
#> TCGA.FG.A6J3.01 1 0.000 0.997 1.00 0.00
#> TCGA.S9.A6TX.01 2 0.000 0.993 0.00 1.00
#> TCGA.VM.A8C8.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.A74L.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.A5TS.01 1 0.000 0.997 1.00 0.00
#> TCGA.DB.A4XA.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.A4DV.01 2 0.000 0.993 0.00 1.00
#> TCGA.E1.5311.01 2 0.000 0.993 0.00 1.00
#> TCGA.E1.A7YI.01 2 0.722 0.754 0.20 0.80
#> TCGA.E1.5305.01 1 0.000 0.997 1.00 0.00
#> TCGA.F6.A8O4.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.8113.01 2 0.000 0.993 0.00 1.00
#> TCGA.DH.A66G.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7620.01 2 0.000 0.993 0.00 1.00
#> TCGA.P5.A731.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7480.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.7689.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.8109.01 2 0.000 0.993 0.00 1.00
#> TCGA.E1.A7YE.01 2 0.680 0.784 0.18 0.82
#> TCGA.S9.A7R1.01 2 0.000 0.993 0.00 1.00
#> TCGA.FG.A710.01 2 0.000 0.993 0.00 1.00
#> TCGA.S9.A7J0.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.A6S6.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.7877.01 2 0.000 0.993 0.00 1.00
#> TCGA.QH.A6CU.01 2 0.000 0.993 0.00 1.00
#> TCGA.HW.7486.01 2 0.000 0.993 0.00 1.00
#> TCGA.FG.7634.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.8163.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.6407.02 2 0.402 0.912 0.08 0.92
#> TCGA.DU.6407.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.8010.01 2 0.000 0.993 0.00 1.00
#> TCGA.P5.A5F1.01 1 0.000 0.997 1.00 0.00
#> TCGA.VM.A8CF.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.6542.01 1 0.000 0.997 1.00 0.00
#> TCGA.FG.7638.01 2 0.000 0.993 0.00 1.00
#> TCGA.DH.5143.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.7299.01 1 0.000 0.997 1.00 0.00
#> TCGA.CS.5393.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.7011.01 1 0.000 0.997 1.00 0.00
#> TCGA.TM.A84Q.01 1 0.000 0.997 1.00 0.00
#> TCGA.DB.5281.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7605.01 2 0.000 0.993 0.00 1.00
#> TCGA.FG.A6J1.01 2 0.000 0.993 0.00 1.00
#> TCGA.DB.5270.01 1 0.000 0.997 1.00 0.00
#> TCGA.S9.A6WQ.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.8106.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7608.01 2 0.000 0.993 0.00 1.00
#> TCGA.E1.A7YU.01 1 0.000 0.997 1.00 0.00
#> TCGA.W9.A837.01 2 0.000 0.993 0.00 1.00
#> TCGA.TM.A7C5.01 2 0.000 0.993 0.00 1.00
#> TCGA.S9.A7QY.01 2 0.000 0.993 0.00 1.00
#> TCGA.QH.A6CW.01 1 0.000 0.997 1.00 0.00
#> TCGA.S9.A6WO.01 1 0.000 0.997 1.00 0.00
#> TCGA.IK.7675.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7601.01 1 0.000 0.997 1.00 0.00
#> TCGA.P5.A5ET.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.7472.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7880.01 1 0.000 0.997 1.00 0.00
#> TCGA.E1.A7Z3.01 1 0.000 0.997 1.00 0.00
#> TCGA.P5.A77X.01 2 0.000 0.993 0.00 1.00
#> TCGA.FG.A6IZ.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.7873.01 1 0.000 0.997 1.00 0.00
#> TCGA.CS.4938.01 1 0.000 0.997 1.00 0.00
#> TCGA.KT.A74X.01 2 0.000 0.993 0.00 1.00
#> TCGA.P5.A5EX.01 2 0.000 0.993 0.00 1.00
#> TCGA.VM.A8CH.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7476.01 1 0.000 0.997 1.00 0.00
#> TCGA.DB.A75L.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.8563.01 1 0.000 0.997 1.00 0.00
#> TCGA.RY.A843.01 1 0.000 0.997 1.00 0.00
#> TCGA.S9.A7IS.01 1 0.000 0.997 1.00 0.00
#> TCGA.TQ.A8XE.02 1 0.000 0.997 1.00 0.00
#> TCGA.E1.A7YO.01 2 0.000 0.993 0.00 1.00
#> TCGA.TQ.A7RG.01 2 0.000 0.993 0.00 1.00
#> TCGA.QH.A6X5.01 2 0.000 0.993 0.00 1.00
#> TCGA.HW.7493.01 1 0.000 0.997 1.00 0.00
#> TCGA.RY.A847.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.8166.01 1 0.000 0.997 1.00 0.00
#> TCGA.VM.A8CA.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.7855.01 1 0.000 0.997 1.00 0.00
#> TCGA.S9.A89Z.01 1 0.000 0.997 1.00 0.00
#> TCGA.DB.A4XG.01 2 0.000 0.993 0.00 1.00
#> TCGA.DH.A7UT.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.7015.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.A616.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7611.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.8018.01 1 0.000 0.997 1.00 0.00
#> TCGA.FG.A60K.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.7856.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.5851.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.A7T6.01 2 0.000 0.993 0.00 1.00
#> TCGA.S9.A6TY.01 2 0.000 0.993 0.00 1.00
#> TCGA.WY.A85C.01 1 0.000 0.997 1.00 0.00
#> TCGA.DB.A4XC.01 1 0.000 0.997 1.00 0.00
#> TCGA.TM.A84O.01 2 0.000 0.993 0.00 1.00
#> TCGA.P5.A72W.01 1 0.000 0.997 1.00 0.00
#> TCGA.S9.A6TU.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.A61A.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.5855.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7884.01 1 0.000 0.997 1.00 0.00
#> TCGA.TQ.A7RQ.01 2 0.000 0.993 0.00 1.00
#> TCGA.IK.8125.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.A74K.01 2 0.000 0.993 0.00 1.00
#> TCGA.WH.A86K.01 1 0.000 0.997 1.00 0.00
#> TCGA.QH.A6X8.01 2 0.000 0.993 0.00 1.00
#> TCGA.WY.A85E.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.A5R5.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.A618.01 1 0.000 0.997 1.00 0.00
#> TCGA.FG.6691.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7467.01 2 0.000 0.993 0.00 1.00
#> TCGA.S9.A7R3.01 1 0.000 0.997 1.00 0.00
#> TCGA.FG.A4MX.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7681.01 2 0.000 0.993 0.00 1.00
#> TCGA.S9.A7IZ.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.A6S7.01 1 0.000 0.997 1.00 0.00
#> TCGA.P5.A72Z.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.8114.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.8168.01 2 0.000 0.993 0.00 1.00
#> TCGA.HW.8321.01 1 0.000 0.997 1.00 0.00
#> TCGA.TQ.A7RN.01 2 0.000 0.993 0.00 1.00
#> TCGA.DH.5141.01 2 0.000 0.993 0.00 1.00
#> TCGA.EZ.7264.01 2 0.000 0.993 0.00 1.00
#> TCGA.P5.A5F4.01 1 0.000 0.997 1.00 0.00
#> TCGA.QH.A65V.01 2 0.000 0.993 0.00 1.00
#> TCGA.FG.8191.01 1 0.000 0.997 1.00 0.00
#> TCGA.DH.5142.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.A6S8.01 2 0.000 0.993 0.00 1.00
#> TCGA.E1.A7YW.01 1 0.000 0.997 1.00 0.00
#> TCGA.CS.6666.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.7298.01 2 0.000 0.993 0.00 1.00
#> TCGA.DB.A64R.01 2 0.000 0.993 0.00 1.00
#> TCGA.FG.A60L.01 1 0.000 0.997 1.00 0.00
#> TCGA.CS.5390.01 2 0.000 0.993 0.00 1.00
#> TCGA.S9.A6WP.01 2 0.000 0.993 0.00 1.00
#> TCGA.DB.5280.01 1 0.000 0.997 1.00 0.00
#> TCGA.TM.A84T.01 1 0.000 0.997 1.00 0.00
#> TCGA.DH.A66D.01 1 0.000 0.997 1.00 0.00
#> TCGA.RY.A83Z.01 1 0.000 0.997 1.00 0.00
#> TCGA.DB.5278.01 2 0.402 0.912 0.08 0.92
#> TCGA.TQ.A7RR.01 1 0.000 0.997 1.00 0.00
#> TCGA.TQ.A7RH.01 1 0.000 0.997 1.00 0.00
#> TCGA.E1.A7YS.01 2 0.000 0.993 0.00 1.00
#> TCGA.P5.A735.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.7294.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.7881.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.7695.01 2 0.000 0.993 0.00 1.00
#> TCGA.P5.A5EU.01 1 0.000 0.997 1.00 0.00
#> TCGA.DB.A64X.01 1 0.000 0.997 1.00 0.00
#> TCGA.FG.7637.01 2 0.000 0.993 0.00 1.00
#> TCGA.VM.A8CE.01 2 0.000 0.993 0.00 1.00
#> TCGA.S9.A6U5.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.7609.01 1 0.000 0.997 1.00 0.00
#> TCGA.DB.5274.01 2 0.000 0.993 0.00 1.00
#> TCGA.HW.7487.01 2 0.000 0.993 0.00 1.00
#> TCGA.HW.7491.01 2 0.000 0.993 0.00 1.00
#> TCGA.CS.4944.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.A6S2.01 2 0.000 0.993 0.00 1.00
#> TCGA.S9.A7R7.01 1 0.000 0.997 1.00 0.00
#> TCGA.TM.A84R.01 2 0.000 0.993 0.00 1.00
#> TCGA.DB.A75M.01 1 0.000 0.997 1.00 0.00
#> TCGA.HW.A5KM.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7477.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.8012.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.8167.01 1 0.000 0.997 1.00 0.00
#> TCGA.S9.A6U1.01 1 0.000 0.997 1.00 0.00
#> TCGA.FG.5965.01 1 0.000 0.997 1.00 0.00
#> TCGA.FG.8187.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.A614.01 1 0.000 0.997 1.00 0.00
#> TCGA.S9.A7QZ.01 2 0.000 0.993 0.00 1.00
#> TCGA.QH.A6X4.01 2 0.000 0.993 0.00 1.00
#> TCGA.P5.A77W.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.7302.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.6399.01 1 0.000 0.997 1.00 0.00
#> TCGA.E1.5307.01 1 0.000 0.997 1.00 0.00
#> TCGA.S9.A7QW.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7604.01 1 0.000 0.997 1.00 0.00
#> TCGA.P5.A733.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7684.01 1 0.000 0.997 1.00 0.00
#> TCGA.HW.7495.01 2 0.000 0.993 0.00 1.00
#> TCGA.QH.A65R.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.A7TG.01 2 0.000 0.993 0.00 1.00
#> TCGA.DH.A7UV.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7879.01 1 0.000 0.997 1.00 0.00
#> TCGA.TM.A84F.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.A7TC.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7610.01 1 0.000 0.997 1.00 0.00
#> TCGA.S9.A6TW.01 2 0.000 0.993 0.00 1.00
#> TCGA.FG.A60J.01 1 0.000 0.997 1.00 0.00
#> TCGA.E1.5303.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7481.01 2 0.000 0.993 0.00 1.00
#> TCGA.FN.7833.01 1 0.000 0.997 1.00 0.00
#> TCGA.E1.A7Z4.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.A5TR.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7875.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.7473.01 1 0.000 0.997 1.00 0.00
#> TCGA.S9.A7IQ.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.7008.01 1 0.000 0.997 1.00 0.00
#> TCGA.S9.A6WG.01 1 0.000 0.997 1.00 0.00
#> TCGA.DB.A75O.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7688.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.7304.02 2 0.242 0.955 0.04 0.96
#> TCGA.DU.6394.01 2 0.000 0.993 0.00 1.00
#> TCGA.S9.A6WD.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.5872.01 1 0.000 0.997 1.00 0.00
#> TCGA.FG.8185.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7902.01 1 0.000 0.997 1.00 0.00
#> TCGA.TQ.A7RU.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.5874.01 2 0.000 0.993 0.00 1.00
#> TCGA.S9.A6WE.01 2 0.584 0.839 0.14 0.86
#> TCGA.FG.6690.01 1 0.000 0.997 1.00 0.00
#> TCGA.HW.8320.01 1 0.000 0.997 1.00 0.00
#> TCGA.R8.A6MK.01 2 0.000 0.993 0.00 1.00
#> TCGA.QH.A6CY.01 2 0.000 0.993 0.00 1.00
#> TCGA.S9.A7J1.01 2 0.000 0.993 0.00 1.00
#> TCGA.P5.A72X.01 1 0.000 0.997 1.00 0.00
#> TCGA.E1.5322.01 1 0.000 0.997 1.00 0.00
#> TCGA.P5.A5F0.01 2 0.000 0.993 0.00 1.00
#> TCGA.R8.A73M.01 2 0.000 0.993 0.00 1.00
#> TCGA.CS.4942.01 1 0.000 0.997 1.00 0.00
#> TCGA.DB.A4X9.01 1 0.000 0.997 1.00 0.00
#> TCGA.DB.A4XF.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.A74O.01 1 0.000 0.997 1.00 0.00
#> TCGA.FG.8188.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.A6S3.01 2 0.000 0.993 0.00 1.00
#> TCGA.DB.A4XH.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.7485.01 1 0.000 0.997 1.00 0.00
#> TCGA.VW.A7QS.01 2 0.000 0.993 0.00 1.00
#> TCGA.S9.A6WI.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.8164.01 2 0.000 0.993 0.00 1.00
#> TCGA.S9.A6TS.01 1 0.000 0.997 1.00 0.00
#> TCGA.DB.A64S.01 1 0.000 0.997 1.00 0.00
#> TCGA.VV.A86M.01 1 0.000 0.997 1.00 0.00
#> TCGA.TQ.A8XE.01 1 0.000 0.997 1.00 0.00
#> TCGA.CS.6667.01 1 0.000 0.997 1.00 0.00
#> TCGA.E1.A7YV.01 1 0.958 0.382 0.62 0.38
#> TCGA.TQ.A7RW.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.5849.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.A7TI.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7468.01 2 0.000 0.993 0.00 1.00
#> TCGA.TQ.A7RI.01 2 0.000 0.993 0.00 1.00
#> TCGA.DB.5279.01 2 0.000 0.993 0.00 1.00
#> TCGA.S9.A6U8.01 1 0.000 0.997 1.00 0.00
#> TCGA.HW.7489.01 1 0.000 0.997 1.00 0.00
#> TCGA.R8.A6YH.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.7018.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.7677.01 2 0.000 0.993 0.00 1.00
#> TCGA.FG.A713.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.7300.01 2 0.000 0.993 0.00 1.00
#> TCGA.TM.A7CA.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7690.01 1 0.000 0.997 1.00 0.00
#> TCGA.FG.6689.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.7007.01 1 0.000 0.997 1.00 0.00
#> TCGA.TQ.A7RF.01 1 0.000 0.997 1.00 0.00
#> TCGA.DB.5277.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7694.01 2 0.000 0.993 0.00 1.00
#> TCGA.TM.A84M.01 2 0.000 0.993 0.00 1.00
#> TCGA.F6.A8O3.01 2 0.000 0.993 0.00 1.00
#> TCGA.QH.A86X.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.8013.01 1 0.000 0.997 1.00 0.00
#> TCGA.HW.7490.01 1 0.000 0.997 1.00 0.00
#> TCGA.QH.A65S.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.A76R.01 2 0.000 0.993 0.00 1.00
#> TCGA.DH.5144.01 2 0.000 0.993 0.00 1.00
#> TCGA.P5.A780.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7606.01 1 0.000 0.997 1.00 0.00
#> TCGA.DB.A64V.01 2 0.000 0.993 0.00 1.00
#> TCGA.RY.A840.01 2 0.000 0.993 0.00 1.00
#> TCGA.E1.5302.01 1 0.000 0.997 1.00 0.00
#> TCGA.HW.A5KJ.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.A615.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.8105.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.7309.01 1 0.000 0.997 1.00 0.00
#> TCGA.E1.A7YK.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7874.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.7471.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.6395.01 1 0.000 0.997 1.00 0.00
#> TCGA.S9.A6TV.01 1 0.000 0.997 1.00 0.00
#> TCGA.P5.A5EW.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.6408.01 1 0.000 0.997 1.00 0.00
#> TCGA.DB.A4XB.01 1 0.000 0.997 1.00 0.00
#> TCGA.FG.A4MT.01 1 0.000 0.997 1.00 0.00
#> TCGA.FG.A4MT.02 1 0.000 0.997 1.00 0.00
#> TCGA.HT.A619.01 2 0.000 0.993 0.00 1.00
#> TCGA.QH.A870.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.A5R9.01 2 0.000 0.993 0.00 1.00
#> TCGA.FG.5964.01 2 0.000 0.993 0.00 1.00
#> TCGA.CS.5396.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.A7TA.01 1 0.000 0.997 1.00 0.00
#> TCGA.HW.8319.01 1 0.000 0.997 1.00 0.00
#> TCGA.DH.A7UR.01 2 0.000 0.993 0.00 1.00
#> TCGA.TM.A84H.01 1 0.000 0.997 1.00 0.00
#> TCGA.S9.A6TZ.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7479.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.6400.01 2 0.000 0.993 0.00 1.00
#> TCGA.S9.A6WL.01 2 0.000 0.993 0.00 1.00
#> TCGA.DB.A75K.01 2 0.000 0.993 0.00 1.00
#> TCGA.DB.A4XD.01 1 0.000 0.997 1.00 0.00
#> TCGA.DB.A64Q.01 2 0.000 0.993 0.00 1.00
#> TCGA.P5.A737.01 2 0.000 0.993 0.00 1.00
#> TCGA.DB.5275.01 1 0.000 0.997 1.00 0.00
#> TCGA.S9.A6WH.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.7602.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.A5TU.01 2 0.327 0.934 0.06 0.94
#> TCGA.HT.A5RB.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7616.01 2 0.000 0.993 0.00 1.00
#> TCGA.S9.A7R8.01 1 0.000 0.997 1.00 0.00
#> TCGA.QH.A6XA.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.8111.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.A5TP.01 1 0.000 0.997 1.00 0.00
#> TCGA.RY.A83Y.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.7482.01 1 0.000 0.997 1.00 0.00
#> TCGA.TQ.A7RK.02 1 0.000 0.997 1.00 0.00
#> TCGA.TQ.A7RK.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7858.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7475.01 1 0.000 0.997 1.00 0.00
#> TCGA.DB.A64U.01 2 0.000 0.993 0.00 1.00
#> TCGA.DB.A64W.01 2 0.000 0.993 0.00 1.00
#> TCGA.R8.A6MO.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.A7T8.01 1 0.000 0.997 1.00 0.00
#> TCGA.HW.8322.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.5870.02 2 0.000 0.993 0.00 1.00
#> TCGA.CS.6668.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.5870.01 2 0.000 0.993 0.00 1.00
#> TCGA.FG.7636.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7692.01 2 0.000 0.993 0.00 1.00
#> TCGA.WY.A859.01 1 0.000 0.997 1.00 0.00
#> TCGA.R8.A6ML.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.7686.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.6410.01 2 0.000 0.993 0.00 1.00
#> TCGA.S9.A6U9.01 1 0.000 0.997 1.00 0.00
#> TCGA.CS.6290.01 1 0.000 0.997 1.00 0.00
#> TCGA.TQ.A7RO.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.7019.01 1 0.000 0.997 1.00 0.00
#> TCGA.FG.A711.01 1 0.000 0.997 1.00 0.00
#> TCGA.TQ.A7RM.01 1 0.000 0.997 1.00 0.00
#> TCGA.S9.A7R4.01 1 0.000 0.997 1.00 0.00
#> TCGA.E1.5318.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.7676.01 1 0.000 0.997 1.00 0.00
#> TCGA.S9.A7J3.01 2 0.000 0.993 0.00 1.00
#> TCGA.P5.A5F2.01 1 0.000 0.997 1.00 0.00
#> TCGA.E1.5304.01 1 0.943 0.433 0.64 0.36
#> TCGA.TM.A84S.01 2 0.000 0.993 0.00 1.00
#> TCGA.WY.A85B.01 1 0.000 0.997 1.00 0.00
#> TCGA.TQ.A7RS.01 2 0.000 0.993 0.00 1.00
#> TCGA.S9.A7QX.01 1 0.000 0.997 1.00 0.00
#> TCGA.CS.4943.01 1 0.000 0.997 1.00 0.00
#> TCGA.QH.A65Z.01 2 0.000 0.993 0.00 1.00
#> TCGA.DB.5276.01 1 0.000 0.997 1.00 0.00
#> TCGA.P5.A730.01 2 0.000 0.993 0.00 1.00
#> TCGA.TM.A84L.01 1 0.000 0.997 1.00 0.00
#> TCGA.WY.A85D.01 1 0.000 0.997 1.00 0.00
#> TCGA.RY.A83X.01 2 0.000 0.993 0.00 1.00
#> TCGA.S9.A6UB.01 2 0.000 0.993 0.00 1.00
#> TCGA.DB.5273.01 1 0.000 0.997 1.00 0.00
#> TCGA.TM.A7C4.01 1 0.000 0.997 1.00 0.00
#> TCGA.DH.A66F.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.7607.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.6393.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.8108.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.7304.01 1 0.000 0.997 1.00 0.00
#> TCGA.S9.A7IY.01 2 0.000 0.993 0.00 1.00
#> TCGA.FG.7641.01 2 0.000 0.993 0.00 1.00
#> TCGA.P5.A736.01 1 0.000 0.997 1.00 0.00
#> TCGA.P5.A5EV.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.7301.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7470.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.7009.01 2 0.000 0.993 0.00 1.00
#> TCGA.P5.A781.01 2 0.000 0.993 0.00 1.00
#> TCGA.FG.A4MY.01 1 0.000 0.997 1.00 0.00
#> TCGA.TM.A7CF.01 1 0.000 0.997 1.00 0.00
#> TCGA.TM.A7CF.02 1 0.000 0.997 1.00 0.00
#> TCGA.FG.8186.01 2 0.000 0.993 0.00 1.00
#> TCGA.S9.A6U6.01 1 0.000 0.997 1.00 0.00
#> TCGA.RY.A845.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.7010.01 2 0.242 0.955 0.04 0.96
#> TCGA.S9.A6U2.01 2 0.000 0.993 0.00 1.00
#> TCGA.S9.A6WN.01 2 0.000 0.993 0.00 1.00
#> TCGA.FG.8182.01 1 0.000 0.997 1.00 0.00
#> TCGA.QH.A6X3.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.6401.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.6396.01 1 0.000 0.997 1.00 0.00
#> TCGA.E1.A7YH.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.7306.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.A74J.01 1 0.000 0.997 1.00 0.00
#> TCGA.DH.A7US.01 2 0.000 0.993 0.00 1.00
#> TCGA.FG.A87N.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.7478.01 1 0.000 0.997 1.00 0.00
#> TCGA.DB.A4XE.01 1 0.000 0.997 1.00 0.00
#> TCGA.DB.A64L.01 2 0.000 0.993 0.00 1.00
#> TCGA.VV.A829.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.A61B.01 1 0.000 0.997 1.00 0.00
#> TCGA.DH.A66B.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7603.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.6397.02 2 0.000 0.993 0.00 1.00
#> TCGA.DU.6397.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.5853.01 1 0.000 0.997 1.00 0.00
#> TCGA.CS.6670.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.7014.01 1 0.000 0.997 1.00 0.00
#> TCGA.QH.A65X.01 2 0.000 0.993 0.00 1.00
#> TCGA.DB.A64P.01 2 0.000 0.993 0.00 1.00
#> TCGA.FG.5965.02 2 0.242 0.955 0.04 0.96
#> TCGA.FG.A70Y.01 1 0.000 0.997 1.00 0.00
#> TCGA.TQ.A7RV.01 1 0.000 0.997 1.00 0.00
#> TCGA.TQ.A7RV.02 1 0.000 0.997 1.00 0.00
#> TCGA.HT.A5R7.01 1 0.000 0.997 1.00 0.00
#> TCGA.HW.A5KL.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7474.01 1 0.000 0.997 1.00 0.00
#> TCGA.DH.A7UU.01 1 0.000 0.997 1.00 0.00
#> TCGA.QH.A6CZ.01 2 0.000 0.993 0.00 1.00
#> TCGA.DH.A669.02 2 0.000 0.993 0.00 1.00
#> TCGA.DH.A669.01 2 0.000 0.993 0.00 1.00
#> TCGA.QH.A6X9.01 1 0.000 0.997 1.00 0.00
#> TCGA.P5.A5EZ.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.5871.01 1 0.000 0.997 1.00 0.00
#> TCGA.TQ.A7RJ.01 1 0.000 0.997 1.00 0.00
#> TCGA.WY.A858.01 1 0.000 0.997 1.00 0.00
#> TCGA.VM.A8CB.01 2 0.000 0.993 0.00 1.00
#> TCGA.HT.7483.01 1 0.000 0.997 1.00 0.00
#> TCGA.HT.7687.01 2 0.000 0.993 0.00 1.00
#> TCGA.TM.A84G.01 2 0.000 0.993 0.00 1.00
#> TCGA.E1.A7Z6.01 1 0.000 0.997 1.00 0.00
#> TCGA.TM.A84I.01 1 0.000 0.997 1.00 0.00
#> TCGA.CS.5394.01 2 0.000 0.993 0.00 1.00
#> TCGA.DU.A76O.01 1 0.000 0.997 1.00 0.00
#> TCGA.DU.A5TW.01 1 0.000 0.997 1.00 0.00
#> TCGA.WY.A85A.01 1 0.000 0.997 1.00 0.00
#> TCGA.FG.5962.01 2 0.000 0.993 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.E1.5319.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.HT.7693.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.CS.6665.01 3 0.0000 0.934 0.00 0.00 1.00
#> TCGA.S9.A7J2.01 2 0.6280 0.149 0.46 0.54 0.00
#> TCGA.FG.A6J3.01 3 0.0000 0.934 0.00 0.00 1.00
#> TCGA.S9.A6TX.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.VM.A8C8.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.A74L.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DU.A5TS.01 1 0.0892 0.974 0.98 0.00 0.02
#> TCGA.DB.A4XA.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.HT.A4DV.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.E1.5311.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.E1.A7YI.01 3 0.0000 0.934 0.00 0.00 1.00
#> TCGA.E1.5305.01 1 0.5397 0.582 0.72 0.00 0.28
#> TCGA.F6.A8O4.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.8113.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DH.A66G.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.7620.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.P5.A731.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.7480.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.HT.7689.01 3 0.4002 0.815 0.16 0.00 0.84
#> TCGA.HT.8109.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.E1.A7YE.01 3 0.0000 0.934 0.00 0.00 1.00
#> TCGA.S9.A7R1.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.FG.A710.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.S9.A7J0.01 3 0.4555 0.768 0.20 0.00 0.80
#> TCGA.DU.A6S6.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.HT.7877.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.QH.A6CU.01 2 0.1529 0.939 0.04 0.96 0.00
#> TCGA.HW.7486.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.FG.7634.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DU.8163.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DU.6407.02 3 0.0000 0.934 0.00 0.00 1.00
#> TCGA.DU.6407.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.8010.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.P5.A5F1.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.VM.A8CF.01 1 0.1529 0.953 0.96 0.00 0.04
#> TCGA.DU.6542.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.FG.7638.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DH.5143.01 1 0.0000 0.993 1.00 0.00 0.00
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#> TCGA.DB.5281.01 1 0.0000 0.993 1.00 0.00 0.00
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#> TCGA.S9.A6WQ.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.8106.01 1 0.5397 0.584 0.72 0.00 0.28
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#> TCGA.IK.7675.01 3 0.0000 0.934 0.00 0.00 1.00
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#> TCGA.DB.A4XG.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DH.A7UT.01 1 0.0000 0.993 1.00 0.00 0.00
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#> TCGA.HT.A616.01 1 0.0000 0.993 1.00 0.00 0.00
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#> TCGA.P5.A72W.01 1 0.0000 0.993 1.00 0.00 0.00
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#> TCGA.HT.A61A.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DU.5855.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.7884.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.TQ.A7RQ.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.IK.8125.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.HT.A74K.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.WH.A86K.01 1 0.0892 0.974 0.98 0.00 0.02
#> TCGA.QH.A6X8.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.WY.A85E.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.A5R5.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.A618.01 3 0.0000 0.934 0.00 0.00 1.00
#> TCGA.FG.6691.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.7467.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.S9.A7R3.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.FG.A4MX.01 1 0.0000 0.993 1.00 0.00 0.00
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#> TCGA.DU.A6S7.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.P5.A72Z.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.HT.8114.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DU.8168.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.HW.8321.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.TQ.A7RN.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DH.5141.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.EZ.7264.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.P5.A5F4.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.QH.A65V.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.FG.8191.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DH.5142.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DU.A6S8.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.E1.A7YW.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.CS.6666.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DU.7298.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DB.A64R.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.FG.A60L.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.CS.5390.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.S9.A6WP.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DB.5280.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.TM.A84T.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DH.A66D.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.RY.A83Z.01 3 0.0000 0.934 0.00 0.00 1.00
#> TCGA.DB.5278.01 2 0.4002 0.752 0.16 0.84 0.00
#> TCGA.TQ.A7RR.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.TQ.A7RH.01 1 0.0000 0.993 1.00 0.00 0.00
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#> TCGA.P5.A735.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DU.7294.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.HT.7881.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.HT.7695.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.P5.A5EU.01 3 0.0000 0.934 0.00 0.00 1.00
#> TCGA.DB.A64X.01 3 0.0000 0.934 0.00 0.00 1.00
#> TCGA.FG.7637.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.VM.A8CE.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.S9.A6U5.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.HT.7609.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DB.5274.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.HW.7487.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.HW.7491.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.CS.4944.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DU.A6S2.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.S9.A7R7.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.TM.A84R.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DB.A75M.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HW.A5KM.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.7477.01 3 0.0000 0.934 0.00 0.00 1.00
#> TCGA.HT.8012.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DU.8167.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.S9.A6U1.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.FG.5965.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.FG.8187.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.HT.A614.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.S9.A7QZ.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.QH.A6X4.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.P5.A77W.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DU.7302.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DU.6399.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.E1.5307.01 1 0.5560 0.538 0.70 0.00 0.30
#> TCGA.S9.A7QW.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.7604.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.P5.A733.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.7684.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HW.7495.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.QH.A65R.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DU.A7TG.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DH.A7UV.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.7879.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.TM.A84F.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DU.A7TC.01 1 0.0000 0.993 1.00 0.00 0.00
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#> TCGA.DU.7008.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.S9.A6WG.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DB.A75O.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.7688.01 1 0.1529 0.953 0.96 0.00 0.04
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#> TCGA.DU.5872.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.FG.8185.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.7902.01 1 0.0000 0.993 1.00 0.00 0.00
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#> TCGA.DU.5874.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.S9.A6WE.01 2 0.4796 0.645 0.22 0.78 0.00
#> TCGA.FG.6690.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HW.8320.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.R8.A6MK.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.QH.A6CY.01 2 0.0000 0.993 0.00 1.00 0.00
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#> TCGA.HT.A74O.01 1 0.0000 0.993 1.00 0.00 0.00
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#> TCGA.CS.6667.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.E1.A7YV.01 3 0.0000 0.934 0.00 0.00 1.00
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#> TCGA.HT.A5RB.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.7616.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.S9.A7R8.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.QH.A6XA.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.8111.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DU.A5TP.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.RY.A83Y.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.HT.7482.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.TQ.A7RK.02 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.TQ.A7RK.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.7858.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.7475.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DB.A64U.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DB.A64W.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.R8.A6MO.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DU.A7T8.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HW.8322.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DU.5870.02 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.CS.6668.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DU.5870.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.FG.7636.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.7692.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.WY.A859.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.R8.A6ML.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.HT.7686.01 3 0.0000 0.934 0.00 0.00 1.00
#> TCGA.DU.6410.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.S9.A6U9.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.CS.6290.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.TQ.A7RO.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DU.7019.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.FG.A711.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.TQ.A7RM.01 3 0.0000 0.934 0.00 0.00 1.00
#> TCGA.S9.A7R4.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.E1.5318.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.HT.7676.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.S9.A7J3.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.P5.A5F2.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.E1.5304.01 3 0.0000 0.934 0.00 0.00 1.00
#> TCGA.TM.A84S.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.WY.A85B.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.TQ.A7RS.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.S9.A7QX.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.CS.4943.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.QH.A65Z.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DB.5276.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.P5.A730.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.TM.A84L.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.WY.A85D.01 1 0.1529 0.953 0.96 0.00 0.04
#> TCGA.RY.A83X.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.S9.A6UB.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DB.5273.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.TM.A7C4.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DH.A66F.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.HT.7607.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DU.6393.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.HT.8108.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DU.7304.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.S9.A7IY.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.FG.7641.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.P5.A736.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.P5.A5EV.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DU.7301.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.7470.01 3 0.3686 0.835 0.14 0.00 0.86
#> TCGA.DU.7009.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.P5.A781.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.FG.A4MY.01 1 0.1529 0.953 0.96 0.00 0.04
#> TCGA.TM.A7CF.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.TM.A7CF.02 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.FG.8186.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.S9.A6U6.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.RY.A845.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DU.7010.01 3 0.0000 0.934 0.00 0.00 1.00
#> TCGA.S9.A6U2.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.S9.A6WN.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.FG.8182.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.QH.A6X3.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DU.6401.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DU.6396.01 3 0.0000 0.934 0.00 0.00 1.00
#> TCGA.E1.A7YH.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DU.7306.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.A74J.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DH.A7US.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.FG.A87N.01 3 0.0000 0.934 0.00 0.00 1.00
#> TCGA.HT.7478.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DB.A4XE.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DB.A64L.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.VV.A829.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.HT.A61B.01 1 0.0892 0.974 0.98 0.00 0.02
#> TCGA.DH.A66B.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.7603.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DU.6397.02 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DU.6397.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DU.5853.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.CS.6670.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DU.7014.01 1 0.1529 0.953 0.96 0.00 0.04
#> TCGA.QH.A65X.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DB.A64P.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.FG.5965.02 3 0.0000 0.934 0.00 0.00 1.00
#> TCGA.FG.A70Y.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.TQ.A7RV.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.TQ.A7RV.02 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.A5R7.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HW.A5KL.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.7474.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DH.A7UU.01 3 0.6045 0.455 0.38 0.00 0.62
#> TCGA.QH.A6CZ.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DH.A669.02 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DH.A669.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.QH.A6X9.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.P5.A5EZ.01 1 0.0892 0.974 0.98 0.00 0.02
#> TCGA.DU.5871.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.TQ.A7RJ.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.WY.A858.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.VM.A8CB.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.HT.7483.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.HT.7687.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.TM.A84G.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.E1.A7Z6.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.TM.A84I.01 3 0.0000 0.934 0.00 0.00 1.00
#> TCGA.CS.5394.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DU.A76O.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.DU.A5TW.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.WY.A85A.01 1 0.0000 0.993 1.00 0.00 0.00
#> TCGA.FG.5962.01 2 0.0000 0.993 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.E1.5319.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HT.7693.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.CS.6665.01 3 0.0000 0.9693 0.00 0.00 1.00 0.00
#> TCGA.S9.A7J2.01 1 0.4977 0.1691 0.54 0.46 0.00 0.00
#> TCGA.FG.A6J3.01 3 0.0000 0.9693 0.00 0.00 1.00 0.00
#> TCGA.S9.A6TX.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.VM.A8C8.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.HT.A74L.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DU.A5TS.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.DB.A4XA.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HT.A4DV.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.E1.5311.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.E1.A7YI.01 3 0.0000 0.9693 0.00 0.00 1.00 0.00
#> TCGA.E1.5305.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.F6.A8O4.01 4 0.4907 0.2710 0.42 0.00 0.00 0.58
#> TCGA.HT.8113.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DH.A66G.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.HT.7620.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.P5.A731.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.HT.7480.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HT.7689.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.HT.8109.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.E1.A7YE.01 3 0.0000 0.9693 0.00 0.00 1.00 0.00
#> TCGA.S9.A7R1.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.FG.A710.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.S9.A7J0.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.DU.A6S6.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HT.7877.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.QH.A6CU.01 1 0.5000 0.0192 0.50 0.50 0.00 0.00
#> TCGA.HW.7486.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.FG.7634.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DU.8163.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DU.6407.02 3 0.0000 0.9693 0.00 0.00 1.00 0.00
#> TCGA.DU.6407.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.HT.8010.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.P5.A5F1.01 1 0.3610 0.7254 0.80 0.00 0.00 0.20
#> TCGA.VM.A8CF.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.DU.6542.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.FG.7638.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DH.5143.01 4 0.4406 0.5680 0.30 0.00 0.00 0.70
#> TCGA.DU.7299.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.CS.5393.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.DU.7011.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.TM.A84Q.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DB.5281.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.HT.7605.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.FG.A6J1.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DB.5270.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.S9.A6WQ.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.HT.8106.01 1 0.0707 0.9012 0.98 0.00 0.02 0.00
#> TCGA.HT.7608.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.E1.A7YU.01 4 0.3975 0.6333 0.00 0.00 0.24 0.76
#> TCGA.W9.A837.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.TM.A7C5.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.S9.A7QY.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.QH.A6CW.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.S9.A6WO.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.IK.7675.01 3 0.0707 0.9539 0.00 0.00 0.98 0.02
#> TCGA.HT.7601.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.P5.A5ET.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HT.7472.01 1 0.4277 0.6008 0.72 0.00 0.00 0.28
#> TCGA.HT.7880.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.E1.A7Z3.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.P5.A77X.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.FG.A6IZ.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HT.7873.01 4 0.3975 0.6525 0.24 0.00 0.00 0.76
#> TCGA.CS.4938.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.KT.A74X.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.P5.A5EX.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.VM.A8CH.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.HT.7476.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.DB.A75L.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.HT.8563.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.RY.A843.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.S9.A7IS.01 3 0.0000 0.9693 0.00 0.00 1.00 0.00
#> TCGA.TQ.A8XE.02 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.E1.A7YO.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.TQ.A7RG.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.QH.A6X5.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HW.7493.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.RY.A847.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DU.8166.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.VM.A8CA.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HT.7855.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.S9.A89Z.01 4 0.2011 0.8482 0.00 0.00 0.08 0.92
#> TCGA.DB.A4XG.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DH.A7UT.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DU.7015.01 1 0.4790 0.4001 0.62 0.00 0.00 0.38
#> TCGA.HT.A616.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.HT.7611.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.HT.8018.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.FG.A60K.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HT.7856.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DU.5851.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DU.A7T6.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.S9.A6TY.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.WY.A85C.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.DB.A4XC.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.TM.A84O.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.P5.A72W.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.S9.A6TU.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.HT.A61A.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DU.5855.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.HT.7884.01 1 0.2011 0.8499 0.92 0.00 0.00 0.08
#> TCGA.TQ.A7RQ.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.IK.8125.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HT.A74K.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.WH.A86K.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.QH.A6X8.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.WY.A85E.01 1 0.4994 0.0736 0.52 0.00 0.00 0.48
#> TCGA.HT.A5R5.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.HT.A618.01 3 0.0000 0.9693 0.00 0.00 1.00 0.00
#> TCGA.FG.6691.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.HT.7467.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.S9.A7R3.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.FG.A4MX.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.HT.7681.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.S9.A7IZ.01 1 0.4977 0.1387 0.54 0.00 0.00 0.46
#> TCGA.DU.A6S7.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.P5.A72Z.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HT.8114.01 1 0.4977 0.1659 0.54 0.00 0.00 0.46
#> TCGA.DU.8168.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HW.8321.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RN.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DH.5141.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.EZ.7264.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.P5.A5F4.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.QH.A65V.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.FG.8191.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DH.5142.01 1 0.4948 0.2002 0.56 0.00 0.00 0.44
#> TCGA.DU.A6S8.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
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#> TCGA.DU.7298.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DB.A64R.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.FG.A60L.01 4 0.4406 0.5769 0.30 0.00 0.00 0.70
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#> TCGA.RY.A83Z.01 3 0.0000 0.9693 0.00 0.00 1.00 0.00
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#> TCGA.P5.A735.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
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#> TCGA.HT.7881.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HT.7695.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.P5.A5EU.01 3 0.0000 0.9693 0.00 0.00 1.00 0.00
#> TCGA.DB.A64X.01 4 0.2011 0.8482 0.00 0.00 0.08 0.92
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#> TCGA.S9.A6U5.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HT.7609.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DB.5274.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HW.7487.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HW.7491.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.CS.4944.01 4 0.0707 0.9042 0.02 0.00 0.00 0.98
#> TCGA.DU.A6S2.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.S9.A7R7.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
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#> TCGA.HW.A5KM.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.HT.7477.01 3 0.0000 0.9693 0.00 0.00 1.00 0.00
#> TCGA.HT.8012.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DU.8167.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.S9.A6U1.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.FG.5965.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.FG.8187.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HT.A614.01 4 0.4713 0.4544 0.36 0.00 0.00 0.64
#> TCGA.S9.A7QZ.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.QH.A6X4.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
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#> TCGA.DU.7302.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DU.6399.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.E1.5307.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.S9.A7QW.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.HT.7604.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.P5.A733.01 4 0.1637 0.8667 0.06 0.00 0.00 0.94
#> TCGA.HT.7684.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.HW.7495.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.QH.A65R.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DU.A7TG.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DH.A7UV.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.HT.7879.01 1 0.4948 0.2325 0.56 0.00 0.00 0.44
#> TCGA.TM.A84F.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DU.A7TC.01 4 0.4855 0.3270 0.40 0.00 0.00 0.60
#> TCGA.HT.7610.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.S9.A6TW.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.FG.A60J.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.E1.5303.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.HT.7481.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.FN.7833.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.E1.A7Z4.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DU.A5TR.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.HT.7875.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HT.7473.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.S9.A7IQ.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DU.7008.01 1 0.2345 0.8312 0.90 0.00 0.00 0.10
#> TCGA.S9.A6WG.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DB.A75O.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.HT.7688.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.DU.7304.02 3 0.0000 0.9693 0.00 0.00 1.00 0.00
#> TCGA.DU.6394.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.S9.A6WD.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DU.5872.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.FG.8185.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.HT.7902.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RU.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DU.5874.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.S9.A6WE.01 1 0.4994 0.0998 0.52 0.48 0.00 0.00
#> TCGA.FG.6690.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.HW.8320.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.R8.A6MK.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.QH.A6CY.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.S9.A7J1.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.P5.A72X.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.E1.5322.01 4 0.4624 0.4967 0.34 0.00 0.00 0.66
#> TCGA.P5.A5F0.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.R8.A73M.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.CS.4942.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DB.A4X9.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DB.A4XF.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.HT.A74O.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.FG.8188.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.DU.A6S3.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DB.A4XH.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HT.7485.01 1 0.4522 0.5258 0.68 0.00 0.00 0.32
#> TCGA.VW.A7QS.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.S9.A6WI.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DU.8164.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.S9.A6TS.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.DB.A64S.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.VV.A86M.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.TQ.A8XE.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.CS.6667.01 1 0.3975 0.6694 0.76 0.00 0.00 0.24
#> TCGA.E1.A7YV.01 3 0.0000 0.9693 0.00 0.00 1.00 0.00
#> TCGA.TQ.A7RW.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.DU.5849.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DU.A7TI.01 1 0.4855 0.3492 0.60 0.00 0.00 0.40
#> TCGA.HT.7468.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.TQ.A7RI.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DB.5279.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.S9.A6U8.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.HW.7489.01 1 0.4907 0.2925 0.58 0.00 0.00 0.42
#> TCGA.R8.A6YH.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DU.7018.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HT.7677.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.FG.A713.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DU.7300.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.TM.A7CA.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.HT.7690.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.FG.6689.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DU.7007.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.TQ.A7RF.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DB.5277.01 4 0.2011 0.8533 0.00 0.00 0.08 0.92
#> TCGA.HT.7694.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.TM.A84M.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.F6.A8O3.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.QH.A86X.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HT.8013.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.HW.7490.01 1 0.3801 0.6947 0.78 0.00 0.00 0.22
#> TCGA.QH.A65S.01 4 0.4277 0.6045 0.28 0.00 0.00 0.72
#> TCGA.DU.A76R.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DH.5144.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.P5.A780.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.HT.7606.01 3 0.4713 0.4585 0.00 0.00 0.64 0.36
#> TCGA.DB.A64V.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.RY.A840.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
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#> TCGA.HW.A5KJ.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HT.A615.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HT.8105.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DU.7309.01 1 0.1211 0.8837 0.96 0.00 0.00 0.04
#> TCGA.E1.A7YK.01 3 0.0000 0.9693 0.00 0.00 1.00 0.00
#> TCGA.HT.7874.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HT.7471.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DU.6395.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
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#> TCGA.P5.A5EW.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DU.6408.01 4 0.4406 0.5758 0.30 0.00 0.00 0.70
#> TCGA.DB.A4XB.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.FG.A4MT.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.FG.A4MT.02 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.HT.A619.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.QH.A870.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.HT.A5R9.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.FG.5964.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.CS.5396.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DU.A7TA.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.HW.8319.01 3 0.0000 0.9693 0.00 0.00 1.00 0.00
#> TCGA.DH.A7UR.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.TM.A84H.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.S9.A6TZ.01 4 0.3801 0.6803 0.22 0.00 0.00 0.78
#> TCGA.HT.7479.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DU.6400.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
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#> TCGA.DB.A75K.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DB.A4XD.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
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#> TCGA.HT.7602.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DU.A5TU.01 3 0.0000 0.9693 0.00 0.00 1.00 0.00
#> TCGA.HT.A5RB.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.HT.7616.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.S9.A7R8.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.QH.A6XA.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
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#> TCGA.RY.A83Y.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HT.7482.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
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#> TCGA.HT.7858.01 1 0.4522 0.5343 0.68 0.00 0.00 0.32
#> TCGA.HT.7475.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
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#> TCGA.DU.A7T8.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
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#> TCGA.DU.5870.02 2 0.0000 1.0000 0.00 1.00 0.00 0.00
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#> TCGA.HT.8108.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DU.7304.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.S9.A7IY.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
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#> TCGA.P5.A5EV.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.DU.7301.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.HT.7470.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.DU.7009.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.P5.A781.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.FG.A4MY.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.TM.A7CF.01 1 0.4522 0.5315 0.68 0.00 0.00 0.32
#> TCGA.TM.A7CF.02 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.FG.8186.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.S9.A6U6.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.RY.A845.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DU.7010.01 3 0.0000 0.9693 0.00 0.00 1.00 0.00
#> TCGA.S9.A6U2.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.S9.A6WN.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.FG.8182.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.QH.A6X3.01 4 0.3172 0.7575 0.16 0.00 0.00 0.84
#> TCGA.DU.6401.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DU.6396.01 3 0.2921 0.8344 0.00 0.00 0.86 0.14
#> TCGA.E1.A7YH.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DU.7306.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.HT.A74J.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DH.A7US.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.FG.A87N.01 3 0.0000 0.9693 0.00 0.00 1.00 0.00
#> TCGA.HT.7478.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DB.A4XE.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DB.A64L.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.VV.A829.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HT.A61B.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.DH.A66B.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.HT.7603.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DU.6397.02 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DU.6397.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DU.5853.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.CS.6670.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DU.7014.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.QH.A65X.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DB.A64P.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.FG.5965.02 3 0.0000 0.9693 0.00 0.00 1.00 0.00
#> TCGA.FG.A70Y.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RV.01 4 0.3172 0.7581 0.16 0.00 0.00 0.84
#> TCGA.TQ.A7RV.02 4 0.4134 0.6347 0.26 0.00 0.00 0.74
#> TCGA.HT.A5R7.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.HW.A5KL.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.HT.7474.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DH.A7UU.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.QH.A6CZ.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DH.A669.02 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DH.A669.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.QH.A6X9.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.P5.A5EZ.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.DU.5871.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.TQ.A7RJ.01 4 0.0000 0.9214 0.00 0.00 0.00 1.00
#> TCGA.WY.A858.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.VM.A8CB.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.HT.7483.01 4 0.0707 0.9041 0.02 0.00 0.00 0.98
#> TCGA.HT.7687.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.TM.A84G.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.E1.A7Z6.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.TM.A84I.01 3 0.0000 0.9693 0.00 0.00 1.00 0.00
#> TCGA.CS.5394.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.DU.A76O.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.DU.A5TW.01 1 0.4948 0.2365 0.56 0.00 0.00 0.44
#> TCGA.WY.A85A.01 1 0.0000 0.9175 1.00 0.00 0.00 0.00
#> TCGA.FG.5962.01 2 0.0000 1.0000 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.E1.5319.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7693.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.CS.6665.01 3 0.0000 0.95970 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A7J2.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.A6J3.01 3 0.0000 0.95970 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6TX.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.VM.A8C8.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A74L.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.A5TS.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.DB.A4XA.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.A4DV.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.5311.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YI.01 3 0.0000 0.95970 0.00 0.00 1.00 0.00 0.00
#> TCGA.E1.5305.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.F6.A8O4.01 1 0.4307 0.00727 0.50 0.00 0.00 0.50 0.00
#> TCGA.HT.8113.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.DH.A66G.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7620.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A731.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7480.01 2 0.2020 0.86586 0.00 0.90 0.00 0.00 0.10
#> TCGA.HT.7689.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.8109.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.E1.A7YE.01 3 0.0000 0.95970 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A7R1.01 5 0.1732 0.88845 0.00 0.08 0.00 0.00 0.92
#> TCGA.FG.A710.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.S9.A7J0.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.A6S6.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7877.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.QH.A6CU.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.HW.7486.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.7634.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.8163.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6407.02 3 0.0000 0.95970 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.6407.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.8010.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A5F1.01 1 0.1732 0.86450 0.92 0.00 0.00 0.08 0.00
#> TCGA.VM.A8CF.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.6542.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7638.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.DH.5143.01 4 0.4060 0.43659 0.36 0.00 0.00 0.64 0.00
#> TCGA.DU.7299.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.CS.5393.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.7011.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84Q.01 1 0.0609 0.91527 0.98 0.00 0.00 0.02 0.00
#> TCGA.DB.5281.01 4 0.0609 0.90208 0.02 0.00 0.00 0.98 0.00
#> TCGA.HT.7605.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.A6J1.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.5270.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WQ.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8106.01 1 0.1043 0.90089 0.96 0.00 0.04 0.00 0.00
#> TCGA.HT.7608.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YU.01 4 0.2516 0.77590 0.00 0.00 0.14 0.86 0.00
#> TCGA.W9.A837.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.TM.A7C5.01 2 0.2732 0.78812 0.00 0.84 0.00 0.00 0.16
#> TCGA.S9.A7QY.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.QH.A6CW.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A6WO.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.IK.7675.01 3 0.0609 0.94268 0.00 0.00 0.98 0.02 0.00
#> TCGA.HT.7601.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A5ET.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7472.01 1 0.2280 0.82721 0.88 0.00 0.00 0.12 0.00
#> TCGA.HT.7880.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7Z3.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A77X.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.A6IZ.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.7873.01 4 0.3561 0.61721 0.26 0.00 0.00 0.74 0.00
#> TCGA.CS.4938.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.KT.A74X.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A5EX.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.VM.A8CH.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7476.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.DB.A75L.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.8563.01 4 0.0609 0.90333 0.00 0.00 0.02 0.98 0.00
#> TCGA.RY.A843.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IS.01 3 0.0000 0.95970 0.00 0.00 1.00 0.00 0.00
#> TCGA.TQ.A8XE.02 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.E1.A7YO.01 5 0.3561 0.61808 0.00 0.26 0.00 0.00 0.74
#> TCGA.TQ.A7RG.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.QH.A6X5.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.HW.7493.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.RY.A847.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.8166.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8CA.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7855.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A89Z.01 4 0.1732 0.84731 0.00 0.00 0.08 0.92 0.00
#> TCGA.DB.A4XG.01 2 0.4060 0.45956 0.00 0.64 0.00 0.00 0.36
#> TCGA.DH.A7UT.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7015.01 1 0.4227 0.29700 0.58 0.00 0.00 0.42 0.00
#> TCGA.HT.A616.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7611.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.8018.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A60K.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7856.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.5851.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A7T6.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.S9.A6TY.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.WY.A85C.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.DB.A4XC.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84O.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.P5.A72W.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TU.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.A61A.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.5855.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7884.01 1 0.1410 0.88263 0.94 0.00 0.00 0.06 0.00
#> TCGA.TQ.A7RQ.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.IK.8125.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.A74K.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.WH.A86K.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.QH.A6X8.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.WY.A85E.01 1 0.4262 0.23046 0.56 0.00 0.00 0.44 0.00
#> TCGA.HT.A5R5.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A618.01 3 0.0000 0.95970 0.00 0.00 1.00 0.00 0.00
#> TCGA.FG.6691.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7467.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A7R3.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.FG.A4MX.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7681.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A7IZ.01 1 0.4126 0.39002 0.62 0.00 0.00 0.38 0.00
#> TCGA.DU.A6S7.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.P5.A72Z.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.8114.01 1 0.4126 0.40827 0.62 0.00 0.00 0.38 0.00
#> TCGA.DU.8168.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.HW.8321.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RN.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.DH.5141.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.EZ.7264.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.P5.A5F4.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A65V.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.8191.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.5142.01 1 0.3684 0.60883 0.72 0.00 0.00 0.28 0.00
#> TCGA.DU.A6S8.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.E1.A7YW.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6666.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.7298.01 2 0.0609 0.95422 0.00 0.98 0.00 0.00 0.02
#> TCGA.DB.A64R.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.A60L.01 4 0.3796 0.56444 0.30 0.00 0.00 0.70 0.00
#> TCGA.CS.5390.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.S9.A6WP.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.DB.5280.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84T.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A66D.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.RY.A83Z.01 3 0.0000 0.95970 0.00 0.00 1.00 0.00 0.00
#> TCGA.DB.5278.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RR.01 1 0.2516 0.80072 0.86 0.00 0.00 0.14 0.00
#> TCGA.TQ.A7RH.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YS.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.P5.A735.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7294.01 5 0.3895 0.51806 0.00 0.32 0.00 0.00 0.68
#> TCGA.HT.7881.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7695.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A5EU.01 3 0.0000 0.95970 0.00 0.00 1.00 0.00 0.00
#> TCGA.DB.A64X.01 4 0.1043 0.88527 0.00 0.00 0.04 0.96 0.00
#> TCGA.FG.7637.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.VM.A8CE.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6U5.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7609.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5274.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.HW.7487.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.HW.7491.01 5 0.1043 0.93973 0.00 0.04 0.00 0.00 0.96
#> TCGA.CS.4944.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.A6S2.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A7R7.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84R.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.A75M.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.HW.A5KM.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7477.01 3 0.0000 0.95970 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.8012.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.8167.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A6U1.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.5965.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8187.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.A614.01 4 0.4262 0.22053 0.44 0.00 0.00 0.56 0.00
#> TCGA.S9.A7QZ.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.QH.A6X4.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A77W.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.7302.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.6399.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.E1.5307.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A7QW.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7604.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.P5.A733.01 4 0.2516 0.77419 0.14 0.00 0.00 0.86 0.00
#> TCGA.HT.7684.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.HW.7495.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.QH.A65R.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.A7TG.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.DH.A7UV.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7879.01 1 0.4182 0.35540 0.60 0.00 0.00 0.40 0.00
#> TCGA.TM.A84F.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A7TC.01 4 0.3895 0.52803 0.32 0.00 0.00 0.68 0.00
#> TCGA.HT.7610.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TW.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.FG.A60J.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5303.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7481.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.FN.7833.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7Z4.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TR.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7875.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7473.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IQ.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7008.01 1 0.2516 0.80346 0.86 0.00 0.00 0.14 0.00
#> TCGA.S9.A6WG.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A75O.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7688.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.7304.02 3 0.0000 0.95970 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.6394.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.S9.A6WD.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.5872.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8185.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7902.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RU.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.5874.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.S9.A6WE.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.6690.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.HW.8320.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.R8.A6MK.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.QH.A6CY.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A7J1.01 2 0.1732 0.88974 0.00 0.92 0.00 0.00 0.08
#> TCGA.P5.A72X.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5322.01 1 0.4302 0.08160 0.52 0.00 0.00 0.48 0.00
#> TCGA.P5.A5F0.01 2 0.1410 0.91230 0.00 0.94 0.00 0.00 0.06
#> TCGA.R8.A73M.01 2 0.3895 0.54918 0.00 0.68 0.00 0.00 0.32
#> TCGA.CS.4942.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4X9.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4XF.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.A74O.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.FG.8188.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.A6S3.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.DB.A4XH.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.7485.01 1 0.3424 0.68149 0.76 0.00 0.00 0.24 0.00
#> TCGA.VW.A7QS.01 5 0.2280 0.83378 0.00 0.12 0.00 0.00 0.88
#> TCGA.S9.A6WI.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.8164.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.S9.A6TS.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.DB.A64S.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.VV.A86M.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.TQ.A8XE.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.CS.6667.01 1 0.3424 0.68026 0.76 0.00 0.00 0.24 0.00
#> TCGA.E1.A7YV.01 3 0.0000 0.95970 0.00 0.00 1.00 0.00 0.00
#> TCGA.TQ.A7RW.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.5849.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.A7TI.01 1 0.4227 0.29589 0.58 0.00 0.00 0.42 0.00
#> TCGA.HT.7468.01 2 0.3109 0.73305 0.00 0.80 0.00 0.00 0.20
#> TCGA.TQ.A7RI.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.5279.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.S9.A6U8.01 1 0.0609 0.91557 0.98 0.00 0.00 0.02 0.00
#> TCGA.HW.7489.01 4 0.4302 0.04978 0.48 0.00 0.00 0.52 0.00
#> TCGA.R8.A6YH.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7018.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.7677.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.FG.A713.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.7300.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.TM.A7CA.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7690.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.6689.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7007.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.TQ.A7RF.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5277.01 4 0.1732 0.84731 0.00 0.00 0.08 0.92 0.00
#> TCGA.HT.7694.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.TM.A84M.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.F6.A8O3.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.QH.A86X.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.8013.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.HW.7490.01 1 0.2732 0.78582 0.84 0.00 0.00 0.16 0.00
#> TCGA.QH.A65S.01 4 0.3561 0.62272 0.26 0.00 0.00 0.74 0.00
#> TCGA.DU.A76R.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.DH.5144.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.P5.A780.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7606.01 3 0.4302 0.11796 0.00 0.00 0.52 0.48 0.00
#> TCGA.DB.A64V.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.RY.A840.01 2 0.3274 0.70249 0.00 0.78 0.00 0.00 0.22
#> TCGA.E1.5302.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.HW.A5KJ.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.A615.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.8105.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.7309.01 1 0.4075 0.70423 0.78 0.16 0.00 0.06 0.00
#> TCGA.E1.A7YK.01 3 0.0000 0.95970 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7874.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7471.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.6395.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TV.01 4 0.0609 0.90323 0.00 0.00 0.02 0.98 0.00
#> TCGA.P5.A5EW.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6408.01 4 0.4227 0.28476 0.42 0.00 0.00 0.58 0.00
#> TCGA.DB.A4XB.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A4MT.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A4MT.02 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A619.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.QH.A870.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A5R9.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.FG.5964.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.CS.5396.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.A7TA.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.HW.8319.01 3 0.0000 0.95970 0.00 0.00 1.00 0.00 0.00
#> TCGA.DH.A7UR.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.TM.A84H.01 4 0.0609 0.90201 0.02 0.00 0.00 0.98 0.00
#> TCGA.S9.A6TZ.01 4 0.2280 0.80066 0.12 0.00 0.00 0.88 0.00
#> TCGA.HT.7479.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6400.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.S9.A6WL.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.DB.A75K.01 2 0.4126 0.40924 0.00 0.62 0.00 0.00 0.38
#> TCGA.DB.A4XD.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.DB.A64Q.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.P5.A737.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.5275.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WH.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.7602.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TU.01 3 0.0000 0.95970 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.A5RB.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7616.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.S9.A7R8.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.QH.A6XA.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8111.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TP.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.RY.A83Y.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.7482.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RK.02 1 0.4182 0.35190 0.60 0.00 0.00 0.40 0.00
#> TCGA.TQ.A7RK.01 1 0.4126 0.40492 0.62 0.00 0.00 0.38 0.00
#> TCGA.HT.7858.01 1 0.4227 0.29865 0.58 0.00 0.00 0.42 0.00
#> TCGA.HT.7475.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64U.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.A64W.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.R8.A6MO.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.A7T8.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.HW.8322.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.5870.02 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.CS.6668.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.5870.01 2 0.0609 0.95415 0.00 0.98 0.00 0.00 0.02
#> TCGA.FG.7636.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7692.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.WY.A859.01 4 0.4060 0.44830 0.36 0.00 0.00 0.64 0.00
#> TCGA.R8.A6ML.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.7686.01 3 0.3561 0.65625 0.00 0.00 0.74 0.26 0.00
#> TCGA.DU.6410.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.S9.A6U9.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6290.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RO.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7019.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.FG.A711.01 1 0.3684 0.61070 0.72 0.00 0.00 0.28 0.00
#> TCGA.TQ.A7RM.01 3 0.0000 0.95970 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A7R4.01 1 0.1043 0.89915 0.96 0.00 0.00 0.04 0.00
#> TCGA.E1.5318.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.7676.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7J3.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.P5.A5F2.01 4 0.1043 0.88397 0.04 0.00 0.00 0.96 0.00
#> TCGA.E1.5304.01 3 0.0000 0.95970 0.00 0.00 1.00 0.00 0.00
#> TCGA.TM.A84S.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.WY.A85B.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RS.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A7QX.01 4 0.3895 0.53209 0.32 0.00 0.00 0.68 0.00
#> TCGA.CS.4943.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.QH.A65Z.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.DB.5276.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A730.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.TM.A84L.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.WY.A85D.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.RY.A83X.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6UB.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.DB.5273.01 4 0.4302 0.06881 0.48 0.00 0.00 0.52 0.00
#> TCGA.TM.A7C4.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A66F.01 2 0.1732 0.89021 0.00 0.92 0.00 0.00 0.08
#> TCGA.HT.7607.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.6393.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.8108.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7304.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A7IY.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.7641.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A736.01 1 0.3424 0.68118 0.76 0.00 0.00 0.24 0.00
#> TCGA.P5.A5EV.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.7301.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7470.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.7009.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A781.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.A4MY.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.TM.A7CF.01 1 0.3561 0.65206 0.74 0.00 0.00 0.26 0.00
#> TCGA.TM.A7CF.02 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8186.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6U6.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.RY.A845.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7010.01 3 0.0000 0.95970 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6U2.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6WN.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.FG.8182.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6X3.01 4 0.3109 0.70149 0.20 0.00 0.00 0.80 0.00
#> TCGA.DU.6401.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6396.01 3 0.2929 0.77377 0.00 0.00 0.82 0.18 0.00
#> TCGA.E1.A7YH.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7306.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.A74J.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A7US.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.A87N.01 3 0.0000 0.95970 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7478.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4XE.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64L.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.VV.A829.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.A61B.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.DH.A66B.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7603.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6397.02 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.6397.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.5853.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6670.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7014.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.QH.A65X.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.A64P.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.5965.02 3 0.0000 0.95970 0.00 0.00 1.00 0.00 0.00
#> TCGA.FG.A70Y.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RV.01 4 0.2280 0.79905 0.12 0.00 0.00 0.88 0.00
#> TCGA.TQ.A7RV.02 4 0.3274 0.67655 0.22 0.00 0.00 0.78 0.00
#> TCGA.HT.A5R7.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.HW.A5KL.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7474.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A7UU.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.QH.A6CZ.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.DH.A669.02 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.DH.A669.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.QH.A6X9.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.P5.A5EZ.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.5871.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.TQ.A7RJ.01 4 0.0000 0.91927 0.00 0.00 0.00 1.00 0.00
#> TCGA.WY.A858.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8CB.01 2 0.0000 0.97392 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7483.01 4 0.2516 0.77785 0.14 0.00 0.00 0.86 0.00
#> TCGA.HT.7687.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.TM.A84G.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.E1.A7Z6.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84I.01 3 0.0000 0.95970 0.00 0.00 1.00 0.00 0.00
#> TCGA.CS.5394.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.A76O.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TW.01 1 0.4262 0.23614 0.56 0.00 0.00 0.44 0.00
#> TCGA.WY.A85A.01 1 0.0000 0.93155 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.5962.01 5 0.0000 0.98750 0.00 0.00 0.00 0.00 1.00
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 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7693.01 4 0.0000 0.79430 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CS.6665.01 3 0.3309 0.56817 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.S9.A7J2.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A6J3.01 3 0.0000 0.90436 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6TX.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.VM.A8C8.01 1 0.0937 0.83184 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.HT.A74L.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TS.01 4 0.2631 0.72272 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.DB.A4XA.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A4DV.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5311.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YI.01 3 0.0000 0.90436 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.5305.01 4 0.3309 0.63455 0.00 0.00 0.00 0.72 0.00 0.28
#> TCGA.F6.A8O4.01 4 0.3864 -0.16155 0.48 0.00 0.00 0.52 0.00 0.00
#> TCGA.HT.8113.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A66G.01 4 0.3592 0.67942 0.02 0.00 0.00 0.74 0.00 0.24
#> TCGA.HT.7620.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A731.01 1 0.1267 0.79489 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.HT.7480.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7689.01 4 0.3499 0.58475 0.00 0.00 0.00 0.68 0.00 0.32
#> TCGA.HT.8109.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.E1.A7YE.01 3 0.0000 0.90436 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A7R1.01 5 0.2048 0.82230 0.00 0.12 0.00 0.00 0.88 0.00
#> TCGA.FG.A710.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A7J0.01 4 0.3499 0.58475 0.00 0.00 0.00 0.68 0.00 0.32
#> TCGA.DU.A6S6.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7877.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CU.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HW.7486.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7634.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.8163.01 1 0.0937 0.83184 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.DU.6407.02 3 0.0937 0.87601 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.DU.6407.01 4 0.0000 0.79430 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.8010.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A5F1.01 1 0.1814 0.81617 0.90 0.00 0.00 0.10 0.00 0.00
#> TCGA.VM.A8CF.01 4 0.3309 0.63455 0.00 0.00 0.00 0.72 0.00 0.28
#> TCGA.DU.6542.01 1 0.1267 0.82176 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.FG.7638.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.5143.01 1 0.3869 0.22808 0.50 0.00 0.00 0.50 0.00 0.00
#> TCGA.DU.7299.01 4 0.3076 0.67645 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.CS.5393.01 4 0.3409 0.61112 0.00 0.00 0.00 0.70 0.00 0.30
#> TCGA.DU.7011.01 1 0.0000 0.82398 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84Q.01 1 0.3076 0.71726 0.76 0.00 0.00 0.24 0.00 0.00
#> TCGA.DB.5281.01 4 0.1267 0.76412 0.06 0.00 0.00 0.94 0.00 0.00
#> TCGA.HT.7605.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A6J1.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5270.01 1 0.1267 0.79336 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.S9.A6WQ.01 1 0.1267 0.83004 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.HT.8106.01 6 0.3198 0.55208 0.26 0.00 0.00 0.00 0.00 0.74
#> TCGA.HT.7608.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YU.01 4 0.4144 0.49510 0.00 0.00 0.02 0.62 0.00 0.36
#> TCGA.W9.A837.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A7C5.01 2 0.1814 0.85977 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.S9.A7QY.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.QH.A6CW.01 4 0.0000 0.79430 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6WO.01 1 0.2260 0.79214 0.86 0.00 0.00 0.14 0.00 0.00
#> TCGA.IK.7675.01 6 0.3409 0.24285 0.00 0.00 0.30 0.00 0.00 0.70
#> TCGA.HT.7601.01 6 0.2941 0.56766 0.22 0.00 0.00 0.00 0.00 0.78
#> TCGA.P5.A5ET.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7472.01 1 0.2941 0.73163 0.78 0.00 0.00 0.22 0.00 0.00
#> TCGA.HT.7880.01 1 0.1267 0.79336 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.E1.A7Z3.01 1 0.3198 0.69836 0.74 0.00 0.00 0.26 0.00 0.00
#> TCGA.P5.A77X.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A6IZ.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7873.01 6 0.0000 0.55600 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CS.4938.01 1 0.1267 0.83004 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.KT.A74X.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A5EX.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8CH.01 1 0.1267 0.83020 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.HT.7476.01 4 0.0547 0.78846 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DB.A75L.01 4 0.0937 0.78655 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.HT.8563.01 6 0.2631 0.44835 0.00 0.00 0.00 0.18 0.00 0.82
#> TCGA.RY.A843.01 1 0.0000 0.82398 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IS.01 3 0.0000 0.90436 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.TQ.A8XE.02 4 0.2793 0.70846 0.00 0.00 0.00 0.80 0.00 0.20
#> TCGA.E1.A7YO.01 5 0.3499 0.48488 0.00 0.32 0.00 0.00 0.68 0.00
#> TCGA.TQ.A7RG.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6X5.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HW.7493.01 1 0.0937 0.83184 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.RY.A847.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.8166.01 1 0.0937 0.83184 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.VM.A8CA.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7855.01 4 0.0547 0.78846 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.S9.A89Z.01 4 0.4348 0.53544 0.00 0.00 0.04 0.64 0.00 0.32
#> TCGA.DB.A4XG.01 2 0.3309 0.58129 0.00 0.72 0.00 0.00 0.28 0.00
#> TCGA.DH.A7UT.01 1 0.3864 -0.11547 0.52 0.00 0.00 0.00 0.00 0.48
#> TCGA.DU.7015.01 1 0.3706 0.52313 0.62 0.00 0.00 0.38 0.00 0.00
#> TCGA.HT.A616.01 4 0.2454 0.73555 0.00 0.00 0.00 0.84 0.00 0.16
#> TCGA.HT.7611.01 4 0.0937 0.77685 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.HT.8018.01 6 0.3499 0.51581 0.32 0.00 0.00 0.00 0.00 0.68
#> TCGA.FG.A60K.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7856.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5851.01 1 0.3309 0.49902 0.72 0.00 0.00 0.00 0.00 0.28
#> TCGA.DU.A7T6.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A6TY.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.WY.A85C.01 4 0.0547 0.78846 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DB.A4XC.01 1 0.0937 0.80534 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.TM.A84O.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.P5.A72W.01 1 0.0000 0.82398 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TU.01 4 0.0000 0.79430 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.A61A.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5855.01 4 0.0000 0.79430 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7884.01 1 0.3499 0.62277 0.68 0.00 0.00 0.32 0.00 0.00
#> TCGA.TQ.A7RQ.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.IK.8125.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.A74K.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.WH.A86K.01 4 0.3309 0.63455 0.00 0.00 0.00 0.72 0.00 0.28
#> TCGA.QH.A6X8.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.WY.A85E.01 1 0.3828 0.36788 0.56 0.00 0.00 0.44 0.00 0.00
#> TCGA.HT.A5R5.01 1 0.1267 0.79336 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.HT.A618.01 3 0.3828 0.24479 0.00 0.00 0.56 0.00 0.00 0.44
#> TCGA.FG.6691.01 1 0.0000 0.82398 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7467.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7R3.01 4 0.1556 0.74583 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.FG.A4MX.01 1 0.1556 0.82368 0.92 0.00 0.00 0.08 0.00 0.00
#> TCGA.HT.7681.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IZ.01 1 0.5945 -0.11870 0.42 0.00 0.00 0.22 0.00 0.36
#> TCGA.DU.A6S7.01 4 0.0547 0.78846 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.P5.A72Z.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.8114.01 1 0.3797 0.44010 0.58 0.00 0.00 0.42 0.00 0.00
#> TCGA.DU.8168.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HW.8321.01 1 0.1267 0.83020 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.TQ.A7RN.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.5141.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EZ.7264.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.P5.A5F4.01 1 0.2941 0.73399 0.78 0.00 0.00 0.22 0.00 0.00
#> TCGA.QH.A65V.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8191.01 1 0.0547 0.82920 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DH.5142.01 6 0.2048 0.58999 0.12 0.00 0.00 0.00 0.00 0.88
#> TCGA.DU.A6S8.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.E1.A7YW.01 1 0.1267 0.83004 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.CS.6666.01 4 0.0547 0.78846 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DU.7298.01 2 0.0547 0.95764 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.DB.A64R.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A60L.01 4 0.3578 0.32878 0.34 0.00 0.00 0.66 0.00 0.00
#> TCGA.CS.5390.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A6WP.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DB.5280.01 1 0.0937 0.83184 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.TM.A84T.01 1 0.0937 0.80534 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.DH.A66D.01 1 0.1556 0.82382 0.92 0.00 0.00 0.08 0.00 0.00
#> TCGA.RY.A83Z.01 3 0.0000 0.90436 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.5278.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RR.01 6 0.1814 0.59267 0.10 0.00 0.00 0.00 0.00 0.90
#> TCGA.TQ.A7RH.01 1 0.1814 0.75992 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.E1.A7YS.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.P5.A735.01 1 0.1267 0.83004 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.DU.7294.01 5 0.3706 0.37545 0.00 0.38 0.00 0.00 0.62 0.00
#> TCGA.HT.7881.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7695.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A5EU.01 6 0.3499 0.28500 0.00 0.00 0.32 0.00 0.00 0.68
#> TCGA.DB.A64X.01 4 0.4348 0.53544 0.00 0.00 0.04 0.64 0.00 0.32
#> TCGA.FG.7637.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8CE.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6U5.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7609.01 1 0.1267 0.83020 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.DB.5274.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HW.7487.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HW.7491.01 5 0.0547 0.95953 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.CS.4944.01 4 0.0547 0.79163 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DU.A6S2.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7R7.01 6 0.3499 0.51581 0.32 0.00 0.00 0.00 0.00 0.68
#> TCGA.TM.A84R.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A75M.01 4 0.2454 0.66615 0.16 0.00 0.00 0.84 0.00 0.00
#> TCGA.HW.A5KM.01 4 0.0937 0.77713 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.HT.7477.01 6 0.3578 0.21080 0.00 0.00 0.34 0.00 0.00 0.66
#> TCGA.HT.8012.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.8167.01 4 0.0000 0.79430 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6U1.01 1 0.1267 0.83020 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.FG.5965.01 6 0.3499 0.51581 0.32 0.00 0.00 0.00 0.00 0.68
#> TCGA.FG.8187.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A614.01 6 0.0937 0.57394 0.04 0.00 0.00 0.00 0.00 0.96
#> TCGA.S9.A7QZ.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.QH.A6X4.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A77W.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.7302.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.6399.01 4 0.0000 0.79430 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E1.5307.01 4 0.2941 0.69275 0.00 0.00 0.00 0.78 0.00 0.22
#> TCGA.S9.A7QW.01 1 0.0000 0.82398 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7604.01 4 0.0547 0.78846 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.P5.A733.01 4 0.3647 0.28079 0.36 0.00 0.00 0.64 0.00 0.00
#> TCGA.HT.7684.01 1 0.3711 0.55791 0.72 0.00 0.00 0.02 0.00 0.26
#> TCGA.HW.7495.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A65R.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.A7TG.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A7UV.01 4 0.0000 0.79430 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7879.01 1 0.3706 0.52376 0.62 0.00 0.00 0.38 0.00 0.00
#> TCGA.TM.A84F.01 6 0.3499 0.51581 0.32 0.00 0.00 0.00 0.00 0.68
#> TCGA.DU.A7TC.01 4 0.3828 -0.00254 0.44 0.00 0.00 0.56 0.00 0.00
#> TCGA.HT.7610.01 1 0.1556 0.82368 0.92 0.00 0.00 0.08 0.00 0.00
#> TCGA.S9.A6TW.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FG.A60J.01 1 0.0937 0.83184 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.E1.5303.01 4 0.0000 0.79430 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7481.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FN.7833.01 1 0.0000 0.82398 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7Z4.01 1 0.0937 0.83184 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.DU.A5TR.01 4 0.0000 0.79430 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7875.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7473.01 1 0.0000 0.82398 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IQ.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7008.01 1 0.3499 0.62482 0.68 0.00 0.00 0.32 0.00 0.00
#> TCGA.S9.A6WG.01 1 0.1267 0.79336 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.DB.A75O.01 1 0.2260 0.71660 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.HT.7688.01 4 0.2048 0.75547 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.DU.7304.02 3 0.0000 0.90436 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.6394.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A6WD.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.5872.01 1 0.1267 0.79336 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.FG.8185.01 4 0.0547 0.78846 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.HT.7902.01 6 0.3578 0.49375 0.34 0.00 0.00 0.00 0.00 0.66
#> TCGA.TQ.A7RU.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.5874.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A6WE.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.6690.01 4 0.0000 0.79430 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HW.8320.01 4 0.0000 0.79430 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.R8.A6MK.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CY.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7J1.01 2 0.0937 0.93503 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.P5.A72X.01 1 0.0000 0.82398 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5322.01 1 0.4576 0.38098 0.56 0.00 0.00 0.40 0.00 0.04
#> TCGA.P5.A5F0.01 2 0.0547 0.95839 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.R8.A73M.01 2 0.3198 0.61714 0.00 0.74 0.00 0.00 0.26 0.00
#> TCGA.CS.4942.01 1 0.0937 0.80534 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.DB.A4X9.01 1 0.0000 0.82398 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4XF.01 4 0.0547 0.78846 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.HT.A74O.01 4 0.0000 0.79430 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FG.8188.01 4 0.2260 0.74563 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.DU.A6S3.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DB.A4XH.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7485.01 1 0.2631 0.76420 0.82 0.00 0.00 0.18 0.00 0.00
#> TCGA.VW.A7QS.01 5 0.2260 0.79168 0.00 0.14 0.00 0.00 0.86 0.00
#> TCGA.S9.A6WI.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.8164.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A6TS.01 4 0.3499 0.58475 0.00 0.00 0.00 0.68 0.00 0.32
#> TCGA.DB.A64S.01 1 0.1267 0.83020 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.VV.A86M.01 4 0.0000 0.79430 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.TQ.A8XE.01 4 0.1267 0.78151 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.CS.6667.01 1 0.3706 0.52385 0.62 0.00 0.00 0.38 0.00 0.00
#> TCGA.E1.A7YV.01 3 0.0000 0.90436 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RW.01 4 0.2454 0.73555 0.00 0.00 0.00 0.84 0.00 0.16
#> TCGA.DU.5849.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.A7TI.01 1 0.3756 0.48406 0.60 0.00 0.00 0.40 0.00 0.00
#> TCGA.HT.7468.01 2 0.2631 0.74530 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.TQ.A7RI.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5279.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A6U8.01 1 0.3198 0.69836 0.74 0.00 0.00 0.26 0.00 0.00
#> TCGA.HW.7489.01 4 0.3828 -0.01777 0.44 0.00 0.00 0.56 0.00 0.00
#> TCGA.R8.A6YH.01 1 0.0937 0.83184 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.DU.7018.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7677.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FG.A713.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.7300.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.TM.A7CA.01 1 0.1814 0.81507 0.90 0.00 0.00 0.10 0.00 0.00
#> TCGA.HT.7690.01 1 0.0547 0.81651 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.FG.6689.01 1 0.0937 0.83184 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.DU.7007.01 4 0.3706 0.49278 0.00 0.00 0.00 0.62 0.00 0.38
#> TCGA.TQ.A7RF.01 1 0.1267 0.83004 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.DB.5277.01 6 0.3756 0.04492 0.00 0.00 0.00 0.40 0.00 0.60
#> TCGA.HT.7694.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.TM.A84M.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.F6.A8O3.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A86X.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8013.01 1 0.0937 0.80534 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.HW.7490.01 1 0.2793 0.75077 0.80 0.00 0.00 0.20 0.00 0.00
#> TCGA.QH.A65S.01 6 0.1807 0.53558 0.02 0.00 0.00 0.06 0.00 0.92
#> TCGA.DU.A76R.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.5144.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.P5.A780.01 4 0.2048 0.75547 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.HT.7606.01 4 0.5992 0.14634 0.00 0.00 0.24 0.42 0.00 0.34
#> TCGA.DB.A64V.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.RY.A840.01 2 0.3076 0.64825 0.00 0.76 0.00 0.00 0.24 0.00
#> TCGA.E1.5302.01 1 0.2631 0.66603 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.HW.A5KJ.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.A615.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8105.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.7309.01 1 0.4078 0.57461 0.64 0.02 0.00 0.34 0.00 0.00
#> TCGA.E1.A7YK.01 6 0.3578 0.23246 0.00 0.00 0.34 0.00 0.00 0.66
#> TCGA.HT.7874.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7471.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.6395.01 1 0.0937 0.83184 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.S9.A6TV.01 4 0.3864 0.28380 0.00 0.00 0.00 0.52 0.00 0.48
#> TCGA.P5.A5EW.01 1 0.0937 0.83184 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.DU.6408.01 6 0.1267 0.58629 0.06 0.00 0.00 0.00 0.00 0.94
#> TCGA.DB.A4XB.01 1 0.3828 0.03480 0.56 0.00 0.00 0.00 0.00 0.44
#> TCGA.FG.A4MT.01 1 0.2454 0.77913 0.84 0.00 0.00 0.16 0.00 0.00
#> TCGA.FG.A4MT.02 1 0.2454 0.77913 0.84 0.00 0.00 0.16 0.00 0.00
#> TCGA.HT.A619.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.QH.A870.01 1 0.0000 0.82398 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A5R9.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FG.5964.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CS.5396.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.A7TA.01 1 0.0547 0.82795 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.HW.8319.01 6 0.3869 -0.16338 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.DH.A7UR.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.TM.A84H.01 4 0.1814 0.73012 0.10 0.00 0.00 0.90 0.00 0.00
#> TCGA.S9.A6TZ.01 4 0.2260 0.68873 0.14 0.00 0.00 0.86 0.00 0.00
#> TCGA.HT.7479.01 1 0.0937 0.83184 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.DU.6400.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A6WL.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DB.A75K.01 2 0.3409 0.54430 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.DB.A4XD.01 4 0.0547 0.78846 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DB.A64Q.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.P5.A737.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5275.01 1 0.0937 0.80534 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.S9.A6WH.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7602.01 1 0.1267 0.79336 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.DU.A5TU.01 3 0.2094 0.82453 0.00 0.00 0.90 0.02 0.00 0.08
#> TCGA.HT.A5RB.01 1 0.1267 0.83020 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.HT.7616.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A7R8.01 4 0.0000 0.79430 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.QH.A6XA.01 1 0.0937 0.80534 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.HT.8111.01 1 0.3647 0.30241 0.64 0.00 0.00 0.00 0.00 0.36
#> TCGA.DU.A5TP.01 1 0.2793 0.63947 0.80 0.00 0.00 0.00 0.00 0.20
#> TCGA.RY.A83Y.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7482.01 1 0.0547 0.82896 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.TQ.A7RK.02 1 0.3828 0.39349 0.56 0.00 0.00 0.44 0.00 0.00
#> TCGA.TQ.A7RK.01 1 0.3828 0.39349 0.56 0.00 0.00 0.44 0.00 0.00
#> TCGA.HT.7858.01 1 0.3756 0.48478 0.60 0.00 0.00 0.40 0.00 0.00
#> TCGA.HT.7475.01 1 0.2454 0.69304 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.DB.A64U.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64W.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.R8.A6MO.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.A7T8.01 1 0.0937 0.83184 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.HW.8322.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5870.02 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CS.6668.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.5870.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7636.01 4 0.2941 0.69432 0.00 0.00 0.00 0.78 0.00 0.22
#> TCGA.HT.7692.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.WY.A859.01 1 0.4651 0.15436 0.48 0.00 0.00 0.48 0.00 0.04
#> TCGA.R8.A6ML.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7686.01 6 0.1807 0.51390 0.00 0.00 0.06 0.02 0.00 0.92
#> TCGA.DU.6410.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A6U9.01 1 0.3076 0.71678 0.76 0.00 0.00 0.24 0.00 0.00
#> TCGA.CS.6290.01 1 0.0937 0.80534 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.TQ.A7RO.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7019.01 4 0.0547 0.79016 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.FG.A711.01 1 0.4377 0.65775 0.72 0.00 0.00 0.12 0.00 0.16
#> TCGA.TQ.A7RM.01 3 0.4348 0.45943 0.00 0.00 0.64 0.04 0.00 0.32
#> TCGA.S9.A7R4.01 1 0.3076 0.71691 0.76 0.00 0.00 0.24 0.00 0.00
#> TCGA.E1.5318.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7676.01 1 0.0000 0.82398 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7J3.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.P5.A5F2.01 4 0.2048 0.72112 0.12 0.00 0.00 0.88 0.00 0.00
#> TCGA.E1.5304.01 3 0.0000 0.90436 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.TM.A84S.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.WY.A85B.01 1 0.1267 0.83020 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.TQ.A7RS.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7QX.01 4 0.3851 -0.09004 0.46 0.00 0.00 0.54 0.00 0.00
#> TCGA.CS.4943.01 4 0.2941 0.69432 0.00 0.00 0.00 0.78 0.00 0.22
#> TCGA.QH.A65Z.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DB.5276.01 1 0.1556 0.82434 0.92 0.00 0.00 0.08 0.00 0.00
#> TCGA.P5.A730.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84L.01 1 0.0000 0.82398 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WY.A85D.01 4 0.2454 0.73533 0.00 0.00 0.00 0.84 0.00 0.16
#> TCGA.RY.A83X.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6UB.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DB.5273.01 1 0.3864 0.24408 0.52 0.00 0.00 0.48 0.00 0.00
#> TCGA.TM.A7C4.01 1 0.0000 0.82398 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A66F.01 2 0.0547 0.95837 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.HT.7607.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.6393.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.8108.01 1 0.0937 0.83184 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.DU.7304.01 4 0.0547 0.79016 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.S9.A7IY.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7641.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A736.01 1 0.3499 0.61696 0.68 0.00 0.00 0.32 0.00 0.00
#> TCGA.P5.A5EV.01 4 0.0000 0.79430 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.7301.01 4 0.0000 0.79430 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7470.01 4 0.3797 0.42359 0.00 0.00 0.00 0.58 0.00 0.42
#> TCGA.DU.7009.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A781.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A4MY.01 4 0.3076 0.67583 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.TM.A7CF.01 1 0.3578 0.59334 0.66 0.00 0.00 0.34 0.00 0.00
#> TCGA.TM.A7CF.02 1 0.1267 0.83020 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.FG.8186.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6U6.01 1 0.1556 0.82368 0.92 0.00 0.00 0.08 0.00 0.00
#> TCGA.RY.A845.01 1 0.0000 0.82398 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7010.01 3 0.0000 0.90436 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6U2.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WN.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FG.8182.01 1 0.0000 0.82398 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6X3.01 4 0.3797 0.07626 0.42 0.00 0.00 0.58 0.00 0.00
#> TCGA.DU.6401.01 1 0.1267 0.83020 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.DU.6396.01 6 0.0547 0.54853 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.E1.A7YH.01 1 0.1267 0.83004 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.DU.7306.01 4 0.0000 0.79430 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.A74J.01 1 0.0937 0.80534 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.DH.A7US.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A87N.01 3 0.0000 0.90436 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7478.01 1 0.1556 0.77824 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.DB.A4XE.01 1 0.0000 0.82398 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64L.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.VV.A829.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.A61B.01 6 0.3797 -0.02602 0.00 0.00 0.00 0.42 0.00 0.58
#> TCGA.DH.A66B.01 4 0.1267 0.77741 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.HT.7603.01 1 0.0000 0.82398 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6397.02 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.6397.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.5853.01 1 0.3076 0.57226 0.76 0.00 0.00 0.00 0.00 0.24
#> TCGA.CS.6670.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7014.01 4 0.1814 0.76331 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.QH.A65X.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64P.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.5965.02 3 0.0000 0.90436 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.A70Y.01 1 0.0000 0.82398 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RV.01 4 0.2260 0.67816 0.14 0.00 0.00 0.86 0.00 0.00
#> TCGA.TQ.A7RV.02 4 0.2631 0.66121 0.18 0.00 0.00 0.82 0.00 0.00
#> TCGA.HT.A5R7.01 6 0.3198 0.55208 0.26 0.00 0.00 0.00 0.00 0.74
#> TCGA.HW.A5KL.01 4 0.0000 0.79430 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7474.01 1 0.0547 0.81520 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DH.A7UU.01 4 0.3309 0.63374 0.00 0.00 0.00 0.72 0.00 0.28
#> TCGA.QH.A6CZ.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A669.02 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DH.A669.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.QH.A6X9.01 4 0.2260 0.74563 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.P5.A5EZ.01 4 0.1814 0.76331 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.DU.5871.01 4 0.2631 0.63906 0.18 0.00 0.00 0.82 0.00 0.00
#> TCGA.TQ.A7RJ.01 4 0.1556 0.74819 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.WY.A858.01 1 0.0937 0.80534 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.VM.A8CB.01 2 0.0000 0.98018 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7483.01 4 0.3578 0.33594 0.34 0.00 0.00 0.66 0.00 0.00
#> TCGA.HT.7687.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.TM.A84G.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.E1.A7Z6.01 1 0.1267 0.83004 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.TM.A84I.01 6 0.3864 -0.10683 0.00 0.00 0.48 0.00 0.00 0.52
#> TCGA.CS.5394.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.A76O.01 1 0.3076 0.71691 0.76 0.00 0.00 0.24 0.00 0.00
#> TCGA.DU.A5TW.01 1 0.3706 0.52313 0.62 0.00 0.00 0.38 0.00 0.00
#> TCGA.WY.A85A.01 1 0.1814 0.75992 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.FG.5962.01 5 0.0000 0.98437 0.00 0.00 0.00 0.00 1.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.E1.5319.01 2 0.0504 0.9487 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.HT.7693.01 4 0.0000 0.6710 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CS.6665.01 3 0.3685 0.6386 0.00 0.00 0.66 0.00 0.00 0.32 0.02
#> TCGA.S9.A7J2.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.FG.A6J3.01 3 0.1166 0.8177 0.00 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.S9.A6TX.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.VM.A8C8.01 1 0.2016 0.7620 0.90 0.00 0.00 0.06 0.00 0.04 0.00
#> TCGA.HT.A74L.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DU.A5TS.01 4 0.3496 0.0163 0.00 0.00 0.00 0.58 0.00 0.00 0.42
#> TCGA.DB.A4XA.01 2 0.0000 0.9573 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A4DV.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.E1.5311.01 2 0.0504 0.9487 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.E1.A7YI.01 3 0.0000 0.8216 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5305.01 7 0.3047 0.5879 0.00 0.00 0.00 0.28 0.00 0.00 0.72
#> TCGA.F6.A8O4.01 4 0.3517 0.4661 0.28 0.00 0.00 0.70 0.00 0.00 0.02
#> TCGA.HT.8113.01 2 0.0000 0.9573 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A66G.01 7 0.5635 0.2137 0.16 0.00 0.00 0.36 0.00 0.02 0.46
#> TCGA.HT.7620.01 2 0.0000 0.9573 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A731.01 1 0.3139 0.5095 0.70 0.00 0.00 0.00 0.00 0.30 0.00
#> TCGA.HT.7480.01 2 0.1671 0.8632 0.00 0.90 0.00 0.00 0.10 0.00 0.00
#> TCGA.HT.7689.01 7 0.3417 0.5934 0.00 0.00 0.00 0.26 0.00 0.02 0.72
#> TCGA.HT.8109.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.E1.A7YE.01 3 0.0504 0.8218 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.S9.A7R1.01 5 0.1886 0.8383 0.00 0.12 0.00 0.00 0.88 0.00 0.00
#> TCGA.FG.A710.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.S9.A7J0.01 7 0.2745 0.6097 0.00 0.00 0.00 0.16 0.00 0.02 0.82
#> TCGA.DU.A6S6.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.HT.7877.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.QH.A6CU.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.HW.7486.01 2 0.0000 0.9573 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7634.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DU.8163.01 1 0.1664 0.7627 0.92 0.00 0.00 0.06 0.00 0.02 0.00
#> TCGA.DU.6407.02 3 0.2081 0.7813 0.00 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.DU.6407.01 4 0.1671 0.6178 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.HT.8010.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.P5.A5F1.01 1 0.3289 0.7205 0.82 0.00 0.00 0.10 0.00 0.02 0.06
#> TCGA.VM.A8CF.01 7 0.3685 0.5454 0.00 0.00 0.00 0.32 0.00 0.02 0.66
#> TCGA.DU.6542.01 1 0.1928 0.7594 0.90 0.00 0.00 0.08 0.00 0.00 0.02
#> TCGA.FG.7638.01 2 0.0000 0.9573 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.5143.01 1 0.4778 0.3406 0.58 0.00 0.00 0.34 0.00 0.02 0.06
#> TCGA.DU.7299.01 7 0.4269 0.5026 0.02 0.00 0.00 0.36 0.00 0.02 0.60
#> TCGA.CS.5393.01 7 0.3606 0.5628 0.00 0.00 0.00 0.30 0.00 0.02 0.68
#> TCGA.DU.7011.01 1 0.3011 0.7110 0.82 0.00 0.00 0.06 0.00 0.12 0.00
#> TCGA.TM.A84Q.01 1 0.3459 0.4849 0.60 0.00 0.00 0.40 0.00 0.00 0.00
#> TCGA.DB.5281.01 4 0.3770 0.6060 0.18 0.00 0.00 0.74 0.00 0.00 0.08
#> TCGA.HT.7605.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.FG.A6J1.01 2 0.0000 0.9573 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5270.01 1 0.2945 0.5699 0.74 0.00 0.00 0.00 0.00 0.26 0.00
#> TCGA.S9.A6WQ.01 1 0.1664 0.7605 0.92 0.00 0.00 0.06 0.00 0.00 0.02
#> TCGA.HT.8106.01 6 0.1006 0.5557 0.02 0.00 0.00 0.00 0.00 0.96 0.02
#> TCGA.HT.7608.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.E1.A7YU.01 7 0.1363 0.5431 0.00 0.00 0.02 0.04 0.00 0.00 0.94
#> TCGA.W9.A837.01 2 0.0504 0.9487 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.TM.A7C5.01 2 0.2259 0.7809 0.00 0.84 0.00 0.00 0.16 0.00 0.00
#> TCGA.S9.A7QY.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.QH.A6CW.01 4 0.4015 0.3886 0.06 0.00 0.00 0.68 0.00 0.00 0.26
#> TCGA.S9.A6WO.01 1 0.2376 0.7475 0.86 0.00 0.00 0.12 0.00 0.00 0.02
#> TCGA.IK.7675.01 7 0.4640 0.1287 0.00 0.00 0.18 0.00 0.00 0.18 0.64
#> TCGA.HT.7601.01 6 0.2803 0.5525 0.06 0.00 0.00 0.00 0.00 0.84 0.10
#> TCGA.P5.A5ET.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.HT.7472.01 1 0.2912 0.7159 0.82 0.00 0.00 0.14 0.00 0.00 0.04
#> TCGA.HT.7880.01 1 0.3358 0.3972 0.64 0.00 0.00 0.00 0.00 0.36 0.00
#> TCGA.E1.A7Z3.01 1 0.3985 0.3615 0.52 0.00 0.00 0.46 0.00 0.02 0.00
#> TCGA.P5.A77X.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.FG.A6IZ.01 5 0.0000 0.9700 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7873.01 7 0.4338 0.2183 0.08 0.00 0.00 0.00 0.00 0.28 0.64
#> TCGA.CS.4938.01 1 0.1664 0.7605 0.92 0.00 0.00 0.06 0.00 0.00 0.02
#> TCGA.KT.A74X.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.P5.A5EX.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.VM.A8CH.01 1 0.3606 0.6451 0.68 0.00 0.00 0.30 0.00 0.02 0.00
#> TCGA.HT.7476.01 4 0.0504 0.6748 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.DB.A75L.01 4 0.3927 0.3078 0.04 0.00 0.00 0.66 0.00 0.00 0.30
#> TCGA.HT.8563.01 6 0.4787 -0.1043 0.00 0.00 0.00 0.12 0.00 0.58 0.30
#> TCGA.RY.A843.01 1 0.4429 0.6195 0.66 0.00 0.00 0.12 0.00 0.22 0.00
#> TCGA.S9.A7IS.01 3 0.1433 0.8122 0.00 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.TQ.A8XE.02 7 0.4386 0.3055 0.02 0.00 0.00 0.42 0.00 0.02 0.54
#> TCGA.E1.A7YO.01 5 0.3139 0.5338 0.00 0.30 0.00 0.00 0.70 0.00 0.00
#> TCGA.TQ.A7RG.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.QH.A6X5.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.HW.7493.01 1 0.1664 0.7627 0.92 0.00 0.00 0.06 0.00 0.02 0.00
#> TCGA.RY.A847.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DU.8166.01 1 0.0863 0.7631 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.VM.A8CA.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.HT.7855.01 4 0.0504 0.6748 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.S9.A89Z.01 7 0.4243 0.5907 0.00 0.00 0.10 0.22 0.00 0.00 0.68
#> TCGA.DB.A4XG.01 2 0.3294 0.4837 0.00 0.66 0.00 0.00 0.34 0.00 0.00
#> TCGA.DH.A7UT.01 6 0.3606 0.5355 0.30 0.00 0.00 0.00 0.00 0.68 0.02
#> TCGA.DU.7015.01 1 0.3685 0.5330 0.66 0.00 0.00 0.32 0.00 0.00 0.02
#> TCGA.HT.A616.01 4 0.4505 -0.0863 0.06 0.00 0.00 0.50 0.00 0.00 0.44
#> TCGA.HT.7611.01 4 0.0504 0.6748 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.HT.8018.01 6 0.1433 0.6139 0.08 0.00 0.00 0.00 0.00 0.92 0.00
#> TCGA.FG.A60K.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.HT.7856.01 2 0.0000 0.9573 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5851.01 6 0.3943 0.2870 0.42 0.00 0.00 0.00 0.00 0.56 0.02
#> TCGA.DU.A7T6.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.S9.A6TY.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.WY.A85C.01 4 0.0504 0.6748 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.DB.A4XC.01 1 0.2016 0.7087 0.90 0.00 0.00 0.00 0.00 0.04 0.06
#> TCGA.TM.A84O.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.P5.A72W.01 1 0.1363 0.7382 0.94 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.S9.A6TU.01 4 0.0504 0.6748 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.HT.A61A.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DU.5855.01 4 0.3745 0.4003 0.04 0.00 0.00 0.70 0.00 0.00 0.26
#> TCGA.HT.7884.01 1 0.3968 0.3373 0.54 0.00 0.00 0.44 0.00 0.00 0.02
#> TCGA.TQ.A7RQ.01 2 0.0504 0.9487 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.IK.8125.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.HT.A74K.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.WH.A86K.01 7 0.4146 0.5055 0.02 0.00 0.00 0.32 0.00 0.02 0.64
#> TCGA.QH.A6X8.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.WY.A85E.01 4 0.4461 0.2525 0.40 0.00 0.00 0.54 0.00 0.00 0.06
#> TCGA.HT.A5R5.01 1 0.2945 0.5699 0.74 0.00 0.00 0.00 0.00 0.26 0.00
#> TCGA.HT.A618.01 3 0.3815 0.5980 0.00 0.00 0.62 0.00 0.00 0.36 0.02
#> TCGA.FG.6691.01 1 0.3058 0.7233 0.82 0.00 0.00 0.08 0.00 0.10 0.00
#> TCGA.HT.7467.01 2 0.0000 0.9573 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7R3.01 4 0.5451 0.3318 0.28 0.00 0.00 0.54 0.00 0.02 0.16
#> TCGA.FG.A4MX.01 1 0.2163 0.7549 0.88 0.00 0.00 0.10 0.00 0.00 0.02
#> TCGA.HT.7681.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.S9.A7IZ.01 1 0.5483 0.0349 0.50 0.00 0.00 0.02 0.00 0.14 0.34
#> TCGA.DU.A6S7.01 4 0.0504 0.6748 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.P5.A72Z.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.HT.8114.01 1 0.3985 0.1800 0.52 0.00 0.00 0.46 0.00 0.00 0.02
#> TCGA.DU.8168.01 5 0.0000 0.9700 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HW.8321.01 1 0.3927 0.6367 0.66 0.00 0.00 0.30 0.00 0.04 0.00
#> TCGA.TQ.A7RN.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DH.5141.01 2 0.0504 0.9487 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.EZ.7264.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.P5.A5F4.01 1 0.3909 0.5061 0.58 0.00 0.00 0.40 0.00 0.02 0.00
#> TCGA.QH.A65V.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.FG.8191.01 1 0.2016 0.7620 0.90 0.00 0.00 0.06 0.00 0.04 0.00
#> TCGA.DH.5142.01 7 0.5128 -0.0142 0.16 0.00 0.00 0.00 0.00 0.32 0.52
#> TCGA.DU.A6S8.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.E1.A7YW.01 1 0.2159 0.7596 0.90 0.00 0.00 0.06 0.00 0.02 0.02
#> TCGA.CS.6666.01 4 0.0000 0.6710 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7298.01 2 0.1363 0.9195 0.00 0.94 0.00 0.02 0.04 0.00 0.00
#> TCGA.DB.A64R.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.FG.A60L.01 4 0.2163 0.6467 0.10 0.00 0.00 0.88 0.00 0.00 0.02
#> TCGA.CS.5390.01 5 0.0000 0.9700 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6WP.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DB.5280.01 1 0.2159 0.7631 0.90 0.00 0.00 0.06 0.00 0.02 0.02
#> TCGA.TM.A84T.01 1 0.1664 0.7272 0.92 0.00 0.00 0.00 0.00 0.06 0.02
#> TCGA.DH.A66D.01 1 0.1664 0.7605 0.92 0.00 0.00 0.06 0.00 0.00 0.02
#> TCGA.RY.A83Z.01 3 0.0863 0.8175 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.DB.5278.01 2 0.0863 0.9454 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.TQ.A7RR.01 7 0.5002 -0.1042 0.12 0.00 0.00 0.00 0.00 0.40 0.48
#> TCGA.TQ.A7RH.01 1 0.3221 0.4419 0.68 0.00 0.00 0.00 0.00 0.32 0.00
#> TCGA.E1.A7YS.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.P5.A735.01 1 0.1664 0.7605 0.92 0.00 0.00 0.06 0.00 0.00 0.02
#> TCGA.DU.7294.01 5 0.3139 0.5336 0.00 0.30 0.00 0.00 0.70 0.00 0.00
#> TCGA.HT.7881.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.HT.7695.01 2 0.0000 0.9573 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A5EU.01 6 0.4939 0.1215 0.02 0.00 0.20 0.00 0.00 0.64 0.14
#> TCGA.DB.A64X.01 7 0.4121 0.5891 0.00 0.00 0.10 0.20 0.00 0.00 0.70
#> TCGA.FG.7637.01 2 0.0000 0.9573 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8CE.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.S9.A6U5.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.HT.7609.01 1 0.2906 0.7310 0.80 0.00 0.00 0.18 0.00 0.02 0.00
#> TCGA.DB.5274.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.HW.7487.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.HW.7491.01 5 0.0863 0.9454 0.00 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.CS.4944.01 4 0.4107 0.4243 0.02 0.00 0.00 0.70 0.00 0.04 0.24
#> TCGA.DU.A6S2.01 2 0.0000 0.9573 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7R7.01 6 0.1671 0.6133 0.10 0.00 0.00 0.00 0.00 0.90 0.00
#> TCGA.TM.A84R.01 2 0.0000 0.9573 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A75M.01 4 0.3186 0.5912 0.22 0.00 0.00 0.76 0.00 0.00 0.02
#> TCGA.HW.A5KM.01 4 0.1664 0.6671 0.06 0.00 0.00 0.92 0.00 0.00 0.02
#> TCGA.HT.7477.01 7 0.5485 -0.1797 0.00 0.00 0.22 0.00 0.00 0.38 0.40
#> TCGA.HT.8012.01 2 0.0504 0.9487 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DU.8167.01 4 0.1166 0.6450 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.S9.A6U1.01 1 0.3927 0.6367 0.66 0.00 0.00 0.30 0.00 0.04 0.00
#> TCGA.FG.5965.01 6 0.4478 0.5696 0.20 0.00 0.00 0.00 0.00 0.66 0.14
#> TCGA.FG.8187.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.HT.A614.01 7 0.5240 0.1775 0.14 0.00 0.00 0.02 0.00 0.26 0.58
#> TCGA.S9.A7QZ.01 5 0.0000 0.9700 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.QH.A6X4.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.P5.A77W.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DU.7302.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DU.6399.01 4 0.2832 0.4427 0.00 0.00 0.00 0.76 0.00 0.00 0.24
#> TCGA.E1.5307.01 7 0.3558 0.2416 0.00 0.00 0.00 0.48 0.00 0.00 0.52
#> TCGA.S9.A7QW.01 1 0.1664 0.7324 0.92 0.00 0.00 0.00 0.00 0.06 0.02
#> TCGA.HT.7604.01 4 0.0504 0.6748 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.P5.A733.01 4 0.3186 0.5909 0.22 0.00 0.00 0.76 0.00 0.00 0.02
#> TCGA.HT.7684.01 1 0.4977 0.0523 0.50 0.00 0.00 0.04 0.00 0.42 0.04
#> TCGA.HW.7495.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.QH.A65R.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DU.A7TG.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DH.A7UV.01 4 0.0863 0.6547 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.HT.7879.01 4 0.3815 0.2532 0.36 0.00 0.00 0.62 0.00 0.00 0.02
#> TCGA.TM.A84F.01 6 0.1433 0.6139 0.08 0.00 0.00 0.00 0.00 0.92 0.00
#> TCGA.DU.A7TC.01 4 0.2259 0.6155 0.16 0.00 0.00 0.84 0.00 0.00 0.00
#> TCGA.HT.7610.01 1 0.3517 0.6611 0.70 0.00 0.00 0.28 0.00 0.02 0.00
#> TCGA.S9.A6TW.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.FG.A60J.01 1 0.2163 0.7566 0.88 0.00 0.00 0.10 0.00 0.00 0.02
#> TCGA.E1.5303.01 4 0.5240 0.3510 0.14 0.00 0.00 0.58 0.00 0.02 0.26
#> TCGA.HT.7481.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.FN.7833.01 1 0.1363 0.7382 0.94 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.E1.A7Z4.01 1 0.1664 0.7605 0.92 0.00 0.00 0.06 0.00 0.00 0.02
#> TCGA.DU.A5TR.01 4 0.0000 0.6710 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7875.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.HT.7473.01 1 0.1363 0.7479 0.94 0.00 0.00 0.02 0.00 0.04 0.00
#> TCGA.S9.A7IQ.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DU.7008.01 1 0.3994 0.2835 0.50 0.00 0.00 0.48 0.00 0.00 0.02
#> TCGA.S9.A6WG.01 1 0.3047 0.5451 0.72 0.00 0.00 0.00 0.00 0.28 0.00
#> TCGA.DB.A75O.01 1 0.3294 0.4408 0.66 0.00 0.00 0.00 0.00 0.34 0.00
#> TCGA.HT.7688.01 4 0.3358 0.2022 0.00 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.DU.7304.02 3 0.2081 0.7813 0.00 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.DU.6394.01 5 0.0000 0.9700 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6WD.01 5 0.0000 0.9700 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.5872.01 1 0.2572 0.6131 0.80 0.00 0.00 0.00 0.00 0.20 0.00
#> TCGA.FG.8185.01 4 0.0504 0.6748 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.HT.7902.01 6 0.1671 0.6104 0.10 0.00 0.00 0.00 0.00 0.90 0.00
#> TCGA.TQ.A7RU.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DU.5874.01 5 0.0000 0.9700 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6WE.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.FG.6690.01 4 0.0863 0.6592 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.HW.8320.01 4 0.0000 0.6710 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.R8.A6MK.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.QH.A6CY.01 2 0.0000 0.9573 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7J1.01 2 0.1166 0.9116 0.00 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.P5.A72X.01 1 0.1363 0.7497 0.94 0.00 0.00 0.02 0.00 0.04 0.00
#> TCGA.E1.5322.01 1 0.4538 0.5189 0.62 0.00 0.00 0.28 0.00 0.00 0.10
#> TCGA.P5.A5F0.01 2 0.0863 0.9326 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.R8.A73M.01 2 0.3221 0.5202 0.00 0.68 0.00 0.00 0.32 0.00 0.00
#> TCGA.CS.4942.01 1 0.1664 0.7272 0.92 0.00 0.00 0.00 0.00 0.06 0.02
#> TCGA.DB.A4X9.01 1 0.1505 0.7488 0.94 0.00 0.00 0.02 0.00 0.02 0.02
#> TCGA.DB.A4XF.01 4 0.0504 0.6748 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.HT.A74O.01 4 0.1433 0.6333 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.FG.8188.01 4 0.3413 0.1473 0.00 0.00 0.00 0.62 0.00 0.00 0.38
#> TCGA.DU.A6S3.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DB.A4XH.01 5 0.0000 0.9700 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7485.01 1 0.3630 0.7211 0.80 0.00 0.00 0.10 0.00 0.04 0.06
#> TCGA.VW.A7QS.01 5 0.2081 0.8080 0.00 0.14 0.00 0.00 0.86 0.00 0.00
#> TCGA.S9.A6WI.01 2 0.0000 0.9573 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.8164.01 5 0.0000 0.9700 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6TS.01 7 0.2832 0.6195 0.00 0.00 0.00 0.24 0.00 0.00 0.76
#> TCGA.DB.A64S.01 1 0.3927 0.6367 0.66 0.00 0.00 0.30 0.00 0.04 0.00
#> TCGA.VV.A86M.01 4 0.3199 0.5882 0.06 0.00 0.00 0.80 0.00 0.00 0.14
#> TCGA.TQ.A8XE.01 4 0.5085 0.3429 0.12 0.00 0.00 0.60 0.00 0.02 0.26
#> TCGA.CS.6667.01 4 0.3815 0.2228 0.36 0.00 0.00 0.62 0.00 0.00 0.02
#> TCGA.E1.A7YV.01 3 0.0863 0.8175 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.TQ.A7RW.01 7 0.4901 0.3320 0.06 0.00 0.00 0.40 0.00 0.02 0.52
#> TCGA.DU.5849.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DU.A7TI.01 1 0.4127 0.4262 0.60 0.00 0.00 0.36 0.00 0.00 0.04
#> TCGA.HT.7468.01 2 0.2708 0.6903 0.00 0.78 0.00 0.00 0.22 0.00 0.00
#> TCGA.TQ.A7RI.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DB.5279.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.S9.A6U8.01 1 0.3546 0.3782 0.54 0.00 0.00 0.46 0.00 0.00 0.00
#> TCGA.HW.7489.01 4 0.2259 0.6196 0.16 0.00 0.00 0.84 0.00 0.00 0.00
#> TCGA.R8.A6YH.01 1 0.1166 0.7631 0.94 0.00 0.00 0.06 0.00 0.00 0.00
#> TCGA.DU.7018.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.HT.7677.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.FG.A713.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DU.7300.01 5 0.0000 0.9700 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.TM.A7CA.01 1 0.2906 0.7177 0.80 0.00 0.00 0.18 0.00 0.00 0.02
#> TCGA.HT.7690.01 1 0.1433 0.7122 0.92 0.00 0.00 0.00 0.00 0.08 0.00
#> TCGA.FG.6689.01 1 0.2159 0.7596 0.90 0.00 0.00 0.06 0.00 0.02 0.02
#> TCGA.DU.7007.01 7 0.2016 0.5533 0.00 0.00 0.00 0.06 0.00 0.04 0.90
#> TCGA.TQ.A7RF.01 1 0.1664 0.7605 0.92 0.00 0.00 0.06 0.00 0.00 0.02
#> TCGA.DB.5277.01 7 0.2213 0.5393 0.00 0.00 0.02 0.04 0.00 0.04 0.90
#> TCGA.HT.7694.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.TM.A84M.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.F6.A8O3.01 2 0.0000 0.9573 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A86X.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.HT.8013.01 1 0.2163 0.6999 0.88 0.00 0.00 0.00 0.00 0.10 0.02
#> TCGA.HW.7490.01 1 0.3186 0.6923 0.76 0.00 0.00 0.22 0.00 0.00 0.02
#> TCGA.QH.A65S.01 7 0.5604 0.0960 0.20 0.00 0.00 0.02 0.00 0.26 0.52
#> TCGA.DU.A76R.01 2 0.0504 0.9487 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DH.5144.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.P5.A780.01 4 0.3221 0.2975 0.00 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.HT.7606.01 7 0.3284 0.5464 0.00 0.00 0.10 0.10 0.00 0.00 0.80
#> TCGA.DB.A64V.01 5 0.0000 0.9700 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.RY.A840.01 2 0.2832 0.6542 0.00 0.76 0.00 0.00 0.24 0.00 0.00
#> TCGA.E1.5302.01 1 0.3221 0.4419 0.68 0.00 0.00 0.00 0.00 0.32 0.00
#> TCGA.HW.A5KJ.01 5 0.0000 0.9700 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.A615.01 2 0.0504 0.9487 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.HT.8105.01 5 0.0000 0.9700 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.7309.01 4 0.3887 0.4461 0.26 0.02 0.00 0.70 0.00 0.02 0.00
#> TCGA.E1.A7YK.01 6 0.5233 -0.1751 0.00 0.00 0.28 0.00 0.00 0.52 0.20
#> TCGA.HT.7874.01 2 0.0504 0.9487 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.HT.7471.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DU.6395.01 1 0.1363 0.7610 0.94 0.00 0.00 0.04 0.00 0.02 0.00
#> TCGA.S9.A6TV.01 7 0.1664 0.5635 0.00 0.00 0.00 0.06 0.00 0.02 0.92
#> TCGA.P5.A5EW.01 1 0.1664 0.7605 0.92 0.00 0.00 0.06 0.00 0.00 0.02
#> TCGA.DU.6408.01 7 0.5065 0.1883 0.10 0.00 0.00 0.02 0.00 0.30 0.58
#> TCGA.DB.A4XB.01 6 0.4426 0.3652 0.38 0.00 0.00 0.00 0.00 0.56 0.06
#> TCGA.FG.A4MT.01 1 0.3685 0.6151 0.66 0.00 0.00 0.32 0.00 0.00 0.02
#> TCGA.FG.A4MT.02 1 0.3755 0.6022 0.64 0.00 0.00 0.34 0.00 0.02 0.00
#> TCGA.HT.A619.01 5 0.0000 0.9700 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.QH.A870.01 1 0.1860 0.7491 0.92 0.00 0.00 0.02 0.00 0.04 0.02
#> TCGA.HT.A5R9.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.FG.5964.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.CS.5396.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DU.A7TA.01 1 0.3911 0.6592 0.70 0.00 0.00 0.24 0.00 0.06 0.00
#> TCGA.HW.8319.01 3 0.5128 0.4968 0.00 0.00 0.52 0.00 0.00 0.32 0.16
#> TCGA.DH.A7UR.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.TM.A84H.01 4 0.4309 0.5306 0.20 0.00 0.00 0.68 0.00 0.00 0.12
#> TCGA.S9.A6TZ.01 4 0.1006 0.6729 0.02 0.00 0.00 0.96 0.00 0.00 0.02
#> TCGA.HT.7479.01 1 0.2722 0.7466 0.84 0.00 0.00 0.12 0.00 0.04 0.00
#> TCGA.DU.6400.01 5 0.0000 0.9700 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6WL.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DB.A75K.01 2 0.3358 0.4447 0.00 0.64 0.00 0.00 0.36 0.00 0.00
#> TCGA.DB.A4XD.01 4 0.0504 0.6748 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.DB.A64Q.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.P5.A737.01 2 0.0504 0.9487 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DB.5275.01 1 0.1664 0.7410 0.92 0.00 0.00 0.02 0.00 0.06 0.00
#> TCGA.S9.A6WH.01 5 0.0000 0.9700 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7602.01 1 0.3139 0.5159 0.70 0.00 0.00 0.00 0.00 0.30 0.00
#> TCGA.DU.A5TU.01 3 0.3413 0.5171 0.00 0.00 0.62 0.00 0.00 0.00 0.38
#> TCGA.HT.A5RB.01 1 0.2163 0.7605 0.88 0.00 0.00 0.10 0.00 0.00 0.02
#> TCGA.HT.7616.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.S9.A7R8.01 4 0.2259 0.5658 0.00 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.QH.A6XA.01 1 0.1363 0.7287 0.94 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.HT.8111.01 6 0.3496 0.3328 0.42 0.00 0.00 0.00 0.00 0.58 0.00
#> TCGA.DU.A5TP.01 1 0.3294 0.3985 0.66 0.00 0.00 0.00 0.00 0.34 0.00
#> TCGA.RY.A83Y.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.HT.7482.01 1 0.1928 0.7613 0.90 0.00 0.00 0.08 0.00 0.02 0.00
#> TCGA.TQ.A7RK.02 4 0.2708 0.5717 0.22 0.00 0.00 0.78 0.00 0.00 0.00
#> TCGA.TQ.A7RK.01 4 0.2708 0.5717 0.22 0.00 0.00 0.78 0.00 0.00 0.00
#> TCGA.HT.7858.01 4 0.2832 0.5441 0.24 0.00 0.00 0.76 0.00 0.00 0.00
#> TCGA.HT.7475.01 1 0.3139 0.4771 0.70 0.00 0.00 0.00 0.00 0.30 0.00
#> TCGA.DB.A64U.01 2 0.0000 0.9573 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64W.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.R8.A6MO.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DU.A7T8.01 1 0.1363 0.7603 0.94 0.00 0.00 0.04 0.00 0.00 0.02
#> TCGA.HW.8322.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DU.5870.02 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.CS.6668.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DU.5870.01 2 0.0863 0.9321 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.FG.7636.01 7 0.4278 0.2067 0.04 0.00 0.00 0.46 0.00 0.00 0.50
#> TCGA.HT.7692.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.WY.A859.01 1 0.5545 0.2784 0.48 0.00 0.00 0.38 0.00 0.04 0.10
#> TCGA.R8.A6ML.01 5 0.0000 0.9700 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7686.01 7 0.4283 -0.0342 0.00 0.00 0.04 0.00 0.00 0.48 0.48
#> TCGA.DU.6410.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.S9.A6U9.01 4 0.3558 -0.2202 0.48 0.00 0.00 0.52 0.00 0.00 0.00
#> TCGA.CS.6290.01 1 0.2313 0.7181 0.88 0.00 0.00 0.00 0.00 0.06 0.06
#> TCGA.TQ.A7RO.01 2 0.0000 0.9573 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7019.01 4 0.2259 0.5480 0.00 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.FG.A711.01 1 0.4773 0.4080 0.66 0.00 0.00 0.02 0.00 0.12 0.20
#> TCGA.TQ.A7RM.01 7 0.4269 -0.0454 0.00 0.00 0.36 0.02 0.00 0.02 0.60
#> TCGA.S9.A7R4.01 1 0.3685 0.5546 0.66 0.00 0.00 0.32 0.00 0.00 0.02
#> TCGA.E1.5318.01 5 0.0000 0.9700 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7676.01 1 0.1006 0.7387 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.S9.A7J3.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.P5.A5F2.01 4 0.5513 0.3010 0.30 0.00 0.00 0.52 0.00 0.02 0.16
#> TCGA.E1.5304.01 3 0.2081 0.7837 0.00 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.TM.A84S.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.WY.A85B.01 1 0.3606 0.6451 0.68 0.00 0.00 0.30 0.00 0.02 0.00
#> TCGA.TQ.A7RS.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.S9.A7QX.01 4 0.4244 0.1909 0.42 0.00 0.00 0.54 0.00 0.00 0.04
#> TCGA.CS.4943.01 7 0.4264 0.5020 0.06 0.00 0.00 0.32 0.00 0.00 0.62
#> TCGA.QH.A65Z.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DB.5276.01 1 0.4998 0.5069 0.54 0.00 0.00 0.32 0.00 0.14 0.00
#> TCGA.P5.A730.01 2 0.0000 0.9573 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84L.01 1 0.2016 0.7620 0.90 0.00 0.00 0.06 0.00 0.04 0.00
#> TCGA.WY.A85D.01 4 0.3525 -0.0581 0.00 0.00 0.00 0.56 0.00 0.00 0.44
#> TCGA.RY.A83X.01 2 0.0504 0.9487 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.S9.A6UB.01 5 0.0000 0.9700 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DB.5273.01 1 0.4610 0.5642 0.66 0.00 0.00 0.24 0.00 0.02 0.08
#> TCGA.TM.A7C4.01 1 0.2722 0.7261 0.84 0.00 0.00 0.04 0.00 0.12 0.00
#> TCGA.DH.A66F.01 2 0.1671 0.8639 0.00 0.90 0.00 0.00 0.10 0.00 0.00
#> TCGA.HT.7607.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DU.6393.01 5 0.0000 0.9700 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.8108.01 1 0.1664 0.7605 0.92 0.00 0.00 0.06 0.00 0.00 0.02
#> TCGA.DU.7304.01 4 0.2259 0.5480 0.00 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.S9.A7IY.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.FG.7641.01 2 0.0504 0.9487 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.P5.A736.01 1 0.4264 0.6066 0.70 0.00 0.00 0.22 0.00 0.02 0.06
#> TCGA.P5.A5EV.01 4 0.2081 0.5842 0.00 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.DU.7301.01 4 0.1166 0.6462 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.HT.7470.01 7 0.3911 0.6272 0.00 0.00 0.00 0.24 0.00 0.06 0.70
#> TCGA.DU.7009.01 2 0.0000 0.9573 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A781.01 2 0.0504 0.9487 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.FG.A4MY.01 7 0.3867 0.4608 0.00 0.00 0.00 0.38 0.00 0.02 0.60
#> TCGA.TM.A7CF.01 1 0.3755 0.5111 0.64 0.00 0.00 0.34 0.00 0.00 0.02
#> TCGA.TM.A7CF.02 1 0.3244 0.7257 0.78 0.00 0.00 0.18 0.00 0.04 0.00
#> TCGA.FG.8186.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.S9.A6U6.01 1 0.2745 0.7387 0.82 0.00 0.00 0.16 0.00 0.02 0.00
#> TCGA.RY.A845.01 1 0.1664 0.7418 0.92 0.00 0.00 0.02 0.00 0.06 0.00
#> TCGA.DU.7010.01 3 0.0000 0.8216 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6U2.01 2 0.0000 0.9573 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WN.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.FG.8182.01 1 0.2422 0.6551 0.82 0.00 0.00 0.00 0.00 0.18 0.00
#> TCGA.QH.A6X3.01 4 0.3186 0.5855 0.22 0.00 0.00 0.76 0.00 0.00 0.02
#> TCGA.DU.6401.01 1 0.3927 0.6367 0.66 0.00 0.00 0.30 0.00 0.04 0.00
#> TCGA.DU.6396.01 6 0.4710 0.0384 0.02 0.00 0.04 0.00 0.00 0.48 0.46
#> TCGA.E1.A7YH.01 1 0.1664 0.7627 0.92 0.00 0.00 0.06 0.00 0.02 0.00
#> TCGA.DU.7306.01 4 0.3011 0.6108 0.06 0.00 0.00 0.82 0.00 0.00 0.12
#> TCGA.HT.A74J.01 1 0.1718 0.7212 0.92 0.00 0.00 0.00 0.00 0.04 0.04
#> TCGA.DH.A7US.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.FG.A87N.01 3 0.0504 0.8218 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.HT.7478.01 1 0.2572 0.6170 0.80 0.00 0.00 0.00 0.00 0.20 0.00
#> TCGA.DB.A4XE.01 1 0.2016 0.7564 0.90 0.00 0.00 0.06 0.00 0.04 0.00
#> TCGA.DB.A64L.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.VV.A829.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.HT.A61B.01 7 0.3114 0.5189 0.04 0.00 0.00 0.04 0.00 0.08 0.84
#> TCGA.DH.A66B.01 4 0.3139 0.3395 0.00 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.HT.7603.01 1 0.2722 0.7294 0.84 0.00 0.00 0.04 0.00 0.12 0.00
#> TCGA.DU.6397.02 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DU.6397.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DU.5853.01 1 0.3244 0.6084 0.78 0.00 0.00 0.00 0.00 0.18 0.04
#> TCGA.CS.6670.01 2 0.0504 0.9487 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DU.7014.01 4 0.3294 0.2504 0.00 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.QH.A65X.01 2 0.0504 0.9487 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DB.A64P.01 2 0.0504 0.9487 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.FG.5965.02 3 0.1886 0.7921 0.00 0.00 0.88 0.00 0.00 0.12 0.00
#> TCGA.FG.A70Y.01 1 0.2829 0.7400 0.84 0.00 0.00 0.08 0.00 0.08 0.00
#> TCGA.TQ.A7RV.01 4 0.3541 0.6019 0.08 0.00 0.00 0.80 0.00 0.02 0.10
#> TCGA.TQ.A7RV.02 4 0.5190 0.4324 0.14 0.00 0.00 0.66 0.00 0.10 0.10
#> TCGA.HT.A5R7.01 6 0.1664 0.6010 0.06 0.00 0.00 0.00 0.00 0.92 0.02
#> TCGA.HW.A5KL.01 4 0.0000 0.6710 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7474.01 1 0.3386 0.6923 0.78 0.00 0.00 0.02 0.00 0.18 0.02
#> TCGA.DH.A7UU.01 7 0.3221 0.5541 0.00 0.00 0.00 0.32 0.00 0.00 0.68
#> TCGA.QH.A6CZ.01 2 0.0504 0.9487 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DH.A669.02 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DH.A669.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.QH.A6X9.01 4 0.3496 0.0187 0.00 0.00 0.00 0.58 0.00 0.00 0.42
#> TCGA.P5.A5EZ.01 4 0.3294 0.2562 0.00 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.DU.5871.01 4 0.2376 0.6342 0.12 0.00 0.00 0.86 0.00 0.00 0.02
#> TCGA.TQ.A7RJ.01 4 0.1006 0.6729 0.02 0.00 0.00 0.96 0.00 0.00 0.02
#> TCGA.WY.A858.01 1 0.1363 0.7287 0.94 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.VM.A8CB.01 2 0.0504 0.9589 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.HT.7483.01 4 0.2745 0.6152 0.16 0.00 0.00 0.82 0.00 0.00 0.02
#> TCGA.HT.7687.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.TM.A84G.01 5 0.0000 0.9700 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.E1.A7Z6.01 1 0.1664 0.7605 0.92 0.00 0.00 0.06 0.00 0.00 0.02
#> TCGA.TM.A84I.01 3 0.5338 0.4349 0.00 0.00 0.48 0.00 0.00 0.32 0.20
#> TCGA.CS.5394.01 5 0.0504 0.9651 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DU.A76O.01 1 0.3294 0.5876 0.66 0.00 0.00 0.34 0.00 0.00 0.00
#> TCGA.DU.A5TW.01 4 0.3909 0.1734 0.40 0.00 0.00 0.58 0.00 0.00 0.02
#> TCGA.WY.A85A.01 1 0.3221 0.4419 0.68 0.00 0.00 0.00 0.00 0.32 0.00
#> TCGA.FG.5962.01 5 0.0504 0.9669 0.00 0.00 0.00 0.00 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.E1.5319.01 2 0.2725 0.77929 0.00 0.82 0.00 0.00 0.14 0.00 0.00 0.04
#> TCGA.HT.7693.01 4 0.0471 0.64517 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CS.6665.01 6 0.3992 -0.08236 0.00 0.00 0.44 0.00 0.00 0.52 0.00 0.04
#> TCGA.S9.A7J2.01 2 0.1557 0.87823 0.00 0.92 0.00 0.00 0.00 0.06 0.00 0.02
#> TCGA.FG.A6J3.01 3 0.3036 0.72335 0.00 0.00 0.78 0.00 0.00 0.18 0.00 0.04
#> TCGA.S9.A6TX.01 5 0.1887 0.86312 0.00 0.06 0.00 0.00 0.90 0.00 0.00 0.04
#> TCGA.VM.A8C8.01 1 0.1091 0.61228 0.94 0.00 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.HT.A74L.01 2 0.1275 0.88051 0.00 0.94 0.00 0.00 0.00 0.04 0.00 0.02
#> TCGA.DU.A5TS.01 4 0.3570 0.21254 0.00 0.00 0.00 0.62 0.00 0.00 0.36 0.02
#> TCGA.DB.A4XA.01 2 0.0808 0.87165 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.HT.A4DV.01 2 0.1887 0.87360 0.00 0.90 0.00 0.00 0.00 0.06 0.00 0.04
#> TCGA.E1.5311.01 2 0.2725 0.77929 0.00 0.82 0.00 0.00 0.14 0.00 0.00 0.04
#> TCGA.E1.A7YI.01 3 0.0471 0.82973 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.E1.5305.01 7 0.3198 0.57181 0.00 0.00 0.00 0.26 0.00 0.00 0.72 0.02
#> TCGA.F6.A8O4.01 4 0.4480 0.26814 0.30 0.00 0.00 0.58 0.00 0.00 0.00 0.12
#> TCGA.HT.8113.01 2 0.1275 0.88005 0.00 0.94 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.DH.A66G.01 7 0.6271 0.28650 0.14 0.00 0.00 0.24 0.00 0.00 0.42 0.20
#> TCGA.HT.7620.01 2 0.1275 0.88005 0.00 0.94 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.P5.A731.01 1 0.3095 0.42221 0.74 0.00 0.00 0.00 0.00 0.02 0.00 0.24
#> TCGA.HT.7480.01 2 0.3036 0.73605 0.00 0.78 0.00 0.00 0.18 0.00 0.00 0.04
#> TCGA.HT.7689.01 7 0.3627 0.56638 0.00 0.00 0.02 0.14 0.00 0.02 0.78 0.04
#> TCGA.HT.8109.01 5 0.1607 0.87222 0.00 0.04 0.00 0.00 0.92 0.00 0.00 0.04
#> TCGA.E1.A7YE.01 3 0.1091 0.82572 0.00 0.00 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.S9.A7R1.01 5 0.3404 0.64965 0.00 0.24 0.00 0.00 0.72 0.00 0.00 0.04
#> TCGA.FG.A710.01 5 0.2940 0.83942 0.00 0.02 0.00 0.00 0.84 0.10 0.02 0.02
#> TCGA.S9.A7J0.01 7 0.2719 0.58258 0.00 0.00 0.00 0.18 0.00 0.00 0.80 0.02
#> TCGA.DU.A6S6.01 2 0.1275 0.88051 0.00 0.94 0.00 0.00 0.00 0.04 0.00 0.02
#> TCGA.HT.7877.01 2 0.2165 0.86406 0.00 0.88 0.00 0.00 0.00 0.06 0.00 0.06
#> TCGA.QH.A6CU.01 2 0.2407 0.85365 0.00 0.86 0.00 0.00 0.00 0.08 0.00 0.06
#> TCGA.HW.7486.01 2 0.0941 0.88365 0.00 0.96 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.FG.7634.01 2 0.1557 0.87823 0.00 0.92 0.00 0.00 0.00 0.06 0.00 0.02
#> TCGA.DU.8163.01 1 0.0000 0.61897 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6407.02 3 0.2350 0.80326 0.00 0.00 0.86 0.00 0.00 0.00 0.10 0.04
#> TCGA.DU.6407.01 4 0.0808 0.63528 0.00 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.HT.8010.01 2 0.2407 0.85365 0.00 0.86 0.00 0.00 0.00 0.08 0.00 0.06
#> TCGA.P5.A5F1.01 1 0.3986 0.45401 0.74 0.00 0.00 0.08 0.00 0.00 0.04 0.14
#> TCGA.VM.A8CF.01 7 0.4191 0.54700 0.02 0.00 0.00 0.26 0.00 0.00 0.66 0.06
#> TCGA.DU.6542.01 1 0.3434 0.53948 0.76 0.00 0.00 0.10 0.00 0.00 0.00 0.14
#> TCGA.FG.7638.01 2 0.1275 0.86401 0.00 0.94 0.00 0.00 0.02 0.00 0.00 0.04
#> TCGA.DH.5143.01 1 0.5448 -0.09073 0.44 0.00 0.00 0.38 0.00 0.00 0.04 0.14
#> TCGA.DU.7299.01 4 0.4619 -0.10800 0.02 0.00 0.00 0.48 0.00 0.00 0.44 0.06
#> TCGA.CS.5393.01 7 0.3095 0.57149 0.00 0.00 0.00 0.24 0.00 0.00 0.74 0.02
#> TCGA.DU.7011.01 1 0.2981 0.51552 0.76 0.00 0.00 0.02 0.00 0.00 0.00 0.22
#> TCGA.TM.A84Q.01 1 0.4255 0.17692 0.58 0.00 0.00 0.34 0.00 0.00 0.00 0.08
#> TCGA.DB.5281.01 4 0.3663 0.60373 0.10 0.00 0.00 0.78 0.00 0.00 0.06 0.06
#> TCGA.HT.7605.01 2 0.1887 0.87242 0.00 0.90 0.00 0.00 0.00 0.06 0.00 0.04
#> TCGA.FG.A6J1.01 2 0.0471 0.87747 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DB.5270.01 1 0.2267 0.52807 0.82 0.00 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.S9.A6WQ.01 1 0.2623 0.57474 0.84 0.00 0.00 0.06 0.00 0.00 0.00 0.10
#> TCGA.HT.8106.01 6 0.3291 0.56971 0.02 0.00 0.00 0.00 0.00 0.70 0.00 0.28
#> TCGA.HT.7608.01 2 0.1887 0.87242 0.00 0.90 0.00 0.00 0.00 0.06 0.00 0.04
#> TCGA.E1.A7YU.01 7 0.2025 0.54630 0.00 0.00 0.02 0.10 0.00 0.00 0.88 0.00
#> TCGA.W9.A837.01 2 0.1275 0.86401 0.00 0.94 0.00 0.00 0.02 0.00 0.00 0.04
#> TCGA.TM.A7C5.01 2 0.3293 0.68430 0.00 0.74 0.00 0.00 0.22 0.00 0.00 0.04
#> TCGA.S9.A7QY.01 5 0.1887 0.86312 0.00 0.06 0.00 0.00 0.90 0.00 0.00 0.04
#> TCGA.QH.A6CW.01 4 0.3434 0.53474 0.00 0.00 0.00 0.76 0.00 0.00 0.14 0.10
#> TCGA.S9.A6WO.01 1 0.3054 0.55433 0.80 0.00 0.00 0.08 0.00 0.00 0.00 0.12
#> TCGA.IK.7675.01 7 0.4593 0.01177 0.00 0.00 0.10 0.00 0.00 0.20 0.66 0.04
#> TCGA.HT.7601.01 6 0.4723 0.51770 0.00 0.00 0.00 0.00 0.00 0.52 0.14 0.34
#> TCGA.P5.A5ET.01 2 0.1275 0.88051 0.00 0.94 0.00 0.00 0.00 0.04 0.00 0.02
#> TCGA.HT.7472.01 1 0.4332 0.32994 0.64 0.00 0.00 0.16 0.00 0.00 0.00 0.20
#> TCGA.HT.7880.01 1 0.3991 0.18022 0.62 0.00 0.00 0.00 0.00 0.06 0.00 0.32
#> TCGA.E1.A7Z3.01 1 0.4873 0.02740 0.48 0.00 0.00 0.36 0.00 0.00 0.00 0.16
#> TCGA.P5.A77X.01 2 0.0808 0.88355 0.00 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.FG.A6IZ.01 5 0.0000 0.88681 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7873.01 7 0.5577 0.32163 0.08 0.00 0.00 0.02 0.00 0.10 0.58 0.22
#> TCGA.CS.4938.01 1 0.1765 0.58560 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.KT.A74X.01 2 0.0471 0.88398 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.P5.A5EX.01 2 0.1275 0.88051 0.00 0.94 0.00 0.00 0.00 0.04 0.00 0.02
#> TCGA.VM.A8CH.01 1 0.4560 0.29176 0.60 0.00 0.00 0.22 0.00 0.00 0.00 0.18
#> TCGA.HT.7476.01 4 0.1563 0.62387 0.00 0.00 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.DB.A75L.01 4 0.3293 0.47638 0.00 0.00 0.00 0.74 0.00 0.00 0.22 0.04
#> TCGA.HT.8563.01 6 0.5017 0.39016 0.00 0.00 0.00 0.08 0.00 0.58 0.28 0.06
#> TCGA.RY.A843.01 1 0.4028 0.38800 0.66 0.00 0.00 0.04 0.00 0.02 0.00 0.28
#> TCGA.S9.A7IS.01 3 0.3169 0.72103 0.00 0.00 0.78 0.00 0.00 0.18 0.02 0.02
#> TCGA.TQ.A8XE.02 4 0.5810 -0.12889 0.06 0.00 0.00 0.42 0.00 0.02 0.40 0.10
#> TCGA.E1.A7YO.01 5 0.3971 0.22553 0.00 0.42 0.00 0.00 0.54 0.00 0.00 0.04
#> TCGA.TQ.A7RG.01 2 0.1557 0.87823 0.00 0.92 0.00 0.00 0.00 0.06 0.00 0.02
#> TCGA.QH.A6X5.01 5 0.2484 0.83786 0.00 0.00 0.00 0.00 0.86 0.10 0.02 0.02
#> TCGA.HW.7493.01 1 0.0808 0.61730 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.RY.A847.01 2 0.1887 0.87242 0.00 0.90 0.00 0.00 0.00 0.06 0.00 0.04
#> TCGA.DU.8166.01 1 0.0471 0.62088 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.VM.A8CA.01 2 0.1091 0.88316 0.00 0.94 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.HT.7855.01 4 0.1341 0.63120 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.S9.A89Z.01 7 0.3794 0.56085 0.00 0.00 0.04 0.18 0.00 0.00 0.74 0.04
#> TCGA.DB.A4XG.01 2 0.3808 0.47075 0.00 0.62 0.00 0.00 0.34 0.00 0.00 0.04
#> TCGA.DH.A7UT.01 1 0.4999 -0.25907 0.42 0.00 0.00 0.00 0.00 0.18 0.00 0.40
#> TCGA.DU.7015.01 1 0.4370 0.09425 0.52 0.00 0.00 0.40 0.00 0.00 0.00 0.08
#> TCGA.HT.A616.01 4 0.5118 0.24683 0.04 0.00 0.00 0.56 0.00 0.00 0.28 0.12
#> TCGA.HT.7611.01 4 0.1804 0.63066 0.00 0.00 0.00 0.90 0.00 0.00 0.02 0.08
#> TCGA.HT.8018.01 6 0.3746 0.51890 0.04 0.00 0.00 0.00 0.00 0.64 0.00 0.32
#> TCGA.FG.A60K.01 2 0.1557 0.87823 0.00 0.92 0.00 0.00 0.00 0.06 0.00 0.02
#> TCGA.HT.7856.01 2 0.2591 0.85868 0.00 0.86 0.00 0.00 0.04 0.02 0.00 0.08
#> TCGA.DU.5851.01 1 0.4804 -0.17031 0.46 0.00 0.00 0.00 0.00 0.14 0.00 0.40
#> TCGA.DU.A7T6.01 5 0.2484 0.83786 0.00 0.00 0.00 0.00 0.86 0.10 0.02 0.02
#> TCGA.S9.A6TY.01 5 0.2350 0.83448 0.00 0.10 0.00 0.00 0.86 0.00 0.00 0.04
#> TCGA.WY.A85C.01 4 0.0808 0.64892 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.DB.A4XC.01 1 0.2406 0.53715 0.80 0.00 0.00 0.00 0.00 0.00 0.00 0.20
#> TCGA.TM.A84O.01 5 0.2484 0.83786 0.00 0.00 0.00 0.00 0.86 0.10 0.02 0.02
#> TCGA.P5.A72W.01 1 0.0941 0.62125 0.96 0.00 0.00 0.02 0.00 0.00 0.00 0.02
#> TCGA.S9.A6TU.01 4 0.1275 0.64349 0.00 0.00 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.HT.A61A.01 2 0.2407 0.85365 0.00 0.86 0.00 0.00 0.00 0.08 0.00 0.06
#> TCGA.DU.5855.01 4 0.2888 0.54249 0.00 0.00 0.00 0.80 0.00 0.00 0.16 0.04
#> TCGA.HT.7884.01 4 0.4554 -0.06265 0.42 0.00 0.00 0.48 0.00 0.00 0.00 0.10
#> TCGA.TQ.A7RQ.01 2 0.1607 0.85449 0.00 0.92 0.00 0.00 0.04 0.00 0.00 0.04
#> TCGA.IK.8125.01 5 0.1804 0.85929 0.00 0.00 0.00 0.00 0.90 0.08 0.00 0.02
#> TCGA.HT.A74K.01 5 0.1804 0.85929 0.00 0.00 0.00 0.00 0.90 0.08 0.00 0.02
#> TCGA.WH.A86K.01 7 0.4758 0.50858 0.02 0.00 0.00 0.26 0.00 0.00 0.60 0.12
#> TCGA.QH.A6X8.01 5 0.1804 0.85929 0.00 0.00 0.00 0.00 0.90 0.08 0.00 0.02
#> TCGA.WY.A85E.01 1 0.5448 0.00194 0.44 0.00 0.00 0.38 0.00 0.00 0.04 0.14
#> TCGA.HT.A5R5.01 1 0.2534 0.45789 0.78 0.00 0.00 0.00 0.00 0.00 0.00 0.22
#> TCGA.HT.A618.01 6 0.4255 0.26074 0.00 0.00 0.34 0.00 0.00 0.58 0.08 0.00
#> TCGA.FG.6691.01 1 0.3293 0.49914 0.74 0.00 0.00 0.04 0.00 0.00 0.00 0.22
#> TCGA.HT.7467.01 2 0.1275 0.88005 0.00 0.94 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.S9.A7R3.01 4 0.6160 0.26209 0.20 0.00 0.00 0.46 0.00 0.00 0.16 0.18
#> TCGA.FG.A4MX.01 1 0.3263 0.54004 0.78 0.00 0.00 0.12 0.00 0.00 0.00 0.10
#> TCGA.HT.7681.01 2 0.2165 0.86406 0.00 0.88 0.00 0.00 0.00 0.06 0.00 0.06
#> TCGA.S9.A7IZ.01 7 0.6129 -0.03242 0.34 0.00 0.00 0.02 0.00 0.04 0.38 0.22
#> TCGA.DU.A6S7.01 4 0.0471 0.64796 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.P5.A72Z.01 5 0.2484 0.83786 0.00 0.00 0.00 0.00 0.86 0.10 0.02 0.02
#> TCGA.HT.8114.01 1 0.4999 0.02371 0.42 0.00 0.00 0.40 0.00 0.00 0.00 0.18
#> TCGA.DU.8168.01 5 0.0000 0.88681 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HW.8321.01 1 0.4069 0.41155 0.68 0.00 0.00 0.14 0.00 0.00 0.00 0.18
#> TCGA.TQ.A7RN.01 2 0.1275 0.88051 0.00 0.94 0.00 0.00 0.00 0.04 0.00 0.02
#> TCGA.DH.5141.01 2 0.2725 0.77929 0.00 0.82 0.00 0.00 0.14 0.00 0.00 0.04
#> TCGA.EZ.7264.01 5 0.2350 0.83448 0.00 0.10 0.00 0.00 0.86 0.00 0.00 0.04
#> TCGA.P5.A5F4.01 1 0.4686 0.19951 0.56 0.00 0.00 0.28 0.00 0.00 0.00 0.16
#> TCGA.QH.A65V.01 2 0.1275 0.88381 0.00 0.94 0.00 0.00 0.00 0.04 0.00 0.02
#> TCGA.FG.8191.01 1 0.0471 0.61731 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DH.5142.01 7 0.6174 0.08273 0.18 0.00 0.00 0.00 0.00 0.12 0.42 0.28
#> TCGA.DU.A6S8.01 5 0.2484 0.83786 0.00 0.00 0.00 0.00 0.86 0.10 0.02 0.02
#> TCGA.E1.A7YW.01 1 0.1947 0.57284 0.86 0.00 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.CS.6666.01 4 0.0808 0.64907 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.DU.7298.01 2 0.4022 0.72369 0.00 0.74 0.00 0.10 0.12 0.00 0.00 0.04
#> TCGA.DB.A64R.01 2 0.1557 0.87823 0.00 0.92 0.00 0.00 0.00 0.06 0.00 0.02
#> TCGA.FG.A60L.01 4 0.3397 0.57406 0.06 0.00 0.00 0.80 0.00 0.00 0.04 0.10
#> TCGA.CS.5390.01 5 0.0808 0.88331 0.00 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.S9.A6WP.01 5 0.1887 0.86312 0.00 0.06 0.00 0.00 0.90 0.00 0.00 0.04
#> TCGA.DB.5280.01 1 0.1275 0.61505 0.94 0.00 0.00 0.04 0.00 0.00 0.00 0.02
#> TCGA.TM.A84T.01 1 0.1765 0.58922 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.DH.A66D.01 1 0.2547 0.57716 0.84 0.00 0.00 0.04 0.00 0.00 0.00 0.12
#> TCGA.RY.A83Z.01 3 0.1607 0.82891 0.00 0.00 0.92 0.00 0.00 0.00 0.04 0.04
#> TCGA.DB.5278.01 2 0.2407 0.85365 0.00 0.86 0.00 0.00 0.00 0.08 0.00 0.06
#> TCGA.TQ.A7RR.01 7 0.6343 -0.14665 0.12 0.00 0.00 0.00 0.00 0.22 0.34 0.32
#> TCGA.TQ.A7RH.01 1 0.2938 0.38342 0.70 0.00 0.00 0.00 0.00 0.00 0.00 0.30
#> TCGA.E1.A7YS.01 5 0.1804 0.85929 0.00 0.00 0.00 0.00 0.90 0.08 0.00 0.02
#> TCGA.P5.A735.01 1 0.1563 0.59450 0.90 0.00 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.DU.7294.01 5 0.3808 0.46579 0.00 0.34 0.00 0.00 0.62 0.00 0.00 0.04
#> TCGA.HT.7881.01 2 0.2165 0.86406 0.00 0.88 0.00 0.00 0.00 0.06 0.00 0.06
#> TCGA.HT.7695.01 2 0.0471 0.88405 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.P5.A5EU.01 6 0.4838 0.51659 0.00 0.00 0.14 0.00 0.00 0.66 0.12 0.08
#> TCGA.DB.A64X.01 7 0.3794 0.56085 0.00 0.00 0.04 0.18 0.00 0.00 0.74 0.04
#> TCGA.FG.7637.01 2 0.0808 0.87165 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.VM.A8CE.01 2 0.2165 0.86406 0.00 0.88 0.00 0.00 0.00 0.06 0.00 0.06
#> TCGA.S9.A6U5.01 2 0.1887 0.87242 0.00 0.90 0.00 0.00 0.00 0.06 0.00 0.04
#> TCGA.HT.7609.01 1 0.3299 0.50985 0.76 0.00 0.00 0.06 0.00 0.00 0.00 0.18
#> TCGA.DB.5274.01 5 0.1607 0.87222 0.00 0.04 0.00 0.00 0.92 0.00 0.00 0.04
#> TCGA.HW.7487.01 5 0.1887 0.86312 0.00 0.06 0.00 0.00 0.90 0.00 0.00 0.04
#> TCGA.HW.7491.01 5 0.2888 0.76617 0.00 0.16 0.00 0.00 0.80 0.00 0.00 0.04
#> TCGA.CS.4944.01 4 0.3986 0.53837 0.04 0.00 0.00 0.74 0.00 0.00 0.14 0.08
#> TCGA.DU.A6S2.01 2 0.1275 0.88005 0.00 0.94 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.S9.A7R7.01 6 0.4860 0.39177 0.06 0.00 0.00 0.00 0.00 0.50 0.04 0.40
#> TCGA.TM.A84R.01 2 0.1275 0.88005 0.00 0.94 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.DB.A75M.01 4 0.5385 0.41102 0.22 0.00 0.00 0.56 0.00 0.00 0.06 0.16
#> TCGA.HW.A5KM.01 4 0.2348 0.64467 0.02 0.00 0.00 0.88 0.00 0.00 0.06 0.04
#> TCGA.HT.7477.01 7 0.5342 -0.38693 0.00 0.00 0.12 0.00 0.00 0.40 0.44 0.04
#> TCGA.HT.8012.01 2 0.2725 0.77929 0.00 0.82 0.00 0.00 0.14 0.00 0.00 0.04
#> TCGA.DU.8167.01 4 0.0941 0.63849 0.00 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.S9.A6U1.01 1 0.4342 0.34997 0.64 0.00 0.00 0.18 0.00 0.00 0.00 0.18
#> TCGA.FG.5965.01 8 0.6186 -0.32796 0.22 0.00 0.00 0.00 0.00 0.28 0.10 0.40
#> TCGA.FG.8187.01 2 0.1887 0.87242 0.00 0.90 0.00 0.00 0.00 0.06 0.00 0.04
#> TCGA.HT.A614.01 7 0.5782 0.25586 0.14 0.00 0.00 0.00 0.00 0.10 0.50 0.26
#> TCGA.S9.A7QZ.01 5 0.0000 0.88681 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.QH.A6X4.01 2 0.0808 0.88355 0.00 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.P5.A77W.01 5 0.1887 0.86312 0.00 0.06 0.00 0.00 0.90 0.00 0.00 0.04
#> TCGA.DU.7302.01 5 0.0000 0.88681 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.6399.01 4 0.2719 0.52614 0.00 0.00 0.00 0.80 0.00 0.00 0.18 0.02
#> TCGA.E1.5307.01 4 0.3714 -0.03177 0.00 0.00 0.00 0.54 0.00 0.00 0.44 0.02
#> TCGA.S9.A7QW.01 1 0.1563 0.60613 0.90 0.00 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.HT.7604.01 4 0.0808 0.64958 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.P5.A733.01 4 0.4073 0.40742 0.24 0.00 0.00 0.66 0.00 0.00 0.00 0.10
#> TCGA.HT.7684.01 1 0.4800 0.11150 0.54 0.00 0.00 0.04 0.00 0.06 0.00 0.36
#> TCGA.HW.7495.01 2 0.1887 0.87242 0.00 0.90 0.00 0.00 0.00 0.06 0.00 0.04
#> TCGA.QH.A65R.01 5 0.1607 0.87222 0.00 0.04 0.00 0.00 0.92 0.00 0.00 0.04
#> TCGA.DU.A7TG.01 2 0.2407 0.85365 0.00 0.86 0.00 0.00 0.00 0.08 0.00 0.06
#> TCGA.DH.A7UV.01 4 0.0471 0.64222 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.HT.7879.01 4 0.4841 0.11352 0.34 0.00 0.00 0.50 0.00 0.00 0.00 0.16
#> TCGA.TM.A84F.01 6 0.3675 0.54058 0.04 0.00 0.00 0.00 0.00 0.66 0.00 0.30
#> TCGA.DU.A7TC.01 4 0.3314 0.55784 0.10 0.00 0.00 0.80 0.00 0.00 0.02 0.08
#> TCGA.HT.7610.01 1 0.4332 0.34296 0.64 0.00 0.00 0.20 0.00 0.00 0.00 0.16
#> TCGA.S9.A6TW.01 5 0.1887 0.86312 0.00 0.06 0.00 0.00 0.90 0.00 0.00 0.04
#> TCGA.FG.A60J.01 1 0.1887 0.60899 0.90 0.00 0.00 0.06 0.00 0.00 0.00 0.04
#> TCGA.E1.5303.01 4 0.5605 0.38317 0.12 0.00 0.00 0.56 0.00 0.00 0.16 0.16
#> TCGA.HT.7481.01 2 0.1275 0.88381 0.00 0.94 0.00 0.00 0.00 0.04 0.00 0.02
#> TCGA.FN.7833.01 1 0.1091 0.61610 0.94 0.00 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.E1.A7Z4.01 1 0.1563 0.60095 0.90 0.00 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.DU.A5TR.01 4 0.0808 0.64578 0.00 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.HT.7875.01 2 0.0808 0.88355 0.00 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.HT.7473.01 1 0.0808 0.61334 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.S9.A7IQ.01 2 0.2407 0.85365 0.00 0.86 0.00 0.00 0.00 0.08 0.00 0.06
#> TCGA.DU.7008.01 1 0.4698 -0.03641 0.44 0.00 0.00 0.44 0.00 0.00 0.00 0.12
#> TCGA.S9.A6WG.01 1 0.2534 0.50113 0.78 0.00 0.00 0.00 0.00 0.00 0.00 0.22
#> TCGA.DB.A75O.01 1 0.3449 0.30347 0.66 0.00 0.00 0.00 0.00 0.02 0.00 0.32
#> TCGA.HT.7688.01 4 0.3449 0.28347 0.00 0.00 0.00 0.66 0.00 0.00 0.32 0.02
#> TCGA.DU.7304.02 3 0.2623 0.78872 0.00 0.00 0.84 0.00 0.00 0.00 0.10 0.06
#> TCGA.DU.6394.01 5 0.0000 0.88681 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6WD.01 5 0.0471 0.88619 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.DU.5872.01 1 0.1947 0.57757 0.86 0.00 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.FG.8185.01 4 0.1091 0.63840 0.00 0.00 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.HT.7902.01 6 0.3675 0.54058 0.04 0.00 0.00 0.00 0.00 0.66 0.00 0.30
#> TCGA.TQ.A7RU.01 5 0.2350 0.83448 0.00 0.10 0.00 0.00 0.86 0.00 0.00 0.04
#> TCGA.DU.5874.01 5 0.0000 0.88681 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6WE.01 2 0.1557 0.87823 0.00 0.92 0.00 0.00 0.00 0.06 0.00 0.02
#> TCGA.FG.6690.01 4 0.1091 0.64376 0.00 0.00 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.HW.8320.01 4 0.0941 0.64431 0.00 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.R8.A6MK.01 2 0.1557 0.87823 0.00 0.92 0.00 0.00 0.00 0.06 0.00 0.02
#> TCGA.QH.A6CY.01 2 0.0941 0.88365 0.00 0.96 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.S9.A7J1.01 2 0.2888 0.75793 0.00 0.80 0.00 0.00 0.16 0.00 0.00 0.04
#> TCGA.P5.A72X.01 1 0.0808 0.61150 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.E1.5322.01 1 0.6156 0.01178 0.44 0.00 0.00 0.24 0.00 0.00 0.12 0.20
#> TCGA.P5.A5F0.01 2 0.3036 0.73584 0.00 0.78 0.00 0.00 0.18 0.00 0.00 0.04
#> TCGA.R8.A73M.01 2 0.3808 0.47105 0.00 0.62 0.00 0.00 0.34 0.00 0.00 0.04
#> TCGA.CS.4942.01 1 0.1341 0.60750 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.DB.A4X9.01 1 0.0808 0.61635 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.DB.A4XF.01 4 0.1091 0.63840 0.00 0.00 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.HT.A74O.01 4 0.1275 0.63674 0.00 0.00 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.FG.8188.01 4 0.3845 0.33429 0.00 0.00 0.00 0.66 0.00 0.00 0.28 0.06
#> TCGA.DU.A6S3.01 5 0.1887 0.86312 0.00 0.06 0.00 0.00 0.90 0.00 0.00 0.04
#> TCGA.DB.A4XH.01 5 0.0000 0.88681 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7485.01 1 0.4646 0.35366 0.66 0.00 0.00 0.12 0.00 0.00 0.04 0.18
#> TCGA.VW.A7QS.01 5 0.3504 0.61781 0.00 0.26 0.00 0.00 0.70 0.00 0.00 0.04
#> TCGA.S9.A6WI.01 2 0.1275 0.88005 0.00 0.94 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.DU.8164.01 5 0.0471 0.88619 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.S9.A6TS.01 7 0.2852 0.56533 0.00 0.00 0.00 0.28 0.00 0.00 0.72 0.00
#> TCGA.DB.A64S.01 1 0.4342 0.34997 0.64 0.00 0.00 0.18 0.00 0.00 0.00 0.18
#> TCGA.VV.A86M.01 4 0.3894 0.58458 0.06 0.00 0.00 0.76 0.00 0.00 0.10 0.08
#> TCGA.TQ.A8XE.01 4 0.5451 0.18932 0.10 0.00 0.00 0.52 0.00 0.00 0.30 0.08
#> TCGA.CS.6667.01 4 0.4799 0.15001 0.32 0.00 0.00 0.52 0.00 0.00 0.00 0.16
#> TCGA.E1.A7YV.01 3 0.1557 0.82960 0.00 0.00 0.92 0.00 0.00 0.00 0.06 0.02
#> TCGA.TQ.A7RW.01 4 0.5947 -0.00273 0.10 0.00 0.00 0.42 0.00 0.00 0.34 0.14
#> TCGA.DU.5849.01 5 0.2132 0.85009 0.00 0.08 0.00 0.00 0.88 0.00 0.00 0.04
#> TCGA.DU.A7TI.01 1 0.4677 0.18220 0.54 0.00 0.00 0.32 0.00 0.00 0.00 0.14
#> TCGA.HT.7468.01 2 0.3404 0.65502 0.00 0.72 0.00 0.00 0.24 0.00 0.00 0.04
#> TCGA.TQ.A7RI.01 2 0.1557 0.87823 0.00 0.92 0.00 0.00 0.00 0.06 0.00 0.02
#> TCGA.DB.5279.01 5 0.2484 0.83786 0.00 0.00 0.00 0.00 0.86 0.10 0.02 0.02
#> TCGA.S9.A6U8.01 1 0.4759 0.05867 0.50 0.00 0.00 0.36 0.00 0.00 0.00 0.14
#> TCGA.HW.7489.01 4 0.3523 0.53138 0.10 0.00 0.00 0.78 0.00 0.00 0.02 0.10
#> TCGA.R8.A6YH.01 1 0.0471 0.62088 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.DU.7018.01 5 0.1557 0.86695 0.00 0.00 0.00 0.00 0.92 0.06 0.00 0.02
#> TCGA.HT.7677.01 5 0.2350 0.83448 0.00 0.10 0.00 0.00 0.86 0.00 0.00 0.04
#> TCGA.FG.A713.01 5 0.2165 0.85442 0.00 0.06 0.00 0.00 0.88 0.00 0.00 0.06
#> TCGA.DU.7300.01 5 0.0000 0.88681 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.TM.A7CA.01 1 0.3299 0.47785 0.76 0.00 0.00 0.18 0.00 0.00 0.00 0.06
#> TCGA.HT.7690.01 1 0.1765 0.58853 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.FG.6689.01 1 0.1563 0.59450 0.90 0.00 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.DU.7007.01 7 0.1563 0.54753 0.00 0.00 0.00 0.10 0.00 0.00 0.90 0.00
#> TCGA.TQ.A7RF.01 1 0.2025 0.60020 0.88 0.00 0.00 0.02 0.00 0.00 0.00 0.10
#> TCGA.DB.5277.01 7 0.2807 0.52598 0.00 0.00 0.00 0.10 0.00 0.02 0.84 0.04
#> TCGA.HT.7694.01 5 0.1091 0.87352 0.00 0.00 0.00 0.00 0.94 0.06 0.00 0.00
#> TCGA.TM.A84M.01 5 0.2484 0.83786 0.00 0.00 0.00 0.00 0.86 0.10 0.02 0.02
#> TCGA.F6.A8O3.01 2 0.1275 0.86401 0.00 0.94 0.00 0.00 0.02 0.00 0.00 0.04
#> TCGA.QH.A86X.01 2 0.1557 0.87823 0.00 0.92 0.00 0.00 0.00 0.06 0.00 0.02
#> TCGA.HT.8013.01 1 0.2114 0.57745 0.84 0.00 0.00 0.00 0.00 0.00 0.00 0.16
#> TCGA.HW.7490.01 1 0.4396 0.32232 0.62 0.00 0.00 0.24 0.00 0.00 0.00 0.14
#> TCGA.QH.A65S.01 7 0.5986 0.28307 0.18 0.00 0.00 0.02 0.00 0.06 0.50 0.24
#> TCGA.DU.A76R.01 2 0.2132 0.82805 0.00 0.88 0.00 0.00 0.08 0.00 0.00 0.04
#> TCGA.DH.5144.01 5 0.1887 0.86312 0.00 0.06 0.00 0.00 0.90 0.00 0.00 0.04
#> TCGA.P5.A780.01 4 0.3449 0.28347 0.00 0.00 0.00 0.66 0.00 0.00 0.32 0.02
#> TCGA.HT.7606.01 7 0.3454 0.54464 0.00 0.00 0.02 0.12 0.00 0.02 0.80 0.04
#> TCGA.DB.A64V.01 5 0.0471 0.88621 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.RY.A840.01 2 0.3404 0.64904 0.00 0.72 0.00 0.00 0.24 0.00 0.00 0.04
#> TCGA.E1.5302.01 1 0.3083 0.30087 0.66 0.00 0.00 0.00 0.00 0.00 0.00 0.34
#> TCGA.HW.A5KJ.01 5 0.0000 0.88681 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.A615.01 2 0.2547 0.79712 0.00 0.84 0.00 0.00 0.12 0.00 0.00 0.04
#> TCGA.HT.8105.01 5 0.0000 0.88681 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7309.01 4 0.4190 0.28376 0.20 0.00 0.00 0.66 0.00 0.00 0.00 0.14
#> TCGA.E1.A7YK.01 6 0.3431 0.52403 0.00 0.00 0.06 0.00 0.00 0.74 0.20 0.00
#> TCGA.HT.7874.01 2 0.3314 0.81722 0.00 0.80 0.00 0.00 0.10 0.02 0.00 0.08
#> TCGA.HT.7471.01 5 0.2350 0.83448 0.00 0.10 0.00 0.00 0.86 0.00 0.00 0.04
#> TCGA.DU.6395.01 1 0.0941 0.61993 0.96 0.00 0.00 0.02 0.00 0.00 0.00 0.02
#> TCGA.S9.A6TV.01 7 0.1563 0.54753 0.00 0.00 0.00 0.10 0.00 0.00 0.90 0.00
#> TCGA.P5.A5EW.01 1 0.1804 0.61073 0.90 0.00 0.00 0.02 0.00 0.00 0.00 0.08
#> TCGA.DU.6408.01 7 0.5713 0.24168 0.14 0.00 0.00 0.00 0.00 0.10 0.52 0.24
#> TCGA.DB.A4XB.01 1 0.5048 -0.08640 0.48 0.00 0.00 0.00 0.00 0.08 0.04 0.40
#> TCGA.FG.A4MT.01 1 0.3970 0.34861 0.68 0.00 0.00 0.22 0.00 0.00 0.00 0.10
#> TCGA.FG.A4MT.02 1 0.4396 0.28565 0.62 0.00 0.00 0.24 0.00 0.00 0.00 0.14
#> TCGA.HT.A619.01 5 0.0471 0.88304 0.00 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.QH.A870.01 1 0.0808 0.61635 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.HT.A5R9.01 5 0.2350 0.83448 0.00 0.10 0.00 0.00 0.86 0.00 0.00 0.04
#> TCGA.FG.5964.01 5 0.2348 0.88030 0.00 0.04 0.00 0.00 0.88 0.06 0.00 0.02
#> TCGA.CS.5396.01 5 0.2484 0.83786 0.00 0.00 0.00 0.00 0.86 0.10 0.02 0.02
#> TCGA.DU.A7TA.01 1 0.3729 0.46056 0.72 0.00 0.00 0.10 0.00 0.00 0.00 0.18
#> TCGA.HW.8319.01 6 0.4873 0.17560 0.00 0.00 0.36 0.00 0.00 0.48 0.16 0.00
#> TCGA.DH.A7UR.01 5 0.1275 0.87896 0.00 0.02 0.00 0.00 0.94 0.00 0.00 0.04
#> TCGA.TM.A84H.01 4 0.5948 0.32798 0.20 0.00 0.00 0.50 0.00 0.00 0.14 0.16
#> TCGA.S9.A6TZ.01 4 0.2071 0.64130 0.02 0.00 0.00 0.90 0.00 0.00 0.04 0.04
#> TCGA.HT.7479.01 1 0.2719 0.53963 0.80 0.00 0.00 0.02 0.00 0.00 0.00 0.18
#> TCGA.DU.6400.01 5 0.0000 0.88681 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6WL.01 5 0.1607 0.87222 0.00 0.04 0.00 0.00 0.92 0.00 0.00 0.04
#> TCGA.DB.A75K.01 2 0.3862 0.41872 0.00 0.60 0.00 0.00 0.36 0.00 0.00 0.04
#> TCGA.DB.A4XD.01 4 0.1275 0.64907 0.00 0.00 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.DB.A64Q.01 5 0.2484 0.83786 0.00 0.00 0.00 0.00 0.86 0.10 0.02 0.02
#> TCGA.P5.A737.01 2 0.1607 0.85452 0.00 0.92 0.00 0.00 0.04 0.00 0.00 0.04
#> TCGA.DB.5275.01 1 0.1765 0.61120 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.S9.A6WH.01 5 0.0000 0.88681 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7602.01 1 0.3660 0.35613 0.70 0.00 0.00 0.00 0.00 0.06 0.00 0.24
#> TCGA.DU.A5TU.01 3 0.3943 0.42154 0.00 0.00 0.56 0.00 0.00 0.00 0.40 0.04
#> TCGA.HT.A5RB.01 1 0.1607 0.60782 0.92 0.00 0.00 0.04 0.00 0.00 0.00 0.04
#> TCGA.HT.7616.01 5 0.2484 0.83786 0.00 0.00 0.00 0.00 0.86 0.10 0.02 0.02
#> TCGA.S9.A7R8.01 4 0.2404 0.59161 0.00 0.00 0.00 0.84 0.00 0.00 0.14 0.02
#> TCGA.QH.A6XA.01 1 0.1947 0.57522 0.86 0.00 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.HT.8111.01 1 0.5207 -0.16880 0.46 0.00 0.00 0.00 0.00 0.10 0.04 0.40
#> TCGA.DU.A5TP.01 1 0.3142 0.26186 0.64 0.00 0.00 0.00 0.00 0.00 0.00 0.36
#> TCGA.RY.A83Y.01 5 0.1887 0.86312 0.00 0.06 0.00 0.00 0.90 0.00 0.00 0.04
#> TCGA.HT.7482.01 1 0.2719 0.54551 0.80 0.00 0.00 0.02 0.00 0.00 0.00 0.18
#> TCGA.TQ.A7RK.02 4 0.3434 0.47563 0.14 0.00 0.00 0.76 0.00 0.00 0.00 0.10
#> TCGA.TQ.A7RK.01 4 0.3729 0.42219 0.18 0.00 0.00 0.72 0.00 0.00 0.00 0.10
#> TCGA.HT.7858.01 4 0.3263 0.51058 0.12 0.00 0.00 0.78 0.00 0.00 0.00 0.10
#> TCGA.HT.7475.01 1 0.3291 0.41411 0.70 0.00 0.00 0.00 0.00 0.00 0.02 0.28
#> TCGA.DB.A64U.01 2 0.0471 0.88359 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DB.A64W.01 5 0.1804 0.85929 0.00 0.00 0.00 0.00 0.90 0.08 0.00 0.02
#> TCGA.R8.A6MO.01 5 0.1275 0.87896 0.00 0.02 0.00 0.00 0.94 0.00 0.00 0.04
#> TCGA.DU.A7T8.01 1 0.1275 0.61960 0.94 0.00 0.00 0.02 0.00 0.00 0.00 0.04
#> TCGA.HW.8322.01 2 0.1275 0.88051 0.00 0.94 0.00 0.00 0.00 0.04 0.00 0.02
#> TCGA.DU.5870.02 5 0.2484 0.83786 0.00 0.00 0.00 0.00 0.86 0.10 0.02 0.02
#> TCGA.CS.6668.01 5 0.2265 0.84947 0.00 0.00 0.00 0.00 0.88 0.08 0.02 0.02
#> TCGA.DU.5870.01 2 0.1607 0.85607 0.00 0.92 0.00 0.00 0.04 0.00 0.00 0.04
#> TCGA.FG.7636.01 7 0.5448 0.24580 0.04 0.00 0.00 0.38 0.00 0.00 0.44 0.14
#> TCGA.HT.7692.01 2 0.0471 0.87742 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.WY.A859.01 4 0.5880 0.12074 0.26 0.00 0.00 0.44 0.00 0.00 0.06 0.24
#> TCGA.R8.A6ML.01 5 0.0000 0.88681 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7686.01 6 0.3658 0.42277 0.00 0.00 0.00 0.00 0.00 0.58 0.40 0.02
#> TCGA.DU.6410.01 5 0.1887 0.86381 0.00 0.06 0.00 0.00 0.90 0.00 0.00 0.04
#> TCGA.S9.A6U9.01 1 0.4896 -0.02896 0.46 0.00 0.00 0.38 0.00 0.00 0.00 0.16
#> TCGA.CS.6290.01 1 0.2725 0.54837 0.82 0.00 0.00 0.00 0.00 0.00 0.04 0.14
#> TCGA.TQ.A7RO.01 2 0.0808 0.87165 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.DU.7019.01 4 0.1091 0.62666 0.00 0.00 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.FG.A711.01 1 0.5741 -0.00370 0.48 0.00 0.00 0.02 0.00 0.02 0.24 0.24
#> TCGA.TQ.A7RM.01 7 0.5187 0.18739 0.00 0.00 0.22 0.02 0.00 0.06 0.62 0.08
#> TCGA.S9.A7R4.01 1 0.4799 0.14955 0.52 0.00 0.00 0.32 0.00 0.00 0.00 0.16
#> TCGA.E1.5318.01 5 0.0808 0.88331 0.00 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.HT.7676.01 1 0.2114 0.57284 0.84 0.00 0.00 0.00 0.00 0.00 0.00 0.16
#> TCGA.S9.A7J3.01 5 0.1091 0.87352 0.00 0.00 0.00 0.00 0.94 0.06 0.00 0.00
#> TCGA.P5.A5F2.01 4 0.6085 0.27607 0.28 0.00 0.00 0.44 0.00 0.00 0.12 0.16
#> TCGA.E1.5304.01 3 0.2407 0.81283 0.00 0.00 0.86 0.00 0.00 0.00 0.08 0.06
#> TCGA.TM.A84S.01 2 0.1887 0.87242 0.00 0.90 0.00 0.00 0.00 0.06 0.00 0.04
#> TCGA.WY.A85B.01 1 0.4458 0.32596 0.62 0.00 0.00 0.20 0.00 0.00 0.00 0.18
#> TCGA.TQ.A7RS.01 2 0.1557 0.87823 0.00 0.92 0.00 0.00 0.00 0.06 0.00 0.02
#> TCGA.S9.A7QX.01 4 0.4813 0.03590 0.42 0.00 0.00 0.44 0.00 0.00 0.00 0.14
#> TCGA.CS.4943.01 7 0.5535 0.42706 0.04 0.00 0.00 0.30 0.00 0.00 0.48 0.18
#> TCGA.QH.A65Z.01 5 0.1607 0.87222 0.00 0.04 0.00 0.00 0.92 0.00 0.00 0.04
#> TCGA.DB.5276.01 8 0.5874 -0.03530 0.30 0.00 0.00 0.32 0.00 0.04 0.00 0.34
#> TCGA.P5.A730.01 2 0.0808 0.87165 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.TM.A84L.01 1 0.0808 0.61150 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.WY.A85D.01 4 0.3618 0.16663 0.00 0.00 0.00 0.60 0.00 0.00 0.38 0.02
#> TCGA.RY.A83X.01 2 0.2350 0.81335 0.00 0.86 0.00 0.00 0.10 0.00 0.00 0.04
#> TCGA.S9.A6UB.01 5 0.0808 0.88331 0.00 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.DB.5273.01 1 0.6009 -0.02182 0.42 0.00 0.00 0.30 0.00 0.00 0.08 0.20
#> TCGA.TM.A7C4.01 1 0.2404 0.57332 0.84 0.00 0.00 0.02 0.00 0.00 0.00 0.14
#> TCGA.DH.A66F.01 2 0.3036 0.73708 0.00 0.78 0.00 0.00 0.18 0.00 0.00 0.04
#> TCGA.HT.7607.01 5 0.2484 0.83786 0.00 0.00 0.00 0.00 0.86 0.10 0.02 0.02
#> TCGA.DU.6393.01 5 0.0808 0.88331 0.00 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.HT.8108.01 1 0.1275 0.61960 0.94 0.00 0.00 0.02 0.00 0.00 0.00 0.04
#> TCGA.DU.7304.01 4 0.2404 0.55037 0.00 0.00 0.00 0.84 0.00 0.00 0.14 0.02
#> TCGA.S9.A7IY.01 2 0.1887 0.87242 0.00 0.90 0.00 0.00 0.00 0.06 0.00 0.04
#> TCGA.FG.7641.01 2 0.2725 0.77929 0.00 0.82 0.00 0.00 0.14 0.00 0.00 0.04
#> TCGA.P5.A736.01 1 0.5171 0.21994 0.58 0.00 0.00 0.18 0.00 0.00 0.04 0.20
#> TCGA.P5.A5EV.01 4 0.2484 0.60865 0.02 0.00 0.00 0.86 0.00 0.00 0.10 0.02
#> TCGA.DU.7301.01 4 0.1607 0.63841 0.00 0.00 0.00 0.92 0.00 0.00 0.04 0.04
#> TCGA.HT.7470.01 7 0.4759 0.56524 0.00 0.00 0.00 0.22 0.00 0.08 0.64 0.06
#> TCGA.DU.7009.01 2 0.0808 0.87165 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.P5.A781.01 2 0.2547 0.79712 0.00 0.84 0.00 0.00 0.12 0.00 0.00 0.04
#> TCGA.FG.A4MY.01 7 0.3729 0.23319 0.00 0.00 0.00 0.46 0.00 0.00 0.52 0.02
#> TCGA.TM.A7CF.01 4 0.4999 -0.03823 0.40 0.00 0.00 0.42 0.00 0.00 0.00 0.18
#> TCGA.TM.A7CF.02 1 0.4213 0.38710 0.66 0.00 0.00 0.18 0.00 0.00 0.00 0.16
#> TCGA.FG.8186.01 2 0.1557 0.87823 0.00 0.92 0.00 0.00 0.00 0.06 0.00 0.02
#> TCGA.S9.A6U6.01 1 0.3450 0.49840 0.76 0.00 0.00 0.12 0.00 0.00 0.00 0.12
#> TCGA.RY.A845.01 1 0.1341 0.59681 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.DU.7010.01 3 0.1275 0.83088 0.00 0.00 0.94 0.00 0.00 0.04 0.00 0.02
#> TCGA.S9.A6U2.01 2 0.0471 0.88405 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.S9.A6WN.01 5 0.2484 0.83786 0.00 0.00 0.00 0.00 0.86 0.10 0.02 0.02
#> TCGA.FG.8182.01 1 0.1563 0.58690 0.90 0.00 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.QH.A6X3.01 4 0.4244 0.38203 0.24 0.00 0.00 0.64 0.00 0.00 0.00 0.12
#> TCGA.DU.6401.01 1 0.4213 0.37805 0.66 0.00 0.00 0.16 0.00 0.00 0.00 0.18
#> TCGA.DU.6396.01 6 0.4554 0.37074 0.00 0.00 0.00 0.00 0.00 0.48 0.42 0.10
#> TCGA.E1.A7YH.01 1 0.1557 0.60927 0.92 0.00 0.00 0.02 0.00 0.00 0.00 0.06
#> TCGA.DU.7306.01 4 0.3185 0.62215 0.04 0.00 0.00 0.82 0.00 0.00 0.06 0.08
#> TCGA.HT.A74J.01 1 0.2569 0.54798 0.82 0.00 0.00 0.00 0.00 0.00 0.02 0.16
#> TCGA.DH.A7US.01 2 0.0808 0.88543 0.00 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.FG.A87N.01 3 0.1741 0.81322 0.00 0.00 0.92 0.00 0.00 0.04 0.02 0.02
#> TCGA.HT.7478.01 1 0.2406 0.54580 0.80 0.00 0.00 0.00 0.00 0.00 0.00 0.20
#> TCGA.DB.A4XE.01 1 0.2404 0.57332 0.84 0.00 0.00 0.02 0.00 0.00 0.00 0.14
#> TCGA.DB.A64L.01 5 0.1557 0.86695 0.00 0.00 0.00 0.00 0.92 0.06 0.00 0.02
#> TCGA.VV.A829.01 5 0.2484 0.83786 0.00 0.00 0.00 0.00 0.86 0.10 0.02 0.02
#> TCGA.HT.A61B.01 7 0.4355 0.46024 0.02 0.00 0.00 0.06 0.00 0.04 0.72 0.16
#> TCGA.DH.A66B.01 4 0.3095 0.42254 0.00 0.00 0.00 0.74 0.00 0.00 0.24 0.02
#> TCGA.HT.7603.01 1 0.1947 0.57344 0.86 0.00 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.DU.6397.02 5 0.2484 0.83786 0.00 0.00 0.00 0.00 0.86 0.10 0.02 0.02
#> TCGA.DU.6397.01 5 0.2547 0.81443 0.00 0.12 0.00 0.00 0.84 0.00 0.00 0.04
#> TCGA.DU.5853.01 1 0.3504 0.46445 0.70 0.00 0.00 0.00 0.00 0.00 0.04 0.26
#> TCGA.CS.6670.01 2 0.0808 0.87165 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.DU.7014.01 4 0.3449 0.29684 0.00 0.00 0.00 0.66 0.00 0.00 0.32 0.02
#> TCGA.QH.A65X.01 2 0.1275 0.86401 0.00 0.94 0.00 0.00 0.02 0.00 0.00 0.04
#> TCGA.DB.A64P.01 2 0.2725 0.77929 0.00 0.82 0.00 0.00 0.14 0.00 0.00 0.04
#> TCGA.FG.5965.02 3 0.2856 0.70980 0.00 0.00 0.78 0.00 0.00 0.20 0.00 0.02
#> TCGA.FG.A70Y.01 1 0.2569 0.59389 0.82 0.00 0.00 0.02 0.00 0.00 0.00 0.16
#> TCGA.TQ.A7RV.01 4 0.3218 0.61778 0.06 0.00 0.00 0.82 0.00 0.00 0.06 0.06
#> TCGA.TQ.A7RV.02 4 0.5157 0.38703 0.14 0.00 0.00 0.60 0.00 0.00 0.06 0.20
#> TCGA.HT.A5R7.01 6 0.4233 0.50195 0.04 0.00 0.00 0.00 0.00 0.60 0.02 0.34
#> TCGA.HW.A5KL.01 4 0.0808 0.64480 0.00 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.HT.7474.01 1 0.2224 0.58202 0.86 0.00 0.00 0.00 0.00 0.00 0.02 0.12
#> TCGA.DH.A7UU.01 7 0.3570 0.44146 0.00 0.00 0.00 0.36 0.00 0.00 0.62 0.02
#> TCGA.QH.A6CZ.01 2 0.1607 0.85452 0.00 0.92 0.00 0.00 0.04 0.00 0.00 0.04
#> TCGA.DH.A669.02 5 0.1804 0.85929 0.00 0.00 0.00 0.00 0.90 0.08 0.00 0.02
#> TCGA.DH.A669.01 5 0.2484 0.83786 0.00 0.00 0.00 0.00 0.86 0.10 0.02 0.02
#> TCGA.QH.A6X9.01 4 0.3808 0.24560 0.00 0.00 0.00 0.62 0.00 0.00 0.34 0.04
#> TCGA.P5.A5EZ.01 4 0.3374 0.32166 0.00 0.00 0.00 0.68 0.00 0.00 0.30 0.02
#> TCGA.DU.5871.01 4 0.3450 0.54699 0.12 0.00 0.00 0.76 0.00 0.00 0.00 0.12
#> TCGA.TQ.A7RJ.01 4 0.2399 0.64379 0.04 0.00 0.00 0.88 0.00 0.00 0.04 0.04
#> TCGA.WY.A858.01 1 0.1765 0.58708 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.VM.A8CB.01 2 0.1275 0.88368 0.00 0.94 0.00 0.00 0.00 0.04 0.00 0.02
#> TCGA.HT.7483.01 4 0.4081 0.45553 0.16 0.00 0.00 0.68 0.00 0.00 0.00 0.16
#> TCGA.HT.7687.01 5 0.1557 0.86695 0.00 0.00 0.00 0.00 0.92 0.06 0.00 0.02
#> TCGA.TM.A84G.01 5 0.0000 0.88681 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.A7Z6.01 1 0.1947 0.57717 0.86 0.00 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.TM.A84I.01 6 0.5886 0.22483 0.00 0.00 0.30 0.00 0.00 0.46 0.14 0.10
#> TCGA.CS.5394.01 5 0.1275 0.87896 0.00 0.02 0.00 0.00 0.94 0.00 0.00 0.04
#> TCGA.DU.A76O.01 1 0.4588 0.13493 0.54 0.00 0.00 0.34 0.00 0.00 0.00 0.12
#> TCGA.DU.A5TW.01 4 0.4693 -0.01386 0.42 0.00 0.00 0.46 0.00 0.00 0.00 0.12
#> TCGA.WY.A85A.01 1 0.2938 0.37663 0.70 0.00 0.00 0.00 0.00 0.00 0.00 0.30
#> TCGA.FG.5962.01 5 0.1804 0.85929 0.00 0.00 0.00 0.00 0.90 0.08 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: Node02. Child nodes: Node0121 , Node0122-leaf , Node0123-leaf , Node0211-leaf , Node0212-leaf , Node0213-leaf , Node0221 , Node0222 , Node0231 , Node0232 .
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 214 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.999 1.000 0.4852 0.515 0.515
#> 3 3 0.972 0.957 0.976 0.3360 0.835 0.680
#> 4 4 0.943 0.920 0.960 0.1068 0.923 0.782
#> 5 5 0.759 0.713 0.870 0.0636 0.911 0.712
#> 6 6 0.753 0.684 0.830 0.0399 0.940 0.765
#> 7 7 0.729 0.613 0.763 0.0237 0.923 0.659
#> 8 8 0.733 0.584 0.780 0.0215 0.949 0.744
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.HT.7693.01 2 0.000 0.999 0.00 1.00
#> TCGA.VM.A8C8.01 2 0.000 0.999 0.00 1.00
#> TCGA.DU.A5TS.01 1 0.000 1.000 1.00 0.00
#> TCGA.E1.5305.01 1 0.000 1.000 1.00 0.00
#> TCGA.F6.A8O4.01 1 0.000 1.000 1.00 0.00
#> TCGA.DH.A66G.01 2 0.000 0.999 0.00 1.00
#> TCGA.P5.A731.01 2 0.000 0.999 0.00 1.00
#> TCGA.DU.8163.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.6407.01 2 0.000 0.999 0.00 1.00
#> TCGA.P5.A5F1.01 1 0.000 1.000 1.00 0.00
#> TCGA.VM.A8CF.01 2 0.000 0.999 0.00 1.00
#> TCGA.DU.6542.01 1 0.000 1.000 1.00 0.00
#> TCGA.DH.5143.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.7299.01 1 0.000 1.000 1.00 0.00
#> TCGA.CS.5393.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.7011.01 1 0.000 1.000 1.00 0.00
#> TCGA.TM.A84Q.01 1 0.000 1.000 1.00 0.00
#> TCGA.DB.5281.01 1 0.000 1.000 1.00 0.00
#> TCGA.DB.5270.01 2 0.000 0.999 0.00 1.00
#> TCGA.S9.A6WQ.01 2 0.000 0.999 0.00 1.00
#> TCGA.HT.8106.01 1 0.000 1.000 1.00 0.00
#> TCGA.QH.A6CW.01 1 0.000 1.000 1.00 0.00
#> TCGA.S9.A6WO.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7601.01 2 0.000 0.999 0.00 1.00
#> TCGA.HT.7472.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7880.01 1 0.000 1.000 1.00 0.00
#> TCGA.E1.A7Z3.01 2 0.000 0.999 0.00 1.00
#> TCGA.HT.7873.01 1 0.000 1.000 1.00 0.00
#> TCGA.CS.4938.01 2 0.000 0.999 0.00 1.00
#> TCGA.VM.A8CH.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7476.01 1 0.000 1.000 1.00 0.00
#> TCGA.DB.A75L.01 2 0.000 0.999 0.00 1.00
#> TCGA.RY.A843.01 1 0.000 1.000 1.00 0.00
#> TCGA.TQ.A8XE.02 2 0.000 0.999 0.00 1.00
#> TCGA.HW.7493.01 2 0.000 0.999 0.00 1.00
#> TCGA.DU.8166.01 2 0.000 0.999 0.00 1.00
#> TCGA.HT.7855.01 1 0.000 1.000 1.00 0.00
#> TCGA.DH.A7UT.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.7015.01 2 0.327 0.936 0.06 0.94
#> TCGA.HT.A616.01 2 0.000 0.999 0.00 1.00
#> TCGA.HT.7611.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.8018.01 2 0.000 0.999 0.00 1.00
#> TCGA.DU.5851.01 2 0.000 0.999 0.00 1.00
#> TCGA.WY.A85C.01 1 0.000 1.000 1.00 0.00
#> TCGA.DB.A4XC.01 1 0.000 1.000 1.00 0.00
#> TCGA.P5.A72W.01 1 0.000 1.000 1.00 0.00
#> TCGA.S9.A6TU.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.5855.01 2 0.000 0.999 0.00 1.00
#> TCGA.HT.7884.01 2 0.000 0.999 0.00 1.00
#> TCGA.WH.A86K.01 1 0.000 1.000 1.00 0.00
#> TCGA.WY.A85E.01 2 0.000 0.999 0.00 1.00
#> TCGA.HT.A5R5.01 2 0.000 0.999 0.00 1.00
#> TCGA.FG.6691.01 2 0.000 0.999 0.00 1.00
#> TCGA.S9.A7R3.01 2 0.000 0.999 0.00 1.00
#> TCGA.FG.A4MX.01 1 0.000 1.000 1.00 0.00
#> TCGA.S9.A7IZ.01 2 0.000 0.999 0.00 1.00
#> TCGA.DU.A6S7.01 2 0.000 0.999 0.00 1.00
#> TCGA.HT.8114.01 1 0.000 1.000 1.00 0.00
#> TCGA.HW.8321.01 1 0.000 1.000 1.00 0.00
#> TCGA.P5.A5F4.01 2 0.000 0.999 0.00 1.00
#> TCGA.FG.8191.01 1 0.000 1.000 1.00 0.00
#> TCGA.DH.5142.01 1 0.000 1.000 1.00 0.00
#> TCGA.E1.A7YW.01 1 0.000 1.000 1.00 0.00
#> TCGA.CS.6666.01 1 0.000 1.000 1.00 0.00
#> TCGA.FG.A60L.01 2 0.000 0.999 0.00 1.00
#> TCGA.DB.5280.01 1 0.000 1.000 1.00 0.00
#> TCGA.TM.A84T.01 1 0.000 1.000 1.00 0.00
#> TCGA.DH.A66D.01 2 0.000 0.999 0.00 1.00
#> TCGA.TQ.A7RR.01 1 0.000 1.000 1.00 0.00
#> TCGA.TQ.A7RH.01 1 0.000 1.000 1.00 0.00
#> TCGA.P5.A735.01 2 0.000 0.999 0.00 1.00
#> TCGA.HT.7609.01 1 0.000 1.000 1.00 0.00
#> TCGA.CS.4944.01 1 0.000 1.000 1.00 0.00
#> TCGA.S9.A7R7.01 1 0.000 1.000 1.00 0.00
#> TCGA.DB.A75M.01 1 0.000 1.000 1.00 0.00
#> TCGA.HW.A5KM.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.8167.01 2 0.000 0.999 0.00 1.00
#> TCGA.S9.A6U1.01 2 0.000 0.999 0.00 1.00
#> TCGA.FG.5965.01 2 0.000 0.999 0.00 1.00
#> TCGA.HT.A614.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.6399.01 1 0.000 1.000 1.00 0.00
#> TCGA.E1.5307.01 2 0.000 0.999 0.00 1.00
#> TCGA.S9.A7QW.01 2 0.000 0.999 0.00 1.00
#> TCGA.HT.7604.01 1 0.000 1.000 1.00 0.00
#> TCGA.P5.A733.01 2 0.000 0.999 0.00 1.00
#> TCGA.HT.7684.01 1 0.000 1.000 1.00 0.00
#> TCGA.DH.A7UV.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7879.01 1 0.000 1.000 1.00 0.00
#> TCGA.TM.A84F.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.A7TC.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7610.01 2 0.000 0.999 0.00 1.00
#> TCGA.FG.A60J.01 2 0.000 0.999 0.00 1.00
#> TCGA.E1.5303.01 1 0.000 1.000 1.00 0.00
#> TCGA.FN.7833.01 1 0.000 1.000 1.00 0.00
#> TCGA.E1.A7Z4.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.A5TR.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7473.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.7008.01 2 0.000 0.999 0.00 1.00
#> TCGA.S9.A6WG.01 1 0.000 1.000 1.00 0.00
#> TCGA.DB.A75O.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7688.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.5872.01 2 0.000 0.999 0.00 1.00
#> TCGA.FG.8185.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7902.01 2 0.000 0.999 0.00 1.00
#> TCGA.FG.6690.01 1 0.000 1.000 1.00 0.00
#> TCGA.HW.8320.01 1 0.000 1.000 1.00 0.00
#> TCGA.P5.A72X.01 1 0.000 1.000 1.00 0.00
#> TCGA.E1.5322.01 2 0.000 0.999 0.00 1.00
#> TCGA.CS.4942.01 2 0.000 0.999 0.00 1.00
#> TCGA.DB.A4X9.01 2 0.000 0.999 0.00 1.00
#> TCGA.DB.A4XF.01 2 0.000 0.999 0.00 1.00
#> TCGA.HT.A74O.01 1 0.000 1.000 1.00 0.00
#> TCGA.FG.8188.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7485.01 1 0.000 1.000 1.00 0.00
#> TCGA.DB.A64S.01 1 0.000 1.000 1.00 0.00
#> TCGA.VV.A86M.01 2 0.000 0.999 0.00 1.00
#> TCGA.TQ.A8XE.01 2 0.000 0.999 0.00 1.00
#> TCGA.CS.6667.01 2 0.000 0.999 0.00 1.00
#> TCGA.TQ.A7RW.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.A7TI.01 1 0.000 1.000 1.00 0.00
#> TCGA.S9.A6U8.01 1 0.000 1.000 1.00 0.00
#> TCGA.HW.7489.01 1 0.000 1.000 1.00 0.00
#> TCGA.R8.A6YH.01 1 0.000 1.000 1.00 0.00
#> TCGA.TM.A7CA.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7690.01 1 0.000 1.000 1.00 0.00
#> TCGA.FG.6689.01 1 0.000 1.000 1.00 0.00
#> TCGA.TQ.A7RF.01 2 0.000 0.999 0.00 1.00
#> TCGA.HT.8013.01 2 0.000 0.999 0.00 1.00
#> TCGA.HW.7490.01 1 0.000 1.000 1.00 0.00
#> TCGA.QH.A65S.01 2 0.000 0.999 0.00 1.00
#> TCGA.P5.A780.01 2 0.000 0.999 0.00 1.00
#> TCGA.E1.5302.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.7309.01 2 0.000 0.999 0.00 1.00
#> TCGA.DU.6395.01 1 0.000 1.000 1.00 0.00
#> TCGA.P5.A5EW.01 2 0.000 0.999 0.00 1.00
#> TCGA.DU.6408.01 2 0.000 0.999 0.00 1.00
#> TCGA.DB.A4XB.01 1 0.000 1.000 1.00 0.00
#> TCGA.FG.A4MT.01 2 0.000 0.999 0.00 1.00
#> TCGA.FG.A4MT.02 2 0.000 0.999 0.00 1.00
#> TCGA.QH.A870.01 2 0.000 0.999 0.00 1.00
#> TCGA.DU.A7TA.01 1 0.000 1.000 1.00 0.00
#> TCGA.TM.A84H.01 2 0.000 0.999 0.00 1.00
#> TCGA.S9.A6TZ.01 2 0.000 0.999 0.00 1.00
#> TCGA.HT.7479.01 1 0.000 1.000 1.00 0.00
#> TCGA.DB.A4XD.01 1 0.000 1.000 1.00 0.00
#> TCGA.DB.5275.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7602.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.A5RB.01 1 0.000 1.000 1.00 0.00
#> TCGA.S9.A7R8.01 2 0.000 0.999 0.00 1.00
#> TCGA.QH.A6XA.01 2 0.000 0.999 0.00 1.00
#> TCGA.HT.8111.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.A5TP.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7482.01 2 0.000 0.999 0.00 1.00
#> TCGA.TQ.A7RK.02 1 0.000 1.000 1.00 0.00
#> TCGA.TQ.A7RK.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.7475.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.A7T8.01 1 0.000 1.000 1.00 0.00
#> TCGA.FG.7636.01 1 0.000 1.000 1.00 0.00
#> TCGA.WY.A859.01 2 0.000 0.999 0.00 1.00
#> TCGA.S9.A6U9.01 1 0.000 1.000 1.00 0.00
#> TCGA.CS.6290.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.7019.01 1 0.000 1.000 1.00 0.00
#> TCGA.FG.A711.01 2 0.000 0.999 0.00 1.00
#> TCGA.S9.A7R4.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7676.01 1 0.000 1.000 1.00 0.00
#> TCGA.P5.A5F2.01 2 0.000 0.999 0.00 1.00
#> TCGA.WY.A85B.01 1 0.000 1.000 1.00 0.00
#> TCGA.S9.A7QX.01 2 0.000 0.999 0.00 1.00
#> TCGA.CS.4943.01 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.WY.A85D.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 2 0.000 0.999 0.00 1.00
#> TCGA.HT.8108.01 2 0.000 0.999 0.00 1.00
#> TCGA.DU.7304.01 1 0.000 1.000 1.00 0.00
#> TCGA.P5.A736.01 2 0.000 0.999 0.00 1.00
#> TCGA.P5.A5EV.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.7301.01 1 0.000 1.000 1.00 0.00
#> TCGA.FG.A4MY.01 2 0.000 0.999 0.00 1.00
#> TCGA.TM.A7CF.01 2 0.000 0.999 0.00 1.00
#> TCGA.TM.A7CF.02 2 0.000 0.999 0.00 1.00
#> TCGA.S9.A6U6.01 1 0.000 1.000 1.00 0.00
#> TCGA.RY.A845.01 2 0.000 0.999 0.00 1.00
#> TCGA.FG.8182.01 1 0.000 1.000 1.00 0.00
#> TCGA.QH.A6X3.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.6401.01 2 0.000 0.999 0.00 1.00
#> TCGA.E1.A7YH.01 2 0.000 0.999 0.00 1.00
#> TCGA.DU.7306.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.A74J.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7478.01 1 0.000 1.000 1.00 0.00
#> TCGA.DB.A4XE.01 2 0.000 0.999 0.00 1.00
#> TCGA.HT.A61B.01 1 0.000 1.000 1.00 0.00
#> TCGA.DH.A66B.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7603.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.5853.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.7014.01 1 0.000 1.000 1.00 0.00
#> TCGA.FG.A70Y.01 2 0.000 0.999 0.00 1.00
#> TCGA.TQ.A7RV.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 0.999 0.00 1.00
#> TCGA.HW.A5KL.01 2 0.000 0.999 0.00 1.00
#> TCGA.HT.7474.01 1 0.000 1.000 1.00 0.00
#> TCGA.QH.A6X9.01 2 0.000 0.999 0.00 1.00
#> TCGA.P5.A5EZ.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.5871.01 2 0.000 0.999 0.00 1.00
#> TCGA.TQ.A7RJ.01 2 0.000 0.999 0.00 1.00
#> TCGA.WY.A858.01 2 0.000 0.999 0.00 1.00
#> TCGA.HT.7483.01 1 0.000 1.000 1.00 0.00
#> TCGA.E1.A7Z6.01 2 0.000 0.999 0.00 1.00
#> TCGA.DU.A76O.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.A5TW.01 2 0.000 0.999 0.00 1.00
#> 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.HT.7693.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.VM.A8C8.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.DU.A5TS.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.E1.5305.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.F6.A8O4.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DH.A66G.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.P5.A731.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.DU.8163.01 1 0.6126 0.310 0.60 0.00 0.40
#> TCGA.DU.6407.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.P5.A5F1.01 1 0.5216 0.646 0.74 0.00 0.26
#> TCGA.VM.A8CF.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.DU.6542.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.DH.5143.01 1 0.3340 0.856 0.88 0.00 0.12
#> TCGA.DU.7299.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.CS.5393.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DU.7011.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.TM.A84Q.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DB.5281.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DB.5270.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.S9.A6WQ.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.HT.8106.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.QH.A6CW.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.S9.A6WO.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.HT.7601.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.HT.7472.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.HT.7880.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.E1.A7Z3.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.HT.7873.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.CS.4938.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.VM.A8CH.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.HT.7476.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DB.A75L.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.RY.A843.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.TQ.A8XE.02 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.HW.7493.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.DU.8166.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.HT.7855.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DH.A7UT.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.DU.7015.01 2 0.3686 0.830 0.14 0.86 0.00
#> TCGA.HT.A616.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.HT.7611.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.HT.8018.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.DU.5851.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.WY.A85C.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DB.A4XC.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.P5.A72W.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.S9.A6TU.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DU.5855.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.HT.7884.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.WH.A86K.01 1 0.2537 0.900 0.92 0.00 0.08
#> TCGA.WY.A85E.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.HT.A5R5.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.FG.6691.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.S9.A7R3.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.FG.A4MX.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.S9.A7IZ.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.DU.A6S7.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.HT.8114.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.HW.8321.01 1 0.5706 0.518 0.68 0.00 0.32
#> TCGA.P5.A5F4.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.FG.8191.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.DH.5142.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.E1.A7YW.01 3 0.5397 0.648 0.28 0.00 0.72
#> TCGA.CS.6666.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.FG.A60L.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.DB.5280.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.TM.A84T.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.DH.A66D.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.TQ.A7RR.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.TQ.A7RH.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.P5.A735.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.HT.7609.01 1 0.0892 0.958 0.98 0.00 0.02
#> TCGA.CS.4944.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.S9.A7R7.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.DB.A75M.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.HW.A5KM.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DU.8167.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.S9.A6U1.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.FG.5965.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.HT.A614.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.DU.6399.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.E1.5307.01 2 0.4555 0.749 0.20 0.80 0.00
#> TCGA.S9.A7QW.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.HT.7604.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.P5.A733.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.HT.7684.01 3 0.5835 0.527 0.34 0.00 0.66
#> TCGA.DH.A7UV.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.HT.7879.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.TM.A84F.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.DU.A7TC.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.HT.7610.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.FG.A60J.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.E1.5303.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.FN.7833.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.E1.A7Z4.01 3 0.6126 0.381 0.40 0.00 0.60
#> TCGA.DU.A5TR.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.HT.7473.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.DU.7008.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.S9.A6WG.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.DB.A75O.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.HT.7688.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DU.5872.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.FG.8185.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.HT.7902.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.FG.6690.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.HW.8320.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.P5.A72X.01 3 0.2959 0.900 0.10 0.00 0.90
#> TCGA.E1.5322.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.CS.4942.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.DB.A4X9.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.DB.A4XF.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.HT.A74O.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.FG.8188.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.HT.7485.01 1 0.4002 0.805 0.84 0.00 0.16
#> TCGA.DB.A64S.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.VV.A86M.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.TQ.A8XE.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.CS.6667.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.TQ.A7RW.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DU.A7TI.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.S9.A6U8.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.HW.7489.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.R8.A6YH.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.TM.A7CA.01 1 0.2537 0.900 0.92 0.00 0.08
#> TCGA.HT.7690.01 3 0.1529 0.951 0.04 0.00 0.96
#> TCGA.FG.6689.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.TQ.A7RF.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.HT.8013.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.HW.7490.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.QH.A65S.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.P5.A780.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.E1.5302.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.DU.7309.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.DU.6395.01 3 0.4002 0.833 0.16 0.00 0.84
#> TCGA.P5.A5EW.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.DU.6408.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.DB.A4XB.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.FG.A4MT.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.FG.A4MT.02 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.QH.A870.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.DU.A7TA.01 3 0.2537 0.919 0.08 0.00 0.92
#> TCGA.TM.A84H.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.S9.A6TZ.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.HT.7479.01 1 0.4002 0.804 0.84 0.00 0.16
#> TCGA.DB.A4XD.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DB.5275.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.HT.7602.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.HT.A5RB.01 1 0.0892 0.958 0.98 0.00 0.02
#> TCGA.S9.A7R8.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.QH.A6XA.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.HT.8111.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.DU.A5TP.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.HT.7482.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.TQ.A7RK.02 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.TQ.A7RK.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.HT.7858.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.HT.7475.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.DU.A7T8.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.FG.7636.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.WY.A859.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.S9.A6U9.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.CS.6290.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.DU.7019.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.FG.A711.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.S9.A7R4.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.HT.7676.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.P5.A5F2.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.WY.A85B.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.S9.A7QX.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.CS.4943.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DB.5276.01 1 0.4291 0.776 0.82 0.00 0.18
#> TCGA.TM.A84L.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.WY.A85D.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DB.5273.01 3 0.2959 0.899 0.10 0.00 0.90
#> TCGA.TM.A7C4.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.HT.8108.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.DU.7304.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.P5.A736.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.P5.A5EV.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DU.7301.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.FG.A4MY.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.TM.A7CF.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.TM.A7CF.02 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.S9.A6U6.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.RY.A845.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.FG.8182.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.QH.A6X3.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DU.6401.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.E1.A7YH.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.DU.7306.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.HT.A74J.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.HT.7478.01 3 0.4002 0.832 0.16 0.00 0.84
#> TCGA.DB.A4XE.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.HT.A61B.01 3 0.1529 0.951 0.04 0.00 0.96
#> TCGA.DH.A66B.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.HT.7603.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DU.5853.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.DU.7014.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.FG.A70Y.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.TQ.A7RV.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.TQ.A7RV.02 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.HT.A5R7.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.HW.A5KL.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.HT.7474.01 3 0.0892 0.965 0.02 0.00 0.98
#> TCGA.QH.A6X9.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.P5.A5EZ.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DU.5871.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.TQ.A7RJ.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.WY.A858.01 2 0.0892 0.985 0.00 0.98 0.02
#> TCGA.HT.7483.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.E1.A7Z6.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.DU.A76O.01 1 0.0000 0.976 1.00 0.00 0.00
#> TCGA.DU.A5TW.01 2 0.0000 0.990 0.00 1.00 0.00
#> TCGA.WY.A85A.01 3 0.0892 0.965 0.02 0.00 0.98
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.HT.7693.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.VM.A8C8.01 2 0.0707 0.9598 0.00 0.98 0.00 0.02
#> TCGA.DU.A5TS.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.E1.5305.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.F6.A8O4.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.DH.A66G.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.P5.A731.01 4 0.1211 0.9633 0.00 0.04 0.00 0.96
#> TCGA.DU.8163.01 3 0.4977 0.1507 0.46 0.00 0.54 0.00
#> TCGA.DU.6407.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.P5.A5F1.01 1 0.4855 0.3335 0.60 0.00 0.40 0.00
#> TCGA.VM.A8CF.01 2 0.0707 0.9597 0.00 0.98 0.00 0.02
#> TCGA.DU.6542.01 3 0.0707 0.9265 0.00 0.00 0.98 0.02
#> TCGA.DH.5143.01 1 0.2921 0.8378 0.86 0.00 0.14 0.00
#> TCGA.DU.7299.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.CS.5393.01 1 0.0707 0.9607 0.98 0.00 0.02 0.00
#> TCGA.DU.7011.01 3 0.0707 0.9265 0.00 0.00 0.98 0.02
#> TCGA.TM.A84Q.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.DB.5281.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.DB.5270.01 4 0.1211 0.9633 0.00 0.04 0.00 0.96
#> TCGA.S9.A6WQ.01 4 0.4977 0.1754 0.00 0.46 0.00 0.54
#> TCGA.HT.8106.01 3 0.0707 0.9224 0.00 0.00 0.98 0.02
#> TCGA.QH.A6CW.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.S9.A6WO.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.HT.7601.01 4 0.1211 0.9633 0.00 0.04 0.00 0.96
#> TCGA.HT.7472.01 3 0.0000 0.9254 0.00 0.00 1.00 0.00
#> TCGA.HT.7880.01 3 0.0707 0.9265 0.00 0.00 0.98 0.02
#> TCGA.E1.A7Z3.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.HT.7873.01 3 0.0707 0.9224 0.00 0.00 0.98 0.02
#> TCGA.CS.4938.01 2 0.1211 0.9469 0.00 0.96 0.00 0.04
#> TCGA.VM.A8CH.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.HT.7476.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.DB.A75L.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.RY.A843.01 1 0.1211 0.9475 0.96 0.00 0.04 0.00
#> TCGA.TQ.A8XE.02 4 0.1637 0.9470 0.00 0.06 0.00 0.94
#> TCGA.HW.7493.01 2 0.1211 0.9469 0.00 0.96 0.00 0.04
#> TCGA.DU.8166.01 2 0.1211 0.9469 0.00 0.96 0.00 0.04
#> TCGA.HT.7855.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.DH.A7UT.01 3 0.1211 0.9207 0.00 0.00 0.96 0.04
#> TCGA.DU.7015.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.HT.A616.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.HT.7611.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.HT.8018.01 4 0.1211 0.9633 0.00 0.04 0.00 0.96
#> TCGA.DU.5851.01 4 0.1211 0.9633 0.00 0.04 0.00 0.96
#> TCGA.WY.A85C.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.DB.A4XC.01 3 0.0707 0.9224 0.00 0.00 0.98 0.02
#> TCGA.P5.A72W.01 3 0.0000 0.9254 0.00 0.00 1.00 0.00
#> TCGA.S9.A6TU.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.DU.5855.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.HT.7884.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.WH.A86K.01 1 0.3606 0.8201 0.84 0.00 0.14 0.02
#> TCGA.WY.A85E.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.HT.A5R5.01 4 0.1211 0.9633 0.00 0.04 0.00 0.96
#> TCGA.FG.6691.01 2 0.2921 0.8366 0.00 0.86 0.00 0.14
#> TCGA.S9.A7R3.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.FG.A4MX.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.S9.A7IZ.01 4 0.1211 0.9633 0.00 0.04 0.00 0.96
#> TCGA.DU.A6S7.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.HT.8114.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.HW.8321.01 3 0.5000 -0.0066 0.50 0.00 0.50 0.00
#> TCGA.P5.A5F4.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.FG.8191.01 3 0.0000 0.9254 0.00 0.00 1.00 0.00
#> TCGA.DH.5142.01 3 0.0707 0.9224 0.00 0.00 0.98 0.02
#> TCGA.E1.A7YW.01 3 0.3400 0.7495 0.18 0.00 0.82 0.00
#> TCGA.CS.6666.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.FG.A60L.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.DB.5280.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.TM.A84T.01 3 0.0707 0.9265 0.00 0.00 0.98 0.02
#> TCGA.DH.A66D.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.TQ.A7RR.01 3 0.0707 0.9224 0.00 0.00 0.98 0.02
#> TCGA.TQ.A7RH.01 3 0.0707 0.9265 0.00 0.00 0.98 0.02
#> TCGA.P5.A735.01 2 0.1211 0.9469 0.00 0.96 0.00 0.04
#> TCGA.HT.7609.01 1 0.1211 0.9415 0.96 0.00 0.04 0.00
#> TCGA.CS.4944.01 3 0.0000 0.9254 0.00 0.00 1.00 0.00
#> TCGA.S9.A7R7.01 3 0.1211 0.9207 0.00 0.00 0.96 0.04
#> TCGA.DB.A75M.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.HW.A5KM.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.DU.8167.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.S9.A6U1.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.FG.5965.01 4 0.1211 0.9633 0.00 0.04 0.00 0.96
#> TCGA.HT.A614.01 3 0.0707 0.9224 0.00 0.00 0.98 0.02
#> TCGA.DU.6399.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.E1.5307.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.S9.A7QW.01 4 0.1211 0.9633 0.00 0.04 0.00 0.96
#> TCGA.HT.7604.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.P5.A733.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.HT.7684.01 3 0.5173 0.5350 0.32 0.00 0.66 0.02
#> TCGA.DH.A7UV.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.HT.7879.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.TM.A84F.01 3 0.1211 0.9207 0.00 0.00 0.96 0.04
#> TCGA.DU.A7TC.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.HT.7610.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.FG.A60J.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.E1.5303.01 1 0.0707 0.9607 0.98 0.00 0.02 0.00
#> TCGA.FN.7833.01 3 0.0707 0.9265 0.00 0.00 0.98 0.02
#> TCGA.E1.A7Z4.01 3 0.4134 0.6480 0.26 0.00 0.74 0.00
#> TCGA.DU.A5TR.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.HT.7473.01 3 0.0707 0.9265 0.00 0.00 0.98 0.02
#> TCGA.DU.7008.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.S9.A6WG.01 3 0.0707 0.9265 0.00 0.00 0.98 0.02
#> TCGA.DB.A75O.01 3 0.0707 0.9265 0.00 0.00 0.98 0.02
#> TCGA.HT.7688.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.DU.5872.01 4 0.1211 0.9633 0.00 0.04 0.00 0.96
#> TCGA.FG.8185.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.HT.7902.01 4 0.1211 0.9633 0.00 0.04 0.00 0.96
#> TCGA.FG.6690.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.HW.8320.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.P5.A72X.01 3 0.2011 0.8617 0.08 0.00 0.92 0.00
#> TCGA.E1.5322.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.CS.4942.01 4 0.1211 0.9633 0.00 0.04 0.00 0.96
#> TCGA.DB.A4X9.01 2 0.4277 0.6138 0.00 0.72 0.00 0.28
#> TCGA.DB.A4XF.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.HT.A74O.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.FG.8188.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.HT.7485.01 1 0.4406 0.5743 0.70 0.00 0.30 0.00
#> TCGA.DB.A64S.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.VV.A86M.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.TQ.A8XE.01 4 0.2011 0.9286 0.00 0.08 0.00 0.92
#> TCGA.CS.6667.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.TQ.A7RW.01 1 0.0707 0.9607 0.98 0.00 0.02 0.00
#> TCGA.DU.A7TI.01 1 0.0707 0.9607 0.98 0.00 0.02 0.00
#> TCGA.S9.A6U8.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.HW.7489.01 1 0.0707 0.9607 0.98 0.00 0.02 0.00
#> TCGA.R8.A6YH.01 1 0.1211 0.9475 0.96 0.00 0.04 0.00
#> TCGA.TM.A7CA.01 1 0.4522 0.5398 0.68 0.00 0.32 0.00
#> TCGA.HT.7690.01 3 0.0707 0.9149 0.02 0.00 0.98 0.00
#> TCGA.FG.6689.01 3 0.0000 0.9254 0.00 0.00 1.00 0.00
#> TCGA.TQ.A7RF.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.HT.8013.01 4 0.1211 0.9633 0.00 0.04 0.00 0.96
#> TCGA.HW.7490.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.QH.A65S.01 4 0.1211 0.9633 0.00 0.04 0.00 0.96
#> TCGA.P5.A780.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.E1.5302.01 3 0.0707 0.9265 0.00 0.00 0.98 0.02
#> TCGA.DU.7309.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.DU.6395.01 3 0.3400 0.7497 0.18 0.00 0.82 0.00
#> TCGA.P5.A5EW.01 2 0.1211 0.9469 0.00 0.96 0.00 0.04
#> TCGA.DU.6408.01 4 0.1211 0.9633 0.00 0.04 0.00 0.96
#> TCGA.DB.A4XB.01 3 0.1211 0.9207 0.00 0.00 0.96 0.04
#> TCGA.FG.A4MT.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.FG.A4MT.02 2 0.0707 0.9597 0.00 0.98 0.00 0.02
#> TCGA.QH.A870.01 4 0.1211 0.9633 0.00 0.04 0.00 0.96
#> TCGA.DU.A7TA.01 3 0.1411 0.9186 0.02 0.00 0.96 0.02
#> TCGA.TM.A84H.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.S9.A6TZ.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.HT.7479.01 1 0.3400 0.7913 0.82 0.00 0.18 0.00
#> TCGA.DB.A4XD.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.DB.5275.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.HT.7602.01 3 0.0707 0.9265 0.00 0.00 0.98 0.02
#> TCGA.HT.A5RB.01 1 0.0707 0.9607 0.98 0.00 0.02 0.00
#> TCGA.S9.A7R8.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.QH.A6XA.01 4 0.1211 0.9633 0.00 0.04 0.00 0.96
#> TCGA.HT.8111.01 3 0.0707 0.9224 0.00 0.00 0.98 0.02
#> TCGA.DU.A5TP.01 3 0.0707 0.9265 0.00 0.00 0.98 0.02
#> TCGA.HT.7482.01 2 0.1211 0.9469 0.00 0.96 0.00 0.04
#> TCGA.TQ.A7RK.02 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RK.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.HT.7858.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.HT.7475.01 3 0.0707 0.9265 0.00 0.00 0.98 0.02
#> TCGA.DU.A7T8.01 1 0.0707 0.9607 0.98 0.00 0.02 0.00
#> TCGA.FG.7636.01 1 0.0707 0.9607 0.98 0.00 0.02 0.00
#> TCGA.WY.A859.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.S9.A6U9.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.CS.6290.01 3 0.0000 0.9254 0.00 0.00 1.00 0.00
#> TCGA.DU.7019.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.FG.A711.01 4 0.1211 0.9633 0.00 0.04 0.00 0.96
#> TCGA.S9.A7R4.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.HT.7676.01 3 0.0000 0.9254 0.00 0.00 1.00 0.00
#> TCGA.P5.A5F2.01 2 0.0707 0.9598 0.00 0.98 0.00 0.02
#> TCGA.WY.A85B.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.S9.A7QX.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.CS.4943.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.DB.5276.01 1 0.3801 0.7321 0.78 0.00 0.22 0.00
#> TCGA.TM.A84L.01 1 0.1211 0.9475 0.96 0.00 0.04 0.00
#> TCGA.WY.A85D.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.DB.5273.01 3 0.2011 0.8624 0.08 0.00 0.92 0.00
#> TCGA.TM.A7C4.01 2 0.0707 0.9598 0.00 0.98 0.00 0.02
#> TCGA.HT.8108.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.DU.7304.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.P5.A736.01 2 0.1211 0.9469 0.00 0.96 0.00 0.04
#> TCGA.P5.A5EV.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.DU.7301.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.FG.A4MY.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.TM.A7CF.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.TM.A7CF.02 2 0.4522 0.5255 0.00 0.68 0.00 0.32
#> TCGA.S9.A6U6.01 1 0.0707 0.9607 0.98 0.00 0.02 0.00
#> TCGA.RY.A845.01 2 0.4134 0.6512 0.00 0.74 0.00 0.26
#> TCGA.FG.8182.01 3 0.0707 0.9265 0.00 0.00 0.98 0.02
#> TCGA.QH.A6X3.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.DU.6401.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.E1.A7YH.01 4 0.4406 0.6116 0.00 0.30 0.00 0.70
#> TCGA.DU.7306.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.HT.A74J.01 3 0.0707 0.9265 0.00 0.00 0.98 0.02
#> TCGA.HT.7478.01 3 0.2647 0.8207 0.12 0.00 0.88 0.00
#> TCGA.DB.A4XE.01 2 0.3975 0.6868 0.00 0.76 0.00 0.24
#> TCGA.HT.A61B.01 3 0.1411 0.9107 0.02 0.00 0.96 0.02
#> TCGA.DH.A66B.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.HT.7603.01 1 0.1211 0.9459 0.96 0.00 0.04 0.00
#> TCGA.DU.5853.01 3 0.0707 0.9265 0.00 0.00 0.98 0.02
#> TCGA.DU.7014.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.FG.A70Y.01 2 0.1211 0.9469 0.00 0.96 0.00 0.04
#> TCGA.TQ.A7RV.01 1 0.0707 0.9607 0.98 0.00 0.02 0.00
#> TCGA.TQ.A7RV.02 3 0.0000 0.9254 0.00 0.00 1.00 0.00
#> TCGA.HT.A5R7.01 4 0.1211 0.9633 0.00 0.04 0.00 0.96
#> TCGA.HW.A5KL.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.HT.7474.01 3 0.0000 0.9254 0.00 0.00 1.00 0.00
#> TCGA.QH.A6X9.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.P5.A5EZ.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.DU.5871.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.TQ.A7RJ.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.WY.A858.01 4 0.1211 0.9633 0.00 0.04 0.00 0.96
#> TCGA.HT.7483.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.E1.A7Z6.01 2 0.1211 0.9469 0.00 0.96 0.00 0.04
#> TCGA.DU.A76O.01 1 0.0000 0.9711 1.00 0.00 0.00 0.00
#> TCGA.DU.A5TW.01 2 0.0000 0.9705 0.00 1.00 0.00 0.00
#> TCGA.WY.A85A.01 3 0.0707 0.9265 0.00 0.00 0.98 0.02
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 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.VM.A8C8.01 2 0.3390 0.86783 0.00 0.84 0.00 0.06 0.10
#> TCGA.DU.A5TS.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5305.01 1 0.3274 0.70077 0.78 0.00 0.22 0.00 0.00
#> TCGA.F6.A8O4.01 1 0.3983 0.39332 0.66 0.00 0.34 0.00 0.00
#> TCGA.DH.A66G.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A731.01 4 0.0000 0.90538 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.8163.01 3 0.1732 0.59268 0.08 0.00 0.92 0.00 0.00
#> TCGA.DU.6407.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A5F1.01 3 0.2732 0.57943 0.16 0.00 0.84 0.00 0.00
#> TCGA.VM.A8CF.01 2 0.3037 0.87799 0.00 0.86 0.00 0.04 0.10
#> TCGA.DU.6542.01 3 0.1732 0.50758 0.00 0.00 0.92 0.00 0.08
#> TCGA.DH.5143.01 3 0.3274 0.55484 0.22 0.00 0.78 0.00 0.00
#> TCGA.DU.7299.01 1 0.1043 0.89061 0.96 0.00 0.04 0.00 0.00
#> TCGA.CS.5393.01 1 0.3561 0.63556 0.74 0.00 0.26 0.00 0.00
#> TCGA.DU.7011.01 3 0.3895 0.03786 0.00 0.00 0.68 0.00 0.32
#> TCGA.TM.A84Q.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5281.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5270.01 4 0.0000 0.90538 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A6WQ.01 4 0.5828 0.14827 0.00 0.38 0.00 0.52 0.10
#> TCGA.HT.8106.01 3 0.4227 0.09971 0.00 0.00 0.58 0.00 0.42
#> TCGA.QH.A6CW.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WO.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7601.01 4 0.1043 0.90263 0.00 0.00 0.00 0.96 0.04
#> TCGA.HT.7472.01 3 0.0000 0.56251 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7880.01 5 0.4302 0.52797 0.00 0.00 0.48 0.00 0.52
#> TCGA.E1.A7Z3.01 2 0.2020 0.89200 0.00 0.90 0.00 0.00 0.10
#> TCGA.HT.7873.01 3 0.4126 0.18568 0.00 0.00 0.62 0.00 0.38
#> TCGA.CS.4938.01 2 0.4216 0.81593 0.00 0.78 0.00 0.12 0.10
#> TCGA.VM.A8CH.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7476.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A75L.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.RY.A843.01 3 0.3796 0.52277 0.30 0.00 0.70 0.00 0.00
#> TCGA.TQ.A8XE.02 4 0.2020 0.87004 0.00 0.00 0.00 0.90 0.10
#> TCGA.HW.7493.01 2 0.3697 0.85346 0.00 0.82 0.00 0.08 0.10
#> TCGA.DU.8166.01 2 0.3697 0.85585 0.00 0.82 0.00 0.08 0.10
#> TCGA.HT.7855.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A7UT.01 5 0.2516 0.78540 0.00 0.00 0.14 0.00 0.86
#> TCGA.DU.7015.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.A616.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7611.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8018.01 4 0.1043 0.90263 0.00 0.00 0.00 0.96 0.04
#> TCGA.DU.5851.01 4 0.1043 0.90263 0.00 0.00 0.00 0.96 0.04
#> TCGA.WY.A85C.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4XC.01 3 0.3424 0.40030 0.00 0.00 0.76 0.00 0.24
#> TCGA.P5.A72W.01 3 0.1732 0.51406 0.00 0.00 0.92 0.00 0.08
#> TCGA.S9.A6TU.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5855.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7884.01 2 0.2020 0.89200 0.00 0.90 0.00 0.00 0.10
#> TCGA.WH.A86K.01 3 0.5646 0.26224 0.40 0.00 0.52 0.00 0.08
#> TCGA.WY.A85E.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.A5R5.01 4 0.0000 0.90538 0.00 0.00 0.00 1.00 0.00
#> TCGA.FG.6691.01 2 0.4637 0.77008 0.00 0.74 0.00 0.16 0.10
#> TCGA.S9.A7R3.01 2 0.2020 0.89200 0.00 0.90 0.00 0.00 0.10
#> TCGA.FG.A4MX.01 1 0.2020 0.84061 0.90 0.00 0.10 0.00 0.00
#> TCGA.S9.A7IZ.01 4 0.1043 0.90263 0.00 0.00 0.00 0.96 0.04
#> TCGA.DU.A6S7.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.8114.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.HW.8321.01 3 0.2732 0.57542 0.16 0.00 0.84 0.00 0.00
#> TCGA.P5.A5F4.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.8191.01 3 0.1410 0.53179 0.00 0.00 0.94 0.00 0.06
#> TCGA.DH.5142.01 3 0.4126 0.18568 0.00 0.00 0.62 0.00 0.38
#> TCGA.E1.A7YW.01 3 0.1410 0.59252 0.06 0.00 0.94 0.00 0.00
#> TCGA.CS.6666.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A60L.01 2 0.3037 0.87644 0.00 0.86 0.00 0.04 0.10
#> TCGA.DB.5280.01 1 0.4302 -0.09416 0.52 0.00 0.48 0.00 0.00
#> TCGA.TM.A84T.01 3 0.4287 -0.42887 0.00 0.00 0.54 0.00 0.46
#> TCGA.DH.A66D.01 2 0.2020 0.89200 0.00 0.90 0.00 0.00 0.10
#> TCGA.TQ.A7RR.01 3 0.4126 0.18568 0.00 0.00 0.62 0.00 0.38
#> TCGA.TQ.A7RH.01 5 0.3895 0.76053 0.00 0.00 0.32 0.00 0.68
#> TCGA.P5.A735.01 2 0.3697 0.85148 0.00 0.82 0.00 0.08 0.10
#> TCGA.HT.7609.01 3 0.4262 0.32649 0.44 0.00 0.56 0.00 0.00
#> TCGA.CS.4944.01 3 0.0609 0.55571 0.00 0.00 0.98 0.00 0.02
#> TCGA.S9.A7R7.01 5 0.2516 0.78540 0.00 0.00 0.14 0.00 0.86
#> TCGA.DB.A75M.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.HW.A5KM.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.8167.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6U1.01 2 0.1216 0.90461 0.00 0.96 0.00 0.02 0.02
#> TCGA.FG.5965.01 4 0.1043 0.90263 0.00 0.00 0.00 0.96 0.04
#> TCGA.HT.A614.01 3 0.4126 0.18568 0.00 0.00 0.62 0.00 0.38
#> TCGA.DU.6399.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5307.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A7QW.01 4 0.0000 0.90538 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7604.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A733.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7684.01 3 0.5263 0.40755 0.10 0.00 0.66 0.00 0.24
#> TCGA.DH.A7UV.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7879.01 1 0.1043 0.88855 0.96 0.00 0.04 0.00 0.00
#> TCGA.TM.A84F.01 5 0.2516 0.78540 0.00 0.00 0.14 0.00 0.86
#> TCGA.DU.A7TC.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7610.01 2 0.2020 0.89200 0.00 0.90 0.00 0.00 0.10
#> TCGA.FG.A60J.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.5303.01 1 0.3796 0.56216 0.70 0.00 0.30 0.00 0.00
#> TCGA.FN.7833.01 3 0.3684 0.15588 0.00 0.00 0.72 0.00 0.28
#> TCGA.E1.A7Z4.01 3 0.1410 0.59079 0.06 0.00 0.94 0.00 0.00
#> TCGA.DU.A5TR.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7473.01 3 0.3895 0.03786 0.00 0.00 0.68 0.00 0.32
#> TCGA.DU.7008.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6WG.01 3 0.3895 0.03786 0.00 0.00 0.68 0.00 0.32
#> TCGA.DB.A75O.01 5 0.3424 0.81162 0.00 0.00 0.24 0.00 0.76
#> TCGA.HT.7688.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5872.01 4 0.2331 0.86775 0.00 0.02 0.00 0.90 0.08
#> TCGA.FG.8185.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7902.01 4 0.1043 0.90263 0.00 0.00 0.00 0.96 0.04
#> TCGA.FG.6690.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.HW.8320.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A72X.01 3 0.1732 0.58094 0.08 0.00 0.92 0.00 0.00
#> TCGA.E1.5322.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.CS.4942.01 4 0.0000 0.90538 0.00 0.00 0.00 1.00 0.00
#> TCGA.DB.A4X9.01 2 0.5895 0.14278 0.00 0.46 0.00 0.44 0.10
#> TCGA.DB.A4XF.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.A74O.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8188.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7485.01 3 0.3561 0.53189 0.26 0.00 0.74 0.00 0.00
#> TCGA.DB.A64S.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.VV.A86M.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.TQ.A8XE.01 4 0.2020 0.87004 0.00 0.00 0.00 0.90 0.10
#> TCGA.CS.6667.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RW.01 3 0.4262 0.21502 0.44 0.00 0.56 0.00 0.00
#> TCGA.DU.A7TI.01 3 0.4307 -0.00209 0.50 0.00 0.50 0.00 0.00
#> TCGA.S9.A6U8.01 1 0.3274 0.64899 0.78 0.00 0.22 0.00 0.00
#> TCGA.HW.7489.01 1 0.2732 0.76730 0.84 0.00 0.16 0.00 0.00
#> TCGA.R8.A6YH.01 3 0.4060 0.47023 0.36 0.00 0.64 0.00 0.00
#> TCGA.TM.A7CA.01 3 0.3109 0.56804 0.20 0.00 0.80 0.00 0.00
#> TCGA.HT.7690.01 3 0.0609 0.57684 0.02 0.00 0.98 0.00 0.00
#> TCGA.FG.6689.01 3 0.0609 0.55574 0.00 0.00 0.98 0.00 0.02
#> TCGA.TQ.A7RF.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.8013.01 4 0.0000 0.90538 0.00 0.00 0.00 1.00 0.00
#> TCGA.HW.7490.01 1 0.2020 0.83864 0.90 0.00 0.10 0.00 0.00
#> TCGA.QH.A65S.01 4 0.1043 0.90263 0.00 0.00 0.00 0.96 0.04
#> TCGA.P5.A780.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.5302.01 5 0.3561 0.80474 0.00 0.00 0.26 0.00 0.74
#> TCGA.DU.7309.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.6395.01 3 0.2077 0.57854 0.04 0.00 0.92 0.00 0.04
#> TCGA.P5.A5EW.01 2 0.3390 0.86783 0.00 0.84 0.00 0.06 0.10
#> TCGA.DU.6408.01 4 0.1043 0.90263 0.00 0.00 0.00 0.96 0.04
#> TCGA.DB.A4XB.01 5 0.2516 0.78540 0.00 0.00 0.14 0.00 0.86
#> TCGA.FG.A4MT.01 2 0.2616 0.88620 0.00 0.88 0.00 0.02 0.10
#> TCGA.FG.A4MT.02 2 0.3390 0.86783 0.00 0.84 0.00 0.06 0.10
#> TCGA.QH.A870.01 4 0.2020 0.87004 0.00 0.00 0.00 0.90 0.10
#> TCGA.DU.A7TA.01 3 0.3513 0.37116 0.02 0.00 0.80 0.00 0.18
#> TCGA.TM.A84H.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6TZ.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7479.01 3 0.3796 0.51195 0.30 0.00 0.70 0.00 0.00
#> TCGA.DB.A4XD.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5275.01 1 0.3109 0.72870 0.80 0.00 0.20 0.00 0.00
#> TCGA.HT.7602.01 5 0.4302 0.52797 0.00 0.00 0.48 0.00 0.52
#> TCGA.HT.A5RB.01 3 0.4262 0.31151 0.44 0.00 0.56 0.00 0.00
#> TCGA.S9.A7R8.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.QH.A6XA.01 4 0.2020 0.87004 0.00 0.00 0.00 0.90 0.10
#> TCGA.HT.8111.01 3 0.3684 0.33224 0.00 0.00 0.72 0.00 0.28
#> TCGA.DU.A5TP.01 5 0.3424 0.81162 0.00 0.00 0.24 0.00 0.76
#> TCGA.HT.7482.01 2 0.3390 0.86783 0.00 0.84 0.00 0.06 0.10
#> TCGA.TQ.A7RK.02 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RK.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7858.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7475.01 3 0.4287 -0.38501 0.00 0.00 0.54 0.00 0.46
#> TCGA.DU.A7T8.01 3 0.3983 0.47904 0.34 0.00 0.66 0.00 0.00
#> TCGA.FG.7636.01 1 0.3274 0.70097 0.78 0.00 0.22 0.00 0.00
#> TCGA.WY.A859.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6U9.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6290.01 3 0.2929 0.42184 0.00 0.00 0.82 0.00 0.18
#> TCGA.DU.7019.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A711.01 4 0.2280 0.88476 0.00 0.00 0.00 0.88 0.12
#> TCGA.S9.A7R4.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7676.01 3 0.0000 0.56251 0.00 0.00 1.00 0.00 0.00
#> TCGA.P5.A5F2.01 2 0.3390 0.86616 0.00 0.84 0.00 0.06 0.10
#> TCGA.WY.A85B.01 1 0.0609 0.90504 0.98 0.00 0.02 0.00 0.00
#> TCGA.S9.A7QX.01 2 0.1732 0.89707 0.00 0.92 0.00 0.00 0.08
#> TCGA.CS.4943.01 1 0.3109 0.72870 0.80 0.00 0.20 0.00 0.00
#> TCGA.DB.5276.01 3 0.3983 0.48011 0.34 0.00 0.66 0.00 0.00
#> TCGA.TM.A84L.01 3 0.4126 0.44673 0.38 0.00 0.62 0.00 0.00
#> TCGA.WY.A85D.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5273.01 3 0.1043 0.58642 0.04 0.00 0.96 0.00 0.00
#> TCGA.TM.A7C4.01 2 0.3390 0.86783 0.00 0.84 0.00 0.06 0.10
#> TCGA.HT.8108.01 2 0.3390 0.86783 0.00 0.84 0.00 0.06 0.10
#> TCGA.DU.7304.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A736.01 2 0.3390 0.86616 0.00 0.84 0.00 0.06 0.10
#> TCGA.P5.A5EV.01 1 0.2516 0.79918 0.86 0.00 0.14 0.00 0.00
#> TCGA.DU.7301.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A4MY.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.TM.A7CF.01 2 0.2020 0.89200 0.00 0.90 0.00 0.00 0.10
#> TCGA.TM.A7CF.02 2 0.5895 0.14363 0.00 0.46 0.00 0.44 0.10
#> TCGA.S9.A6U6.01 1 0.4302 -0.09183 0.52 0.00 0.48 0.00 0.00
#> TCGA.RY.A845.01 2 0.5895 0.14425 0.00 0.46 0.00 0.44 0.10
#> TCGA.FG.8182.01 3 0.4060 -0.11231 0.00 0.00 0.64 0.00 0.36
#> TCGA.QH.A6X3.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6401.01 2 0.0609 0.90521 0.00 0.98 0.00 0.02 0.00
#> TCGA.E1.A7YH.01 4 0.5130 0.58283 0.00 0.22 0.00 0.68 0.10
#> TCGA.DU.7306.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A74J.01 5 0.4182 0.66542 0.00 0.00 0.40 0.00 0.60
#> TCGA.HT.7478.01 3 0.1410 0.59223 0.06 0.00 0.94 0.00 0.00
#> TCGA.DB.A4XE.01 2 0.5487 0.57487 0.00 0.62 0.00 0.28 0.10
#> TCGA.HT.A61B.01 3 0.4675 0.21502 0.02 0.00 0.60 0.00 0.38
#> TCGA.DH.A66B.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7603.01 3 0.3424 0.54962 0.24 0.00 0.76 0.00 0.00
#> TCGA.DU.5853.01 3 0.3424 0.27526 0.00 0.00 0.76 0.00 0.24
#> TCGA.DU.7014.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A70Y.01 2 0.3390 0.86783 0.00 0.84 0.00 0.06 0.10
#> TCGA.TQ.A7RV.01 1 0.4287 0.13847 0.54 0.00 0.46 0.00 0.00
#> TCGA.TQ.A7RV.02 3 0.0000 0.56251 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.A5R7.01 4 0.1043 0.90263 0.00 0.00 0.00 0.96 0.04
#> TCGA.HW.A5KL.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7474.01 3 0.0000 0.56251 0.00 0.00 1.00 0.00 0.00
#> TCGA.QH.A6X9.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A5EZ.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5871.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RJ.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.WY.A858.01 4 0.2280 0.87219 0.00 0.00 0.00 0.88 0.12
#> TCGA.HT.7483.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7Z6.01 2 0.3697 0.85346 0.00 0.82 0.00 0.08 0.10
#> TCGA.DU.A76O.01 1 0.0000 0.92102 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TW.01 2 0.0000 0.91024 0.00 1.00 0.00 0.00 0.00
#> TCGA.WY.A85A.01 3 0.4307 -0.52909 0.00 0.00 0.50 0.00 0.50
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 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8C8.01 2 0.4345 0.7735 0.00 0.74 0.00 0.18 0.02 0.06
#> TCGA.DU.A5TS.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5305.01 1 0.5150 0.3234 0.62 0.00 0.16 0.00 0.00 0.22
#> TCGA.F6.A8O4.01 1 0.4328 0.0418 0.52 0.00 0.46 0.00 0.00 0.02
#> TCGA.DH.A66G.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A731.01 4 0.1556 0.7303 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.DU.8163.01 3 0.3156 0.4482 0.02 0.00 0.80 0.00 0.00 0.18
#> TCGA.DU.6407.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A5F1.01 3 0.2190 0.5804 0.06 0.00 0.90 0.00 0.00 0.04
#> TCGA.VM.A8CF.01 2 0.2454 0.8312 0.00 0.84 0.00 0.16 0.00 0.00
#> TCGA.DU.6542.01 3 0.2350 0.6007 0.00 0.00 0.88 0.00 0.10 0.02
#> TCGA.DH.5143.01 3 0.5110 -0.4199 0.08 0.00 0.48 0.00 0.00 0.44
#> TCGA.DU.7299.01 1 0.1556 0.8571 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.CS.5393.01 6 0.5867 0.5379 0.28 0.00 0.24 0.00 0.00 0.48
#> TCGA.DU.7011.01 3 0.3950 0.4108 0.00 0.00 0.72 0.00 0.24 0.04
#> TCGA.TM.A84Q.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5281.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5270.01 4 0.2260 0.7272 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.S9.A6WQ.01 4 0.4222 0.5072 0.00 0.26 0.00 0.70 0.02 0.02
#> TCGA.HT.8106.01 6 0.5267 0.6002 0.00 0.00 0.32 0.00 0.12 0.56
#> TCGA.QH.A6CW.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WO.01 1 0.1807 0.8615 0.92 0.00 0.06 0.00 0.00 0.02
#> TCGA.HT.7601.01 4 0.3982 0.7002 0.00 0.00 0.00 0.74 0.06 0.20
#> TCGA.HT.7472.01 3 0.2793 0.3970 0.00 0.00 0.80 0.00 0.00 0.20
#> TCGA.HT.7880.01 5 0.5144 0.4902 0.00 0.00 0.34 0.00 0.56 0.10
#> TCGA.E1.A7Z3.01 2 0.2629 0.8572 0.00 0.88 0.00 0.08 0.02 0.02
#> TCGA.HT.7873.01 6 0.4798 0.7078 0.00 0.00 0.30 0.00 0.08 0.62
#> TCGA.CS.4938.01 2 0.5244 0.4777 0.00 0.56 0.00 0.36 0.02 0.06
#> TCGA.VM.A8CH.01 1 0.0547 0.9065 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.HT.7476.01 1 0.0547 0.9065 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DB.A75L.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RY.A843.01 3 0.3787 0.5100 0.10 0.00 0.78 0.00 0.00 0.12
#> TCGA.TQ.A8XE.02 4 0.1635 0.7273 0.00 0.02 0.00 0.94 0.02 0.02
#> TCGA.HW.7493.01 2 0.5007 0.6880 0.00 0.66 0.00 0.24 0.02 0.08
#> TCGA.DU.8166.01 2 0.5455 0.6370 0.00 0.62 0.00 0.26 0.04 0.08
#> TCGA.HT.7855.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A7UT.01 5 0.2454 0.7294 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.DU.7015.01 2 0.0547 0.8734 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.HT.A616.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7611.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8018.01 4 0.3982 0.7002 0.00 0.00 0.00 0.74 0.06 0.20
#> TCGA.DU.5851.01 4 0.3982 0.7002 0.00 0.00 0.00 0.74 0.06 0.20
#> TCGA.WY.A85C.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4XC.01 6 0.4199 0.6698 0.00 0.00 0.38 0.00 0.02 0.60
#> TCGA.P5.A72W.01 3 0.1480 0.6088 0.00 0.00 0.94 0.00 0.04 0.02
#> TCGA.S9.A6TU.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5855.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7884.01 2 0.2345 0.8646 0.00 0.90 0.00 0.06 0.02 0.02
#> TCGA.WH.A86K.01 6 0.5267 0.6660 0.12 0.00 0.32 0.00 0.00 0.56
#> TCGA.WY.A85E.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A5R5.01 4 0.2048 0.7352 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.FG.6691.01 4 0.6043 -0.0526 0.00 0.40 0.00 0.46 0.04 0.10
#> TCGA.S9.A7R3.01 2 0.0937 0.8791 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.FG.A4MX.01 1 0.3679 0.6692 0.76 0.00 0.20 0.00 0.00 0.04
#> TCGA.S9.A7IZ.01 4 0.3660 0.7098 0.00 0.00 0.00 0.78 0.06 0.16
#> TCGA.DU.A6S7.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8114.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HW.8321.01 3 0.1480 0.6167 0.04 0.00 0.94 0.00 0.00 0.02
#> TCGA.P5.A5F4.01 2 0.1480 0.8771 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.FG.8191.01 3 0.1092 0.6116 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.DH.5142.01 6 0.5012 0.6963 0.00 0.00 0.30 0.00 0.10 0.60
#> TCGA.E1.A7YW.01 3 0.1267 0.5864 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.CS.6666.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A60L.01 2 0.3111 0.8380 0.00 0.84 0.00 0.12 0.02 0.02
#> TCGA.DB.5280.01 3 0.4078 0.3422 0.34 0.00 0.64 0.00 0.00 0.02
#> TCGA.TM.A84T.01 3 0.3851 -0.1595 0.00 0.00 0.54 0.00 0.46 0.00
#> TCGA.DH.A66D.01 2 0.3318 0.8306 0.00 0.82 0.00 0.14 0.02 0.02
#> TCGA.TQ.A7RR.01 6 0.4552 0.7103 0.00 0.00 0.30 0.00 0.06 0.64
#> TCGA.TQ.A7RH.01 5 0.2454 0.7455 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.P5.A735.01 2 0.4334 0.7429 0.00 0.72 0.00 0.22 0.02 0.04
#> TCGA.HT.7609.01 3 0.3819 0.4330 0.28 0.00 0.70 0.00 0.00 0.02
#> TCGA.CS.4944.01 3 0.4993 -0.0783 0.00 0.00 0.56 0.00 0.08 0.36
#> TCGA.S9.A7R7.01 5 0.2454 0.7294 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.DB.A75M.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HW.A5KM.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.8167.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6U1.01 2 0.3697 0.8321 0.00 0.82 0.00 0.06 0.04 0.08
#> TCGA.FG.5965.01 4 0.3829 0.7053 0.00 0.00 0.00 0.76 0.06 0.18
#> TCGA.HT.A614.01 6 0.4929 0.6971 0.00 0.00 0.28 0.00 0.10 0.62
#> TCGA.DU.6399.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5307.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7QW.01 4 0.2094 0.7333 0.00 0.00 0.00 0.90 0.02 0.08
#> TCGA.HT.7604.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A733.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7684.01 6 0.4913 0.7067 0.02 0.00 0.34 0.00 0.04 0.60
#> TCGA.DH.A7UV.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7879.01 1 0.1556 0.8589 0.92 0.00 0.08 0.00 0.00 0.00
#> TCGA.TM.A84F.01 5 0.2454 0.7294 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.DU.A7TC.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7610.01 2 0.3600 0.8359 0.00 0.82 0.00 0.08 0.02 0.08
#> TCGA.FG.A60J.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5303.01 6 0.6010 0.4369 0.36 0.00 0.24 0.00 0.00 0.40
#> TCGA.FN.7833.01 3 0.3592 0.4362 0.00 0.00 0.74 0.00 0.24 0.02
#> TCGA.E1.A7Z4.01 3 0.0547 0.6050 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.DU.A5TR.01 1 0.0547 0.9065 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.HT.7473.01 3 0.3819 0.3429 0.00 0.00 0.70 0.00 0.28 0.02
#> TCGA.DU.7008.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WG.01 3 0.3711 0.3734 0.00 0.00 0.72 0.00 0.26 0.02
#> TCGA.DB.A75O.01 5 0.1814 0.7742 0.00 0.00 0.10 0.00 0.90 0.00
#> TCGA.HT.7688.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5872.01 4 0.2190 0.7016 0.00 0.04 0.00 0.90 0.00 0.06
#> TCGA.FG.8185.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7902.01 4 0.3982 0.7002 0.00 0.00 0.00 0.74 0.06 0.20
#> TCGA.FG.6690.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HW.8320.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A72X.01 3 0.0937 0.6124 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.E1.5322.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.4942.01 4 0.1814 0.7369 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.DB.A4X9.01 4 0.4913 0.2878 0.00 0.34 0.00 0.60 0.02 0.04
#> TCGA.DB.A4XF.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A74O.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8188.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7485.01 6 0.5071 0.6167 0.08 0.00 0.40 0.00 0.00 0.52
#> TCGA.DB.A64S.01 1 0.2094 0.8406 0.90 0.00 0.08 0.00 0.00 0.02
#> TCGA.VV.A86M.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A8XE.01 4 0.2345 0.7129 0.00 0.06 0.00 0.90 0.02 0.02
#> TCGA.CS.6667.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RW.01 6 0.5987 0.5385 0.26 0.00 0.30 0.00 0.00 0.44
#> TCGA.DU.A7TI.01 3 0.6129 -0.4663 0.32 0.00 0.34 0.00 0.00 0.34
#> TCGA.S9.A6U8.01 1 0.4246 0.2523 0.58 0.00 0.40 0.00 0.00 0.02
#> TCGA.HW.7489.01 1 0.4475 0.5478 0.70 0.00 0.20 0.00 0.00 0.10
#> TCGA.R8.A6YH.01 3 0.3163 0.5622 0.14 0.00 0.82 0.00 0.00 0.04
#> TCGA.TM.A7CA.01 3 0.1092 0.6049 0.02 0.00 0.96 0.00 0.00 0.02
#> TCGA.HT.7690.01 3 0.0547 0.6050 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.FG.6689.01 3 0.2048 0.5402 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.TQ.A7RF.01 2 0.1092 0.8809 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.HT.8013.01 4 0.1556 0.7364 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.HW.7490.01 1 0.3321 0.7374 0.82 0.00 0.10 0.00 0.00 0.08
#> TCGA.QH.A65S.01 4 0.3829 0.7053 0.00 0.00 0.00 0.76 0.06 0.18
#> TCGA.P5.A780.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5302.01 5 0.1814 0.7742 0.00 0.00 0.10 0.00 0.90 0.00
#> TCGA.DU.7309.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6395.01 3 0.0937 0.6052 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.P5.A5EW.01 2 0.5106 0.7188 0.00 0.68 0.00 0.20 0.04 0.08
#> TCGA.DU.6408.01 4 0.3829 0.7053 0.00 0.00 0.00 0.76 0.06 0.18
#> TCGA.DB.A4XB.01 5 0.2454 0.7294 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.FG.A4MT.01 2 0.4626 0.7798 0.00 0.74 0.00 0.14 0.04 0.08
#> TCGA.FG.A4MT.02 2 0.5106 0.7188 0.00 0.68 0.00 0.20 0.04 0.08
#> TCGA.QH.A870.01 4 0.2882 0.6828 0.00 0.02 0.00 0.86 0.02 0.10
#> TCGA.DU.A7TA.01 3 0.3592 0.4047 0.00 0.00 0.74 0.00 0.24 0.02
#> TCGA.TM.A84H.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TZ.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7479.01 3 0.3270 0.5760 0.12 0.00 0.82 0.00 0.00 0.06
#> TCGA.DB.A4XD.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5275.01 1 0.5027 0.3820 0.64 0.00 0.20 0.00 0.00 0.16
#> TCGA.HT.7602.01 5 0.5144 0.4902 0.00 0.00 0.34 0.00 0.56 0.10
#> TCGA.HT.A5RB.01 3 0.3523 0.5015 0.18 0.00 0.78 0.00 0.00 0.04
#> TCGA.S9.A7R8.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6XA.01 4 0.1480 0.7118 0.00 0.00 0.00 0.94 0.02 0.04
#> TCGA.HT.8111.01 6 0.4144 0.6851 0.00 0.00 0.36 0.00 0.02 0.62
#> TCGA.DU.A5TP.01 5 0.2350 0.7744 0.00 0.00 0.10 0.00 0.88 0.02
#> TCGA.HT.7482.01 2 0.5106 0.7188 0.00 0.68 0.00 0.20 0.04 0.08
#> TCGA.TQ.A7RK.02 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RK.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7858.01 1 0.1092 0.8927 0.96 0.00 0.02 0.00 0.00 0.02
#> TCGA.HT.7475.01 3 0.4758 0.1389 0.00 0.00 0.58 0.00 0.36 0.06
#> TCGA.DU.A7T8.01 3 0.3475 0.4598 0.14 0.00 0.80 0.00 0.00 0.06
#> TCGA.FG.7636.01 1 0.4890 0.4302 0.66 0.00 0.18 0.00 0.00 0.16
#> TCGA.WY.A859.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6U9.01 1 0.0547 0.9065 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CS.6290.01 3 0.5083 0.0361 0.00 0.00 0.58 0.00 0.10 0.32
#> TCGA.DU.7019.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A711.01 4 0.2350 0.7374 0.00 0.00 0.00 0.88 0.02 0.10
#> TCGA.S9.A7R4.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7676.01 3 0.0937 0.5973 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.P5.A5F2.01 2 0.3318 0.8252 0.00 0.82 0.00 0.14 0.02 0.02
#> TCGA.WY.A85B.01 1 0.2350 0.8192 0.88 0.00 0.10 0.00 0.00 0.02
#> TCGA.S9.A7QX.01 2 0.3007 0.8545 0.00 0.86 0.00 0.08 0.02 0.04
#> TCGA.CS.4943.01 1 0.4377 0.5741 0.72 0.00 0.12 0.00 0.00 0.16
#> TCGA.DB.5276.01 3 0.6046 0.2174 0.28 0.00 0.52 0.00 0.02 0.18
#> TCGA.TM.A84L.01 3 0.4566 0.4667 0.16 0.00 0.70 0.00 0.00 0.14
#> TCGA.WY.A85D.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5273.01 3 0.3819 0.1512 0.02 0.00 0.70 0.00 0.00 0.28
#> TCGA.TM.A7C4.01 2 0.4803 0.7606 0.00 0.72 0.00 0.16 0.04 0.08
#> TCGA.HT.8108.01 2 0.5236 0.6927 0.00 0.66 0.00 0.22 0.04 0.08
#> TCGA.DU.7304.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A736.01 2 0.3506 0.8114 0.00 0.80 0.00 0.16 0.02 0.02
#> TCGA.P5.A5EV.01 1 0.3985 0.6457 0.76 0.00 0.14 0.00 0.00 0.10
#> TCGA.DU.7301.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A4MY.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A7CF.01 2 0.3795 0.8225 0.00 0.80 0.00 0.12 0.02 0.06
#> TCGA.TM.A7CF.02 4 0.5833 0.0805 0.00 0.38 0.00 0.50 0.04 0.08
#> TCGA.S9.A6U6.01 3 0.3819 0.4182 0.28 0.00 0.70 0.00 0.00 0.02
#> TCGA.RY.A845.01 4 0.5832 0.3146 0.00 0.30 0.00 0.56 0.04 0.10
#> TCGA.FG.8182.01 3 0.4002 0.2588 0.00 0.00 0.66 0.00 0.32 0.02
#> TCGA.QH.A6X3.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6401.01 2 0.3697 0.8321 0.00 0.82 0.00 0.06 0.04 0.08
#> TCGA.E1.A7YH.01 4 0.4495 0.5756 0.00 0.20 0.00 0.72 0.02 0.06
#> TCGA.DU.7306.01 1 0.1480 0.8738 0.94 0.00 0.02 0.00 0.00 0.04
#> TCGA.HT.A74J.01 5 0.5029 0.5951 0.00 0.00 0.26 0.00 0.62 0.12
#> TCGA.HT.7478.01 3 0.2094 0.5767 0.02 0.00 0.90 0.00 0.00 0.08
#> TCGA.DB.A4XE.01 4 0.5949 0.1865 0.00 0.34 0.00 0.52 0.04 0.10
#> TCGA.HT.A61B.01 6 0.4798 0.7078 0.00 0.00 0.30 0.00 0.08 0.62
#> TCGA.DH.A66B.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7603.01 3 0.5029 0.1130 0.12 0.00 0.62 0.00 0.00 0.26
#> TCGA.DU.5853.01 3 0.3821 0.4868 0.00 0.00 0.74 0.00 0.22 0.04
#> TCGA.DU.7014.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A70Y.01 2 0.5106 0.7188 0.00 0.68 0.00 0.20 0.04 0.08
#> TCGA.TQ.A7RV.01 6 0.6116 0.4518 0.30 0.00 0.34 0.00 0.00 0.36
#> TCGA.TQ.A7RV.02 3 0.5037 -0.1679 0.00 0.00 0.54 0.00 0.08 0.38
#> TCGA.HT.A5R7.01 4 0.3982 0.7002 0.00 0.00 0.00 0.74 0.06 0.20
#> TCGA.HW.A5KL.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7474.01 3 0.3578 0.0825 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.QH.A6X9.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A5EZ.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5871.01 2 0.1092 0.8806 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.TQ.A7RJ.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.WY.A858.01 4 0.1480 0.7384 0.00 0.00 0.00 0.94 0.02 0.04
#> TCGA.HT.7483.01 1 0.0000 0.9176 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7Z6.01 2 0.4042 0.7867 0.00 0.76 0.00 0.18 0.02 0.04
#> TCGA.DU.A76O.01 1 0.0547 0.9065 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DU.A5TW.01 2 0.0000 0.8865 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.WY.A85A.01 5 0.4310 0.3487 0.00 0.00 0.44 0.00 0.54 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.HT.7693.01 2 0.3221 0.92756 0.00 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.VM.A8C8.01 7 0.2422 0.54210 0.00 0.18 0.00 0.00 0.00 0.00 0.82
#> TCGA.DU.A5TS.01 1 0.1363 0.89518 0.94 0.00 0.02 0.00 0.00 0.04 0.00
#> TCGA.E1.5305.01 1 0.4264 0.41808 0.62 0.00 0.06 0.00 0.00 0.32 0.00
#> TCGA.F6.A8O4.01 3 0.3459 0.23128 0.40 0.00 0.60 0.00 0.00 0.00 0.00
#> TCGA.DH.A66G.01 2 0.3221 0.92756 0.00 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.P5.A731.01 4 0.4461 0.61075 0.00 0.00 0.00 0.54 0.00 0.06 0.40
#> TCGA.DU.8163.01 3 0.4264 0.41647 0.02 0.06 0.70 0.00 0.00 0.22 0.00
#> TCGA.DU.6407.01 2 0.3139 0.91387 0.00 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.P5.A5F1.01 3 0.2569 0.54875 0.00 0.02 0.84 0.00 0.00 0.14 0.00
#> TCGA.VM.A8CF.01 7 0.3815 0.00275 0.00 0.36 0.00 0.02 0.00 0.00 0.62
#> TCGA.DU.6542.01 3 0.3630 0.55151 0.00 0.04 0.80 0.00 0.06 0.10 0.00
#> TCGA.DH.5143.01 6 0.4657 0.44795 0.04 0.02 0.40 0.00 0.00 0.54 0.00
#> TCGA.DU.7299.01 1 0.2422 0.77491 0.82 0.00 0.00 0.00 0.00 0.18 0.00
#> TCGA.CS.5393.01 6 0.4538 0.47636 0.28 0.00 0.10 0.00 0.00 0.62 0.00
#> TCGA.DU.7011.01 3 0.4535 0.19130 0.00 0.12 0.64 0.00 0.24 0.00 0.00
#> TCGA.TM.A84Q.01 1 0.0863 0.89964 0.96 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.DB.5281.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5270.01 4 0.4353 0.72057 0.00 0.00 0.00 0.66 0.00 0.10 0.24
#> TCGA.S9.A6WQ.01 7 0.4248 0.37274 0.00 0.08 0.00 0.26 0.00 0.00 0.66
#> TCGA.HT.8106.01 6 0.5876 0.46274 0.00 0.10 0.26 0.00 0.10 0.54 0.00
#> TCGA.QH.A6CW.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WO.01 1 0.2259 0.80431 0.84 0.00 0.16 0.00 0.00 0.00 0.00
#> TCGA.HT.7601.01 4 0.0000 0.78285 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7472.01 3 0.3294 0.20792 0.00 0.00 0.66 0.00 0.00 0.34 0.00
#> TCGA.HT.7880.01 5 0.5545 0.54204 0.00 0.14 0.26 0.00 0.56 0.04 0.00
#> TCGA.E1.A7Z3.01 7 0.3496 -0.24746 0.00 0.42 0.00 0.00 0.00 0.00 0.58
#> TCGA.HT.7873.01 6 0.3991 0.68274 0.00 0.04 0.22 0.00 0.02 0.72 0.00
#> TCGA.CS.4938.01 7 0.3000 0.59026 0.00 0.10 0.00 0.04 0.00 0.02 0.84
#> TCGA.VM.A8CH.01 1 0.2803 0.82760 0.84 0.06 0.10 0.00 0.00 0.00 0.00
#> TCGA.HT.7476.01 1 0.1433 0.87738 0.92 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.DB.A75L.01 2 0.3221 0.92756 0.00 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.RY.A843.01 3 0.3833 0.51020 0.12 0.04 0.78 0.00 0.00 0.06 0.00
#> TCGA.TQ.A8XE.02 7 0.3943 -0.27990 0.00 0.00 0.00 0.42 0.00 0.02 0.56
#> TCGA.HW.7493.01 7 0.2572 0.52388 0.00 0.20 0.00 0.00 0.00 0.00 0.80
#> TCGA.DU.8166.01 7 0.1166 0.58661 0.00 0.06 0.00 0.00 0.00 0.00 0.94
#> TCGA.HT.7855.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A7UT.01 5 0.2569 0.64765 0.00 0.02 0.00 0.00 0.84 0.14 0.00
#> TCGA.DU.7015.01 2 0.4211 0.75654 0.00 0.68 0.02 0.00 0.00 0.04 0.26
#> TCGA.HT.A616.01 2 0.3221 0.92756 0.00 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.HT.7611.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8018.01 4 0.0000 0.78285 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.5851.01 4 0.0000 0.78285 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.WY.A85C.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4XC.01 6 0.2945 0.67790 0.00 0.00 0.26 0.00 0.00 0.74 0.00
#> TCGA.P5.A72W.01 3 0.2213 0.58751 0.00 0.02 0.90 0.00 0.04 0.04 0.00
#> TCGA.S9.A6TU.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5855.01 2 0.3221 0.92756 0.00 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.HT.7884.01 2 0.3562 0.53748 0.00 0.50 0.00 0.00 0.00 0.00 0.50
#> TCGA.WH.A86K.01 6 0.4377 0.68106 0.06 0.02 0.24 0.00 0.00 0.68 0.00
#> TCGA.WY.A85E.01 2 0.3139 0.91387 0.00 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.HT.A5R5.01 4 0.5620 0.62980 0.00 0.02 0.00 0.52 0.02 0.10 0.34
#> TCGA.FG.6691.01 7 0.3772 0.46914 0.00 0.06 0.00 0.02 0.02 0.10 0.80
#> TCGA.S9.A7R3.01 2 0.3562 0.52673 0.00 0.50 0.00 0.00 0.00 0.00 0.50
#> TCGA.FG.A4MX.01 1 0.3526 0.73074 0.76 0.00 0.18 0.00 0.00 0.06 0.00
#> TCGA.S9.A7IZ.01 4 0.1363 0.77961 0.00 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.DU.A6S7.01 2 0.3221 0.92756 0.00 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.HT.8114.01 1 0.0504 0.90954 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.HW.8321.01 3 0.0504 0.59577 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.P5.A5F4.01 2 0.3294 0.90422 0.00 0.66 0.00 0.00 0.00 0.00 0.34
#> TCGA.FG.8191.01 3 0.2159 0.59541 0.00 0.06 0.90 0.00 0.02 0.02 0.00
#> TCGA.DH.5142.01 6 0.3991 0.68274 0.00 0.04 0.22 0.00 0.02 0.72 0.00
#> TCGA.E1.A7YW.01 3 0.2572 0.49344 0.00 0.00 0.80 0.00 0.00 0.20 0.00
#> TCGA.CS.6666.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A60L.01 7 0.2945 0.42093 0.00 0.26 0.00 0.00 0.00 0.00 0.74
#> TCGA.DB.5280.01 3 0.2572 0.48160 0.20 0.00 0.80 0.00 0.00 0.00 0.00
#> TCGA.TM.A84T.01 5 0.4848 0.41334 0.00 0.10 0.40 0.00 0.50 0.00 0.00
#> TCGA.DH.A66D.01 7 0.2832 0.46103 0.00 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.TQ.A7RR.01 6 0.3519 0.68576 0.00 0.04 0.22 0.00 0.00 0.74 0.00
#> TCGA.TQ.A7RH.01 5 0.3487 0.67566 0.00 0.10 0.12 0.00 0.78 0.00 0.00
#> TCGA.P5.A735.01 7 0.2906 0.54126 0.00 0.18 0.00 0.02 0.00 0.00 0.80
#> TCGA.HT.7609.01 3 0.2722 0.55022 0.12 0.00 0.84 0.00 0.04 0.00 0.00
#> TCGA.CS.4944.01 3 0.5408 -0.19294 0.00 0.08 0.46 0.00 0.04 0.42 0.00
#> TCGA.S9.A7R7.01 5 0.2745 0.63696 0.00 0.02 0.00 0.00 0.82 0.16 0.00
#> TCGA.DB.A75M.01 1 0.0504 0.90954 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.HW.A5KM.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.8167.01 2 0.3221 0.92756 0.00 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.S9.A6U1.01 7 0.4923 -0.18672 0.00 0.42 0.00 0.00 0.02 0.06 0.50
#> TCGA.FG.5965.01 4 0.0000 0.78285 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.A614.01 6 0.4193 0.66962 0.00 0.04 0.20 0.00 0.04 0.72 0.00
#> TCGA.DU.6399.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5307.01 2 0.3417 0.85256 0.00 0.72 0.00 0.00 0.00 0.02 0.26
#> TCGA.S9.A7QW.01 4 0.4487 0.58000 0.00 0.00 0.00 0.52 0.00 0.06 0.42
#> TCGA.HT.7604.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A733.01 2 0.3307 0.82893 0.00 0.74 0.00 0.00 0.00 0.02 0.24
#> TCGA.HT.7684.01 6 0.3307 0.68697 0.00 0.02 0.24 0.00 0.00 0.74 0.00
#> TCGA.DH.A7UV.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7879.01 1 0.2259 0.79633 0.84 0.00 0.16 0.00 0.00 0.00 0.00
#> TCGA.TM.A84F.01 5 0.2745 0.63696 0.00 0.02 0.00 0.00 0.82 0.16 0.00
#> TCGA.DU.A7TC.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7610.01 7 0.3294 0.09032 0.00 0.34 0.00 0.00 0.00 0.00 0.66
#> TCGA.FG.A60J.01 2 0.3221 0.92756 0.00 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.E1.5303.01 6 0.5128 0.46109 0.28 0.00 0.18 0.00 0.00 0.54 0.00
#> TCGA.FN.7833.01 3 0.3722 0.42153 0.00 0.04 0.76 0.00 0.18 0.02 0.00
#> TCGA.E1.A7Z4.01 3 0.1886 0.56485 0.00 0.00 0.88 0.00 0.00 0.12 0.00
#> TCGA.DU.A5TR.01 1 0.1433 0.87848 0.92 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.HT.7473.01 3 0.5293 -0.02666 0.00 0.12 0.54 0.00 0.32 0.02 0.00
#> TCGA.DU.7008.01 2 0.3221 0.92756 0.00 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.S9.A6WG.01 3 0.5085 0.13252 0.00 0.12 0.60 0.00 0.26 0.02 0.00
#> TCGA.DB.A75O.01 5 0.1718 0.68860 0.00 0.00 0.04 0.00 0.92 0.04 0.00
#> TCGA.HT.7688.01 1 0.0504 0.90954 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DU.5872.01 7 0.4264 -0.10136 0.00 0.00 0.00 0.32 0.00 0.06 0.62
#> TCGA.FG.8185.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7902.01 4 0.1006 0.76655 0.00 0.02 0.00 0.96 0.00 0.02 0.00
#> TCGA.FG.6690.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HW.8320.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A72X.01 3 0.1363 0.59090 0.00 0.04 0.94 0.00 0.00 0.02 0.00
#> TCGA.E1.5322.01 2 0.3221 0.92756 0.00 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.CS.4942.01 4 0.3927 0.69387 0.00 0.00 0.00 0.66 0.00 0.04 0.30
#> TCGA.DB.A4X9.01 7 0.3228 0.42949 0.00 0.02 0.00 0.16 0.00 0.02 0.80
#> TCGA.DB.A4XF.01 2 0.3221 0.92756 0.00 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.HT.A74O.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8188.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7485.01 6 0.3685 0.62242 0.02 0.00 0.32 0.00 0.00 0.66 0.00
#> TCGA.DB.A64S.01 1 0.2708 0.73729 0.78 0.00 0.22 0.00 0.00 0.00 0.00
#> TCGA.VV.A86M.01 2 0.3517 0.87561 0.00 0.70 0.00 0.00 0.00 0.02 0.28
#> TCGA.TQ.A8XE.01 7 0.3685 0.07996 0.00 0.00 0.00 0.32 0.00 0.02 0.66
#> TCGA.CS.6667.01 2 0.3307 0.82893 0.00 0.74 0.00 0.00 0.00 0.02 0.24
#> TCGA.TQ.A7RW.01 6 0.4451 0.62541 0.10 0.00 0.26 0.00 0.00 0.64 0.00
#> TCGA.DU.A7TI.01 6 0.5560 0.36567 0.28 0.00 0.30 0.00 0.00 0.42 0.00
#> TCGA.S9.A6U8.01 3 0.3562 -0.08240 0.50 0.00 0.50 0.00 0.00 0.00 0.00
#> TCGA.HW.7489.01 1 0.4908 0.47049 0.62 0.02 0.26 0.00 0.00 0.10 0.00
#> TCGA.R8.A6YH.01 3 0.1671 0.57152 0.10 0.00 0.90 0.00 0.00 0.00 0.00
#> TCGA.TM.A7CA.01 3 0.2163 0.57563 0.02 0.00 0.88 0.00 0.00 0.10 0.00
#> TCGA.HT.7690.01 3 0.2081 0.55196 0.00 0.00 0.86 0.00 0.00 0.14 0.00
#> TCGA.FG.6689.01 3 0.3530 0.47747 0.00 0.02 0.76 0.00 0.02 0.20 0.00
#> TCGA.TQ.A7RF.01 2 0.3358 0.87442 0.00 0.64 0.00 0.00 0.00 0.00 0.36
#> TCGA.HT.8013.01 4 0.4127 0.65579 0.00 0.00 0.00 0.60 0.00 0.04 0.36
#> TCGA.HW.7490.01 1 0.2803 0.79193 0.84 0.00 0.06 0.00 0.00 0.10 0.00
#> TCGA.QH.A65S.01 4 0.0000 0.78285 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.P5.A780.01 2 0.3221 0.92756 0.00 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.E1.5302.01 5 0.1718 0.68884 0.00 0.04 0.04 0.00 0.92 0.00 0.00
#> TCGA.DU.7309.01 2 0.3139 0.91145 0.00 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.DU.6395.01 3 0.1166 0.58995 0.00 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.P5.A5EW.01 7 0.2081 0.56431 0.00 0.14 0.00 0.00 0.00 0.00 0.86
#> TCGA.DU.6408.01 4 0.0000 0.78285 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.A4XB.01 5 0.2569 0.64765 0.00 0.02 0.00 0.00 0.84 0.14 0.00
#> TCGA.FG.A4MT.01 7 0.2572 0.51951 0.00 0.20 0.00 0.00 0.00 0.00 0.80
#> TCGA.FG.A4MT.02 7 0.2422 0.54091 0.00 0.18 0.00 0.00 0.00 0.00 0.82
#> TCGA.QH.A870.01 7 0.3517 0.05784 0.00 0.00 0.00 0.28 0.00 0.02 0.70
#> TCGA.DU.A7TA.01 3 0.3770 0.38321 0.00 0.08 0.74 0.00 0.18 0.00 0.00
#> TCGA.TM.A84H.01 2 0.3517 0.87561 0.00 0.70 0.00 0.00 0.00 0.02 0.28
#> TCGA.S9.A6TZ.01 2 0.3221 0.92756 0.00 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.HT.7479.01 3 0.2509 0.57811 0.02 0.06 0.88 0.00 0.00 0.04 0.00
#> TCGA.DB.A4XD.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5275.01 1 0.4353 0.51391 0.66 0.00 0.10 0.00 0.00 0.24 0.00
#> TCGA.HT.7602.01 5 0.5861 0.49204 0.00 0.14 0.28 0.00 0.52 0.06 0.00
#> TCGA.HT.A5RB.01 3 0.2259 0.52134 0.16 0.00 0.84 0.00 0.00 0.00 0.00
#> TCGA.S9.A7R8.01 2 0.3221 0.92756 0.00 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.QH.A6XA.01 7 0.3358 -0.18254 0.00 0.00 0.00 0.36 0.00 0.00 0.64
#> TCGA.HT.8111.01 6 0.4015 0.65809 0.00 0.06 0.26 0.00 0.00 0.68 0.00
#> TCGA.DU.A5TP.01 5 0.1363 0.68886 0.00 0.00 0.04 0.00 0.94 0.02 0.00
#> TCGA.HT.7482.01 7 0.2569 0.55973 0.00 0.14 0.00 0.00 0.00 0.02 0.84
#> TCGA.TQ.A7RK.02 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RK.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7858.01 1 0.1671 0.86253 0.90 0.00 0.10 0.00 0.00 0.00 0.00
#> TCGA.HT.7475.01 5 0.6473 0.19854 0.00 0.08 0.36 0.00 0.36 0.20 0.00
#> TCGA.DU.A7T8.01 3 0.4429 0.36722 0.22 0.00 0.66 0.00 0.00 0.12 0.00
#> TCGA.FG.7636.01 1 0.4264 0.43198 0.62 0.00 0.06 0.00 0.00 0.32 0.00
#> TCGA.WY.A859.01 2 0.3307 0.82893 0.00 0.74 0.00 0.00 0.00 0.02 0.24
#> TCGA.S9.A6U9.01 1 0.1433 0.87738 0.92 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.CS.6290.01 6 0.5817 0.21580 0.00 0.08 0.40 0.00 0.08 0.44 0.00
#> TCGA.DU.7019.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A711.01 4 0.3459 0.55866 0.00 0.00 0.00 0.60 0.00 0.00 0.40
#> TCGA.S9.A7R4.01 1 0.0504 0.90921 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.HT.7676.01 3 0.2572 0.49149 0.00 0.00 0.80 0.00 0.00 0.20 0.00
#> TCGA.P5.A5F2.01 7 0.3047 0.37343 0.00 0.28 0.00 0.00 0.00 0.00 0.72
#> TCGA.WY.A85B.01 1 0.2832 0.70639 0.76 0.00 0.24 0.00 0.00 0.00 0.00
#> TCGA.S9.A7QX.01 7 0.3546 -0.41780 0.00 0.46 0.00 0.00 0.00 0.00 0.54
#> TCGA.CS.4943.01 1 0.3139 0.60499 0.70 0.00 0.00 0.00 0.00 0.30 0.00
#> TCGA.DB.5276.01 3 0.4748 0.43305 0.14 0.06 0.70 0.00 0.00 0.10 0.00
#> TCGA.TM.A84L.01 3 0.4114 0.48829 0.12 0.06 0.76 0.00 0.00 0.06 0.00
#> TCGA.WY.A85D.01 1 0.0504 0.90954 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DB.5273.01 3 0.3985 -0.20320 0.00 0.02 0.52 0.00 0.00 0.46 0.00
#> TCGA.TM.A7C4.01 7 0.2906 0.52085 0.00 0.18 0.00 0.00 0.00 0.02 0.80
#> TCGA.HT.8108.01 7 0.2259 0.55649 0.00 0.16 0.00 0.00 0.00 0.00 0.84
#> TCGA.DU.7304.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A736.01 7 0.2945 0.42693 0.00 0.26 0.00 0.00 0.00 0.00 0.74
#> TCGA.P5.A5EV.01 1 0.3487 0.72186 0.78 0.00 0.10 0.00 0.00 0.12 0.00
#> TCGA.DU.7301.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A4MY.01 2 0.3221 0.92756 0.00 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.TM.A7CF.01 7 0.3047 0.37068 0.00 0.28 0.00 0.00 0.00 0.00 0.72
#> TCGA.TM.A7CF.02 7 0.3848 0.45993 0.00 0.06 0.00 0.16 0.00 0.02 0.76
#> TCGA.S9.A6U6.01 3 0.2572 0.47220 0.20 0.00 0.80 0.00 0.00 0.00 0.00
#> TCGA.RY.A845.01 7 0.3244 0.33859 0.00 0.00 0.00 0.18 0.00 0.04 0.78
#> TCGA.FG.8182.01 3 0.4994 -0.02088 0.00 0.08 0.56 0.00 0.34 0.02 0.00
#> TCGA.QH.A6X3.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6401.01 2 0.4936 0.45830 0.00 0.48 0.00 0.00 0.02 0.06 0.44
#> TCGA.E1.A7YH.01 7 0.3307 0.25050 0.00 0.00 0.00 0.24 0.00 0.02 0.74
#> TCGA.DU.7306.01 1 0.1433 0.87064 0.92 0.00 0.00 0.00 0.00 0.08 0.00
#> TCGA.HT.A74J.01 5 0.6087 0.36910 0.00 0.10 0.34 0.00 0.46 0.10 0.00
#> TCGA.HT.7478.01 3 0.3530 0.47318 0.02 0.02 0.76 0.00 0.00 0.20 0.00
#> TCGA.DB.A4XE.01 7 0.4022 0.41211 0.00 0.02 0.00 0.10 0.02 0.08 0.78
#> TCGA.HT.A61B.01 6 0.3661 0.68758 0.00 0.02 0.22 0.00 0.02 0.74 0.00
#> TCGA.DH.A66B.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7603.01 3 0.5189 0.20822 0.08 0.06 0.62 0.00 0.00 0.24 0.00
#> TCGA.DU.5853.01 3 0.4939 0.39863 0.00 0.02 0.64 0.00 0.20 0.14 0.00
#> TCGA.DU.7014.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A70Y.01 7 0.2259 0.55277 0.00 0.16 0.00 0.00 0.00 0.00 0.84
#> TCGA.TQ.A7RV.01 6 0.6028 0.25743 0.34 0.02 0.30 0.00 0.00 0.34 0.00
#> TCGA.TQ.A7RV.02 3 0.4505 -0.19812 0.00 0.06 0.50 0.00 0.00 0.44 0.00
#> TCGA.HT.A5R7.01 4 0.0000 0.78285 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HW.A5KL.01 2 0.3221 0.92756 0.00 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.HT.7474.01 3 0.4487 -0.12961 0.00 0.06 0.52 0.00 0.00 0.42 0.00
#> TCGA.QH.A6X9.01 2 0.3221 0.92756 0.00 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.P5.A5EZ.01 1 0.0504 0.90954 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DU.5871.01 2 0.3294 0.90422 0.00 0.66 0.00 0.00 0.00 0.00 0.34
#> TCGA.TQ.A7RJ.01 2 0.3221 0.92756 0.00 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.WY.A858.01 7 0.3558 -0.36130 0.00 0.00 0.00 0.48 0.00 0.00 0.52
#> TCGA.HT.7483.01 1 0.0000 0.91652 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7Z6.01 7 0.2832 0.46718 0.00 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.DU.A76O.01 1 0.0504 0.90921 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TW.01 2 0.3221 0.92756 0.00 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.WY.A85A.01 5 0.5293 0.50429 0.00 0.12 0.32 0.00 0.54 0.02 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.HT.7693.01 2 0.0471 0.78140 0.00 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8C8.01 2 0.3318 0.11244 0.00 0.54 0.00 0.00 0.00 0.00 0.46 0.00
#> TCGA.DU.A5TS.01 1 0.3128 0.78829 0.82 0.00 0.04 0.00 0.00 0.04 0.00 0.10
#> TCGA.E1.5305.01 6 0.3714 0.11549 0.44 0.00 0.00 0.00 0.00 0.54 0.00 0.02
#> TCGA.F6.A8O4.01 8 0.4165 0.43408 0.26 0.00 0.10 0.00 0.00 0.00 0.00 0.64
#> TCGA.DH.A66G.01 2 0.0471 0.78355 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.P5.A731.01 7 0.4759 -0.26597 0.00 0.00 0.14 0.36 0.00 0.00 0.50 0.00
#> TCGA.DU.8163.01 8 0.3856 0.52801 0.00 0.00 0.10 0.00 0.00 0.20 0.00 0.70
#> TCGA.DU.6407.01 2 0.0471 0.78140 0.00 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A5F1.01 8 0.3385 0.61715 0.00 0.00 0.08 0.00 0.00 0.16 0.00 0.76
#> TCGA.VM.A8CF.01 2 0.5257 0.10221 0.00 0.54 0.14 0.04 0.00 0.00 0.28 0.00
#> TCGA.DU.6542.01 8 0.4355 0.58035 0.00 0.00 0.04 0.00 0.06 0.16 0.02 0.72
#> TCGA.DH.5143.01 6 0.3991 0.38669 0.00 0.00 0.06 0.00 0.00 0.62 0.00 0.32
#> TCGA.DU.7299.01 1 0.3374 0.53556 0.68 0.00 0.00 0.00 0.00 0.30 0.00 0.02
#> TCGA.CS.5393.01 6 0.3154 0.60935 0.16 0.00 0.00 0.00 0.00 0.78 0.00 0.06
#> TCGA.DU.7011.01 8 0.3970 0.51536 0.00 0.00 0.08 0.00 0.18 0.00 0.02 0.72
#> TCGA.TM.A84Q.01 1 0.1091 0.85170 0.94 0.00 0.06 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5281.01 1 0.0000 0.87413 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5270.01 4 0.3907 0.47830 0.00 0.00 0.04 0.58 0.00 0.00 0.38 0.00
#> TCGA.S9.A6WQ.01 7 0.5459 0.52546 0.00 0.22 0.08 0.14 0.00 0.00 0.56 0.00
#> TCGA.HT.8106.01 6 0.5639 0.47922 0.00 0.00 0.16 0.00 0.06 0.60 0.04 0.14
#> TCGA.QH.A6CW.01 1 0.0000 0.87413 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WO.01 1 0.3551 0.66435 0.72 0.00 0.06 0.00 0.00 0.00 0.00 0.22
#> TCGA.HT.7601.01 4 0.0471 0.73766 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.HT.7472.01 8 0.4559 0.40823 0.00 0.00 0.08 0.00 0.00 0.30 0.02 0.60
#> TCGA.HT.7880.01 5 0.5758 0.59727 0.00 0.00 0.20 0.00 0.56 0.04 0.04 0.16
#> TCGA.E1.A7Z3.01 2 0.2938 0.52744 0.00 0.70 0.00 0.00 0.00 0.00 0.30 0.00
#> TCGA.HT.7873.01 6 0.2020 0.62957 0.00 0.00 0.06 0.00 0.02 0.90 0.00 0.02
#> TCGA.CS.4938.01 7 0.4847 0.53524 0.00 0.30 0.08 0.04 0.00 0.00 0.58 0.00
#> TCGA.VM.A8CH.01 1 0.3657 0.68859 0.72 0.00 0.20 0.00 0.00 0.00 0.00 0.08
#> TCGA.HT.7476.01 1 0.2132 0.81800 0.88 0.00 0.08 0.00 0.00 0.00 0.00 0.04
#> TCGA.DB.A75L.01 2 0.0000 0.78667 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RY.A843.01 8 0.4468 0.56884 0.08 0.00 0.14 0.00 0.00 0.08 0.00 0.70
#> TCGA.TQ.A8XE.02 7 0.5861 0.05286 0.00 0.08 0.24 0.20 0.00 0.00 0.48 0.00
#> TCGA.HW.7493.01 7 0.3995 0.43662 0.00 0.36 0.02 0.02 0.00 0.00 0.60 0.00
#> TCGA.DU.8166.01 7 0.3291 0.54267 0.00 0.28 0.02 0.00 0.00 0.00 0.70 0.00
#> TCGA.HT.7855.01 1 0.0000 0.87413 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A7UT.01 5 0.2818 0.75066 0.00 0.00 0.06 0.00 0.82 0.12 0.00 0.00
#> TCGA.DU.7015.01 2 0.4530 0.46119 0.00 0.66 0.24 0.00 0.00 0.02 0.02 0.06
#> TCGA.HT.A616.01 2 0.0471 0.78355 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.HT.7611.01 1 0.0000 0.87413 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8018.01 4 0.1091 0.70834 0.00 0.00 0.06 0.94 0.00 0.00 0.00 0.00
#> TCGA.DU.5851.01 4 0.0471 0.73790 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.WY.A85C.01 1 0.0000 0.87413 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A4XC.01 6 0.2350 0.66861 0.00 0.00 0.04 0.00 0.00 0.86 0.00 0.10
#> TCGA.P5.A72W.01 8 0.3637 0.62793 0.00 0.00 0.06 0.00 0.04 0.08 0.02 0.80
#> TCGA.S9.A6TU.01 1 0.0000 0.87413 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5855.01 2 0.0000 0.78667 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7884.01 2 0.2569 0.68662 0.00 0.82 0.02 0.00 0.00 0.00 0.16 0.00
#> TCGA.WH.A86K.01 6 0.1341 0.67640 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.WY.A85E.01 2 0.0471 0.78140 0.00 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A5R5.01 4 0.4693 0.36954 0.00 0.00 0.12 0.46 0.00 0.00 0.42 0.00
#> TCGA.FG.6691.01 7 0.4081 0.50343 0.00 0.16 0.16 0.00 0.00 0.00 0.68 0.00
#> TCGA.S9.A7R3.01 2 0.2569 0.67214 0.00 0.82 0.02 0.00 0.00 0.00 0.16 0.00
#> TCGA.FG.A4MX.01 1 0.4870 0.52054 0.62 0.00 0.04 0.00 0.00 0.12 0.00 0.22
#> TCGA.S9.A7IZ.01 4 0.3856 0.65922 0.00 0.00 0.10 0.70 0.00 0.00 0.20 0.00
#> TCGA.DU.A6S7.01 2 0.0471 0.78140 0.00 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8114.01 1 0.0808 0.86190 0.96 0.00 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.HW.8321.01 8 0.2020 0.65386 0.02 0.00 0.06 0.00 0.02 0.00 0.00 0.90
#> TCGA.P5.A5F4.01 2 0.1947 0.71522 0.00 0.86 0.00 0.00 0.00 0.00 0.14 0.00
#> TCGA.FG.8191.01 8 0.2532 0.65428 0.00 0.00 0.04 0.00 0.02 0.04 0.02 0.88
#> TCGA.DH.5142.01 6 0.2020 0.62957 0.00 0.00 0.06 0.00 0.02 0.90 0.00 0.02
#> TCGA.E1.A7YW.01 8 0.3537 0.53501 0.00 0.00 0.02 0.00 0.00 0.24 0.02 0.72
#> TCGA.CS.6666.01 1 0.0000 0.87413 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A60L.01 2 0.3237 0.30581 0.00 0.60 0.00 0.00 0.00 0.00 0.40 0.00
#> TCGA.DB.5280.01 8 0.2818 0.61116 0.12 0.00 0.06 0.00 0.00 0.00 0.00 0.82
#> TCGA.TM.A84T.01 8 0.4794 0.00438 0.00 0.00 0.08 0.00 0.42 0.00 0.02 0.48
#> TCGA.DH.A66D.01 2 0.4059 0.38798 0.00 0.64 0.08 0.00 0.00 0.00 0.28 0.00
#> TCGA.TQ.A7RR.01 6 0.1557 0.64648 0.00 0.00 0.06 0.00 0.00 0.92 0.00 0.02
#> TCGA.TQ.A7RH.01 5 0.2623 0.73023 0.00 0.00 0.10 0.00 0.84 0.00 0.00 0.06
#> TCGA.P5.A735.01 2 0.4914 -0.28876 0.00 0.42 0.16 0.00 0.00 0.00 0.42 0.00
#> TCGA.HT.7609.01 8 0.3270 0.60872 0.12 0.00 0.06 0.00 0.02 0.00 0.00 0.80
#> TCGA.CS.4944.01 6 0.5511 0.15784 0.00 0.00 0.16 0.00 0.00 0.46 0.04 0.34
#> TCGA.S9.A7R7.01 5 0.2818 0.75066 0.00 0.00 0.06 0.00 0.82 0.12 0.00 0.00
#> TCGA.DB.A75M.01 1 0.0471 0.86984 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.HW.A5KM.01 1 0.0471 0.86984 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.DU.8167.01 2 0.0000 0.78667 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6U1.01 2 0.4628 0.18251 0.00 0.52 0.12 0.00 0.00 0.00 0.36 0.00
#> TCGA.FG.5965.01 4 0.1804 0.73690 0.00 0.00 0.08 0.90 0.00 0.00 0.02 0.00
#> TCGA.HT.A614.01 6 0.2020 0.62868 0.00 0.00 0.06 0.00 0.02 0.90 0.00 0.02
#> TCGA.DU.6399.01 1 0.0471 0.86984 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.E1.5307.01 2 0.1557 0.74208 0.02 0.92 0.06 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7QW.01 4 0.4914 0.30562 0.00 0.00 0.16 0.42 0.00 0.00 0.42 0.00
#> TCGA.HT.7604.01 1 0.0000 0.87413 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A733.01 2 0.1091 0.76100 0.00 0.94 0.06 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7684.01 6 0.1804 0.67584 0.00 0.00 0.02 0.00 0.00 0.90 0.00 0.08
#> TCGA.DH.A7UV.01 1 0.0000 0.87413 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7879.01 1 0.3970 0.69360 0.72 0.00 0.08 0.00 0.00 0.02 0.00 0.18
#> TCGA.TM.A84F.01 5 0.2818 0.75066 0.00 0.00 0.06 0.00 0.82 0.12 0.00 0.00
#> TCGA.DU.A7TC.01 1 0.0471 0.86984 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.HT.7610.01 2 0.3083 0.45743 0.00 0.66 0.00 0.00 0.00 0.00 0.34 0.00
#> TCGA.FG.A60J.01 2 0.0471 0.78341 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.E1.5303.01 6 0.3975 0.52624 0.26 0.00 0.00 0.00 0.00 0.66 0.00 0.08
#> TCGA.FN.7833.01 8 0.3873 0.55152 0.00 0.00 0.06 0.00 0.20 0.02 0.00 0.72
#> TCGA.E1.A7Z4.01 8 0.2569 0.60731 0.00 0.00 0.00 0.00 0.00 0.16 0.02 0.82
#> TCGA.DU.A5TR.01 1 0.2994 0.74885 0.80 0.00 0.06 0.00 0.00 0.00 0.00 0.14
#> TCGA.HT.7473.01 8 0.4672 0.41289 0.00 0.00 0.12 0.00 0.24 0.00 0.02 0.62
#> TCGA.DU.7008.01 2 0.0000 0.78667 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WG.01 8 0.4467 0.47920 0.00 0.00 0.12 0.00 0.20 0.00 0.02 0.66
#> TCGA.DB.A75O.01 5 0.1557 0.76851 0.00 0.00 0.02 0.00 0.92 0.06 0.00 0.00
#> TCGA.HT.7688.01 1 0.0808 0.86190 0.96 0.00 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.DU.5872.01 7 0.3154 0.28735 0.00 0.00 0.06 0.16 0.00 0.00 0.78 0.00
#> TCGA.FG.8185.01 1 0.0000 0.87413 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7902.01 4 0.1557 0.69019 0.00 0.00 0.06 0.92 0.00 0.00 0.02 0.00
#> TCGA.FG.6690.01 1 0.0471 0.86984 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.HW.8320.01 1 0.0000 0.87413 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A72X.01 8 0.2484 0.64975 0.00 0.00 0.10 0.00 0.02 0.00 0.02 0.86
#> TCGA.E1.5322.01 2 0.0471 0.78140 0.00 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.4942.01 7 0.4804 -0.32506 0.00 0.00 0.14 0.40 0.00 0.00 0.46 0.00
#> TCGA.DB.A4X9.01 7 0.5619 0.44430 0.00 0.14 0.16 0.14 0.00 0.00 0.56 0.00
#> TCGA.DB.A4XF.01 2 0.0471 0.78140 0.00 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A74O.01 1 0.0000 0.87413 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8188.01 1 0.0471 0.86984 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.HT.7485.01 6 0.2859 0.64640 0.00 0.00 0.02 0.00 0.00 0.82 0.02 0.14
#> TCGA.DB.A64S.01 1 0.3975 0.57065 0.66 0.00 0.08 0.00 0.00 0.00 0.00 0.26
#> TCGA.VV.A86M.01 2 0.1091 0.76100 0.00 0.94 0.06 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A8XE.01 7 0.5975 0.17367 0.00 0.12 0.24 0.16 0.00 0.00 0.48 0.00
#> TCGA.CS.6667.01 2 0.1091 0.76100 0.00 0.94 0.06 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RW.01 6 0.3895 0.61518 0.12 0.00 0.00 0.00 0.00 0.74 0.02 0.12
#> TCGA.DU.A7TI.01 6 0.4757 0.44223 0.24 0.00 0.00 0.00 0.00 0.56 0.00 0.20
#> TCGA.S9.A6U8.01 8 0.4318 0.39055 0.30 0.00 0.10 0.00 0.00 0.00 0.00 0.60
#> TCGA.HW.7489.01 1 0.5350 0.35269 0.54 0.00 0.12 0.00 0.00 0.06 0.00 0.28
#> TCGA.R8.A6YH.01 8 0.1887 0.64864 0.04 0.00 0.06 0.00 0.00 0.00 0.00 0.90
#> TCGA.TM.A7CA.01 8 0.4355 0.59755 0.06 0.00 0.04 0.00 0.00 0.16 0.02 0.72
#> TCGA.HT.7690.01 8 0.1947 0.62492 0.00 0.00 0.00 0.00 0.00 0.14 0.00 0.86
#> TCGA.FG.6689.01 8 0.4033 0.52814 0.00 0.00 0.12 0.00 0.00 0.20 0.00 0.68
#> TCGA.TQ.A7RF.01 2 0.2132 0.75429 0.00 0.88 0.04 0.00 0.00 0.00 0.08 0.00
#> TCGA.HT.8013.01 4 0.4999 0.35834 0.00 0.00 0.18 0.42 0.00 0.00 0.40 0.00
#> TCGA.HW.7490.01 1 0.3036 0.70058 0.78 0.00 0.00 0.00 0.00 0.18 0.00 0.04
#> TCGA.QH.A65S.01 4 0.0941 0.73840 0.00 0.00 0.02 0.96 0.00 0.00 0.02 0.00
#> TCGA.P5.A780.01 2 0.0000 0.78667 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5302.01 5 0.0471 0.75510 0.00 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.DU.7309.01 2 0.1091 0.76678 0.00 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.DU.6395.01 8 0.2204 0.65447 0.00 0.00 0.02 0.00 0.02 0.04 0.02 0.90
#> TCGA.P5.A5EW.01 7 0.3237 0.31230 0.00 0.40 0.00 0.00 0.00 0.00 0.60 0.00
#> TCGA.DU.6408.01 4 0.1607 0.74046 0.00 0.00 0.04 0.92 0.00 0.00 0.04 0.00
#> TCGA.DB.A4XB.01 5 0.3263 0.73012 0.00 0.00 0.10 0.00 0.78 0.12 0.00 0.00
#> TCGA.FG.A4MT.01 7 0.3737 0.04986 0.00 0.48 0.02 0.00 0.00 0.00 0.50 0.00
#> TCGA.FG.A4MT.02 7 0.3570 0.39773 0.00 0.36 0.02 0.00 0.00 0.00 0.62 0.00
#> TCGA.QH.A870.01 7 0.3785 0.25607 0.00 0.00 0.14 0.14 0.00 0.00 0.72 0.00
#> TCGA.DU.A7TA.01 8 0.3154 0.55088 0.00 0.00 0.06 0.00 0.16 0.00 0.00 0.78
#> TCGA.TM.A84H.01 2 0.1091 0.76100 0.00 0.94 0.06 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TZ.01 2 0.0471 0.78379 0.00 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7479.01 8 0.4160 0.61107 0.06 0.00 0.10 0.00 0.00 0.04 0.04 0.76
#> TCGA.DB.A4XD.01 1 0.0000 0.87413 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5275.01 1 0.3992 0.10761 0.52 0.00 0.00 0.00 0.00 0.44 0.00 0.04
#> TCGA.HT.7602.01 5 0.5871 0.56257 0.00 0.00 0.20 0.00 0.54 0.04 0.04 0.18
#> TCGA.HT.A5RB.01 8 0.3637 0.62540 0.08 0.00 0.06 0.00 0.00 0.04 0.02 0.80
#> TCGA.S9.A7R8.01 2 0.0000 0.78667 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6XA.01 7 0.3845 0.15826 0.00 0.00 0.06 0.28 0.00 0.00 0.66 0.00
#> TCGA.HT.8111.01 6 0.2807 0.66459 0.00 0.00 0.04 0.00 0.00 0.84 0.02 0.10
#> TCGA.DU.A5TP.01 5 0.1275 0.76045 0.00 0.00 0.02 0.00 0.94 0.04 0.00 0.00
#> TCGA.HT.7482.01 7 0.3272 0.25492 0.00 0.42 0.00 0.00 0.00 0.00 0.58 0.00
#> TCGA.TQ.A7RK.02 1 0.0000 0.87413 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RK.01 1 0.0000 0.87413 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7858.01 1 0.3528 0.68567 0.74 0.00 0.08 0.00 0.00 0.00 0.00 0.18
#> TCGA.HT.7475.01 8 0.6044 0.39122 0.00 0.00 0.10 0.00 0.22 0.14 0.02 0.52
#> TCGA.DU.A7T8.01 8 0.4804 0.56219 0.12 0.00 0.04 0.00 0.00 0.14 0.02 0.68
#> TCGA.FG.7636.01 1 0.4004 0.02704 0.50 0.00 0.00 0.00 0.00 0.46 0.00 0.04
#> TCGA.WY.A859.01 2 0.1341 0.75354 0.00 0.92 0.08 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6U9.01 1 0.2132 0.81800 0.88 0.00 0.08 0.00 0.00 0.00 0.00 0.04
#> TCGA.CS.6290.01 6 0.6404 0.17000 0.00 0.00 0.18 0.00 0.06 0.42 0.04 0.30
#> TCGA.DU.7019.01 1 0.0000 0.87413 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A711.01 4 0.4588 0.42151 0.00 0.00 0.12 0.54 0.00 0.00 0.34 0.00
#> TCGA.S9.A7R4.01 1 0.1408 0.85982 0.94 0.00 0.02 0.00 0.00 0.02 0.00 0.02
#> TCGA.HT.7676.01 8 0.3178 0.60804 0.00 0.00 0.04 0.00 0.00 0.14 0.02 0.80
#> TCGA.P5.A5F2.01 2 0.3675 0.42511 0.00 0.66 0.04 0.00 0.00 0.00 0.30 0.00
#> TCGA.WY.A85B.01 1 0.4059 0.52906 0.64 0.00 0.08 0.00 0.00 0.00 0.00 0.28
#> TCGA.S9.A7QX.01 2 0.2267 0.66910 0.00 0.82 0.00 0.00 0.00 0.00 0.18 0.00
#> TCGA.CS.4943.01 1 0.3737 0.07214 0.50 0.00 0.00 0.00 0.00 0.48 0.00 0.02
#> TCGA.DB.5276.01 8 0.6177 0.39347 0.16 0.00 0.14 0.00 0.00 0.12 0.04 0.54
#> TCGA.TM.A84L.01 8 0.4528 0.53856 0.14 0.00 0.14 0.00 0.00 0.04 0.00 0.68
#> TCGA.WY.A85D.01 1 0.0808 0.86190 0.96 0.00 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.DB.5273.01 8 0.4777 0.11368 0.00 0.00 0.08 0.00 0.00 0.40 0.02 0.50
#> TCGA.TM.A7C4.01 2 0.3333 -0.05860 0.00 0.50 0.00 0.00 0.00 0.00 0.50 0.00
#> TCGA.HT.8108.01 7 0.3237 0.31230 0.00 0.40 0.00 0.00 0.00 0.00 0.60 0.00
#> TCGA.DU.7304.01 1 0.0000 0.87413 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A736.01 2 0.4050 0.26447 0.00 0.60 0.06 0.00 0.00 0.00 0.34 0.00
#> TCGA.P5.A5EV.01 1 0.3337 0.71027 0.78 0.00 0.00 0.00 0.00 0.16 0.02 0.04
#> TCGA.DU.7301.01 1 0.0000 0.87413 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A4MY.01 2 0.0471 0.78355 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.TM.A7CF.01 2 0.3142 0.39633 0.00 0.64 0.00 0.00 0.00 0.00 0.36 0.00
#> TCGA.TM.A7CF.02 7 0.3757 0.57263 0.00 0.26 0.00 0.06 0.00 0.00 0.68 0.00
#> TCGA.S9.A6U6.01 8 0.3227 0.58667 0.14 0.00 0.08 0.00 0.00 0.00 0.00 0.78
#> TCGA.RY.A845.01 7 0.4460 0.50910 0.00 0.12 0.12 0.06 0.00 0.00 0.70 0.00
#> TCGA.FG.8182.01 8 0.5089 0.20288 0.00 0.00 0.14 0.00 0.32 0.00 0.02 0.52
#> TCGA.QH.A6X3.01 1 0.0471 0.86984 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.DU.6401.01 2 0.4255 0.31545 0.00 0.58 0.08 0.00 0.00 0.00 0.34 0.00
#> TCGA.E1.A7YH.01 7 0.3263 0.53906 0.00 0.12 0.00 0.10 0.00 0.00 0.78 0.00
#> TCGA.DU.7306.01 1 0.2404 0.76992 0.84 0.00 0.00 0.00 0.00 0.14 0.00 0.02
#> TCGA.HT.A74J.01 5 0.6375 0.56659 0.00 0.00 0.16 0.00 0.48 0.18 0.02 0.16
#> TCGA.HT.7478.01 8 0.4834 0.44088 0.02 0.00 0.08 0.00 0.00 0.26 0.02 0.62
#> TCGA.DB.A4XE.01 7 0.3385 0.54668 0.00 0.16 0.08 0.00 0.00 0.00 0.76 0.00
#> TCGA.HT.A61B.01 6 0.1275 0.64687 0.00 0.00 0.04 0.00 0.00 0.94 0.00 0.02
#> TCGA.DH.A66B.01 1 0.0000 0.87413 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7603.01 8 0.5815 0.22297 0.06 0.00 0.12 0.00 0.00 0.30 0.02 0.50
#> TCGA.DU.5853.01 8 0.5317 0.45935 0.00 0.00 0.12 0.00 0.08 0.22 0.00 0.58
#> TCGA.DU.7014.01 1 0.0000 0.87413 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A70Y.01 7 0.3299 0.18744 0.00 0.44 0.00 0.00 0.00 0.00 0.56 0.00
#> TCGA.TQ.A7RV.01 6 0.5933 0.24484 0.26 0.00 0.06 0.00 0.00 0.42 0.00 0.26
#> TCGA.TQ.A7RV.02 6 0.5477 0.21940 0.00 0.00 0.16 0.00 0.00 0.48 0.04 0.32
#> TCGA.HT.A5R7.01 4 0.0471 0.72863 0.00 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.HW.A5KL.01 2 0.0000 0.78667 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7474.01 8 0.5273 0.10212 0.00 0.00 0.16 0.00 0.00 0.36 0.02 0.46
#> TCGA.QH.A6X9.01 2 0.0000 0.78667 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A5EZ.01 1 0.1557 0.85345 0.92 0.00 0.06 0.00 0.00 0.02 0.00 0.00
#> TCGA.DU.5871.01 2 0.1765 0.73088 0.00 0.88 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.TQ.A7RJ.01 2 0.0000 0.78667 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WY.A858.01 7 0.4518 0.00322 0.00 0.02 0.06 0.36 0.00 0.00 0.56 0.00
#> TCGA.HT.7483.01 1 0.0000 0.87413 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7Z6.01 2 0.4174 0.07409 0.00 0.54 0.06 0.00 0.00 0.00 0.40 0.00
#> TCGA.DU.A76O.01 1 0.1557 0.84131 0.92 0.00 0.06 0.00 0.00 0.00 0.00 0.02
#> TCGA.DU.A5TW.01 2 0.0000 0.78667 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WY.A85A.01 5 0.4314 0.55893 0.00 0.00 0.08 0.00 0.66 0.00 0.02 0.24
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: Node0121 , Node0122-leaf , Node0123-leaf , Node0211-leaf , Node0212-leaf , Node0213-leaf , Node0221 , Node0222 , Node0231 , Node0232 .
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 180 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 0.4971 0.503 0.503
#> 3 3 0.941 0.925 0.953 0.3042 0.847 0.696
#> 4 4 0.853 0.881 0.931 0.1475 0.901 0.717
#> 5 5 0.704 0.665 0.812 0.0579 0.961 0.847
#> 6 6 0.704 0.637 0.783 0.0307 0.956 0.817
#> 7 7 0.686 0.553 0.726 0.0180 0.954 0.798
#> 8 8 0.678 0.516 0.713 0.0121 0.912 0.623
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 1 1 0
#> TCGA.S9.A7J2.01 2 0 1 0 1
#> TCGA.S9.A6TX.01 2 0 1 0 1
#> TCGA.HT.A74L.01 1 0 1 1 0
#> TCGA.DB.A4XA.01 2 0 1 0 1
#> TCGA.HT.A4DV.01 1 0 1 1 0
#> TCGA.E1.5311.01 2 0 1 0 1
#> TCGA.HT.8113.01 1 0 1 1 0
#> TCGA.HT.7620.01 2 0 1 0 1
#> TCGA.HT.7480.01 2 0 1 0 1
#> TCGA.HT.8109.01 2 0 1 0 1
#> TCGA.S9.A7R1.01 2 0 1 0 1
#> TCGA.FG.A710.01 1 0 1 1 0
#> TCGA.DU.A6S6.01 1 0 1 1 0
#> TCGA.HT.7877.01 1 0 1 1 0
#> TCGA.QH.A6CU.01 1 0 1 1 0
#> TCGA.HW.7486.01 2 0 1 0 1
#> TCGA.FG.7634.01 2 0 1 0 1
#> TCGA.HT.8010.01 1 0 1 1 0
#> TCGA.FG.7638.01 1 0 1 1 0
#> TCGA.HT.7605.01 2 0 1 0 1
#> TCGA.FG.A6J1.01 1 0 1 1 0
#> TCGA.HT.7608.01 2 0 1 0 1
#> TCGA.W9.A837.01 2 0 1 0 1
#> TCGA.TM.A7C5.01 2 0 1 0 1
#> TCGA.S9.A7QY.01 1 0 1 1 0
#> TCGA.P5.A5ET.01 2 0 1 0 1
#> TCGA.P5.A77X.01 1 0 1 1 0
#> TCGA.FG.A6IZ.01 2 0 1 0 1
#> TCGA.KT.A74X.01 2 0 1 0 1
#> TCGA.P5.A5EX.01 1 0 1 1 0
#> TCGA.E1.A7YO.01 2 0 1 0 1
#> TCGA.TQ.A7RG.01 2 0 1 0 1
#> TCGA.QH.A6X5.01 1 0 1 1 0
#> TCGA.RY.A847.01 2 0 1 0 1
#> TCGA.VM.A8CA.01 2 0 1 0 1
#> TCGA.DB.A4XG.01 2 0 1 0 1
#> TCGA.FG.A60K.01 1 0 1 1 0
#> TCGA.HT.7856.01 2 0 1 0 1
#> TCGA.DU.A7T6.01 1 0 1 1 0
#> TCGA.S9.A6TY.01 2 0 1 0 1
#> TCGA.TM.A84O.01 1 0 1 1 0
#> TCGA.HT.A61A.01 1 0 1 1 0
#> TCGA.TQ.A7RQ.01 1 0 1 1 0
#> TCGA.IK.8125.01 2 0 1 0 1
#> TCGA.HT.A74K.01 1 0 1 1 0
#> TCGA.QH.A6X8.01 1 0 1 1 0
#> TCGA.HT.7467.01 2 0 1 0 1
#> TCGA.HT.7681.01 1 0 1 1 0
#> TCGA.P5.A72Z.01 1 0 1 1 0
#> TCGA.DU.8168.01 1 0 1 1 0
#> TCGA.TQ.A7RN.01 2 0 1 0 1
#> TCGA.DH.5141.01 2 0 1 0 1
#> TCGA.EZ.7264.01 1 0 1 1 0
#> TCGA.QH.A65V.01 1 0 1 1 0
#> TCGA.DU.A6S8.01 1 0 1 1 0
#> TCGA.DU.7298.01 1 0 1 1 0
#> TCGA.DB.A64R.01 1 0 1 1 0
#> TCGA.CS.5390.01 1 0 1 1 0
#> TCGA.S9.A6WP.01 2 0 1 0 1
#> TCGA.DB.5278.01 2 0 1 0 1
#> TCGA.E1.A7YS.01 2 0 1 0 1
#> TCGA.DU.7294.01 1 0 1 1 0
#> TCGA.HT.7881.01 2 0 1 0 1
#> TCGA.HT.7695.01 1 0 1 1 0
#> TCGA.FG.7637.01 2 0 1 0 1
#> TCGA.VM.A8CE.01 2 0 1 0 1
#> TCGA.S9.A6U5.01 2 0 1 0 1
#> TCGA.DB.5274.01 1 0 1 1 0
#> TCGA.HW.7487.01 2 0 1 0 1
#> TCGA.HW.7491.01 2 0 1 0 1
#> TCGA.DU.A6S2.01 1 0 1 1 0
#> TCGA.TM.A84R.01 2 0 1 0 1
#> TCGA.HT.8012.01 1 0 1 1 0
#> TCGA.FG.8187.01 2 0 1 0 1
#> TCGA.S9.A7QZ.01 2 0 1 0 1
#> TCGA.QH.A6X4.01 2 0 1 0 1
#> TCGA.P5.A77W.01 1 0 1 1 0
#> TCGA.DU.7302.01 1 0 1 1 0
#> TCGA.HW.7495.01 1 0 1 1 0
#> TCGA.QH.A65R.01 1 0 1 1 0
#> TCGA.DU.A7TG.01 2 0 1 0 1
#> TCGA.S9.A6TW.01 2 0 1 0 1
#> TCGA.HT.7481.01 2 0 1 0 1
#> TCGA.HT.7875.01 2 0 1 0 1
#> TCGA.S9.A7IQ.01 1 0 1 1 0
#> TCGA.DU.6394.01 2 0 1 0 1
#> TCGA.S9.A6WD.01 2 0 1 0 1
#> TCGA.TQ.A7RU.01 2 0 1 0 1
#> TCGA.DU.5874.01 1 0 1 1 0
#> TCGA.S9.A6WE.01 2 0 1 0 1
#> TCGA.R8.A6MK.01 2 0 1 0 1
#> TCGA.QH.A6CY.01 2 0 1 0 1
#> TCGA.S9.A7J1.01 2 0 1 0 1
#> TCGA.P5.A5F0.01 2 0 1 0 1
#> TCGA.R8.A73M.01 1 0 1 1 0
#> TCGA.DU.A6S3.01 2 0 1 0 1
#> TCGA.DB.A4XH.01 1 0 1 1 0
#> TCGA.VW.A7QS.01 1 0 1 1 0
#> TCGA.S9.A6WI.01 1 0 1 1 0
#> TCGA.DU.8164.01 2 0 1 0 1
#> TCGA.DU.5849.01 2 0 1 0 1
#> TCGA.HT.7468.01 2 0 1 0 1
#> TCGA.TQ.A7RI.01 1 0 1 1 0
#> TCGA.DB.5279.01 2 0 1 0 1
#> TCGA.DU.7018.01 1 0 1 1 0
#> TCGA.HT.7677.01 2 0 1 0 1
#> TCGA.FG.A713.01 1 0 1 1 0
#> TCGA.DU.7300.01 1 0 1 1 0
#> TCGA.HT.7694.01 2 0 1 0 1
#> TCGA.TM.A84M.01 2 0 1 0 1
#> TCGA.F6.A8O3.01 2 0 1 0 1
#> TCGA.QH.A86X.01 2 0 1 0 1
#> TCGA.DU.A76R.01 2 0 1 0 1
#> TCGA.DH.5144.01 1 0 1 1 0
#> TCGA.DB.A64V.01 2 0 1 0 1
#> TCGA.RY.A840.01 2 0 1 0 1
#> TCGA.HW.A5KJ.01 2 0 1 0 1
#> TCGA.HT.A615.01 1 0 1 1 0
#> TCGA.HT.8105.01 2 0 1 0 1
#> TCGA.HT.7874.01 1 0 1 1 0
#> TCGA.HT.7471.01 1 0 1 1 0
#> TCGA.HT.A619.01 2 0 1 0 1
#> TCGA.HT.A5R9.01 1 0 1 1 0
#> TCGA.FG.5964.01 2 0 1 0 1
#> TCGA.CS.5396.01 1 0 1 1 0
#> TCGA.DH.A7UR.01 1 0 1 1 0
#> TCGA.DU.6400.01 1 0 1 1 0
#> TCGA.S9.A6WL.01 2 0 1 0 1
#> TCGA.DB.A75K.01 1 0 1 1 0
#> TCGA.DB.A64Q.01 1 0 1 1 0
#> TCGA.P5.A737.01 2 0 1 0 1
#> TCGA.S9.A6WH.01 1 0 1 1 0
#> TCGA.HT.7616.01 2 0 1 0 1
#> TCGA.RY.A83Y.01 2 0 1 0 1
#> TCGA.DB.A64U.01 1 0 1 1 0
#> TCGA.DB.A64W.01 1 0 1 1 0
#> TCGA.R8.A6MO.01 1 0 1 1 0
#> TCGA.HW.8322.01 2 0 1 0 1
#> TCGA.DU.5870.02 1 0 1 1 0
#> TCGA.CS.6668.01 1 0 1 1 0
#> TCGA.DU.5870.01 1 0 1 1 0
#> TCGA.HT.7692.01 2 0 1 0 1
#> TCGA.R8.A6ML.01 2 0 1 0 1
#> TCGA.DU.6410.01 2 0 1 0 1
#> TCGA.TQ.A7RO.01 2 0 1 0 1
#> TCGA.E1.5318.01 1 0 1 1 0
#> TCGA.S9.A7J3.01 1 0 1 1 0
#> TCGA.TM.A84S.01 2 0 1 0 1
#> TCGA.TQ.A7RS.01 1 0 1 1 0
#> TCGA.QH.A65Z.01 2 0 1 0 1
#> TCGA.P5.A730.01 2 0 1 0 1
#> TCGA.RY.A83X.01 1 0 1 1 0
#> TCGA.S9.A6UB.01 2 0 1 0 1
#> TCGA.DH.A66F.01 2 0 1 0 1
#> TCGA.HT.7607.01 1 0 1 1 0
#> TCGA.DU.6393.01 2 0 1 0 1
#> TCGA.S9.A7IY.01 2 0 1 0 1
#> TCGA.FG.7641.01 2 0 1 0 1
#> TCGA.DU.7009.01 1 0 1 1 0
#> TCGA.P5.A781.01 1 0 1 1 0
#> TCGA.FG.8186.01 1 0 1 1 0
#> TCGA.S9.A6U2.01 1 0 1 1 0
#> TCGA.S9.A6WN.01 1 0 1 1 0
#> TCGA.DH.A7US.01 2 0 1 0 1
#> TCGA.DB.A64L.01 1 0 1 1 0
#> TCGA.VV.A829.01 2 0 1 0 1
#> TCGA.DU.6397.02 2 0 1 0 1
#> TCGA.DU.6397.01 2 0 1 0 1
#> TCGA.CS.6670.01 2 0 1 0 1
#> TCGA.QH.A65X.01 1 0 1 1 0
#> TCGA.DB.A64P.01 2 0 1 0 1
#> TCGA.QH.A6CZ.01 2 0 1 0 1
#> TCGA.DH.A669.02 2 0 1 0 1
#> TCGA.DH.A669.01 2 0 1 0 1
#> TCGA.VM.A8CB.01 2 0 1 0 1
#> TCGA.HT.7687.01 2 0 1 0 1
#> TCGA.TM.A84G.01 1 0 1 1 0
#> TCGA.CS.5394.01 2 0 1 0 1
#> TCGA.FG.5962.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.E1.5319.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.S9.A7J2.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.S9.A6TX.01 2 0.2959 0.893 0.00 0.90 0.10
#> TCGA.HT.A74L.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.DB.A4XA.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.HT.A4DV.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.E1.5311.01 3 0.2066 0.919 0.00 0.06 0.94
#> TCGA.HT.8113.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.HT.7620.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.HT.7480.01 2 0.2537 0.912 0.00 0.92 0.08
#> TCGA.HT.8109.01 2 0.1529 0.936 0.00 0.96 0.04
#> TCGA.S9.A7R1.01 2 0.1529 0.936 0.00 0.96 0.04
#> TCGA.FG.A710.01 1 0.0000 0.977 1.00 0.00 0.00
#> TCGA.DU.A6S6.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.HT.7877.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.QH.A6CU.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.HW.7486.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.FG.7634.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.HT.8010.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.FG.7638.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.HT.7605.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.FG.A6J1.01 1 0.0000 0.977 1.00 0.00 0.00
#> TCGA.HT.7608.01 3 0.2959 0.883 0.00 0.10 0.90
#> TCGA.W9.A837.01 2 0.1529 0.936 0.00 0.96 0.04
#> TCGA.TM.A7C5.01 2 0.1529 0.936 0.00 0.96 0.04
#> TCGA.S9.A7QY.01 1 0.0000 0.977 1.00 0.00 0.00
#> TCGA.P5.A5ET.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.P5.A77X.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.FG.A6IZ.01 2 0.0000 0.931 0.00 1.00 0.00
#> TCGA.KT.A74X.01 3 0.4796 0.740 0.00 0.22 0.78
#> TCGA.P5.A5EX.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.E1.A7YO.01 2 0.1529 0.936 0.00 0.96 0.04
#> TCGA.TQ.A7RG.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.QH.A6X5.01 1 0.0000 0.977 1.00 0.00 0.00
#> TCGA.RY.A847.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.VM.A8CA.01 3 0.5948 0.451 0.00 0.36 0.64
#> TCGA.DB.A4XG.01 2 0.1529 0.936 0.00 0.96 0.04
#> TCGA.FG.A60K.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.HT.7856.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.DU.A7T6.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.S9.A6TY.01 2 0.1529 0.936 0.00 0.96 0.04
#> TCGA.TM.A84O.01 1 0.0000 0.977 1.00 0.00 0.00
#> TCGA.HT.A61A.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.TQ.A7RQ.01 1 0.0000 0.977 1.00 0.00 0.00
#> TCGA.IK.8125.01 2 0.0000 0.931 0.00 1.00 0.00
#> TCGA.HT.A74K.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.QH.A6X8.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.HT.7467.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.HT.7681.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.P5.A72Z.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.DU.8168.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.TQ.A7RN.01 2 0.5948 0.484 0.00 0.64 0.36
#> TCGA.DH.5141.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.EZ.7264.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.QH.A65V.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.DU.A6S8.01 1 0.0000 0.977 1.00 0.00 0.00
#> TCGA.DU.7298.01 1 0.0000 0.977 1.00 0.00 0.00
#> TCGA.DB.A64R.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.CS.5390.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.S9.A6WP.01 2 0.1529 0.936 0.00 0.96 0.04
#> TCGA.DB.5278.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.E1.A7YS.01 2 0.0000 0.931 0.00 1.00 0.00
#> TCGA.DU.7294.01 1 0.0892 0.974 0.98 0.02 0.00
#> TCGA.HT.7881.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.HT.7695.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.FG.7637.01 3 0.2066 0.919 0.00 0.06 0.94
#> TCGA.VM.A8CE.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.S9.A6U5.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.DB.5274.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.HW.7487.01 2 0.1529 0.936 0.00 0.96 0.04
#> TCGA.HW.7491.01 2 0.2066 0.926 0.00 0.94 0.06
#> TCGA.DU.A6S2.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.TM.A84R.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.HT.8012.01 1 0.0000 0.977 1.00 0.00 0.00
#> TCGA.FG.8187.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.S9.A7QZ.01 2 0.0000 0.931 0.00 1.00 0.00
#> TCGA.QH.A6X4.01 2 0.4796 0.756 0.00 0.78 0.22
#> TCGA.P5.A77W.01 1 0.0000 0.977 1.00 0.00 0.00
#> TCGA.DU.7302.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.HW.7495.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.QH.A65R.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.DU.A7TG.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.S9.A6TW.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.HT.7481.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.HT.7875.01 2 0.4796 0.755 0.00 0.78 0.22
#> TCGA.S9.A7IQ.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.DU.6394.01 2 0.0000 0.931 0.00 1.00 0.00
#> TCGA.S9.A6WD.01 2 0.0892 0.937 0.00 0.98 0.02
#> TCGA.TQ.A7RU.01 2 0.0892 0.937 0.00 0.98 0.02
#> TCGA.DU.5874.01 1 0.5216 0.692 0.74 0.26 0.00
#> TCGA.S9.A6WE.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.R8.A6MK.01 3 0.1529 0.933 0.00 0.04 0.96
#> TCGA.QH.A6CY.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.S9.A7J1.01 3 0.2066 0.921 0.00 0.06 0.94
#> TCGA.P5.A5F0.01 2 0.5560 0.624 0.00 0.70 0.30
#> TCGA.R8.A73M.01 1 0.0000 0.977 1.00 0.00 0.00
#> TCGA.DU.A6S3.01 2 0.1529 0.936 0.00 0.96 0.04
#> TCGA.DB.A4XH.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.VW.A7QS.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.S9.A6WI.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.DU.8164.01 2 0.0892 0.937 0.00 0.98 0.02
#> TCGA.DU.5849.01 2 0.1529 0.936 0.00 0.96 0.04
#> TCGA.HT.7468.01 2 0.1529 0.936 0.00 0.96 0.04
#> TCGA.TQ.A7RI.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.DB.5279.01 2 0.0000 0.931 0.00 1.00 0.00
#> TCGA.DU.7018.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.HT.7677.01 2 0.1529 0.936 0.00 0.96 0.04
#> TCGA.FG.A713.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.DU.7300.01 1 0.0000 0.977 1.00 0.00 0.00
#> TCGA.HT.7694.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.TM.A84M.01 2 0.0892 0.937 0.00 0.98 0.02
#> TCGA.F6.A8O3.01 2 0.2066 0.926 0.00 0.94 0.06
#> TCGA.QH.A86X.01 3 0.2066 0.920 0.00 0.06 0.94
#> TCGA.DU.A76R.01 3 0.5948 0.470 0.00 0.36 0.64
#> TCGA.DH.5144.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.DB.A64V.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.RY.A840.01 2 0.0892 0.937 0.00 0.98 0.02
#> TCGA.HW.A5KJ.01 2 0.0000 0.931 0.00 1.00 0.00
#> TCGA.HT.A615.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.HT.8105.01 2 0.0000 0.931 0.00 1.00 0.00
#> TCGA.HT.7874.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.HT.7471.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.HT.A619.01 2 0.0000 0.931 0.00 1.00 0.00
#> TCGA.HT.A5R9.01 1 0.0000 0.977 1.00 0.00 0.00
#> TCGA.FG.5964.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.CS.5396.01 1 0.0000 0.977 1.00 0.00 0.00
#> TCGA.DH.A7UR.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.DU.6400.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.S9.A6WL.01 2 0.0000 0.931 0.00 1.00 0.00
#> TCGA.DB.A75K.01 1 0.0000 0.977 1.00 0.00 0.00
#> TCGA.DB.A64Q.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.P5.A737.01 2 0.4555 0.785 0.00 0.80 0.20
#> TCGA.S9.A6WH.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.HT.7616.01 2 0.0000 0.931 0.00 1.00 0.00
#> TCGA.RY.A83Y.01 2 0.1529 0.936 0.00 0.96 0.04
#> TCGA.DB.A64U.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.DB.A64W.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.R8.A6MO.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.HW.8322.01 2 0.5948 0.483 0.00 0.64 0.36
#> TCGA.DU.5870.02 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.CS.6668.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.DU.5870.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.HT.7692.01 3 0.4555 0.765 0.00 0.20 0.80
#> TCGA.R8.A6ML.01 2 0.0892 0.937 0.00 0.98 0.02
#> TCGA.DU.6410.01 2 0.0000 0.931 0.00 1.00 0.00
#> TCGA.TQ.A7RO.01 3 0.2537 0.904 0.00 0.08 0.92
#> TCGA.E1.5318.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.S9.A7J3.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.TM.A84S.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.TQ.A7RS.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.QH.A65Z.01 2 0.0892 0.937 0.00 0.98 0.02
#> TCGA.P5.A730.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.RY.A83X.01 1 0.0000 0.977 1.00 0.00 0.00
#> TCGA.S9.A6UB.01 2 0.0892 0.937 0.00 0.98 0.02
#> TCGA.DH.A66F.01 2 0.1529 0.936 0.00 0.96 0.04
#> TCGA.HT.7607.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.DU.6393.01 2 0.0000 0.931 0.00 1.00 0.00
#> TCGA.S9.A7IY.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.FG.7641.01 2 0.3686 0.854 0.00 0.86 0.14
#> TCGA.DU.7009.01 1 0.0000 0.977 1.00 0.00 0.00
#> TCGA.P5.A781.01 1 0.0000 0.977 1.00 0.00 0.00
#> TCGA.FG.8186.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.S9.A6U2.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.S9.A6WN.01 1 0.0892 0.976 0.98 0.00 0.02
#> TCGA.DH.A7US.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.DB.A64L.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.VV.A829.01 2 0.0000 0.931 0.00 1.00 0.00
#> TCGA.DU.6397.02 3 0.5948 0.461 0.00 0.36 0.64
#> TCGA.DU.6397.01 3 0.0892 0.946 0.00 0.02 0.98
#> TCGA.CS.6670.01 3 0.6126 0.357 0.00 0.40 0.60
#> TCGA.QH.A65X.01 1 0.0000 0.977 1.00 0.00 0.00
#> TCGA.DB.A64P.01 2 0.2066 0.926 0.00 0.94 0.06
#> TCGA.QH.A6CZ.01 2 0.5216 0.694 0.00 0.74 0.26
#> TCGA.DH.A669.02 2 0.0000 0.931 0.00 1.00 0.00
#> TCGA.DH.A669.01 2 0.0000 0.931 0.00 1.00 0.00
#> TCGA.VM.A8CB.01 2 0.5016 0.729 0.00 0.76 0.24
#> TCGA.HT.7687.01 2 0.0000 0.931 0.00 1.00 0.00
#> TCGA.TM.A84G.01 1 0.1529 0.969 0.96 0.04 0.00
#> TCGA.CS.5394.01 2 0.0892 0.937 0.00 0.98 0.02
#> TCGA.FG.5962.01 2 0.1529 0.936 0.00 0.96 0.04
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.E1.5319.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.S9.A7J2.01 3 0.1913 0.913 0.04 0.02 0.94 0.00
#> TCGA.S9.A6TX.01 2 0.3525 0.830 0.04 0.86 0.10 0.00
#> TCGA.HT.A74L.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.DB.A4XA.01 3 0.1913 0.913 0.04 0.02 0.94 0.00
#> TCGA.HT.A4DV.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.E1.5311.01 3 0.3821 0.849 0.04 0.12 0.84 0.00
#> TCGA.HT.8113.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.HT.7620.01 3 0.0000 0.919 0.00 0.00 1.00 0.00
#> TCGA.HT.7480.01 2 0.2345 0.864 0.00 0.90 0.10 0.00
#> TCGA.HT.8109.01 2 0.0000 0.926 0.00 1.00 0.00 0.00
#> TCGA.S9.A7R1.01 2 0.0707 0.919 0.00 0.98 0.02 0.00
#> TCGA.FG.A710.01 1 0.2921 0.889 0.86 0.00 0.00 0.14
#> TCGA.DU.A6S6.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.HT.7877.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.QH.A6CU.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.HW.7486.01 3 0.0000 0.919 0.00 0.00 1.00 0.00
#> TCGA.FG.7634.01 3 0.0000 0.919 0.00 0.00 1.00 0.00
#> TCGA.HT.8010.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.FG.7638.01 4 0.1637 0.906 0.06 0.00 0.00 0.94
#> TCGA.HT.7605.01 3 0.0000 0.919 0.00 0.00 1.00 0.00
#> TCGA.FG.A6J1.01 4 0.4713 0.409 0.36 0.00 0.00 0.64
#> TCGA.HT.7608.01 3 0.3335 0.844 0.02 0.12 0.86 0.00
#> TCGA.W9.A837.01 2 0.2011 0.882 0.00 0.92 0.08 0.00
#> TCGA.TM.A7C5.01 2 0.0000 0.926 0.00 1.00 0.00 0.00
#> TCGA.S9.A7QY.01 1 0.4948 0.297 0.56 0.00 0.00 0.44
#> TCGA.P5.A5ET.01 3 0.0707 0.918 0.00 0.02 0.98 0.00
#> TCGA.P5.A77X.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.FG.A6IZ.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.KT.A74X.01 3 0.5713 0.516 0.04 0.34 0.62 0.00
#> TCGA.P5.A5EX.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.E1.A7YO.01 2 0.0000 0.926 0.00 1.00 0.00 0.00
#> TCGA.TQ.A7RG.01 3 0.1913 0.913 0.04 0.02 0.94 0.00
#> TCGA.QH.A6X5.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.RY.A847.01 3 0.0707 0.918 0.02 0.00 0.98 0.00
#> TCGA.VM.A8CA.01 3 0.5355 0.480 0.02 0.36 0.62 0.00
#> TCGA.DB.A4XG.01 2 0.0707 0.919 0.00 0.98 0.02 0.00
#> TCGA.FG.A60K.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.HT.7856.01 3 0.0000 0.919 0.00 0.00 1.00 0.00
#> TCGA.DU.A7T6.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.S9.A6TY.01 2 0.0000 0.926 0.00 1.00 0.00 0.00
#> TCGA.TM.A84O.01 1 0.2345 0.932 0.90 0.00 0.00 0.10
#> TCGA.HT.A61A.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.TQ.A7RQ.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.IK.8125.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.HT.A74K.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.QH.A6X8.01 1 0.1211 0.953 0.96 0.00 0.00 0.04
#> TCGA.HT.7467.01 3 0.0000 0.919 0.00 0.00 1.00 0.00
#> TCGA.HT.7681.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.P5.A72Z.01 1 0.1211 0.953 0.96 0.00 0.00 0.04
#> TCGA.DU.8168.01 1 0.1211 0.953 0.96 0.00 0.00 0.04
#> TCGA.TQ.A7RN.01 2 0.5428 0.341 0.02 0.60 0.38 0.00
#> TCGA.DH.5141.01 3 0.0000 0.919 0.00 0.00 1.00 0.00
#> TCGA.EZ.7264.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.QH.A65V.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.DU.A6S8.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.DU.7298.01 4 0.3610 0.741 0.20 0.00 0.00 0.80
#> TCGA.DB.A64R.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.CS.5390.01 1 0.1211 0.953 0.96 0.00 0.00 0.04
#> TCGA.S9.A6WP.01 2 0.0000 0.926 0.00 1.00 0.00 0.00
#> TCGA.DB.5278.01 3 0.0000 0.919 0.00 0.00 1.00 0.00
#> TCGA.E1.A7YS.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.DU.7294.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.HT.7881.01 3 0.0000 0.919 0.00 0.00 1.00 0.00
#> TCGA.HT.7695.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.FG.7637.01 3 0.4088 0.829 0.04 0.14 0.82 0.00
#> TCGA.VM.A8CE.01 3 0.0000 0.919 0.00 0.00 1.00 0.00
#> TCGA.S9.A6U5.01 3 0.1913 0.913 0.04 0.02 0.94 0.00
#> TCGA.DB.5274.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.HW.7487.01 2 0.0707 0.919 0.00 0.98 0.02 0.00
#> TCGA.HW.7491.01 2 0.1211 0.908 0.00 0.96 0.04 0.00
#> TCGA.DU.A6S2.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.TM.A84R.01 3 0.0000 0.919 0.00 0.00 1.00 0.00
#> TCGA.HT.8012.01 4 0.3400 0.774 0.18 0.00 0.00 0.82
#> TCGA.FG.8187.01 3 0.0000 0.919 0.00 0.00 1.00 0.00
#> TCGA.S9.A7QZ.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.QH.A6X4.01 2 0.5256 0.593 0.04 0.70 0.26 0.00
#> TCGA.P5.A77W.01 1 0.4406 0.644 0.70 0.00 0.00 0.30
#> TCGA.DU.7302.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.HW.7495.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.QH.A65R.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.DU.A7TG.01 3 0.0000 0.919 0.00 0.00 1.00 0.00
#> TCGA.S9.A6TW.01 3 0.1211 0.915 0.04 0.00 0.96 0.00
#> TCGA.HT.7481.01 3 0.0000 0.919 0.00 0.00 1.00 0.00
#> TCGA.HT.7875.01 2 0.4079 0.760 0.02 0.80 0.18 0.00
#> TCGA.S9.A7IQ.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.DU.6394.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.S9.A6WD.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.TQ.A7RU.01 2 0.0000 0.926 0.00 1.00 0.00 0.00
#> TCGA.DU.5874.01 1 0.1211 0.953 0.96 0.00 0.00 0.04
#> TCGA.S9.A6WE.01 3 0.1913 0.913 0.04 0.02 0.94 0.00
#> TCGA.R8.A6MK.01 3 0.0707 0.918 0.02 0.00 0.98 0.00
#> TCGA.QH.A6CY.01 3 0.0000 0.919 0.00 0.00 1.00 0.00
#> TCGA.S9.A7J1.01 3 0.3198 0.881 0.04 0.08 0.88 0.00
#> TCGA.P5.A5F0.01 2 0.4134 0.658 0.00 0.74 0.26 0.00
#> TCGA.R8.A73M.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.DU.A6S3.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.DB.A4XH.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.VW.A7QS.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.S9.A6WI.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.DU.8164.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.DU.5849.01 2 0.0707 0.919 0.00 0.98 0.02 0.00
#> TCGA.HT.7468.01 2 0.0707 0.920 0.02 0.98 0.00 0.00
#> TCGA.TQ.A7RI.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.DB.5279.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.DU.7018.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.HT.7677.01 2 0.0000 0.926 0.00 1.00 0.00 0.00
#> TCGA.FG.A713.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.DU.7300.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.HT.7694.01 3 0.0000 0.919 0.00 0.00 1.00 0.00
#> TCGA.TM.A84M.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.F6.A8O3.01 2 0.2345 0.863 0.00 0.90 0.10 0.00
#> TCGA.QH.A86X.01 3 0.1411 0.915 0.02 0.02 0.96 0.00
#> TCGA.DU.A76R.01 3 0.5793 0.458 0.04 0.36 0.60 0.00
#> TCGA.DH.5144.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.DB.A64V.01 3 0.2011 0.887 0.00 0.08 0.92 0.00
#> TCGA.RY.A840.01 2 0.0707 0.920 0.02 0.98 0.00 0.00
#> TCGA.HW.A5KJ.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.HT.A615.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.HT.8105.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.HT.7874.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.HT.7471.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.HT.A619.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.HT.A5R9.01 1 0.4406 0.641 0.70 0.00 0.00 0.30
#> TCGA.FG.5964.01 3 0.1913 0.913 0.04 0.02 0.94 0.00
#> TCGA.CS.5396.01 1 0.2345 0.931 0.90 0.00 0.00 0.10
#> TCGA.DH.A7UR.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.DU.6400.01 1 0.1211 0.953 0.96 0.00 0.00 0.04
#> TCGA.S9.A6WL.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.DB.A75K.01 1 0.2011 0.949 0.92 0.00 0.00 0.08
#> TCGA.DB.A64Q.01 4 0.3172 0.790 0.16 0.00 0.00 0.84
#> TCGA.P5.A737.01 2 0.3801 0.724 0.00 0.78 0.22 0.00
#> TCGA.S9.A6WH.01 1 0.1211 0.953 0.96 0.00 0.00 0.04
#> TCGA.HT.7616.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.RY.A83Y.01 2 0.0707 0.920 0.00 0.98 0.02 0.00
#> TCGA.DB.A64U.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.DB.A64W.01 1 0.1211 0.953 0.96 0.00 0.00 0.04
#> TCGA.R8.A6MO.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.HW.8322.01 2 0.5355 0.407 0.02 0.62 0.36 0.00
#> TCGA.DU.5870.02 1 0.1211 0.953 0.96 0.00 0.00 0.04
#> TCGA.CS.6668.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.DU.5870.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.HT.7692.01 3 0.4079 0.786 0.02 0.18 0.80 0.00
#> TCGA.R8.A6ML.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.DU.6410.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.TQ.A7RO.01 3 0.3198 0.882 0.04 0.08 0.88 0.00
#> TCGA.E1.5318.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.S9.A7J3.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.TM.A84S.01 3 0.0707 0.918 0.00 0.02 0.98 0.00
#> TCGA.TQ.A7RS.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.QH.A65Z.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.P5.A730.01 3 0.1637 0.902 0.00 0.06 0.94 0.00
#> TCGA.RY.A83X.01 4 0.2647 0.848 0.12 0.00 0.00 0.88
#> TCGA.S9.A6UB.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.DH.A66F.01 2 0.0000 0.926 0.00 1.00 0.00 0.00
#> TCGA.HT.7607.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.DU.6393.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.S9.A7IY.01 3 0.0000 0.919 0.00 0.00 1.00 0.00
#> TCGA.FG.7641.01 2 0.3400 0.778 0.00 0.82 0.18 0.00
#> TCGA.DU.7009.01 4 0.2647 0.847 0.12 0.00 0.00 0.88
#> TCGA.P5.A781.01 4 0.2011 0.886 0.08 0.00 0.00 0.92
#> TCGA.FG.8186.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.S9.A6U2.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.S9.A6WN.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.DH.A7US.01 3 0.1913 0.913 0.04 0.02 0.94 0.00
#> TCGA.DB.A64L.01 1 0.1637 0.964 0.94 0.00 0.00 0.06
#> TCGA.VV.A829.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.DU.6397.02 3 0.6212 0.351 0.06 0.38 0.56 0.00
#> TCGA.DU.6397.01 3 0.2411 0.907 0.04 0.04 0.92 0.00
#> TCGA.CS.6670.01 3 0.5915 0.352 0.04 0.40 0.56 0.00
#> TCGA.QH.A65X.01 4 0.4977 0.071 0.46 0.00 0.00 0.54
#> TCGA.DB.A64P.01 2 0.2011 0.881 0.00 0.92 0.08 0.00
#> TCGA.QH.A6CZ.01 2 0.4855 0.339 0.00 0.60 0.40 0.00
#> TCGA.DH.A669.02 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.DH.A669.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.VM.A8CB.01 2 0.3801 0.728 0.00 0.78 0.22 0.00
#> TCGA.HT.7687.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.TM.A84G.01 1 0.1211 0.953 0.96 0.00 0.00 0.04
#> TCGA.CS.5394.01 2 0.0707 0.928 0.02 0.98 0.00 0.00
#> TCGA.FG.5962.01 2 0.0000 0.926 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.E1.5319.01 4 0.3697 0.8155 0.10 0.00 0.00 0.82 0.08
#> TCGA.S9.A7J2.01 5 0.5157 0.3207 0.00 0.04 0.44 0.00 0.52
#> TCGA.S9.A6TX.01 2 0.4829 -0.1815 0.00 0.50 0.02 0.00 0.48
#> TCGA.HT.A74L.01 4 0.1648 0.8915 0.02 0.00 0.00 0.94 0.04
#> TCGA.DB.A4XA.01 3 0.4675 0.1784 0.00 0.02 0.60 0.00 0.38
#> TCGA.HT.A4DV.01 4 0.0609 0.9050 0.00 0.00 0.00 0.98 0.02
#> TCGA.E1.5311.01 5 0.5680 0.5708 0.00 0.14 0.24 0.00 0.62
#> TCGA.HT.8113.01 4 0.0609 0.9050 0.00 0.00 0.00 0.98 0.02
#> TCGA.HT.7620.01 3 0.0000 0.7275 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7480.01 2 0.4990 0.5657 0.00 0.60 0.04 0.00 0.36
#> TCGA.HT.8109.01 2 0.3852 0.6852 0.00 0.76 0.02 0.00 0.22
#> TCGA.S9.A7R1.01 2 0.4252 0.6709 0.00 0.70 0.02 0.00 0.28
#> TCGA.FG.A710.01 1 0.4254 0.6924 0.74 0.00 0.00 0.22 0.04
#> TCGA.DU.A6S6.01 4 0.2077 0.8814 0.04 0.00 0.00 0.92 0.04
#> TCGA.HT.7877.01 4 0.0609 0.9050 0.00 0.00 0.00 0.98 0.02
#> TCGA.QH.A6CU.01 4 0.0609 0.9050 0.00 0.00 0.00 0.98 0.02
#> TCGA.HW.7486.01 3 0.0000 0.7275 0.00 0.00 1.00 0.00 0.00
#> TCGA.FG.7634.01 3 0.1732 0.6839 0.00 0.00 0.92 0.00 0.08
#> TCGA.HT.8010.01 4 0.0609 0.9050 0.00 0.00 0.00 0.98 0.02
#> TCGA.FG.7638.01 4 0.3110 0.8463 0.08 0.00 0.00 0.86 0.06
#> TCGA.HT.7605.01 3 0.0609 0.7226 0.00 0.00 0.98 0.00 0.02
#> TCGA.FG.A6J1.01 4 0.5447 0.1361 0.44 0.00 0.00 0.50 0.06
#> TCGA.HT.7608.01 3 0.6455 -0.2688 0.00 0.20 0.48 0.00 0.32
#> TCGA.W9.A837.01 2 0.5579 0.3501 0.00 0.60 0.10 0.00 0.30
#> TCGA.TM.A7C5.01 2 0.3561 0.6798 0.00 0.74 0.00 0.00 0.26
#> TCGA.S9.A7QY.01 1 0.5157 0.0827 0.52 0.00 0.00 0.44 0.04
#> TCGA.P5.A5ET.01 3 0.2929 0.5892 0.00 0.00 0.82 0.00 0.18
#> TCGA.P5.A77X.01 4 0.1043 0.8988 0.00 0.00 0.00 0.96 0.04
#> TCGA.FG.A6IZ.01 2 0.0609 0.6894 0.00 0.98 0.00 0.00 0.02
#> TCGA.KT.A74X.01 5 0.6265 0.5178 0.00 0.24 0.22 0.00 0.54
#> TCGA.P5.A5EX.01 4 0.0609 0.9050 0.00 0.00 0.00 0.98 0.02
#> TCGA.E1.A7YO.01 2 0.3684 0.6573 0.00 0.72 0.00 0.00 0.28
#> TCGA.TQ.A7RG.01 5 0.5425 0.3049 0.00 0.06 0.42 0.00 0.52
#> TCGA.QH.A6X5.01 1 0.2331 0.8886 0.90 0.00 0.00 0.02 0.08
#> TCGA.RY.A847.01 3 0.2929 0.5991 0.00 0.00 0.82 0.00 0.18
#> TCGA.VM.A8CA.01 2 0.6794 -0.4275 0.00 0.38 0.32 0.00 0.30
#> TCGA.DB.A4XG.01 2 0.4252 0.6709 0.00 0.70 0.02 0.00 0.28
#> TCGA.FG.A60K.01 4 0.2438 0.8731 0.04 0.00 0.00 0.90 0.06
#> TCGA.HT.7856.01 3 0.0000 0.7275 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.A7T6.01 1 0.1732 0.8874 0.92 0.00 0.00 0.00 0.08
#> TCGA.S9.A6TY.01 2 0.4360 0.6533 0.00 0.68 0.02 0.00 0.30
#> TCGA.TM.A84O.01 1 0.3946 0.8293 0.80 0.00 0.00 0.12 0.08
#> TCGA.HT.A61A.01 4 0.0609 0.9050 0.00 0.00 0.00 0.98 0.02
#> TCGA.TQ.A7RQ.01 1 0.1732 0.8936 0.92 0.00 0.00 0.00 0.08
#> TCGA.IK.8125.01 2 0.2929 0.6956 0.00 0.82 0.00 0.00 0.18
#> TCGA.HT.A74K.01 1 0.1410 0.8945 0.94 0.00 0.00 0.00 0.06
#> TCGA.QH.A6X8.01 1 0.1410 0.8945 0.94 0.00 0.00 0.00 0.06
#> TCGA.HT.7467.01 3 0.0000 0.7275 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7681.01 4 0.0609 0.9050 0.00 0.00 0.00 0.98 0.02
#> TCGA.P5.A72Z.01 1 0.1410 0.8945 0.94 0.00 0.00 0.00 0.06
#> TCGA.DU.8168.01 1 0.1410 0.8945 0.94 0.00 0.00 0.00 0.06
#> TCGA.TQ.A7RN.01 2 0.6732 0.2506 0.00 0.40 0.26 0.00 0.34
#> TCGA.DH.5141.01 3 0.3319 0.5842 0.00 0.02 0.82 0.00 0.16
#> TCGA.EZ.7264.01 1 0.2012 0.9025 0.92 0.00 0.00 0.02 0.06
#> TCGA.QH.A65V.01 4 0.1648 0.8913 0.02 0.00 0.00 0.94 0.04
#> TCGA.DU.A6S8.01 1 0.1648 0.8940 0.94 0.00 0.00 0.02 0.04
#> TCGA.DU.7298.01 4 0.4728 0.6566 0.24 0.00 0.00 0.70 0.06
#> TCGA.DB.A64R.01 4 0.0000 0.9042 0.00 0.00 0.00 1.00 0.00
#> TCGA.CS.5390.01 1 0.0609 0.9011 0.98 0.00 0.00 0.00 0.02
#> TCGA.S9.A6WP.01 2 0.3274 0.6958 0.00 0.78 0.00 0.00 0.22
#> TCGA.DB.5278.01 3 0.0000 0.7275 0.00 0.00 1.00 0.00 0.00
#> TCGA.E1.A7YS.01 2 0.1648 0.6706 0.02 0.94 0.00 0.00 0.04
#> TCGA.DU.7294.01 1 0.2012 0.8939 0.92 0.00 0.00 0.02 0.06
#> TCGA.HT.7881.01 3 0.2929 0.5681 0.00 0.00 0.82 0.00 0.18
#> TCGA.HT.7695.01 4 0.2012 0.8830 0.02 0.00 0.00 0.92 0.06
#> TCGA.FG.7637.01 5 0.5927 0.3535 0.00 0.12 0.34 0.00 0.54
#> TCGA.VM.A8CE.01 3 0.0000 0.7275 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6U5.01 5 0.5157 0.3207 0.00 0.04 0.44 0.00 0.52
#> TCGA.DB.5274.01 1 0.1216 0.9015 0.96 0.00 0.00 0.02 0.02
#> TCGA.HW.7487.01 2 0.5068 0.6423 0.00 0.64 0.06 0.00 0.30
#> TCGA.HW.7491.01 2 0.5048 0.4174 0.00 0.58 0.04 0.00 0.38
#> TCGA.DU.A6S2.01 4 0.0609 0.9014 0.00 0.00 0.00 0.98 0.02
#> TCGA.TM.A84R.01 3 0.0609 0.7226 0.00 0.00 0.98 0.00 0.02
#> TCGA.HT.8012.01 4 0.5425 0.4738 0.32 0.00 0.00 0.60 0.08
#> TCGA.FG.8187.01 3 0.1043 0.7148 0.00 0.00 0.96 0.00 0.04
#> TCGA.S9.A7QZ.01 2 0.2280 0.7085 0.00 0.88 0.00 0.00 0.12
#> TCGA.QH.A6X4.01 5 0.5673 0.3710 0.00 0.42 0.08 0.00 0.50
#> TCGA.P5.A77W.01 1 0.4558 0.7278 0.74 0.00 0.00 0.18 0.08
#> TCGA.DU.7302.01 1 0.1410 0.9008 0.94 0.00 0.00 0.00 0.06
#> TCGA.HW.7495.01 4 0.0609 0.9050 0.00 0.00 0.00 0.98 0.02
#> TCGA.QH.A65R.01 1 0.2331 0.8884 0.90 0.00 0.00 0.02 0.08
#> TCGA.DU.A7TG.01 3 0.0609 0.7226 0.00 0.00 0.98 0.00 0.02
#> TCGA.S9.A6TW.01 3 0.3319 0.5906 0.00 0.02 0.82 0.00 0.16
#> TCGA.HT.7481.01 3 0.0000 0.7275 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7875.01 2 0.4540 0.3810 0.00 0.64 0.02 0.00 0.34
#> TCGA.S9.A7IQ.01 4 0.0609 0.9050 0.00 0.00 0.00 0.98 0.02
#> TCGA.DU.6394.01 2 0.0000 0.6906 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6WD.01 2 0.1732 0.6889 0.00 0.92 0.00 0.00 0.08
#> TCGA.TQ.A7RU.01 2 0.3999 0.6863 0.00 0.74 0.02 0.00 0.24
#> TCGA.DU.5874.01 1 0.1043 0.8983 0.96 0.00 0.00 0.00 0.04
#> TCGA.S9.A6WE.01 3 0.5178 -0.3300 0.00 0.04 0.48 0.00 0.48
#> TCGA.R8.A6MK.01 3 0.4748 0.2879 0.00 0.04 0.66 0.00 0.30
#> TCGA.QH.A6CY.01 3 0.0000 0.7275 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A7J1.01 5 0.6275 0.5887 0.00 0.18 0.30 0.00 0.52
#> TCGA.P5.A5F0.01 2 0.6498 0.3618 0.00 0.46 0.20 0.00 0.34
#> TCGA.R8.A73M.01 1 0.2331 0.8884 0.90 0.00 0.00 0.02 0.08
#> TCGA.DU.A6S3.01 2 0.3274 0.6984 0.00 0.78 0.00 0.00 0.22
#> TCGA.DB.A4XH.01 1 0.1216 0.9002 0.96 0.00 0.00 0.02 0.02
#> TCGA.VW.A7QS.01 1 0.2331 0.8884 0.90 0.00 0.00 0.02 0.08
#> TCGA.S9.A6WI.01 4 0.0609 0.9050 0.00 0.00 0.00 0.98 0.02
#> TCGA.DU.8164.01 2 0.1732 0.6565 0.00 0.92 0.00 0.00 0.08
#> TCGA.DU.5849.01 2 0.4748 0.6508 0.00 0.66 0.04 0.00 0.30
#> TCGA.HT.7468.01 2 0.3690 0.7005 0.00 0.78 0.02 0.00 0.20
#> TCGA.TQ.A7RI.01 4 0.0609 0.9050 0.00 0.00 0.00 0.98 0.02
#> TCGA.DB.5279.01 2 0.1410 0.6835 0.00 0.94 0.00 0.00 0.06
#> TCGA.DU.7018.01 1 0.1410 0.8945 0.94 0.00 0.00 0.00 0.06
#> TCGA.HT.7677.01 2 0.4132 0.6826 0.00 0.72 0.02 0.00 0.26
#> TCGA.FG.A713.01 4 0.0609 0.9050 0.00 0.00 0.00 0.98 0.02
#> TCGA.DU.7300.01 1 0.2438 0.8855 0.90 0.00 0.00 0.04 0.06
#> TCGA.HT.7694.01 3 0.2331 0.6742 0.00 0.02 0.90 0.00 0.08
#> TCGA.TM.A84M.01 2 0.2732 0.5939 0.00 0.84 0.00 0.00 0.16
#> TCGA.F6.A8O3.01 2 0.5788 0.5717 0.00 0.58 0.12 0.00 0.30
#> TCGA.QH.A86X.01 3 0.5558 -0.0276 0.00 0.08 0.56 0.00 0.36
#> TCGA.DU.A76R.01 5 0.6102 0.4678 0.00 0.34 0.14 0.00 0.52
#> TCGA.DH.5144.01 1 0.2331 0.8884 0.90 0.00 0.00 0.02 0.08
#> TCGA.DB.A64V.01 3 0.5355 0.3158 0.00 0.12 0.66 0.00 0.22
#> TCGA.RY.A840.01 2 0.4840 0.2442 0.00 0.64 0.04 0.00 0.32
#> TCGA.HW.A5KJ.01 2 0.2020 0.6866 0.00 0.90 0.00 0.00 0.10
#> TCGA.HT.A615.01 4 0.0000 0.9042 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.8105.01 2 0.1732 0.7105 0.00 0.92 0.00 0.00 0.08
#> TCGA.HT.7874.01 4 0.0609 0.9050 0.00 0.00 0.00 0.98 0.02
#> TCGA.HT.7471.01 1 0.0609 0.9017 0.98 0.00 0.00 0.00 0.02
#> TCGA.HT.A619.01 2 0.2438 0.6409 0.04 0.90 0.00 0.00 0.06
#> TCGA.HT.A5R9.01 1 0.4558 0.7303 0.74 0.00 0.00 0.18 0.08
#> TCGA.FG.5964.01 5 0.5689 0.3688 0.00 0.08 0.44 0.00 0.48
#> TCGA.CS.5396.01 1 0.3521 0.8046 0.82 0.00 0.00 0.14 0.04
#> TCGA.DH.A7UR.01 1 0.2331 0.8884 0.90 0.00 0.00 0.02 0.08
#> TCGA.DU.6400.01 1 0.1410 0.8945 0.94 0.00 0.00 0.00 0.06
#> TCGA.S9.A6WL.01 2 0.3274 0.6949 0.00 0.78 0.00 0.00 0.22
#> TCGA.DB.A75K.01 1 0.2754 0.8672 0.88 0.00 0.00 0.08 0.04
#> TCGA.DB.A64Q.01 4 0.3037 0.8346 0.10 0.00 0.00 0.86 0.04
#> TCGA.P5.A737.01 2 0.5341 0.4740 0.00 0.62 0.08 0.00 0.30
#> TCGA.S9.A6WH.01 1 0.1410 0.8945 0.94 0.00 0.00 0.00 0.06
#> TCGA.HT.7616.01 2 0.1732 0.6814 0.00 0.92 0.00 0.00 0.08
#> TCGA.RY.A83Y.01 2 0.4132 0.5442 0.00 0.72 0.02 0.00 0.26
#> TCGA.DB.A64U.01 4 0.0000 0.9042 0.00 0.00 0.00 1.00 0.00
#> TCGA.DB.A64W.01 1 0.1410 0.8945 0.94 0.00 0.00 0.00 0.06
#> TCGA.R8.A6MO.01 1 0.2331 0.8884 0.90 0.00 0.00 0.02 0.08
#> TCGA.HW.8322.01 2 0.6047 -0.0426 0.00 0.48 0.12 0.00 0.40
#> TCGA.DU.5870.02 1 0.1410 0.8945 0.94 0.00 0.00 0.00 0.06
#> TCGA.CS.6668.01 1 0.1043 0.8987 0.96 0.00 0.00 0.00 0.04
#> TCGA.DU.5870.01 1 0.1410 0.8945 0.94 0.00 0.00 0.00 0.06
#> TCGA.HT.7692.01 3 0.5888 0.1157 0.00 0.14 0.58 0.00 0.28
#> TCGA.R8.A6ML.01 2 0.3561 0.5614 0.00 0.74 0.00 0.00 0.26
#> TCGA.DU.6410.01 2 0.2516 0.6914 0.00 0.86 0.00 0.00 0.14
#> TCGA.TQ.A7RO.01 5 0.6337 0.5694 0.00 0.18 0.32 0.00 0.50
#> TCGA.E1.5318.01 1 0.2331 0.8884 0.90 0.00 0.00 0.02 0.08
#> TCGA.S9.A7J3.01 1 0.1410 0.9008 0.94 0.00 0.00 0.00 0.06
#> TCGA.TM.A84S.01 3 0.2280 0.6766 0.00 0.00 0.88 0.00 0.12
#> TCGA.TQ.A7RS.01 4 0.1043 0.8978 0.00 0.00 0.00 0.96 0.04
#> TCGA.QH.A65Z.01 2 0.3852 0.6852 0.00 0.76 0.02 0.00 0.22
#> TCGA.P5.A730.01 3 0.5788 0.1609 0.00 0.12 0.58 0.00 0.30
#> TCGA.RY.A83X.01 4 0.5136 0.5978 0.26 0.00 0.00 0.66 0.08
#> TCGA.S9.A6UB.01 2 0.2516 0.6570 0.00 0.86 0.00 0.00 0.14
#> TCGA.DH.A66F.01 2 0.3561 0.5560 0.00 0.74 0.00 0.00 0.26
#> TCGA.HT.7607.01 4 0.0609 0.9050 0.00 0.00 0.00 0.98 0.02
#> TCGA.DU.6393.01 2 0.2732 0.7018 0.00 0.84 0.00 0.00 0.16
#> TCGA.S9.A7IY.01 3 0.0609 0.7190 0.00 0.00 0.98 0.00 0.02
#> TCGA.FG.7641.01 2 0.6275 0.4878 0.00 0.52 0.18 0.00 0.30
#> TCGA.DU.7009.01 4 0.5341 0.5177 0.30 0.00 0.00 0.62 0.08
#> TCGA.P5.A781.01 4 0.3521 0.8024 0.14 0.00 0.00 0.82 0.04
#> TCGA.FG.8186.01 4 0.1648 0.8910 0.02 0.00 0.00 0.94 0.04
#> TCGA.S9.A6U2.01 4 0.1216 0.8971 0.02 0.00 0.00 0.96 0.02
#> TCGA.S9.A6WN.01 4 0.1043 0.8988 0.00 0.00 0.00 0.96 0.04
#> TCGA.DH.A7US.01 3 0.5457 -0.2308 0.00 0.06 0.48 0.00 0.46
#> TCGA.DB.A64L.01 1 0.0000 0.9022 1.00 0.00 0.00 0.00 0.00
#> TCGA.VV.A829.01 2 0.1410 0.6835 0.00 0.94 0.00 0.00 0.06
#> TCGA.DU.6397.02 5 0.5487 0.5895 0.00 0.28 0.10 0.00 0.62
#> TCGA.DU.6397.01 5 0.5892 0.5986 0.00 0.18 0.22 0.00 0.60
#> TCGA.CS.6670.01 5 0.6054 0.6124 0.00 0.28 0.16 0.00 0.56
#> TCGA.QH.A65X.01 1 0.5341 0.4949 0.62 0.00 0.00 0.30 0.08
#> TCGA.DB.A64P.01 2 0.4456 0.6318 0.00 0.66 0.02 0.00 0.32
#> TCGA.QH.A6CZ.01 2 0.6019 0.1442 0.00 0.50 0.12 0.00 0.38
#> TCGA.DH.A669.02 2 0.1648 0.6706 0.02 0.94 0.00 0.00 0.04
#> TCGA.DH.A669.01 2 0.1648 0.6706 0.02 0.94 0.00 0.00 0.04
#> TCGA.VM.A8CB.01 2 0.6532 0.3630 0.00 0.48 0.24 0.00 0.28
#> TCGA.HT.7687.01 2 0.0000 0.6906 0.00 1.00 0.00 0.00 0.00
#> TCGA.TM.A84G.01 1 0.1648 0.9029 0.94 0.00 0.00 0.02 0.04
#> TCGA.CS.5394.01 2 0.3852 0.6852 0.00 0.76 0.02 0.00 0.22
#> TCGA.FG.5962.01 2 0.3561 0.5024 0.00 0.74 0.00 0.00 0.26
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.E1.5319.01 4 0.3787 0.7670 0.12 0.00 0.10 0.78 0.00 0.00
#> TCGA.S9.A7J2.01 5 0.4812 0.4131 0.00 0.04 0.04 0.00 0.68 0.24
#> TCGA.S9.A6TX.01 5 0.3821 0.5008 0.00 0.22 0.04 0.00 0.74 0.00
#> TCGA.HT.A74L.01 4 0.1556 0.8475 0.00 0.00 0.08 0.92 0.00 0.00
#> TCGA.DB.A4XA.01 6 0.6564 0.1181 0.00 0.06 0.14 0.00 0.38 0.42
#> TCGA.HT.A4DV.01 4 0.2048 0.8476 0.00 0.00 0.12 0.88 0.00 0.00
#> TCGA.E1.5311.01 5 0.6556 0.4354 0.00 0.22 0.12 0.00 0.54 0.12
#> TCGA.HT.8113.01 4 0.1267 0.8620 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.HT.7620.01 6 0.1480 0.7246 0.00 0.00 0.02 0.00 0.04 0.94
#> TCGA.HT.7480.01 2 0.5705 0.3802 0.00 0.62 0.14 0.00 0.20 0.04
#> TCGA.HT.8109.01 2 0.1814 0.6377 0.00 0.90 0.10 0.00 0.00 0.00
#> TCGA.S9.A7R1.01 2 0.3697 0.5815 0.00 0.82 0.08 0.00 0.04 0.06
#> TCGA.FG.A710.01 1 0.4680 0.6999 0.68 0.00 0.20 0.12 0.00 0.00
#> TCGA.DU.A6S6.01 4 0.2094 0.8411 0.02 0.00 0.08 0.90 0.00 0.00
#> TCGA.HT.7877.01 4 0.0547 0.8649 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.QH.A6CU.01 4 0.1267 0.8620 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.HW.7486.01 6 0.0547 0.7310 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.FG.7634.01 6 0.2784 0.6883 0.00 0.04 0.04 0.00 0.04 0.88
#> TCGA.HT.8010.01 4 0.1267 0.8620 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.FG.7638.01 4 0.3985 0.7655 0.14 0.00 0.10 0.76 0.00 0.00
#> TCGA.HT.7605.01 6 0.2581 0.6810 0.00 0.00 0.02 0.00 0.12 0.86
#> TCGA.FG.A6J1.01 4 0.5071 0.2587 0.40 0.00 0.08 0.52 0.00 0.00
#> TCGA.HT.7608.01 5 0.7333 0.4016 0.00 0.20 0.14 0.00 0.40 0.26
#> TCGA.W9.A837.01 5 0.6762 0.1996 0.00 0.38 0.14 0.00 0.40 0.08
#> TCGA.TM.A7C5.01 2 0.3928 0.5747 0.00 0.76 0.08 0.00 0.16 0.00
#> TCGA.S9.A7QY.01 1 0.5509 0.3428 0.54 0.00 0.16 0.30 0.00 0.00
#> TCGA.P5.A5ET.01 6 0.4453 0.6075 0.00 0.10 0.10 0.00 0.04 0.76
#> TCGA.P5.A77X.01 4 0.2631 0.8195 0.00 0.00 0.18 0.82 0.00 0.00
#> TCGA.FG.A6IZ.01 2 0.4094 0.6130 0.00 0.74 0.18 0.00 0.08 0.00
#> TCGA.KT.A74X.01 5 0.7153 0.3138 0.00 0.32 0.14 0.00 0.40 0.14
#> TCGA.P5.A5EX.01 4 0.2260 0.8390 0.00 0.00 0.14 0.86 0.00 0.00
#> TCGA.E1.A7YO.01 2 0.4004 0.5803 0.00 0.76 0.12 0.00 0.12 0.00
#> TCGA.TQ.A7RG.01 5 0.6491 0.3801 0.00 0.14 0.12 0.00 0.56 0.18
#> TCGA.QH.A6X5.01 1 0.2790 0.8210 0.84 0.00 0.02 0.14 0.00 0.00
#> TCGA.RY.A847.01 6 0.4195 0.5733 0.00 0.02 0.04 0.00 0.20 0.74
#> TCGA.VM.A8CA.01 5 0.7401 0.3537 0.00 0.30 0.14 0.00 0.36 0.20
#> TCGA.DB.A4XG.01 2 0.2794 0.6016 0.00 0.86 0.08 0.00 0.06 0.00
#> TCGA.FG.A60K.01 4 0.2350 0.8327 0.02 0.00 0.10 0.88 0.00 0.00
#> TCGA.HT.7856.01 6 0.0000 0.7306 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.A7T6.01 1 0.2260 0.8644 0.86 0.00 0.14 0.00 0.00 0.00
#> TCGA.S9.A6TY.01 2 0.4004 0.5552 0.00 0.76 0.12 0.00 0.12 0.00
#> TCGA.TM.A84O.01 1 0.4723 0.6824 0.68 0.00 0.14 0.18 0.00 0.00
#> TCGA.HT.A61A.01 4 0.1267 0.8620 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.TQ.A7RQ.01 1 0.2350 0.8794 0.88 0.00 0.10 0.02 0.00 0.00
#> TCGA.IK.8125.01 2 0.3523 0.6186 0.00 0.78 0.18 0.00 0.04 0.00
#> TCGA.HT.A74K.01 1 0.0937 0.9090 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.QH.A6X8.01 1 0.0547 0.9128 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.HT.7467.01 6 0.1814 0.7062 0.00 0.00 0.00 0.00 0.10 0.90
#> TCGA.HT.7681.01 4 0.0547 0.8649 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.P5.A72Z.01 1 0.1267 0.9037 0.94 0.00 0.06 0.00 0.00 0.00
#> TCGA.DU.8168.01 1 0.0547 0.9128 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.TQ.A7RN.01 2 0.6480 0.0694 0.00 0.48 0.14 0.00 0.06 0.32
#> TCGA.DH.5141.01 6 0.5679 0.4720 0.00 0.18 0.12 0.00 0.06 0.64
#> TCGA.EZ.7264.01 1 0.0547 0.9112 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.QH.A65V.01 4 0.1267 0.8565 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.DU.A6S8.01 1 0.2631 0.8356 0.82 0.00 0.18 0.00 0.00 0.00
#> TCGA.DU.7298.01 4 0.4503 0.6395 0.24 0.00 0.08 0.68 0.00 0.00
#> TCGA.DB.A64R.01 4 0.1267 0.8550 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.CS.5390.01 1 0.0547 0.9129 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.S9.A6WP.01 2 0.2474 0.6185 0.00 0.88 0.04 0.00 0.08 0.00
#> TCGA.DB.5278.01 6 0.0000 0.7306 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.E1.A7YS.01 2 0.4380 0.5950 0.00 0.70 0.22 0.00 0.08 0.00
#> TCGA.DU.7294.01 1 0.0547 0.9129 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.HT.7881.01 6 0.2941 0.6039 0.00 0.00 0.00 0.00 0.22 0.78
#> TCGA.HT.7695.01 4 0.0937 0.8595 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.FG.7637.01 6 0.7656 -0.1241 0.00 0.26 0.18 0.00 0.28 0.28
#> TCGA.VM.A8CE.01 6 0.0000 0.7306 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.S9.A6U5.01 5 0.4328 0.3926 0.00 0.00 0.10 0.00 0.72 0.18
#> TCGA.DB.5274.01 1 0.0000 0.9131 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HW.7487.01 2 0.3697 0.5735 0.00 0.82 0.06 0.00 0.04 0.08
#> TCGA.HW.7491.01 2 0.5898 0.2717 0.00 0.56 0.08 0.00 0.30 0.06
#> TCGA.DU.A6S2.01 4 0.0000 0.8641 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.TM.A84R.01 6 0.0547 0.7310 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.HT.8012.01 4 0.4834 0.5864 0.26 0.00 0.10 0.64 0.00 0.00
#> TCGA.FG.8187.01 6 0.1807 0.7148 0.00 0.00 0.02 0.00 0.06 0.92
#> TCGA.S9.A7QZ.01 2 0.2728 0.6442 0.00 0.86 0.10 0.00 0.04 0.00
#> TCGA.QH.A6X4.01 5 0.5422 0.3962 0.00 0.28 0.10 0.00 0.60 0.02
#> TCGA.P5.A77W.01 1 0.4503 0.6008 0.68 0.00 0.08 0.24 0.00 0.00
#> TCGA.DU.7302.01 1 0.0547 0.9128 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.HW.7495.01 4 0.0547 0.8649 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.QH.A65R.01 1 0.1267 0.9017 0.94 0.00 0.06 0.00 0.00 0.00
#> TCGA.DU.A7TG.01 6 0.0547 0.7310 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.S9.A6TW.01 6 0.4042 0.6138 0.00 0.04 0.02 0.00 0.18 0.76
#> TCGA.HT.7481.01 6 0.0000 0.7306 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.7875.01 5 0.6564 0.1689 0.00 0.38 0.14 0.00 0.42 0.06
#> TCGA.S9.A7IQ.01 4 0.1267 0.8620 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.DU.6394.01 2 0.4244 0.6039 0.00 0.72 0.20 0.00 0.08 0.00
#> TCGA.S9.A6WD.01 2 0.3321 0.6187 0.00 0.82 0.08 0.00 0.10 0.00
#> TCGA.TQ.A7RU.01 2 0.1814 0.6254 0.00 0.90 0.10 0.00 0.00 0.00
#> TCGA.DU.5874.01 1 0.0000 0.9131 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WE.01 5 0.4765 0.3535 0.00 0.04 0.02 0.00 0.64 0.30
#> TCGA.R8.A6MK.01 6 0.6276 0.1820 0.00 0.06 0.12 0.00 0.30 0.52
#> TCGA.QH.A6CY.01 6 0.2728 0.6879 0.00 0.00 0.04 0.00 0.10 0.86
#> TCGA.S9.A7J1.01 5 0.4444 0.5289 0.00 0.08 0.02 0.00 0.74 0.16
#> TCGA.P5.A5F0.01 2 0.6538 0.1651 0.00 0.54 0.10 0.00 0.14 0.22
#> TCGA.R8.A73M.01 1 0.0547 0.9122 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.DU.A6S3.01 2 0.2094 0.6355 0.00 0.90 0.02 0.00 0.08 0.00
#> TCGA.DB.A4XH.01 1 0.0000 0.9131 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VW.A7QS.01 1 0.0937 0.9072 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.S9.A6WI.01 4 0.1267 0.8620 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.DU.8164.01 2 0.4723 0.5171 0.00 0.68 0.14 0.00 0.18 0.00
#> TCGA.DU.5849.01 2 0.4251 0.5525 0.00 0.78 0.10 0.00 0.06 0.06
#> TCGA.HT.7468.01 2 0.4380 0.4776 0.00 0.70 0.08 0.00 0.22 0.00
#> TCGA.TQ.A7RI.01 4 0.1814 0.8612 0.00 0.00 0.10 0.90 0.00 0.00
#> TCGA.DB.5279.01 2 0.4247 0.5899 0.00 0.70 0.24 0.00 0.06 0.00
#> TCGA.DU.7018.01 1 0.0937 0.9090 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.HT.7677.01 2 0.2956 0.5956 0.00 0.84 0.12 0.00 0.04 0.00
#> TCGA.FG.A713.01 4 0.1267 0.8639 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.DU.7300.01 1 0.1865 0.8923 0.92 0.00 0.04 0.04 0.00 0.00
#> TCGA.HT.7694.01 6 0.4179 0.6135 0.00 0.06 0.02 0.00 0.16 0.76
#> TCGA.TM.A84M.01 2 0.5684 0.3813 0.00 0.52 0.20 0.00 0.28 0.00
#> TCGA.F6.A8O3.01 2 0.6595 0.1614 0.00 0.50 0.22 0.00 0.06 0.22
#> TCGA.QH.A86X.01 6 0.7260 -0.2442 0.00 0.14 0.16 0.00 0.32 0.38
#> TCGA.DU.A76R.01 5 0.5797 0.3901 0.00 0.36 0.04 0.00 0.52 0.08
#> TCGA.DH.5144.01 1 0.1807 0.8926 0.92 0.00 0.06 0.02 0.00 0.00
#> TCGA.DB.A64V.01 6 0.4754 0.4692 0.00 0.24 0.06 0.00 0.02 0.68
#> TCGA.RY.A840.01 2 0.5883 0.3029 0.00 0.56 0.18 0.00 0.24 0.02
#> TCGA.HW.A5KJ.01 2 0.3351 0.6313 0.00 0.80 0.16 0.00 0.04 0.00
#> TCGA.HT.A615.01 4 0.0547 0.8665 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.HT.8105.01 2 0.2190 0.6495 0.00 0.90 0.04 0.00 0.06 0.00
#> TCGA.HT.7874.01 4 0.2048 0.8476 0.00 0.00 0.12 0.88 0.00 0.00
#> TCGA.HT.7471.01 1 0.0547 0.9122 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.HT.A619.01 2 0.5569 0.5444 0.04 0.62 0.24 0.00 0.10 0.00
#> TCGA.HT.A5R9.01 1 0.4244 0.6816 0.72 0.00 0.08 0.20 0.00 0.00
#> TCGA.FG.5964.01 5 0.4675 0.3482 0.00 0.02 0.04 0.00 0.66 0.28
#> TCGA.CS.5396.01 1 0.3982 0.7738 0.74 0.00 0.20 0.06 0.00 0.00
#> TCGA.DH.A7UR.01 1 0.1267 0.9023 0.94 0.00 0.06 0.00 0.00 0.00
#> TCGA.DU.6400.01 1 0.0937 0.9090 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.S9.A6WL.01 2 0.2094 0.6429 0.00 0.90 0.08 0.00 0.02 0.00
#> TCGA.DB.A75K.01 1 0.2474 0.8577 0.88 0.00 0.04 0.08 0.00 0.00
#> TCGA.DB.A64Q.01 4 0.4723 0.6938 0.14 0.00 0.18 0.68 0.00 0.00
#> TCGA.P5.A737.01 2 0.6849 -0.0481 0.00 0.46 0.12 0.00 0.30 0.12
#> TCGA.S9.A6WH.01 1 0.0000 0.9131 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7616.01 2 0.3982 0.6049 0.00 0.74 0.20 0.00 0.06 0.00
#> TCGA.RY.A83Y.01 2 0.5363 0.4529 0.00 0.64 0.14 0.00 0.20 0.02
#> TCGA.DB.A64U.01 4 0.0937 0.8650 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.DB.A64W.01 1 0.0937 0.9090 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.R8.A6MO.01 1 0.0547 0.9112 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.HW.8322.01 5 0.7078 0.4294 0.00 0.24 0.16 0.00 0.46 0.14
#> TCGA.DU.5870.02 1 0.2094 0.8877 0.90 0.00 0.08 0.00 0.02 0.00
#> TCGA.CS.6668.01 1 0.0547 0.9132 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.DU.5870.01 1 0.2350 0.8815 0.88 0.00 0.10 0.00 0.02 0.00
#> TCGA.HT.7692.01 2 0.6862 -0.0802 0.00 0.40 0.16 0.00 0.08 0.36
#> TCGA.R8.A6ML.01 2 0.5102 0.4573 0.00 0.62 0.14 0.00 0.24 0.00
#> TCGA.DU.6410.01 2 0.3475 0.6346 0.00 0.80 0.14 0.00 0.06 0.00
#> TCGA.TQ.A7RO.01 5 0.6620 0.5130 0.00 0.28 0.06 0.00 0.48 0.18
#> TCGA.E1.5318.01 1 0.0937 0.9078 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.S9.A7J3.01 1 0.0937 0.9120 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.TM.A84S.01 6 0.5100 0.5880 0.00 0.06 0.16 0.00 0.08 0.70
#> TCGA.TQ.A7RS.01 4 0.1267 0.8617 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.QH.A65Z.01 2 0.1814 0.6371 0.00 0.90 0.10 0.00 0.00 0.00
#> TCGA.P5.A730.01 6 0.6718 0.3169 0.00 0.20 0.22 0.00 0.08 0.50
#> TCGA.RY.A83X.01 4 0.4608 0.6534 0.22 0.00 0.10 0.68 0.00 0.00
#> TCGA.S9.A6UB.01 2 0.4566 0.5538 0.00 0.70 0.14 0.00 0.16 0.00
#> TCGA.DH.A66F.01 2 0.5027 0.4809 0.00 0.64 0.16 0.00 0.20 0.00
#> TCGA.HT.7607.01 4 0.2260 0.8390 0.00 0.00 0.14 0.86 0.00 0.00
#> TCGA.DU.6393.01 2 0.2094 0.6397 0.00 0.90 0.08 0.00 0.02 0.00
#> TCGA.S9.A7IY.01 6 0.1807 0.7228 0.00 0.00 0.06 0.00 0.02 0.92
#> TCGA.FG.7641.01 2 0.6012 0.3003 0.00 0.60 0.16 0.00 0.06 0.18
#> TCGA.DU.7009.01 4 0.5202 0.5543 0.26 0.00 0.14 0.60 0.00 0.00
#> TCGA.P5.A781.01 4 0.2512 0.8514 0.06 0.00 0.06 0.88 0.00 0.00
#> TCGA.FG.8186.01 4 0.0937 0.8595 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.S9.A6U2.01 4 0.2474 0.8479 0.04 0.00 0.08 0.88 0.00 0.00
#> TCGA.S9.A6WN.01 4 0.2260 0.8390 0.00 0.00 0.14 0.86 0.00 0.00
#> TCGA.DH.A7US.01 5 0.6556 0.3383 0.00 0.12 0.12 0.00 0.54 0.22
#> TCGA.DB.A64L.01 1 0.0000 0.9131 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VV.A829.01 2 0.4121 0.6010 0.00 0.72 0.22 0.00 0.06 0.00
#> TCGA.DU.6397.02 5 0.2403 0.5243 0.00 0.04 0.04 0.00 0.90 0.02
#> TCGA.DU.6397.01 5 0.2725 0.4996 0.00 0.02 0.04 0.00 0.88 0.06
#> TCGA.CS.6670.01 5 0.6376 0.4719 0.00 0.34 0.06 0.00 0.48 0.12
#> TCGA.QH.A65X.01 4 0.5285 0.2182 0.42 0.00 0.10 0.48 0.00 0.00
#> TCGA.DB.A64P.01 2 0.5226 0.4877 0.00 0.70 0.12 0.00 0.10 0.08
#> TCGA.QH.A6CZ.01 5 0.7347 0.2356 0.00 0.32 0.14 0.00 0.36 0.18
#> TCGA.DH.A669.02 2 0.4380 0.5950 0.00 0.70 0.22 0.00 0.08 0.00
#> TCGA.DH.A669.01 2 0.4380 0.5950 0.00 0.70 0.22 0.00 0.08 0.00
#> TCGA.VM.A8CB.01 2 0.6504 0.0490 0.00 0.44 0.18 0.00 0.04 0.34
#> TCGA.HT.7687.01 2 0.3928 0.6192 0.00 0.76 0.16 0.00 0.08 0.00
#> TCGA.TM.A84G.01 1 0.0937 0.9112 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.CS.5394.01 2 0.3163 0.6077 0.00 0.82 0.14 0.00 0.04 0.00
#> TCGA.FG.5962.01 2 0.5199 0.3511 0.00 0.58 0.12 0.00 0.30 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 4 0.3908 0.704980 0.20 0.00 0.08 0.72 0.00 0.00 0.00
#> TCGA.S9.A7J2.01 5 0.4699 0.482661 0.00 0.00 0.04 0.00 0.66 0.24 0.06
#> TCGA.S9.A6TX.01 5 0.5059 0.505196 0.00 0.14 0.04 0.00 0.70 0.04 0.08
#> TCGA.HT.A74L.01 4 0.3289 0.832241 0.06 0.00 0.10 0.82 0.02 0.00 0.00
#> TCGA.DB.A4XA.01 6 0.6229 0.025745 0.00 0.02 0.02 0.00 0.22 0.44 0.30
#> TCGA.HT.A4DV.01 4 0.0863 0.860055 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.E1.5311.01 5 0.6996 0.316045 0.00 0.12 0.02 0.00 0.42 0.20 0.24
#> TCGA.HT.8113.01 4 0.0504 0.865354 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.HT.7620.01 6 0.1006 0.667334 0.00 0.00 0.02 0.00 0.00 0.96 0.02
#> TCGA.HT.7480.01 2 0.7176 -0.068449 0.00 0.38 0.08 0.00 0.16 0.06 0.32
#> TCGA.HT.8109.01 2 0.3307 0.470435 0.00 0.74 0.00 0.00 0.02 0.00 0.24
#> TCGA.S9.A7R1.01 2 0.5513 0.041234 0.00 0.50 0.02 0.00 0.02 0.08 0.38
#> TCGA.FG.A710.01 1 0.5240 0.621010 0.58 0.00 0.26 0.14 0.00 0.00 0.02
#> TCGA.DU.A6S6.01 4 0.3199 0.813885 0.06 0.00 0.14 0.80 0.00 0.00 0.00
#> TCGA.HT.7877.01 4 0.0504 0.865354 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.QH.A6CU.01 4 0.0504 0.867142 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.HW.7486.01 6 0.0863 0.663910 0.00 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.FG.7634.01 6 0.3417 0.558533 0.00 0.00 0.02 0.00 0.00 0.72 0.26
#> TCGA.HT.8010.01 4 0.0504 0.865354 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.FG.7638.01 4 0.5218 0.636744 0.20 0.00 0.18 0.60 0.02 0.00 0.00
#> TCGA.HT.7605.01 6 0.1006 0.656770 0.00 0.00 0.02 0.00 0.02 0.96 0.00
#> TCGA.FG.A6J1.01 1 0.5086 0.092937 0.50 0.00 0.14 0.36 0.00 0.00 0.00
#> TCGA.HT.7608.01 5 0.7967 0.071519 0.00 0.12 0.12 0.00 0.28 0.24 0.24
#> TCGA.W9.A837.01 2 0.6735 0.214738 0.00 0.50 0.06 0.00 0.22 0.06 0.16
#> TCGA.TM.A7C5.01 2 0.4610 0.420471 0.00 0.66 0.02 0.00 0.08 0.00 0.24
#> TCGA.S9.A7QY.01 1 0.5190 0.328681 0.52 0.00 0.18 0.30 0.00 0.00 0.00
#> TCGA.P5.A5ET.01 6 0.5437 0.308471 0.00 0.02 0.08 0.00 0.02 0.54 0.34
#> TCGA.P5.A77X.01 4 0.3530 0.782758 0.00 0.00 0.20 0.76 0.02 0.00 0.02
#> TCGA.FG.A6IZ.01 2 0.0504 0.564820 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.KT.A74X.01 5 0.7217 0.095399 0.00 0.16 0.02 0.00 0.36 0.18 0.28
#> TCGA.P5.A5EX.01 4 0.1433 0.856620 0.00 0.00 0.08 0.92 0.00 0.00 0.00
#> TCGA.E1.A7YO.01 2 0.5614 0.380274 0.00 0.60 0.08 0.00 0.14 0.00 0.18
#> TCGA.TQ.A7RG.01 5 0.6620 0.481887 0.00 0.04 0.08 0.00 0.52 0.18 0.18
#> TCGA.QH.A6X5.01 1 0.1928 0.854219 0.90 0.00 0.08 0.00 0.02 0.00 0.00
#> TCGA.RY.A847.01 6 0.4295 0.548454 0.00 0.00 0.06 0.00 0.14 0.74 0.06
#> TCGA.VM.A8CA.01 6 0.7864 -0.177290 0.00 0.18 0.08 0.00 0.22 0.32 0.20
#> TCGA.DB.A4XG.01 2 0.5223 0.256489 0.00 0.58 0.04 0.00 0.04 0.02 0.32
#> TCGA.FG.A60K.01 4 0.3011 0.811601 0.12 0.00 0.06 0.82 0.00 0.00 0.00
#> TCGA.HT.7856.01 6 0.0504 0.665755 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.DU.A7T6.01 1 0.3530 0.803439 0.76 0.00 0.20 0.00 0.02 0.00 0.02
#> TCGA.S9.A6TY.01 2 0.4381 0.269092 0.00 0.58 0.00 0.00 0.06 0.00 0.36
#> TCGA.TM.A84O.01 1 0.3566 0.807858 0.78 0.00 0.16 0.04 0.02 0.00 0.00
#> TCGA.HT.A61A.01 4 0.0504 0.865354 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.TQ.A7RQ.01 1 0.2376 0.850349 0.86 0.00 0.12 0.00 0.02 0.00 0.00
#> TCGA.IK.8125.01 2 0.3833 0.553879 0.00 0.78 0.06 0.00 0.04 0.00 0.12
#> TCGA.HT.A74K.01 1 0.1664 0.850596 0.92 0.00 0.06 0.00 0.02 0.00 0.00
#> TCGA.QH.A6X8.01 1 0.2376 0.838727 0.86 0.00 0.12 0.00 0.02 0.00 0.00
#> TCGA.HT.7467.01 6 0.1860 0.658679 0.00 0.00 0.02 0.00 0.02 0.92 0.04
#> TCGA.HT.7681.01 4 0.0504 0.865528 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.P5.A72Z.01 1 0.2906 0.810727 0.80 0.00 0.18 0.00 0.02 0.00 0.00
#> TCGA.DU.8168.01 1 0.1363 0.853883 0.94 0.00 0.04 0.00 0.02 0.00 0.00
#> TCGA.TQ.A7RN.01 7 0.4248 0.513278 0.00 0.26 0.00 0.00 0.00 0.08 0.66
#> TCGA.DH.5141.01 6 0.4266 0.072468 0.00 0.04 0.00 0.00 0.00 0.52 0.44
#> TCGA.EZ.7264.01 1 0.1166 0.854630 0.94 0.00 0.06 0.00 0.00 0.00 0.00
#> TCGA.QH.A65V.01 4 0.1664 0.860978 0.02 0.00 0.06 0.92 0.00 0.00 0.00
#> TCGA.DU.A6S8.01 1 0.3052 0.811682 0.78 0.00 0.20 0.02 0.00 0.00 0.00
#> TCGA.DU.7298.01 4 0.4820 0.344541 0.38 0.00 0.10 0.52 0.00 0.00 0.00
#> TCGA.DB.A64R.01 4 0.2163 0.845382 0.02 0.00 0.10 0.88 0.00 0.00 0.00
#> TCGA.CS.5390.01 1 0.1433 0.850569 0.92 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WP.01 2 0.4331 0.485412 0.00 0.72 0.04 0.00 0.06 0.00 0.18
#> TCGA.DB.5278.01 6 0.1166 0.662060 0.00 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.E1.A7YS.01 2 0.2163 0.538072 0.00 0.88 0.10 0.00 0.02 0.00 0.00
#> TCGA.DU.7294.01 1 0.1166 0.856136 0.94 0.00 0.06 0.00 0.00 0.00 0.00
#> TCGA.HT.7881.01 6 0.2745 0.531445 0.00 0.00 0.00 0.00 0.16 0.82 0.02
#> TCGA.HT.7695.01 4 0.2803 0.840634 0.06 0.00 0.10 0.84 0.00 0.00 0.00
#> TCGA.FG.7637.01 7 0.6745 0.420445 0.00 0.16 0.04 0.00 0.14 0.14 0.52
#> TCGA.VM.A8CE.01 6 0.0504 0.665755 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.S9.A6U5.01 5 0.3991 0.503968 0.00 0.00 0.02 0.00 0.72 0.22 0.04
#> TCGA.DB.5274.01 1 0.1433 0.846290 0.92 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.HW.7487.01 2 0.5852 -0.213176 0.00 0.44 0.02 0.00 0.02 0.12 0.40
#> TCGA.HW.7491.01 2 0.7530 -0.116183 0.00 0.36 0.08 0.00 0.28 0.10 0.18
#> TCGA.DU.A6S2.01 4 0.0504 0.867384 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.TM.A84R.01 6 0.0504 0.657948 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.HT.8012.01 1 0.5143 -0.099726 0.44 0.00 0.14 0.42 0.00 0.00 0.00
#> TCGA.FG.8187.01 6 0.3058 0.623065 0.00 0.00 0.10 0.00 0.00 0.82 0.08
#> TCGA.S9.A7QZ.01 2 0.3228 0.520465 0.00 0.80 0.02 0.00 0.02 0.00 0.16
#> TCGA.QH.A6X4.01 5 0.6404 0.419247 0.00 0.18 0.06 0.00 0.56 0.06 0.14
#> TCGA.P5.A77W.01 1 0.3487 0.740271 0.78 0.00 0.12 0.10 0.00 0.00 0.00
#> TCGA.DU.7302.01 1 0.2081 0.841645 0.86 0.00 0.14 0.00 0.00 0.00 0.00
#> TCGA.HW.7495.01 4 0.0504 0.865528 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.QH.A65R.01 1 0.1886 0.822162 0.88 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.DU.A7TG.01 6 0.0504 0.657948 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.S9.A6TW.01 6 0.4825 0.427925 0.00 0.00 0.02 0.00 0.16 0.66 0.16
#> TCGA.HT.7481.01 6 0.0863 0.666337 0.00 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.HT.7875.01 2 0.7858 -0.154464 0.00 0.32 0.14 0.00 0.26 0.10 0.18
#> TCGA.S9.A7IQ.01 4 0.0504 0.865354 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.DU.6394.01 2 0.1363 0.562628 0.00 0.94 0.04 0.00 0.02 0.00 0.00
#> TCGA.S9.A6WD.01 2 0.3691 0.552068 0.00 0.80 0.06 0.00 0.08 0.00 0.06
#> TCGA.TQ.A7RU.01 2 0.4003 0.367226 0.00 0.64 0.00 0.00 0.04 0.00 0.32
#> TCGA.DU.5874.01 1 0.1433 0.853272 0.92 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WE.01 5 0.4832 0.399114 0.00 0.00 0.04 0.00 0.58 0.34 0.04
#> TCGA.R8.A6MK.01 6 0.7345 -0.024660 0.00 0.06 0.12 0.00 0.22 0.42 0.18
#> TCGA.QH.A6CY.01 6 0.4100 0.570258 0.00 0.00 0.04 0.00 0.10 0.76 0.10
#> TCGA.S9.A7J1.01 5 0.5330 0.558976 0.00 0.06 0.04 0.00 0.68 0.14 0.08
#> TCGA.P5.A5F0.01 2 0.7328 -0.317011 0.00 0.34 0.06 0.00 0.16 0.10 0.34
#> TCGA.R8.A73M.01 1 0.0504 0.850006 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.DU.A6S3.01 2 0.4378 0.469989 0.00 0.70 0.02 0.00 0.08 0.00 0.20
#> TCGA.DB.A4XH.01 1 0.0504 0.850006 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.VW.A7QS.01 1 0.1671 0.831378 0.90 0.00 0.10 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WI.01 4 0.0504 0.865354 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.DU.8164.01 2 0.4181 0.499526 0.00 0.74 0.04 0.00 0.16 0.00 0.06
#> TCGA.DU.5849.01 2 0.4915 0.281377 0.00 0.60 0.02 0.00 0.02 0.04 0.32
#> TCGA.HT.7468.01 2 0.6435 0.117175 0.00 0.48 0.10 0.00 0.10 0.02 0.30
#> TCGA.TQ.A7RI.01 4 0.1433 0.862483 0.00 0.00 0.08 0.92 0.00 0.00 0.00
#> TCGA.DB.5279.01 2 0.3199 0.517859 0.00 0.80 0.14 0.00 0.00 0.00 0.06
#> TCGA.DU.7018.01 1 0.2569 0.840512 0.84 0.00 0.14 0.00 0.02 0.00 0.00
#> TCGA.HT.7677.01 2 0.4317 0.261300 0.00 0.58 0.00 0.00 0.02 0.02 0.38
#> TCGA.FG.A713.01 4 0.0504 0.865354 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.DU.7300.01 1 0.1671 0.840093 0.90 0.00 0.10 0.00 0.00 0.00 0.00
#> TCGA.HT.7694.01 6 0.4418 0.543215 0.00 0.06 0.02 0.00 0.08 0.76 0.08
#> TCGA.TM.A84M.01 2 0.5208 0.416834 0.00 0.66 0.10 0.00 0.12 0.00 0.12
#> TCGA.F6.A8O3.01 7 0.4615 0.463543 0.00 0.30 0.00 0.00 0.00 0.10 0.60
#> TCGA.QH.A86X.01 6 0.7516 -0.175834 0.00 0.10 0.06 0.00 0.28 0.32 0.24
#> TCGA.DU.A76R.01 5 0.6421 -0.035765 0.00 0.30 0.00 0.00 0.42 0.08 0.20
#> TCGA.DH.5144.01 1 0.1363 0.849560 0.94 0.00 0.04 0.00 0.02 0.00 0.00
#> TCGA.DB.A64V.01 6 0.6656 -0.340534 0.00 0.18 0.04 0.00 0.04 0.42 0.32
#> TCGA.RY.A840.01 2 0.5711 0.303347 0.00 0.56 0.06 0.00 0.24 0.00 0.14
#> TCGA.HW.A5KJ.01 2 0.2163 0.540330 0.00 0.88 0.02 0.00 0.00 0.00 0.10
#> TCGA.HT.A615.01 4 0.1363 0.867853 0.02 0.00 0.04 0.94 0.00 0.00 0.00
#> TCGA.HT.8105.01 2 0.3000 0.546990 0.00 0.84 0.02 0.00 0.04 0.00 0.10
#> TCGA.HT.7874.01 4 0.0504 0.865354 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.HT.7471.01 1 0.2163 0.841575 0.88 0.00 0.10 0.00 0.02 0.00 0.00
#> TCGA.HT.A619.01 2 0.2163 0.542699 0.00 0.88 0.10 0.00 0.02 0.00 0.00
#> TCGA.HT.A5R9.01 1 0.3670 0.724561 0.76 0.00 0.14 0.10 0.00 0.00 0.00
#> TCGA.FG.5964.01 5 0.5477 0.352002 0.00 0.00 0.04 0.00 0.52 0.34 0.10
#> TCGA.CS.5396.01 1 0.5152 0.639342 0.60 0.00 0.24 0.14 0.00 0.00 0.02
#> TCGA.DH.A7UR.01 1 0.1166 0.841994 0.94 0.00 0.06 0.00 0.00 0.00 0.00
#> TCGA.DU.6400.01 1 0.2163 0.844878 0.88 0.00 0.10 0.00 0.02 0.00 0.00
#> TCGA.S9.A6WL.01 2 0.2572 0.496181 0.00 0.80 0.00 0.00 0.00 0.00 0.20
#> TCGA.DB.A75K.01 1 0.1928 0.835199 0.90 0.00 0.08 0.02 0.00 0.00 0.00
#> TCGA.DB.A64Q.01 4 0.5447 0.591079 0.12 0.00 0.24 0.60 0.02 0.00 0.02
#> TCGA.P5.A737.01 2 0.6923 0.000296 0.00 0.40 0.04 0.00 0.20 0.06 0.30
#> TCGA.S9.A6WH.01 1 0.2163 0.849828 0.88 0.00 0.10 0.00 0.02 0.00 0.00
#> TCGA.HT.7616.01 2 0.2512 0.537957 0.00 0.86 0.10 0.00 0.00 0.00 0.04
#> TCGA.RY.A83Y.01 2 0.5652 0.340754 0.00 0.58 0.06 0.00 0.20 0.00 0.16
#> TCGA.DB.A64U.01 4 0.1718 0.859938 0.04 0.00 0.04 0.92 0.00 0.00 0.00
#> TCGA.DB.A64W.01 1 0.2163 0.841489 0.88 0.00 0.10 0.00 0.02 0.00 0.00
#> TCGA.R8.A6MO.01 1 0.0504 0.850006 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.HW.8322.01 7 0.7777 0.005584 0.00 0.26 0.08 0.00 0.26 0.12 0.28
#> TCGA.DU.5870.02 1 0.3530 0.782912 0.76 0.00 0.20 0.00 0.02 0.00 0.02
#> TCGA.CS.6668.01 1 0.1928 0.847557 0.90 0.00 0.08 0.00 0.02 0.00 0.00
#> TCGA.DU.5870.01 1 0.3530 0.782912 0.76 0.00 0.20 0.00 0.02 0.00 0.02
#> TCGA.HT.7692.01 7 0.7383 0.400623 0.00 0.24 0.08 0.00 0.06 0.28 0.34
#> TCGA.R8.A6ML.01 2 0.4536 0.491615 0.00 0.72 0.08 0.00 0.14 0.00 0.06
#> TCGA.DU.6410.01 2 0.1886 0.534860 0.00 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.TQ.A7RO.01 5 0.7117 0.356647 0.00 0.08 0.06 0.00 0.42 0.28 0.16
#> TCGA.E1.5318.01 1 0.0504 0.850006 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.S9.A7J3.01 1 0.1928 0.847557 0.90 0.00 0.08 0.00 0.02 0.00 0.00
#> TCGA.TM.A84S.01 6 0.5322 0.394966 0.00 0.02 0.02 0.00 0.08 0.58 0.30
#> TCGA.TQ.A7RS.01 4 0.2159 0.859545 0.02 0.00 0.06 0.90 0.02 0.00 0.00
#> TCGA.QH.A65Z.01 2 0.3815 0.333612 0.00 0.62 0.00 0.00 0.02 0.00 0.36
#> TCGA.P5.A730.01 7 0.5317 0.468804 0.00 0.14 0.02 0.00 0.00 0.28 0.56
#> TCGA.RY.A83X.01 4 0.4998 0.457200 0.32 0.00 0.14 0.54 0.00 0.00 0.00
#> TCGA.S9.A6UB.01 2 0.4016 0.513457 0.00 0.76 0.04 0.00 0.14 0.00 0.06
#> TCGA.DH.A66F.01 2 0.5731 0.337734 0.00 0.58 0.08 0.00 0.20 0.00 0.14
#> TCGA.HT.7607.01 4 0.0863 0.863177 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.DU.6393.01 2 0.3052 0.494339 0.00 0.78 0.00 0.00 0.02 0.00 0.20
#> TCGA.S9.A7IY.01 6 0.3086 0.617612 0.00 0.00 0.00 0.00 0.04 0.80 0.16
#> TCGA.FG.7641.01 7 0.5223 0.346861 0.00 0.36 0.00 0.00 0.02 0.10 0.52
#> TCGA.DU.7009.01 4 0.5002 0.294022 0.40 0.00 0.12 0.48 0.00 0.00 0.00
#> TCGA.P5.A781.01 4 0.3617 0.765830 0.16 0.00 0.08 0.76 0.00 0.00 0.00
#> TCGA.FG.8186.01 4 0.1505 0.866069 0.02 0.00 0.02 0.94 0.02 0.00 0.00
#> TCGA.S9.A6U2.01 4 0.3011 0.824888 0.06 0.00 0.12 0.82 0.00 0.00 0.00
#> TCGA.S9.A6WN.01 4 0.1928 0.852259 0.00 0.00 0.08 0.90 0.00 0.00 0.02
#> TCGA.DH.A7US.01 5 0.6704 0.448414 0.00 0.02 0.10 0.00 0.48 0.20 0.20
#> TCGA.DB.A64L.01 1 0.0863 0.849089 0.96 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.VV.A829.01 2 0.2512 0.536871 0.00 0.86 0.10 0.00 0.00 0.00 0.04
#> TCGA.DU.6397.02 5 0.5193 0.533522 0.00 0.06 0.12 0.00 0.70 0.06 0.06
#> TCGA.DU.6397.01 5 0.4766 0.511462 0.00 0.00 0.12 0.00 0.70 0.12 0.06
#> TCGA.CS.6670.01 5 0.6996 0.203022 0.00 0.26 0.02 0.00 0.42 0.16 0.14
#> TCGA.QH.A65X.01 1 0.5234 0.335196 0.56 0.00 0.12 0.30 0.00 0.00 0.02
#> TCGA.DB.A64P.01 2 0.6660 0.024379 0.00 0.44 0.02 0.00 0.16 0.08 0.30
#> TCGA.QH.A6CZ.01 7 0.7943 0.116247 0.00 0.24 0.12 0.00 0.22 0.12 0.30
#> TCGA.DH.A669.02 2 0.3055 0.523181 0.00 0.82 0.14 0.00 0.02 0.00 0.02
#> TCGA.DH.A669.01 2 0.3055 0.523181 0.00 0.82 0.14 0.00 0.02 0.00 0.02
#> TCGA.VM.A8CB.01 7 0.7253 0.496467 0.00 0.24 0.10 0.00 0.08 0.14 0.44
#> TCGA.HT.7687.01 2 0.1006 0.562024 0.00 0.96 0.02 0.00 0.02 0.00 0.00
#> TCGA.TM.A84G.01 1 0.1886 0.847734 0.88 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.CS.5394.01 2 0.3294 0.368021 0.00 0.66 0.00 0.00 0.00 0.00 0.34
#> TCGA.FG.5962.01 2 0.5025 0.416766 0.00 0.64 0.10 0.00 0.22 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.E1.5319.01 8 0.4059 0.71197 0.08 0.00 0.00 0.28 0.00 0.00 0.00 0.64
#> TCGA.S9.A7J2.01 5 0.4841 0.54582 0.00 0.00 0.10 0.00 0.64 0.20 0.06 0.00
#> TCGA.S9.A6TX.01 5 0.5579 0.35343 0.00 0.20 0.02 0.06 0.58 0.00 0.14 0.00
#> TCGA.HT.A74L.01 8 0.3594 0.74815 0.04 0.00 0.00 0.28 0.00 0.00 0.00 0.68
#> TCGA.DB.A4XA.01 5 0.6080 0.15021 0.00 0.00 0.02 0.04 0.38 0.36 0.20 0.00
#> TCGA.HT.A4DV.01 8 0.0000 0.80736 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.E1.5311.01 7 0.5669 -0.04115 0.00 0.04 0.04 0.02 0.36 0.04 0.50 0.00
#> TCGA.HT.8113.01 8 0.0000 0.80736 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.7620.01 6 0.0941 0.76014 0.00 0.00 0.00 0.02 0.00 0.96 0.02 0.00
#> TCGA.HT.7480.01 7 0.4896 0.29799 0.00 0.12 0.12 0.00 0.06 0.02 0.68 0.00
#> TCGA.HT.8109.01 2 0.4399 0.41678 0.00 0.50 0.04 0.02 0.00 0.00 0.44 0.00
#> TCGA.S9.A7R1.01 7 0.3918 0.40313 0.00 0.16 0.02 0.02 0.02 0.02 0.76 0.00
#> TCGA.FG.A710.01 1 0.4808 0.66072 0.66 0.00 0.08 0.10 0.00 0.00 0.00 0.16
#> TCGA.DU.A6S6.01 8 0.3095 0.77327 0.02 0.00 0.00 0.24 0.00 0.00 0.00 0.74
#> TCGA.HT.7877.01 8 0.0471 0.80623 0.00 0.00 0.02 0.00 0.00 0.00 0.00 0.98
#> TCGA.QH.A6CU.01 8 0.1275 0.80677 0.00 0.00 0.02 0.04 0.00 0.00 0.00 0.94
#> TCGA.HW.7486.01 6 0.1275 0.75413 0.00 0.00 0.00 0.00 0.04 0.94 0.02 0.00
#> TCGA.FG.7634.01 6 0.5024 0.50991 0.00 0.00 0.10 0.04 0.02 0.64 0.20 0.00
#> TCGA.HT.8010.01 8 0.0000 0.80736 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.FG.7638.01 8 0.5069 0.61701 0.18 0.00 0.02 0.24 0.00 0.00 0.00 0.56
#> TCGA.HT.7605.01 6 0.2724 0.73798 0.00 0.00 0.02 0.02 0.02 0.86 0.08 0.00
#> TCGA.FG.A6J1.01 8 0.5183 0.09489 0.38 0.00 0.00 0.24 0.00 0.00 0.00 0.38
#> TCGA.HT.7608.01 7 0.7643 -0.34116 0.00 0.08 0.24 0.06 0.06 0.24 0.32 0.00
#> TCGA.W9.A837.01 3 0.7105 0.46425 0.00 0.30 0.32 0.02 0.08 0.04 0.24 0.00
#> TCGA.TM.A7C5.01 7 0.3735 0.27912 0.00 0.22 0.04 0.00 0.02 0.00 0.72 0.00
#> TCGA.S9.A7QY.01 1 0.5065 -0.07790 0.44 0.00 0.04 0.08 0.00 0.00 0.00 0.44
#> TCGA.P5.A5ET.01 7 0.5430 -0.00104 0.00 0.00 0.08 0.02 0.04 0.38 0.48 0.00
#> TCGA.P5.A77X.01 8 0.1887 0.79715 0.00 0.00 0.06 0.04 0.00 0.00 0.00 0.90
#> TCGA.FG.A6IZ.01 2 0.2650 0.63033 0.00 0.76 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.KT.A74X.01 5 0.6845 0.27883 0.00 0.16 0.00 0.12 0.42 0.06 0.24 0.00
#> TCGA.P5.A5EX.01 8 0.1275 0.80718 0.00 0.00 0.04 0.02 0.00 0.00 0.00 0.94
#> TCGA.E1.A7YO.01 7 0.5668 0.05406 0.00 0.30 0.10 0.00 0.06 0.02 0.52 0.00
#> TCGA.TQ.A7RG.01 5 0.6470 0.52199 0.00 0.04 0.06 0.04 0.54 0.16 0.16 0.00
#> TCGA.QH.A6X5.01 1 0.3170 0.78664 0.76 0.00 0.00 0.20 0.00 0.00 0.00 0.04
#> TCGA.RY.A847.01 6 0.6218 0.50553 0.00 0.04 0.18 0.06 0.08 0.58 0.06 0.00
#> TCGA.VM.A8CA.01 7 0.7847 -0.47223 0.00 0.14 0.18 0.02 0.14 0.22 0.30 0.00
#> TCGA.DB.A4XG.01 7 0.5348 0.36902 0.00 0.16 0.06 0.06 0.04 0.02 0.66 0.00
#> TCGA.FG.A60K.01 8 0.3449 0.74008 0.02 0.00 0.00 0.32 0.00 0.00 0.00 0.66
#> TCGA.HT.7856.01 6 0.0000 0.75782 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.A7T6.01 1 0.3270 0.76136 0.80 0.02 0.06 0.12 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TY.01 7 0.4575 0.35202 0.00 0.22 0.02 0.00 0.12 0.00 0.64 0.00
#> TCGA.TM.A84O.01 1 0.4882 0.59997 0.60 0.02 0.00 0.18 0.00 0.00 0.00 0.20
#> TCGA.HT.A61A.01 8 0.0941 0.80223 0.00 0.00 0.02 0.02 0.00 0.00 0.00 0.96
#> TCGA.TQ.A7RQ.01 1 0.2534 0.79331 0.78 0.00 0.00 0.22 0.00 0.00 0.00 0.00
#> TCGA.IK.8125.01 2 0.3291 0.60663 0.00 0.70 0.02 0.00 0.00 0.00 0.28 0.00
#> TCGA.HT.A74K.01 1 0.0000 0.84133 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6X8.01 1 0.0941 0.83527 0.96 0.02 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.HT.7467.01 6 0.1607 0.75196 0.00 0.00 0.04 0.00 0.04 0.92 0.00 0.00
#> TCGA.HT.7681.01 8 0.0471 0.80623 0.00 0.00 0.02 0.00 0.00 0.00 0.00 0.98
#> TCGA.P5.A72Z.01 1 0.2020 0.80808 0.90 0.02 0.02 0.06 0.00 0.00 0.00 0.00
#> TCGA.DU.8168.01 1 0.0000 0.84133 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RN.01 7 0.4951 0.31425 0.00 0.02 0.06 0.04 0.04 0.14 0.70 0.00
#> TCGA.DH.5141.01 7 0.4655 0.19343 0.00 0.00 0.04 0.02 0.02 0.34 0.58 0.00
#> TCGA.EZ.7264.01 1 0.1804 0.83645 0.90 0.00 0.02 0.08 0.00 0.00 0.00 0.00
#> TCGA.QH.A65V.01 8 0.2406 0.79708 0.00 0.00 0.00 0.20 0.00 0.00 0.00 0.80
#> TCGA.DU.A6S8.01 1 0.3817 0.75727 0.76 0.00 0.08 0.12 0.00 0.00 0.00 0.04
#> TCGA.DU.7298.01 8 0.5557 0.37454 0.28 0.00 0.02 0.28 0.00 0.00 0.00 0.42
#> TCGA.DB.A64R.01 8 0.2114 0.80765 0.00 0.00 0.00 0.16 0.00 0.00 0.00 0.84
#> TCGA.CS.5390.01 1 0.0000 0.84133 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WP.01 7 0.4375 0.25029 0.00 0.26 0.04 0.02 0.02 0.00 0.66 0.00
#> TCGA.DB.5278.01 6 0.2020 0.73537 0.00 0.00 0.06 0.02 0.02 0.90 0.00 0.00
#> TCGA.E1.A7YS.01 2 0.2224 0.60040 0.02 0.86 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.DU.7294.01 1 0.2224 0.83386 0.86 0.00 0.02 0.12 0.00 0.00 0.00 0.00
#> TCGA.HT.7881.01 6 0.3337 0.63560 0.00 0.00 0.00 0.04 0.16 0.78 0.02 0.00
#> TCGA.HT.7695.01 8 0.3095 0.78278 0.00 0.00 0.02 0.24 0.00 0.00 0.00 0.74
#> TCGA.FG.7637.01 7 0.6295 0.07560 0.00 0.04 0.06 0.02 0.28 0.10 0.50 0.00
#> TCGA.VM.A8CE.01 6 0.0000 0.75782 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6U5.01 5 0.3483 0.56162 0.00 0.00 0.02 0.04 0.76 0.18 0.00 0.00
#> TCGA.DB.5274.01 1 0.1804 0.84072 0.90 0.00 0.02 0.08 0.00 0.00 0.00 0.00
#> TCGA.HW.7487.01 7 0.5280 0.33452 0.00 0.18 0.04 0.04 0.04 0.04 0.66 0.00
#> TCGA.HW.7491.01 7 0.6888 -0.15520 0.00 0.20 0.16 0.04 0.20 0.00 0.40 0.00
#> TCGA.DU.A6S2.01 8 0.1091 0.80744 0.00 0.00 0.00 0.06 0.00 0.00 0.00 0.94
#> TCGA.TM.A84R.01 6 0.0471 0.75615 0.00 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.HT.8012.01 8 0.5211 0.36807 0.26 0.00 0.00 0.34 0.00 0.00 0.00 0.40
#> TCGA.FG.8187.01 6 0.3369 0.72304 0.00 0.00 0.08 0.02 0.04 0.82 0.04 0.00
#> TCGA.S9.A7QZ.01 2 0.4399 0.37647 0.00 0.50 0.04 0.02 0.00 0.00 0.44 0.00
#> TCGA.QH.A6X4.01 5 0.6333 0.13617 0.00 0.24 0.10 0.00 0.46 0.02 0.18 0.00
#> TCGA.P5.A77W.01 1 0.4621 0.62355 0.64 0.00 0.02 0.20 0.00 0.00 0.00 0.14
#> TCGA.DU.7302.01 1 0.0471 0.83934 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.HW.7495.01 8 0.0471 0.80910 0.00 0.00 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.QH.A65R.01 1 0.2981 0.77802 0.76 0.00 0.02 0.22 0.00 0.00 0.00 0.00
#> TCGA.DU.A7TG.01 6 0.0941 0.75623 0.00 0.00 0.00 0.02 0.00 0.96 0.02 0.00
#> TCGA.S9.A6TW.01 6 0.5103 0.48747 0.00 0.00 0.04 0.02 0.14 0.64 0.16 0.00
#> TCGA.HT.7481.01 6 0.2204 0.75585 0.00 0.00 0.04 0.02 0.02 0.90 0.02 0.00
#> TCGA.HT.7875.01 2 0.7830 -0.62246 0.00 0.26 0.26 0.04 0.12 0.08 0.24 0.00
#> TCGA.S9.A7IQ.01 8 0.0941 0.80223 0.00 0.00 0.02 0.02 0.00 0.00 0.00 0.96
#> TCGA.DU.6394.01 2 0.2856 0.62569 0.00 0.78 0.02 0.00 0.00 0.00 0.20 0.00
#> TCGA.S9.A6WD.01 2 0.4800 0.48226 0.00 0.54 0.06 0.00 0.04 0.00 0.36 0.00
#> TCGA.TQ.A7RU.01 7 0.2981 0.32017 0.00 0.22 0.00 0.02 0.00 0.00 0.76 0.00
#> TCGA.DU.5874.01 1 0.0000 0.84133 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WE.01 5 0.6264 0.49958 0.00 0.02 0.18 0.00 0.48 0.22 0.10 0.00
#> TCGA.R8.A6MK.01 6 0.7158 -0.00242 0.00 0.06 0.30 0.04 0.06 0.38 0.16 0.00
#> TCGA.QH.A6CY.01 6 0.4155 0.58576 0.00 0.00 0.02 0.02 0.10 0.74 0.12 0.00
#> TCGA.S9.A7J1.01 5 0.6207 0.48111 0.00 0.10 0.12 0.06 0.60 0.08 0.04 0.00
#> TCGA.P5.A5F0.01 7 0.3637 0.37482 0.00 0.06 0.02 0.04 0.00 0.08 0.80 0.00
#> TCGA.R8.A73M.01 1 0.2404 0.82682 0.84 0.00 0.02 0.14 0.00 0.00 0.00 0.00
#> TCGA.DU.A6S3.01 7 0.4522 -0.04874 0.00 0.34 0.04 0.00 0.04 0.00 0.58 0.00
#> TCGA.DB.A4XH.01 1 0.1091 0.84346 0.94 0.00 0.00 0.06 0.00 0.00 0.00 0.00
#> TCGA.VW.A7QS.01 1 0.1765 0.83133 0.88 0.00 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WI.01 8 0.0471 0.80435 0.00 0.00 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.DU.8164.01 2 0.4759 0.45729 0.00 0.64 0.08 0.00 0.06 0.00 0.22 0.00
#> TCGA.DU.5849.01 7 0.3021 0.40915 0.00 0.16 0.00 0.00 0.02 0.02 0.80 0.00
#> TCGA.HT.7468.01 2 0.6775 0.04540 0.00 0.36 0.04 0.12 0.16 0.00 0.32 0.00
#> TCGA.TQ.A7RI.01 8 0.2719 0.79850 0.00 0.00 0.02 0.18 0.00 0.00 0.00 0.80
#> TCGA.DB.5279.01 2 0.2680 0.58710 0.02 0.84 0.02 0.00 0.00 0.00 0.12 0.00
#> TCGA.DU.7018.01 1 0.0000 0.84133 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7677.01 7 0.4057 0.38875 0.00 0.20 0.02 0.04 0.02 0.00 0.72 0.00
#> TCGA.FG.A713.01 8 0.0471 0.80623 0.00 0.00 0.02 0.00 0.00 0.00 0.00 0.98
#> TCGA.DU.7300.01 1 0.4022 0.75437 0.74 0.00 0.04 0.12 0.00 0.00 0.00 0.10
#> TCGA.HT.7694.01 6 0.5646 0.49974 0.00 0.04 0.06 0.04 0.06 0.64 0.16 0.00
#> TCGA.TM.A84M.01 2 0.4971 0.15110 0.00 0.62 0.22 0.00 0.08 0.00 0.08 0.00
#> TCGA.F6.A8O3.01 7 0.3854 0.37903 0.00 0.06 0.04 0.02 0.02 0.06 0.80 0.00
#> TCGA.QH.A86X.01 7 0.7161 -0.37369 0.00 0.02 0.24 0.02 0.14 0.26 0.32 0.00
#> TCGA.DU.A76R.01 7 0.6440 -0.08615 0.00 0.08 0.08 0.04 0.34 0.02 0.44 0.00
#> TCGA.DH.5144.01 1 0.1563 0.83968 0.90 0.00 0.00 0.10 0.00 0.00 0.00 0.00
#> TCGA.DB.A64V.01 7 0.5021 0.20209 0.00 0.02 0.02 0.04 0.02 0.32 0.58 0.00
#> TCGA.RY.A840.01 2 0.6556 0.04027 0.00 0.42 0.12 0.02 0.22 0.00 0.22 0.00
#> TCGA.HW.A5KJ.01 2 0.2852 0.61958 0.00 0.72 0.00 0.00 0.00 0.00 0.28 0.00
#> TCGA.HT.A615.01 8 0.2404 0.80751 0.00 0.00 0.02 0.14 0.00 0.00 0.00 0.84
#> TCGA.HT.8105.01 2 0.3729 0.39011 0.00 0.52 0.00 0.00 0.02 0.00 0.46 0.00
#> TCGA.HT.7874.01 8 0.0000 0.80736 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.HT.7471.01 1 0.1563 0.83586 0.90 0.00 0.00 0.10 0.00 0.00 0.00 0.00
#> TCGA.HT.A619.01 2 0.3078 0.58061 0.06 0.82 0.02 0.00 0.00 0.00 0.10 0.00
#> TCGA.HT.A5R9.01 1 0.4904 0.37431 0.50 0.00 0.00 0.32 0.00 0.00 0.00 0.18
#> TCGA.FG.5964.01 5 0.6563 0.45183 0.00 0.02 0.14 0.06 0.46 0.28 0.04 0.00
#> TCGA.CS.5396.01 1 0.5563 0.54169 0.56 0.00 0.10 0.16 0.00 0.00 0.00 0.18
#> TCGA.DH.A7UR.01 1 0.2406 0.80932 0.80 0.00 0.00 0.20 0.00 0.00 0.00 0.00
#> TCGA.DU.6400.01 1 0.0471 0.83717 0.98 0.02 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WL.01 7 0.3237 -0.03767 0.00 0.40 0.00 0.00 0.00 0.00 0.60 0.00
#> TCGA.DB.A75K.01 1 0.3771 0.71331 0.72 0.00 0.00 0.16 0.00 0.00 0.00 0.12
#> TCGA.DB.A64Q.01 8 0.4873 0.61318 0.12 0.00 0.10 0.12 0.00 0.00 0.00 0.66
#> TCGA.P5.A737.01 7 0.6958 -0.19510 0.00 0.18 0.14 0.02 0.08 0.10 0.48 0.00
#> TCGA.S9.A6WH.01 1 0.0000 0.84133 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7616.01 2 0.2719 0.60690 0.02 0.80 0.00 0.00 0.00 0.00 0.18 0.00
#> TCGA.RY.A83Y.01 7 0.6147 -0.07176 0.00 0.30 0.06 0.02 0.18 0.00 0.44 0.00
#> TCGA.DB.A64U.01 8 0.2719 0.79994 0.00 0.00 0.02 0.18 0.00 0.00 0.00 0.80
#> TCGA.DB.A64W.01 1 0.0941 0.83527 0.96 0.02 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.R8.A6MO.01 1 0.1804 0.83861 0.90 0.00 0.02 0.08 0.00 0.00 0.00 0.00
#> TCGA.HW.8322.01 3 0.7982 0.45627 0.00 0.16 0.28 0.04 0.18 0.10 0.24 0.00
#> TCGA.DU.5870.02 1 0.3178 0.75871 0.80 0.04 0.02 0.14 0.00 0.00 0.00 0.00
#> TCGA.CS.6668.01 1 0.0941 0.83107 0.96 0.02 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.DU.5870.01 1 0.3178 0.75871 0.80 0.04 0.02 0.14 0.00 0.00 0.00 0.00
#> TCGA.HT.7692.01 7 0.6370 0.07596 0.00 0.04 0.08 0.08 0.02 0.30 0.48 0.00
#> TCGA.R8.A6ML.01 2 0.6003 0.39758 0.00 0.48 0.08 0.02 0.12 0.00 0.30 0.00
#> TCGA.DU.6410.01 2 0.2938 0.62426 0.00 0.70 0.00 0.00 0.00 0.00 0.30 0.00
#> TCGA.TQ.A7RO.01 7 0.7072 -0.33286 0.00 0.08 0.14 0.00 0.26 0.14 0.38 0.00
#> TCGA.E1.5318.01 1 0.1557 0.84120 0.92 0.00 0.02 0.06 0.00 0.00 0.00 0.00
#> TCGA.S9.A7J3.01 1 0.0808 0.84158 0.96 0.00 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.TM.A84S.01 6 0.6908 0.02577 0.00 0.02 0.16 0.02 0.12 0.36 0.32 0.00
#> TCGA.TQ.A7RS.01 8 0.2856 0.79810 0.00 0.00 0.02 0.20 0.00 0.00 0.00 0.78
#> TCGA.QH.A65Z.01 7 0.2406 0.35134 0.00 0.20 0.00 0.00 0.00 0.00 0.80 0.00
#> TCGA.P5.A730.01 7 0.4022 0.33678 0.00 0.00 0.10 0.04 0.00 0.12 0.74 0.00
#> TCGA.RY.A83X.01 8 0.5190 0.37858 0.26 0.00 0.00 0.32 0.00 0.00 0.00 0.42
#> TCGA.S9.A6UB.01 2 0.5692 0.44756 0.00 0.52 0.08 0.02 0.08 0.00 0.30 0.00
#> TCGA.DH.A66F.01 2 0.5798 0.29955 0.00 0.50 0.12 0.00 0.12 0.00 0.26 0.00
#> TCGA.HT.7607.01 8 0.0808 0.80558 0.00 0.00 0.04 0.00 0.00 0.00 0.00 0.96
#> TCGA.DU.6393.01 2 0.3714 0.41611 0.00 0.54 0.00 0.00 0.02 0.00 0.44 0.00
#> TCGA.S9.A7IY.01 6 0.2674 0.74145 0.00 0.00 0.06 0.04 0.00 0.86 0.04 0.00
#> TCGA.FG.7641.01 7 0.4401 0.39781 0.00 0.06 0.04 0.02 0.04 0.08 0.76 0.00
#> TCGA.DU.7009.01 8 0.5653 0.36587 0.28 0.00 0.04 0.22 0.00 0.00 0.00 0.46
#> TCGA.P5.A781.01 8 0.4318 0.68820 0.10 0.00 0.00 0.30 0.00 0.00 0.00 0.60
#> TCGA.FG.8186.01 8 0.2114 0.80927 0.00 0.00 0.00 0.16 0.00 0.00 0.00 0.84
#> TCGA.S9.A6U2.01 8 0.3021 0.79741 0.02 0.00 0.02 0.16 0.00 0.00 0.00 0.80
#> TCGA.S9.A6WN.01 8 0.0471 0.80878 0.00 0.00 0.02 0.00 0.00 0.00 0.00 0.98
#> TCGA.DH.A7US.01 5 0.5880 0.48220 0.00 0.02 0.02 0.06 0.56 0.10 0.24 0.00
#> TCGA.DB.A64L.01 1 0.0000 0.84133 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VV.A829.01 2 0.3503 0.55993 0.02 0.78 0.08 0.00 0.00 0.00 0.12 0.00
#> TCGA.DU.6397.02 5 0.5283 0.45764 0.00 0.10 0.10 0.04 0.68 0.02 0.06 0.00
#> TCGA.DU.6397.01 5 0.5390 0.47653 0.00 0.08 0.10 0.04 0.68 0.04 0.06 0.00
#> TCGA.CS.6670.01 7 0.6950 -0.25621 0.00 0.20 0.10 0.00 0.28 0.06 0.36 0.00
#> TCGA.QH.A65X.01 1 0.5550 0.08113 0.42 0.00 0.02 0.26 0.00 0.00 0.00 0.30
#> TCGA.DB.A64P.01 7 0.3185 0.39352 0.00 0.08 0.04 0.00 0.00 0.06 0.82 0.00
#> TCGA.QH.A6CZ.01 7 0.7170 -0.31986 0.00 0.08 0.24 0.08 0.12 0.04 0.44 0.00
#> TCGA.DH.A669.02 2 0.2025 0.58823 0.02 0.88 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.DH.A669.01 2 0.2025 0.58823 0.02 0.88 0.00 0.00 0.00 0.00 0.10 0.00
#> TCGA.VM.A8CB.01 7 0.6981 0.05404 0.00 0.08 0.14 0.10 0.08 0.08 0.52 0.00
#> TCGA.HT.7687.01 2 0.2938 0.62225 0.00 0.70 0.00 0.00 0.00 0.00 0.30 0.00
#> TCGA.TM.A84G.01 1 0.0471 0.83934 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.CS.5394.01 7 0.3291 0.25254 0.00 0.28 0.00 0.00 0.02 0.00 0.70 0.00
#> TCGA.FG.5962.01 2 0.5804 0.21496 0.00 0.56 0.08 0.00 0.16 0.02 0.18 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node022. Child nodes: Node01211-leaf , Node01212-leaf , Node01213-leaf , Node02211 , Node02212 , Node02221 , Node02222-leaf , Node02223 , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02321-leaf , Node02322-leaf , Node02323-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 80 columns.
#> Top rows (1000) are extracted by 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.997 0.999 0.4950 0.505 0.505
#> 3 3 0.509 0.745 0.857 0.3276 0.715 0.489
#> 4 4 0.681 0.607 0.807 0.1270 0.830 0.550
#> 5 5 0.663 0.634 0.794 0.0612 0.855 0.522
#> 6 6 0.734 0.721 0.837 0.0348 0.931 0.693
#> 7 7 0.758 0.697 0.831 0.0243 0.981 0.896
#> 8 8 0.836 0.732 0.841 0.0197 0.965 0.803
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.E1.5319.01 1 0.000 1.000 1.0 0.0
#> TCGA.HT.A74L.01 1 0.000 1.000 1.0 0.0
#> TCGA.HT.A4DV.01 1 0.000 1.000 1.0 0.0
#> TCGA.HT.8113.01 1 0.000 1.000 1.0 0.0
#> TCGA.FG.A710.01 1 0.000 1.000 1.0 0.0
#> TCGA.DU.A6S6.01 1 0.000 1.000 1.0 0.0
#> TCGA.HT.7877.01 1 0.000 1.000 1.0 0.0
#> TCGA.QH.A6CU.01 1 0.000 1.000 1.0 0.0
#> TCGA.HT.8010.01 1 0.000 1.000 1.0 0.0
#> TCGA.FG.7638.01 1 0.000 1.000 1.0 0.0
#> TCGA.FG.A6J1.01 1 0.000 1.000 1.0 0.0
#> TCGA.S9.A7QY.01 1 0.000 1.000 1.0 0.0
#> TCGA.P5.A77X.01 1 0.000 1.000 1.0 0.0
#> TCGA.P5.A5EX.01 1 0.000 1.000 1.0 0.0
#> TCGA.QH.A6X5.01 1 0.000 1.000 1.0 0.0
#> TCGA.FG.A60K.01 1 0.000 1.000 1.0 0.0
#> TCGA.DU.A7T6.01 1 0.000 1.000 1.0 0.0
#> TCGA.TM.A84O.01 1 0.000 1.000 1.0 0.0
#> TCGA.HT.A61A.01 1 0.000 1.000 1.0 0.0
#> TCGA.TQ.A7RQ.01 1 0.000 1.000 1.0 0.0
#> TCGA.HT.A74K.01 2 0.000 0.997 0.0 1.0
#> TCGA.QH.A6X8.01 2 0.000 0.997 0.0 1.0
#> TCGA.HT.7681.01 1 0.000 1.000 1.0 0.0
#> TCGA.P5.A72Z.01 2 0.000 0.997 0.0 1.0
#> TCGA.DU.8168.01 2 0.000 0.997 0.0 1.0
#> TCGA.EZ.7264.01 2 0.000 0.997 0.0 1.0
#> TCGA.QH.A65V.01 1 0.000 1.000 1.0 0.0
#> TCGA.DU.A6S8.01 1 0.000 1.000 1.0 0.0
#> TCGA.DU.7298.01 2 0.000 0.997 0.0 1.0
#> TCGA.DB.A64R.01 1 0.000 1.000 1.0 0.0
#> TCGA.CS.5390.01 2 0.000 0.997 0.0 1.0
#> TCGA.DU.7294.01 2 0.000 0.997 0.0 1.0
#> TCGA.HT.7695.01 1 0.000 1.000 1.0 0.0
#> TCGA.DB.5274.01 2 0.000 0.997 0.0 1.0
#> TCGA.DU.A6S2.01 1 0.000 1.000 1.0 0.0
#> TCGA.HT.8012.01 2 0.000 0.997 0.0 1.0
#> TCGA.P5.A77W.01 2 0.000 0.997 0.0 1.0
#> TCGA.DU.7302.01 2 0.000 0.997 0.0 1.0
#> TCGA.HW.7495.01 1 0.000 1.000 1.0 0.0
#> TCGA.QH.A65R.01 2 0.000 0.997 0.0 1.0
#> TCGA.S9.A7IQ.01 1 0.000 1.000 1.0 0.0
#> TCGA.DU.5874.01 2 0.000 0.997 0.0 1.0
#> TCGA.R8.A73M.01 2 0.000 0.997 0.0 1.0
#> TCGA.DB.A4XH.01 2 0.000 0.997 0.0 1.0
#> TCGA.VW.A7QS.01 2 0.000 0.997 0.0 1.0
#> TCGA.S9.A6WI.01 1 0.000 1.000 1.0 0.0
#> TCGA.TQ.A7RI.01 1 0.000 1.000 1.0 0.0
#> TCGA.DU.7018.01 2 0.000 0.997 0.0 1.0
#> TCGA.FG.A713.01 1 0.000 1.000 1.0 0.0
#> TCGA.DU.7300.01 2 0.469 0.889 0.1 0.9
#> TCGA.DH.5144.01 2 0.000 0.997 0.0 1.0
#> TCGA.HT.A615.01 1 0.000 1.000 1.0 0.0
#> TCGA.HT.7874.01 1 0.000 1.000 1.0 0.0
#> TCGA.HT.7471.01 2 0.000 0.997 0.0 1.0
#> TCGA.HT.A5R9.01 2 0.000 0.997 0.0 1.0
#> TCGA.CS.5396.01 1 0.000 1.000 1.0 0.0
#> TCGA.DH.A7UR.01 2 0.000 0.997 0.0 1.0
#> TCGA.DU.6400.01 2 0.000 0.997 0.0 1.0
#> TCGA.DB.A75K.01 2 0.000 0.997 0.0 1.0
#> TCGA.DB.A64Q.01 1 0.000 1.000 1.0 0.0
#> TCGA.S9.A6WH.01 2 0.000 0.997 0.0 1.0
#> TCGA.DB.A64U.01 1 0.000 1.000 1.0 0.0
#> TCGA.DB.A64W.01 2 0.000 0.997 0.0 1.0
#> TCGA.R8.A6MO.01 2 0.000 0.997 0.0 1.0
#> TCGA.DU.5870.02 2 0.000 0.997 0.0 1.0
#> TCGA.CS.6668.01 2 0.000 0.997 0.0 1.0
#> TCGA.DU.5870.01 1 0.000 1.000 1.0 0.0
#> TCGA.E1.5318.01 2 0.000 0.997 0.0 1.0
#> TCGA.S9.A7J3.01 2 0.000 0.997 0.0 1.0
#> TCGA.TQ.A7RS.01 1 0.000 1.000 1.0 0.0
#> TCGA.RY.A83X.01 1 0.000 1.000 1.0 0.0
#> TCGA.HT.7607.01 1 0.000 1.000 1.0 0.0
#> TCGA.DU.7009.01 1 0.000 1.000 1.0 0.0
#> TCGA.P5.A781.01 1 0.000 1.000 1.0 0.0
#> TCGA.FG.8186.01 1 0.000 1.000 1.0 0.0
#> TCGA.S9.A6U2.01 1 0.000 1.000 1.0 0.0
#> TCGA.S9.A6WN.01 1 0.000 1.000 1.0 0.0
#> TCGA.DB.A64L.01 2 0.000 0.997 0.0 1.0
#> TCGA.QH.A65X.01 1 0.000 1.000 1.0 0.0
#> TCGA.TM.A84G.01 2 0.000 0.997 0.0 1.0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.E1.5319.01 3 0.4291 0.745 0.18 0.00 0.82
#> TCGA.HT.A74L.01 3 0.5560 0.654 0.30 0.00 0.70
#> TCGA.HT.A4DV.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.HT.8113.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.FG.A710.01 3 0.5706 0.531 0.32 0.00 0.68
#> TCGA.DU.A6S6.01 3 0.5835 0.596 0.34 0.00 0.66
#> TCGA.HT.7877.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.QH.A6CU.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.HT.8010.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.FG.7638.01 3 0.4002 0.748 0.16 0.00 0.84
#> TCGA.FG.A6J1.01 3 0.2959 0.739 0.10 0.00 0.90
#> TCGA.S9.A7QY.01 3 0.3340 0.744 0.12 0.00 0.88
#> TCGA.P5.A77X.01 1 0.0892 0.948 0.98 0.00 0.02
#> TCGA.P5.A5EX.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.QH.A6X5.01 3 0.3340 0.724 0.12 0.00 0.88
#> TCGA.FG.A60K.01 3 0.6309 0.269 0.50 0.00 0.50
#> TCGA.DU.A7T6.01 3 0.5706 0.531 0.32 0.00 0.68
#> TCGA.TM.A84O.01 3 0.3340 0.724 0.12 0.00 0.88
#> TCGA.HT.A61A.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.TQ.A7RQ.01 3 0.0892 0.702 0.02 0.00 0.98
#> TCGA.HT.A74K.01 2 0.5397 0.715 0.00 0.72 0.28
#> TCGA.QH.A6X8.01 2 0.0892 0.812 0.00 0.98 0.02
#> TCGA.HT.7681.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.P5.A72Z.01 2 0.4796 0.699 0.00 0.78 0.22
#> TCGA.DU.8168.01 2 0.0000 0.813 0.00 1.00 0.00
#> TCGA.EZ.7264.01 3 0.5216 0.365 0.00 0.26 0.74
#> TCGA.QH.A65V.01 1 0.5397 0.481 0.72 0.00 0.28
#> TCGA.DU.A6S8.01 3 0.2959 0.724 0.10 0.00 0.90
#> TCGA.DU.7298.01 3 0.4555 0.589 0.00 0.20 0.80
#> TCGA.DB.A64R.01 3 0.6244 0.398 0.44 0.00 0.56
#> TCGA.CS.5390.01 2 0.0000 0.813 0.00 1.00 0.00
#> TCGA.DU.7294.01 3 0.4796 0.467 0.00 0.22 0.78
#> TCGA.HT.7695.01 3 0.6192 0.463 0.42 0.00 0.58
#> TCGA.DB.5274.01 2 0.5397 0.700 0.00 0.72 0.28
#> TCGA.DU.A6S2.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.HT.8012.01 3 0.6045 0.222 0.00 0.38 0.62
#> TCGA.P5.A77W.01 2 0.5560 0.679 0.00 0.70 0.30
#> TCGA.DU.7302.01 2 0.0892 0.812 0.00 0.98 0.02
#> TCGA.HW.7495.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.QH.A65R.01 2 0.0000 0.813 0.00 1.00 0.00
#> TCGA.S9.A7IQ.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.DU.5874.01 2 0.0000 0.813 0.00 1.00 0.00
#> TCGA.R8.A73M.01 3 0.3340 0.620 0.00 0.12 0.88
#> TCGA.DB.A4XH.01 2 0.0000 0.813 0.00 1.00 0.00
#> TCGA.VW.A7QS.01 2 0.5835 0.625 0.00 0.66 0.34
#> TCGA.S9.A6WI.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.TQ.A7RI.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.DU.7018.01 2 0.0892 0.812 0.00 0.98 0.02
#> TCGA.FG.A713.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.DU.7300.01 3 0.3340 0.655 0.00 0.12 0.88
#> TCGA.DH.5144.01 2 0.5706 0.671 0.00 0.68 0.32
#> TCGA.HT.A615.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.HT.7874.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.HT.7471.01 2 0.6045 0.598 0.00 0.62 0.38
#> TCGA.HT.A5R9.01 2 0.5835 0.625 0.00 0.66 0.34
#> TCGA.CS.5396.01 3 0.5560 0.566 0.30 0.00 0.70
#> TCGA.DH.A7UR.01 2 0.5016 0.734 0.00 0.76 0.24
#> TCGA.DU.6400.01 2 0.0892 0.812 0.00 0.98 0.02
#> TCGA.DB.A75K.01 3 0.4002 0.626 0.00 0.16 0.84
#> TCGA.DB.A64Q.01 1 0.2537 0.881 0.92 0.00 0.08
#> TCGA.S9.A6WH.01 2 0.0892 0.812 0.00 0.98 0.02
#> TCGA.DB.A64U.01 1 0.3340 0.819 0.88 0.00 0.12
#> TCGA.DB.A64W.01 2 0.0892 0.812 0.00 0.98 0.02
#> TCGA.R8.A6MO.01 2 0.5706 0.671 0.00 0.68 0.32
#> TCGA.DU.5870.02 3 0.6045 0.056 0.00 0.38 0.62
#> TCGA.CS.6668.01 2 0.5216 0.725 0.00 0.74 0.26
#> TCGA.DU.5870.01 3 0.3340 0.724 0.12 0.00 0.88
#> TCGA.E1.5318.01 2 0.0000 0.813 0.00 1.00 0.00
#> TCGA.S9.A7J3.01 2 0.5397 0.715 0.00 0.72 0.28
#> TCGA.TQ.A7RS.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.RY.A83X.01 3 0.4291 0.745 0.18 0.00 0.82
#> TCGA.HT.7607.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.DU.7009.01 3 0.4002 0.748 0.16 0.00 0.84
#> TCGA.P5.A781.01 3 0.5397 0.694 0.28 0.00 0.72
#> TCGA.FG.8186.01 1 0.0892 0.948 0.98 0.00 0.02
#> TCGA.S9.A6U2.01 1 0.2537 0.878 0.92 0.00 0.08
#> TCGA.S9.A6WN.01 1 0.0000 0.967 1.00 0.00 0.00
#> TCGA.DB.A64L.01 2 0.3340 0.791 0.00 0.88 0.12
#> TCGA.QH.A65X.01 3 0.4291 0.745 0.18 0.00 0.82
#> TCGA.TM.A84G.01 2 0.6244 0.471 0.00 0.56 0.44
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.E1.5319.01 3 0.4994 0.50343 0.00 0.00 0.52 0.48
#> TCGA.HT.A74L.01 3 0.5535 0.51692 0.02 0.00 0.56 0.42
#> TCGA.HT.A4DV.01 1 0.0000 0.93158 1.00 0.00 0.00 0.00
#> TCGA.HT.8113.01 1 0.0000 0.93158 1.00 0.00 0.00 0.00
#> TCGA.FG.A710.01 4 0.0000 0.67802 0.00 0.00 0.00 1.00
#> TCGA.DU.A6S6.01 3 0.5487 0.52407 0.02 0.00 0.58 0.40
#> TCGA.HT.7877.01 1 0.0000 0.93158 1.00 0.00 0.00 0.00
#> TCGA.QH.A6CU.01 1 0.0000 0.93158 1.00 0.00 0.00 0.00
#> TCGA.HT.8010.01 1 0.0000 0.93158 1.00 0.00 0.00 0.00
#> TCGA.FG.7638.01 3 0.4994 0.50343 0.00 0.00 0.52 0.48
#> TCGA.FG.A6J1.01 3 0.4977 0.51484 0.00 0.00 0.54 0.46
#> TCGA.S9.A7QY.01 3 0.4994 0.50343 0.00 0.00 0.52 0.48
#> TCGA.P5.A77X.01 1 0.3400 0.78449 0.82 0.00 0.00 0.18
#> TCGA.P5.A5EX.01 1 0.0000 0.93158 1.00 0.00 0.00 0.00
#> TCGA.QH.A6X5.01 4 0.0707 0.67282 0.00 0.00 0.02 0.98
#> TCGA.FG.A60K.01 4 0.7550 -0.05467 0.30 0.00 0.22 0.48
#> TCGA.DU.A7T6.01 4 0.0000 0.67802 0.00 0.00 0.00 1.00
#> TCGA.TM.A84O.01 4 0.0707 0.67282 0.00 0.00 0.02 0.98
#> TCGA.HT.A61A.01 1 0.0000 0.93158 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RQ.01 4 0.1211 0.65382 0.00 0.00 0.04 0.96
#> TCGA.HT.A74K.01 2 0.7745 0.12078 0.00 0.42 0.24 0.34
#> TCGA.QH.A6X8.01 2 0.2011 0.72042 0.00 0.92 0.08 0.00
#> TCGA.HT.7681.01 1 0.0000 0.93158 1.00 0.00 0.00 0.00
#> TCGA.P5.A72Z.01 2 0.6201 0.38476 0.00 0.62 0.08 0.30
#> TCGA.DU.8168.01 2 0.2345 0.78068 0.00 0.90 0.10 0.00
#> TCGA.EZ.7264.01 4 0.7544 0.29683 0.00 0.20 0.34 0.46
#> TCGA.QH.A65V.01 1 0.4907 0.28239 0.58 0.00 0.00 0.42
#> TCGA.DU.A6S8.01 4 0.0000 0.67802 0.00 0.00 0.00 1.00
#> TCGA.DU.7298.01 3 0.3853 0.54849 0.00 0.02 0.82 0.16
#> TCGA.DB.A64R.01 3 0.5535 0.51692 0.02 0.00 0.56 0.42
#> TCGA.CS.5390.01 2 0.2345 0.78068 0.00 0.90 0.10 0.00
#> TCGA.DU.7294.01 4 0.7357 0.37513 0.00 0.18 0.32 0.50
#> TCGA.HT.7695.01 3 0.6011 0.46022 0.04 0.00 0.48 0.48
#> TCGA.DB.5274.01 3 0.4713 0.13542 0.00 0.36 0.64 0.00
#> TCGA.DU.A6S2.01 1 0.0000 0.93158 1.00 0.00 0.00 0.00
#> TCGA.HT.8012.01 3 0.2830 0.52943 0.00 0.06 0.90 0.04
#> TCGA.P5.A77W.01 3 0.3610 0.41722 0.00 0.20 0.80 0.00
#> TCGA.DU.7302.01 2 0.2011 0.72042 0.00 0.92 0.08 0.00
#> TCGA.HW.7495.01 1 0.0000 0.93158 1.00 0.00 0.00 0.00
#> TCGA.QH.A65R.01 2 0.3610 0.70849 0.00 0.80 0.20 0.00
#> TCGA.S9.A7IQ.01 1 0.0000 0.93158 1.00 0.00 0.00 0.00
#> TCGA.DU.5874.01 2 0.2345 0.78068 0.00 0.90 0.10 0.00
#> TCGA.R8.A73M.01 3 0.5147 0.45505 0.00 0.06 0.74 0.20
#> TCGA.DB.A4XH.01 2 0.2647 0.77052 0.00 0.88 0.12 0.00
#> TCGA.VW.A7QS.01 3 0.2345 0.51713 0.00 0.10 0.90 0.00
#> TCGA.S9.A6WI.01 1 0.0000 0.93158 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RI.01 1 0.0707 0.91882 0.98 0.00 0.00 0.02
#> TCGA.DU.7018.01 2 0.1211 0.77120 0.00 0.96 0.04 0.00
#> TCGA.FG.A713.01 1 0.0000 0.93158 1.00 0.00 0.00 0.00
#> TCGA.DU.7300.01 3 0.4277 0.54611 0.00 0.00 0.72 0.28
#> TCGA.DH.5144.01 3 0.4406 0.18660 0.00 0.30 0.70 0.00
#> TCGA.HT.A615.01 1 0.0707 0.91916 0.98 0.00 0.00 0.02
#> TCGA.HT.7874.01 1 0.0000 0.93158 1.00 0.00 0.00 0.00
#> TCGA.HT.7471.01 3 0.1637 0.49753 0.00 0.06 0.94 0.00
#> TCGA.HT.A5R9.01 3 0.2345 0.51713 0.00 0.10 0.90 0.00
#> TCGA.CS.5396.01 4 0.0000 0.67802 0.00 0.00 0.00 1.00
#> TCGA.DH.A7UR.01 3 0.4790 0.08142 0.00 0.38 0.62 0.00
#> TCGA.DU.6400.01 2 0.2011 0.77948 0.00 0.92 0.08 0.00
#> TCGA.DB.A75K.01 3 0.3610 0.54875 0.00 0.00 0.80 0.20
#> TCGA.DB.A64Q.01 1 0.2647 0.83503 0.88 0.00 0.00 0.12
#> TCGA.S9.A6WH.01 2 0.2345 0.78068 0.00 0.90 0.10 0.00
#> TCGA.DB.A64U.01 1 0.4713 0.43023 0.64 0.00 0.00 0.36
#> TCGA.DB.A64W.01 2 0.0000 0.75740 0.00 1.00 0.00 0.00
#> TCGA.R8.A6MO.01 3 0.4406 0.15002 0.00 0.30 0.70 0.00
#> TCGA.DU.5870.02 4 0.7274 0.27374 0.00 0.22 0.24 0.54
#> TCGA.CS.6668.01 2 0.7654 0.14655 0.00 0.44 0.22 0.34
#> TCGA.DU.5870.01 4 0.2335 0.66321 0.00 0.02 0.06 0.92
#> TCGA.E1.5318.01 2 0.3172 0.74224 0.00 0.84 0.16 0.00
#> TCGA.S9.A7J3.01 2 0.7654 0.14655 0.00 0.44 0.22 0.34
#> TCGA.TQ.A7RS.01 1 0.0000 0.93158 1.00 0.00 0.00 0.00
#> TCGA.RY.A83X.01 3 0.4994 0.50343 0.00 0.00 0.52 0.48
#> TCGA.HT.7607.01 1 0.0000 0.93158 1.00 0.00 0.00 0.00
#> TCGA.DU.7009.01 3 0.4994 0.50343 0.00 0.00 0.52 0.48
#> TCGA.P5.A781.01 3 0.4977 0.51484 0.00 0.00 0.54 0.46
#> TCGA.FG.8186.01 1 0.0707 0.91916 0.98 0.00 0.00 0.02
#> TCGA.S9.A6U2.01 1 0.5256 0.56607 0.70 0.00 0.04 0.26
#> TCGA.S9.A6WN.01 1 0.0000 0.93158 1.00 0.00 0.00 0.00
#> TCGA.DB.A64L.01 3 0.4994 -0.28575 0.00 0.48 0.52 0.00
#> TCGA.QH.A65X.01 3 0.4994 0.50343 0.00 0.00 0.52 0.48
#> TCGA.TM.A84G.01 4 0.7745 0.00279 0.00 0.34 0.24 0.42
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.E1.5319.01 3 0.0000 0.7443 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.A74L.01 3 0.2929 0.6179 0.00 0.00 0.82 0.00 0.18
#> TCGA.HT.A4DV.01 1 0.0000 0.9065 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8113.01 1 0.0609 0.9144 0.98 0.00 0.02 0.00 0.00
#> TCGA.FG.A710.01 4 0.3513 0.5595 0.02 0.00 0.18 0.80 0.00
#> TCGA.DU.A6S6.01 3 0.3109 0.5903 0.00 0.00 0.80 0.00 0.20
#> TCGA.HT.7877.01 1 0.0609 0.9144 0.98 0.00 0.02 0.00 0.00
#> TCGA.QH.A6CU.01 1 0.0609 0.9144 0.98 0.00 0.02 0.00 0.00
#> TCGA.HT.8010.01 1 0.0609 0.9144 0.98 0.00 0.02 0.00 0.00
#> TCGA.FG.7638.01 3 0.0609 0.7447 0.00 0.00 0.98 0.02 0.00
#> TCGA.FG.A6J1.01 3 0.1043 0.7403 0.00 0.00 0.96 0.04 0.00
#> TCGA.S9.A7QY.01 3 0.1410 0.7305 0.00 0.00 0.94 0.06 0.00
#> TCGA.P5.A77X.01 1 0.3999 0.6626 0.74 0.00 0.02 0.24 0.00
#> TCGA.P5.A5EX.01 1 0.0000 0.9065 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6X5.01 3 0.4818 -0.0249 0.00 0.00 0.52 0.46 0.02
#> TCGA.FG.A60K.01 3 0.1732 0.7150 0.08 0.00 0.92 0.00 0.00
#> TCGA.DU.A7T6.01 4 0.3513 0.5595 0.02 0.00 0.18 0.80 0.00
#> TCGA.TM.A84O.01 3 0.4818 -0.0249 0.00 0.00 0.52 0.46 0.02
#> TCGA.HT.A61A.01 1 0.0609 0.9144 0.98 0.00 0.02 0.00 0.00
#> TCGA.TQ.A7RQ.01 4 0.6207 0.2913 0.00 0.00 0.40 0.46 0.14
#> TCGA.HT.A74K.01 4 0.5979 0.4719 0.00 0.12 0.00 0.52 0.36
#> TCGA.QH.A6X8.01 2 0.3421 0.7643 0.00 0.84 0.00 0.08 0.08
#> TCGA.HT.7681.01 1 0.0609 0.9144 0.98 0.00 0.02 0.00 0.00
#> TCGA.P5.A72Z.01 4 0.6265 0.4890 0.00 0.24 0.00 0.54 0.22
#> TCGA.DU.8168.01 2 0.0000 0.8935 0.00 1.00 0.00 0.00 0.00
#> TCGA.EZ.7264.01 5 0.5684 -0.3873 0.00 0.02 0.04 0.44 0.50
#> TCGA.QH.A65V.01 3 0.3561 0.5646 0.26 0.00 0.74 0.00 0.00
#> TCGA.DU.A6S8.01 4 0.3513 0.5595 0.02 0.00 0.18 0.80 0.00
#> TCGA.DU.7298.01 5 0.4613 0.4725 0.00 0.02 0.36 0.00 0.62
#> TCGA.DB.A64R.01 3 0.2732 0.6372 0.00 0.00 0.84 0.00 0.16
#> TCGA.CS.5390.01 2 0.0000 0.8935 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7294.01 4 0.6539 0.3270 0.00 0.04 0.08 0.46 0.42
#> TCGA.HT.7695.01 3 0.0609 0.7462 0.02 0.00 0.98 0.00 0.00
#> TCGA.DB.5274.01 5 0.6623 0.5733 0.00 0.34 0.10 0.04 0.52
#> TCGA.DU.A6S2.01 1 0.3561 0.6442 0.74 0.00 0.26 0.00 0.00
#> TCGA.HT.8012.01 5 0.5156 0.5320 0.00 0.06 0.32 0.00 0.62
#> TCGA.P5.A77W.01 5 0.5599 0.6219 0.00 0.26 0.12 0.00 0.62
#> TCGA.DU.7302.01 2 0.4637 0.6559 0.00 0.74 0.00 0.10 0.16
#> TCGA.HW.7495.01 1 0.0609 0.9144 0.98 0.00 0.02 0.00 0.00
#> TCGA.QH.A65R.01 2 0.3684 0.5122 0.00 0.72 0.00 0.00 0.28
#> TCGA.S9.A7IQ.01 1 0.0609 0.9144 0.98 0.00 0.02 0.00 0.00
#> TCGA.DU.5874.01 2 0.1043 0.8757 0.00 0.96 0.00 0.00 0.04
#> TCGA.R8.A73M.01 5 0.7066 -0.0282 0.00 0.02 0.22 0.32 0.44
#> TCGA.DB.A4XH.01 2 0.1043 0.8757 0.00 0.96 0.00 0.00 0.04
#> TCGA.VW.A7QS.01 5 0.5083 0.6593 0.00 0.16 0.14 0.00 0.70
#> TCGA.S9.A6WI.01 1 0.0609 0.9144 0.98 0.00 0.02 0.00 0.00
#> TCGA.TQ.A7RI.01 1 0.0609 0.9144 0.98 0.00 0.02 0.00 0.00
#> TCGA.DU.7018.01 2 0.0609 0.8853 0.00 0.98 0.00 0.00 0.02
#> TCGA.FG.A713.01 1 0.0609 0.9144 0.98 0.00 0.02 0.00 0.00
#> TCGA.DU.7300.01 3 0.4798 -0.2032 0.00 0.00 0.54 0.02 0.44
#> TCGA.DH.5144.01 5 0.7099 0.5514 0.00 0.22 0.10 0.12 0.56
#> TCGA.HT.A615.01 1 0.2929 0.7624 0.82 0.00 0.18 0.00 0.00
#> TCGA.HT.7874.01 1 0.0000 0.9065 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7471.01 5 0.4957 0.6192 0.00 0.10 0.10 0.04 0.76
#> TCGA.HT.A5R9.01 5 0.5273 0.6550 0.00 0.16 0.16 0.00 0.68
#> TCGA.CS.5396.01 4 0.3513 0.5595 0.02 0.00 0.18 0.80 0.00
#> TCGA.DH.A7UR.01 5 0.5727 0.5459 0.00 0.34 0.10 0.00 0.56
#> TCGA.DU.6400.01 2 0.0000 0.8935 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.A75K.01 5 0.4990 0.4882 0.00 0.00 0.36 0.04 0.60
#> TCGA.DB.A64Q.01 1 0.3424 0.6847 0.76 0.00 0.00 0.24 0.00
#> TCGA.S9.A6WH.01 2 0.0000 0.8935 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.A64U.01 3 0.4227 0.2207 0.42 0.00 0.58 0.00 0.00
#> TCGA.DB.A64W.01 2 0.1043 0.8720 0.00 0.96 0.00 0.00 0.04
#> TCGA.R8.A6MO.01 5 0.7003 0.6301 0.00 0.26 0.14 0.06 0.54
#> TCGA.DU.5870.02 4 0.4132 0.5753 0.00 0.02 0.00 0.72 0.26
#> TCGA.CS.6668.01 4 0.5979 0.4719 0.00 0.12 0.00 0.52 0.36
#> TCGA.DU.5870.01 4 0.5355 0.5931 0.00 0.00 0.12 0.66 0.22
#> TCGA.E1.5318.01 2 0.1732 0.8451 0.00 0.92 0.00 0.00 0.08
#> TCGA.S9.A7J3.01 4 0.6296 0.4270 0.00 0.16 0.00 0.48 0.36
#> TCGA.TQ.A7RS.01 1 0.2516 0.8125 0.86 0.00 0.14 0.00 0.00
#> TCGA.RY.A83X.01 3 0.0000 0.7443 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7607.01 1 0.0000 0.9065 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7009.01 3 0.1043 0.7403 0.00 0.00 0.96 0.04 0.00
#> TCGA.P5.A781.01 3 0.1648 0.7360 0.02 0.00 0.94 0.00 0.04
#> TCGA.FG.8186.01 1 0.4287 0.1473 0.54 0.00 0.46 0.00 0.00
#> TCGA.S9.A6U2.01 3 0.4726 0.2638 0.40 0.00 0.58 0.02 0.00
#> TCGA.S9.A6WN.01 1 0.0000 0.9065 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64L.01 5 0.6727 0.4339 0.00 0.32 0.02 0.16 0.50
#> TCGA.QH.A65X.01 3 0.0000 0.7443 0.00 0.00 1.00 0.00 0.00
#> TCGA.TM.A84G.01 4 0.6302 0.3125 0.00 0.06 0.04 0.48 0.42
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.E1.5319.01 3 0.0000 0.8037 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.A74L.01 3 0.3163 0.7561 0.00 0.00 0.82 0.00 0.14 0.04
#> TCGA.HT.A4DV.01 1 0.0000 0.9625 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8113.01 1 0.0000 0.9625 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A710.01 6 0.3318 0.6598 0.02 0.00 0.14 0.02 0.00 0.82
#> TCGA.DU.A6S6.01 3 0.3163 0.7561 0.00 0.00 0.82 0.00 0.14 0.04
#> TCGA.HT.7877.01 1 0.0000 0.9625 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CU.01 1 0.0000 0.9625 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8010.01 1 0.0000 0.9625 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7638.01 3 0.0547 0.8063 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.FG.A6J1.01 3 0.0937 0.8046 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.S9.A7QY.01 3 0.2020 0.7923 0.00 0.00 0.92 0.02 0.02 0.04
#> TCGA.P5.A77X.01 6 0.4282 0.4056 0.42 0.00 0.02 0.00 0.00 0.56
#> TCGA.P5.A5EX.01 1 0.0000 0.9625 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6X5.01 3 0.3982 0.5831 0.00 0.00 0.74 0.06 0.00 0.20
#> TCGA.FG.A60K.01 3 0.0547 0.8047 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.DU.A7T6.01 6 0.3483 0.6729 0.02 0.00 0.12 0.04 0.00 0.82
#> TCGA.TM.A84O.01 3 0.4462 0.4542 0.00 0.00 0.66 0.06 0.00 0.28
#> TCGA.HT.A61A.01 1 0.0000 0.9625 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RQ.01 3 0.5636 0.2002 0.00 0.00 0.52 0.30 0.00 0.18
#> TCGA.HT.A74K.01 4 0.5392 0.6414 0.00 0.04 0.00 0.66 0.12 0.18
#> TCGA.QH.A6X8.01 2 0.3198 0.6075 0.00 0.74 0.00 0.26 0.00 0.00
#> TCGA.HT.7681.01 1 0.0000 0.9625 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A72Z.01 4 0.5150 0.4682 0.00 0.16 0.00 0.62 0.00 0.22
#> TCGA.DU.8168.01 2 0.0000 0.8449 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EZ.7264.01 4 0.5049 0.5135 0.00 0.00 0.02 0.62 0.30 0.06
#> TCGA.QH.A65V.01 3 0.2260 0.7348 0.14 0.00 0.86 0.00 0.00 0.00
#> TCGA.DU.A6S8.01 6 0.3483 0.6729 0.02 0.00 0.12 0.04 0.00 0.82
#> TCGA.DU.7298.01 5 0.3156 0.6961 0.00 0.00 0.18 0.00 0.80 0.02
#> TCGA.DB.A64R.01 3 0.3163 0.7561 0.00 0.00 0.82 0.00 0.14 0.04
#> TCGA.CS.5390.01 2 0.0547 0.8418 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.DU.7294.01 4 0.6710 0.5178 0.00 0.00 0.10 0.50 0.26 0.14
#> TCGA.HT.7695.01 3 0.1092 0.8063 0.02 0.00 0.96 0.00 0.00 0.02
#> TCGA.DB.5274.01 5 0.4375 0.7392 0.00 0.12 0.02 0.04 0.78 0.04
#> TCGA.DU.A6S2.01 1 0.2941 0.6581 0.78 0.00 0.22 0.00 0.00 0.00
#> TCGA.HT.8012.01 5 0.3156 0.6961 0.00 0.00 0.18 0.00 0.80 0.02
#> TCGA.P5.A77W.01 5 0.3483 0.7658 0.00 0.12 0.04 0.02 0.82 0.00
#> TCGA.DU.7302.01 2 0.5873 0.0730 0.00 0.46 0.00 0.42 0.08 0.04
#> TCGA.HW.7495.01 1 0.0000 0.9625 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A65R.01 2 0.3864 -0.0335 0.00 0.52 0.00 0.00 0.48 0.00
#> TCGA.S9.A7IQ.01 1 0.0000 0.9625 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5874.01 2 0.0547 0.8416 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.R8.A73M.01 4 0.6642 0.3931 0.00 0.00 0.16 0.44 0.34 0.06
#> TCGA.DB.A4XH.01 2 0.0547 0.8416 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.VW.A7QS.01 5 0.1807 0.7807 0.00 0.02 0.06 0.00 0.92 0.00
#> TCGA.S9.A6WI.01 1 0.0000 0.9625 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RI.01 1 0.0547 0.9398 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.DU.7018.01 2 0.1092 0.8343 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.FG.A713.01 1 0.0000 0.9625 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7300.01 5 0.4067 0.6791 0.00 0.00 0.26 0.04 0.70 0.00
#> TCGA.DH.5144.01 5 0.6116 0.4222 0.00 0.04 0.06 0.22 0.62 0.06
#> TCGA.HT.A615.01 1 0.2260 0.7841 0.86 0.00 0.14 0.00 0.00 0.00
#> TCGA.HT.7874.01 1 0.0000 0.9625 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7471.01 5 0.2581 0.7281 0.00 0.00 0.00 0.12 0.86 0.02
#> TCGA.HT.A5R9.01 5 0.1807 0.7807 0.00 0.02 0.06 0.00 0.92 0.00
#> TCGA.CS.5396.01 6 0.3483 0.6729 0.02 0.00 0.12 0.04 0.00 0.82
#> TCGA.DH.A7UR.01 5 0.3111 0.7572 0.00 0.12 0.02 0.02 0.84 0.00
#> TCGA.DU.6400.01 2 0.0000 0.8449 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A75K.01 5 0.3483 0.7573 0.00 0.00 0.12 0.02 0.82 0.04
#> TCGA.DB.A64Q.01 6 0.3828 0.3619 0.44 0.00 0.00 0.00 0.00 0.56
#> TCGA.S9.A6WH.01 2 0.0000 0.8449 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64U.01 3 0.2793 0.6670 0.20 0.00 0.80 0.00 0.00 0.00
#> TCGA.DB.A64W.01 2 0.1556 0.8002 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.R8.A6MO.01 5 0.3910 0.7529 0.00 0.08 0.04 0.04 0.82 0.02
#> TCGA.DU.5870.02 4 0.3819 0.4786 0.00 0.00 0.02 0.70 0.00 0.28
#> TCGA.CS.6668.01 4 0.4733 0.6389 0.00 0.06 0.00 0.74 0.08 0.12
#> TCGA.DU.5870.01 4 0.4265 0.4489 0.00 0.00 0.04 0.66 0.00 0.30
#> TCGA.E1.5318.01 2 0.0937 0.8319 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.S9.A7J3.01 4 0.5615 0.6477 0.00 0.08 0.00 0.66 0.14 0.12
#> TCGA.TQ.A7RS.01 1 0.1807 0.8758 0.92 0.00 0.06 0.00 0.00 0.02
#> TCGA.RY.A83X.01 3 0.0547 0.8063 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.HT.7607.01 1 0.0000 0.9625 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7009.01 3 0.0547 0.8065 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.P5.A781.01 3 0.2403 0.7947 0.02 0.00 0.90 0.00 0.04 0.04
#> TCGA.FG.8186.01 3 0.4246 0.3656 0.40 0.00 0.58 0.00 0.00 0.02
#> TCGA.S9.A6U2.01 3 0.3578 0.4943 0.34 0.00 0.66 0.00 0.00 0.00
#> TCGA.S9.A6WN.01 1 0.0000 0.9625 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64L.01 5 0.4125 0.7261 0.00 0.08 0.02 0.08 0.80 0.02
#> TCGA.QH.A65X.01 3 0.1807 0.7949 0.00 0.00 0.92 0.00 0.02 0.06
#> TCGA.TM.A84G.01 4 0.5691 0.5506 0.00 0.00 0.02 0.58 0.26 0.14
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 3 0.0504 0.80836 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.HT.A74L.01 3 0.5482 0.55683 0.00 0.00 0.62 0.02 0.22 0.04 0.10
#> TCGA.HT.A4DV.01 1 0.0000 0.94708 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8113.01 1 0.0000 0.94708 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A710.01 6 0.1664 0.84697 0.00 0.00 0.06 0.00 0.02 0.92 0.00
#> TCGA.DU.A6S6.01 3 0.5747 0.45315 0.00 0.00 0.56 0.02 0.28 0.04 0.10
#> TCGA.HT.7877.01 1 0.0000 0.94708 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CU.01 1 0.0000 0.94708 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8010.01 1 0.0000 0.94708 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7638.01 3 0.2163 0.79862 0.00 0.00 0.88 0.10 0.00 0.00 0.02
#> TCGA.FG.A6J1.01 3 0.2376 0.79574 0.00 0.00 0.86 0.12 0.00 0.00 0.02
#> TCGA.S9.A7QY.01 3 0.3257 0.78565 0.00 0.00 0.84 0.08 0.04 0.02 0.02
#> TCGA.P5.A77X.01 6 0.3052 0.71343 0.20 0.00 0.00 0.00 0.02 0.78 0.00
#> TCGA.P5.A5EX.01 1 0.0000 0.94708 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6X5.01 3 0.2803 0.76752 0.00 0.00 0.84 0.10 0.00 0.06 0.00
#> TCGA.FG.A60K.01 3 0.1006 0.80426 0.02 0.00 0.96 0.00 0.00 0.00 0.02
#> TCGA.DU.A7T6.01 6 0.1166 0.84697 0.00 0.00 0.06 0.00 0.00 0.94 0.00
#> TCGA.TM.A84O.01 3 0.3487 0.74185 0.00 0.00 0.78 0.12 0.00 0.10 0.00
#> TCGA.HT.A61A.01 1 0.0000 0.94708 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RQ.01 3 0.5718 0.32861 0.00 0.00 0.54 0.18 0.00 0.04 0.24
#> TCGA.HT.A74K.01 4 0.6459 0.00392 0.00 0.08 0.00 0.46 0.08 0.04 0.34
#> TCGA.QH.A6X8.01 2 0.3487 0.66076 0.00 0.78 0.00 0.12 0.00 0.00 0.10
#> TCGA.HT.7681.01 1 0.0000 0.94708 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A72Z.01 7 0.5686 0.55473 0.00 0.18 0.00 0.12 0.02 0.06 0.62
#> TCGA.DU.8168.01 2 0.0000 0.85634 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EZ.7264.01 4 0.3617 0.51861 0.00 0.00 0.00 0.76 0.08 0.00 0.16
#> TCGA.QH.A65V.01 3 0.1671 0.77440 0.10 0.00 0.90 0.00 0.00 0.00 0.00
#> TCGA.DU.A6S8.01 6 0.1664 0.84697 0.00 0.00 0.06 0.00 0.02 0.92 0.00
#> TCGA.DU.7298.01 5 0.3011 0.63773 0.00 0.00 0.12 0.00 0.82 0.00 0.06
#> TCGA.DB.A64R.01 3 0.5269 0.64329 0.00 0.00 0.68 0.04 0.14 0.04 0.10
#> TCGA.CS.5390.01 2 0.1664 0.84374 0.00 0.92 0.00 0.00 0.02 0.00 0.06
#> TCGA.DU.7294.01 4 0.2652 0.56736 0.00 0.00 0.02 0.88 0.06 0.02 0.02
#> TCGA.HT.7695.01 3 0.0504 0.80543 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.DB.5274.01 5 0.5338 0.55225 0.00 0.06 0.02 0.28 0.60 0.00 0.04
#> TCGA.DU.A6S2.01 1 0.3294 0.49798 0.66 0.00 0.34 0.00 0.00 0.00 0.00
#> TCGA.HT.8012.01 5 0.3289 0.64778 0.00 0.02 0.10 0.00 0.82 0.00 0.06
#> TCGA.P5.A77W.01 5 0.4491 0.64769 0.00 0.06 0.02 0.14 0.74 0.00 0.04
#> TCGA.DU.7302.01 4 0.4431 0.39667 0.00 0.24 0.00 0.68 0.04 0.00 0.04
#> TCGA.HW.7495.01 1 0.0000 0.94708 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A65R.01 2 0.4977 -0.01871 0.00 0.50 0.00 0.04 0.42 0.00 0.04
#> TCGA.S9.A7IQ.01 1 0.0000 0.94708 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5874.01 2 0.1006 0.84637 0.00 0.96 0.00 0.02 0.00 0.00 0.02
#> TCGA.R8.A73M.01 4 0.2804 0.53527 0.00 0.00 0.06 0.86 0.06 0.00 0.02
#> TCGA.DB.A4XH.01 2 0.1006 0.84637 0.00 0.96 0.00 0.02 0.00 0.00 0.02
#> TCGA.VW.A7QS.01 5 0.2355 0.68325 0.00 0.02 0.02 0.04 0.90 0.00 0.02
#> TCGA.S9.A6WI.01 1 0.0000 0.94708 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RI.01 1 0.0504 0.93033 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.DU.7018.01 2 0.1860 0.83396 0.00 0.92 0.00 0.02 0.02 0.00 0.04
#> TCGA.FG.A713.01 1 0.0000 0.94708 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7300.01 5 0.4763 0.56246 0.00 0.00 0.20 0.18 0.62 0.00 0.00
#> TCGA.DH.5144.01 4 0.5336 -0.11577 0.00 0.02 0.02 0.50 0.40 0.00 0.06
#> TCGA.HT.A615.01 1 0.2832 0.67630 0.76 0.00 0.24 0.00 0.00 0.00 0.00
#> TCGA.HT.7874.01 1 0.0000 0.94708 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7471.01 5 0.3370 0.63436 0.00 0.00 0.00 0.16 0.78 0.00 0.06
#> TCGA.HT.A5R9.01 5 0.2652 0.68483 0.00 0.02 0.06 0.02 0.88 0.00 0.02
#> TCGA.CS.5396.01 6 0.1166 0.84697 0.00 0.00 0.06 0.00 0.00 0.94 0.00
#> TCGA.DH.A7UR.01 5 0.5282 0.58395 0.00 0.08 0.02 0.22 0.64 0.00 0.04
#> TCGA.DU.6400.01 2 0.0504 0.85478 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DB.A75K.01 5 0.3744 0.66633 0.00 0.00 0.08 0.12 0.78 0.00 0.02
#> TCGA.DB.A64Q.01 6 0.2572 0.71343 0.20 0.00 0.00 0.00 0.00 0.80 0.00
#> TCGA.S9.A6WH.01 2 0.0000 0.85634 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64U.01 3 0.2081 0.73845 0.14 0.00 0.86 0.00 0.00 0.00 0.00
#> TCGA.DB.A64W.01 2 0.1363 0.83852 0.00 0.94 0.00 0.02 0.00 0.00 0.04
#> TCGA.R8.A6MO.01 5 0.5474 0.49680 0.00 0.06 0.02 0.32 0.56 0.00 0.04
#> TCGA.DU.5870.02 7 0.3263 0.63275 0.00 0.00 0.00 0.08 0.00 0.12 0.80
#> TCGA.CS.6668.01 7 0.5429 0.11926 0.00 0.12 0.00 0.40 0.02 0.00 0.46
#> TCGA.DU.5870.01 7 0.3680 0.61513 0.00 0.00 0.02 0.06 0.00 0.14 0.78
#> TCGA.E1.5318.01 2 0.2857 0.77701 0.00 0.86 0.00 0.04 0.06 0.00 0.04
#> TCGA.S9.A7J3.01 4 0.5279 -0.12176 0.00 0.10 0.00 0.48 0.02 0.00 0.40
#> TCGA.TQ.A7RS.01 1 0.2745 0.76989 0.82 0.00 0.16 0.00 0.00 0.00 0.02
#> TCGA.RY.A83X.01 3 0.0863 0.80690 0.00 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.HT.7607.01 1 0.0000 0.94708 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7009.01 3 0.2376 0.79574 0.00 0.00 0.86 0.12 0.00 0.00 0.02
#> TCGA.P5.A781.01 3 0.1006 0.80785 0.00 0.00 0.96 0.00 0.02 0.02 0.00
#> TCGA.FG.8186.01 3 0.3685 0.48955 0.32 0.00 0.66 0.00 0.00 0.00 0.02
#> TCGA.S9.A6U2.01 3 0.4331 0.69437 0.18 0.00 0.72 0.06 0.00 0.00 0.04
#> TCGA.S9.A6WN.01 1 0.0000 0.94708 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64L.01 5 0.5295 0.39602 0.00 0.08 0.00 0.34 0.54 0.00 0.04
#> TCGA.QH.A65X.01 3 0.1860 0.80564 0.00 0.00 0.92 0.04 0.02 0.00 0.02
#> TCGA.TM.A84G.01 4 0.3000 0.55722 0.00 0.00 0.00 0.84 0.04 0.02 0.10
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.E1.5319.01 3 0.0471 0.6624 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.HT.A74L.01 8 0.4174 0.9245 0.00 0.00 0.40 0.00 0.06 0.00 0.00 0.54
#> TCGA.HT.A4DV.01 1 0.0000 0.9349 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8113.01 1 0.0000 0.9349 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A710.01 6 0.0808 0.9224 0.00 0.00 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.DU.A6S6.01 8 0.4340 0.9017 0.00 0.00 0.38 0.00 0.08 0.00 0.00 0.54
#> TCGA.HT.7877.01 1 0.0000 0.9349 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CU.01 1 0.0000 0.9349 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8010.01 1 0.0000 0.9349 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7638.01 3 0.2756 0.3909 0.00 0.00 0.74 0.00 0.00 0.00 0.00 0.26
#> TCGA.FG.A6J1.01 3 0.2852 0.4594 0.00 0.00 0.72 0.00 0.00 0.00 0.00 0.28
#> TCGA.S9.A7QY.01 3 0.3637 0.3331 0.00 0.00 0.70 0.00 0.02 0.02 0.00 0.26
#> TCGA.P5.A77X.01 6 0.1341 0.8902 0.08 0.00 0.00 0.00 0.00 0.92 0.00 0.00
#> TCGA.P5.A5EX.01 1 0.0000 0.9349 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6X5.01 3 0.1275 0.6555 0.00 0.00 0.94 0.02 0.00 0.00 0.00 0.04
#> TCGA.FG.A60K.01 3 0.0471 0.6536 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DU.A7T6.01 6 0.0941 0.9325 0.00 0.00 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.TM.A84O.01 3 0.1557 0.6491 0.00 0.00 0.92 0.02 0.00 0.00 0.00 0.06
#> TCGA.HT.A61A.01 1 0.0000 0.9349 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RQ.01 3 0.4760 0.2774 0.00 0.00 0.62 0.02 0.00 0.00 0.16 0.20
#> TCGA.HT.A74K.01 7 0.5404 0.5070 0.00 0.00 0.00 0.32 0.06 0.04 0.54 0.04
#> TCGA.QH.A6X8.01 2 0.3744 0.7560 0.00 0.74 0.00 0.06 0.00 0.00 0.18 0.02
#> TCGA.HT.7681.01 1 0.0000 0.9349 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A72Z.01 7 0.3185 0.5990 0.00 0.08 0.00 0.04 0.00 0.06 0.82 0.00
#> TCGA.DU.8168.01 2 0.0000 0.8966 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EZ.7264.01 4 0.1408 0.8106 0.00 0.00 0.00 0.94 0.02 0.00 0.02 0.02
#> TCGA.QH.A65V.01 3 0.0941 0.6575 0.02 0.00 0.96 0.00 0.00 0.00 0.00 0.02
#> TCGA.DU.A6S8.01 6 0.0471 0.9322 0.00 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DU.7298.01 5 0.2591 0.7298 0.00 0.00 0.04 0.00 0.86 0.00 0.02 0.08
#> TCGA.DB.A64R.01 8 0.3690 0.8787 0.00 0.00 0.42 0.00 0.02 0.00 0.00 0.56
#> TCGA.CS.5390.01 2 0.2818 0.8607 0.00 0.82 0.00 0.00 0.00 0.00 0.12 0.06
#> TCGA.DU.7294.01 4 0.1091 0.8249 0.00 0.00 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.HT.7695.01 3 0.1557 0.6355 0.00 0.00 0.92 0.00 0.00 0.00 0.02 0.06
#> TCGA.DB.5274.01 5 0.4616 0.7333 0.00 0.06 0.00 0.20 0.68 0.00 0.02 0.04
#> TCGA.DU.A6S2.01 1 0.3449 0.5273 0.66 0.00 0.32 0.00 0.00 0.00 0.02 0.00
#> TCGA.HT.8012.01 5 0.2724 0.7387 0.00 0.02 0.02 0.00 0.86 0.00 0.02 0.08
#> TCGA.P5.A77W.01 5 0.2864 0.7643 0.00 0.06 0.00 0.08 0.84 0.00 0.00 0.02
#> TCGA.DU.7302.01 4 0.3314 0.6570 0.00 0.08 0.00 0.80 0.00 0.00 0.10 0.02
#> TCGA.HW.7495.01 1 0.0471 0.9209 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.QH.A65R.01 5 0.3862 0.4255 0.00 0.36 0.00 0.00 0.60 0.00 0.00 0.04
#> TCGA.S9.A7IQ.01 1 0.0000 0.9349 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5874.01 2 0.0471 0.8912 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.R8.A73M.01 4 0.2547 0.7552 0.00 0.00 0.04 0.84 0.00 0.00 0.00 0.12
#> TCGA.DB.A4XH.01 2 0.0471 0.8912 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.VW.A7QS.01 5 0.1887 0.7644 0.00 0.04 0.00 0.00 0.90 0.00 0.00 0.06
#> TCGA.S9.A6WI.01 1 0.0000 0.9349 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RI.01 1 0.1557 0.8679 0.92 0.00 0.06 0.00 0.00 0.00 0.00 0.02
#> TCGA.DU.7018.01 2 0.3078 0.8594 0.00 0.82 0.00 0.02 0.00 0.00 0.10 0.06
#> TCGA.FG.A713.01 1 0.0000 0.9349 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7300.01 5 0.4880 0.6867 0.00 0.00 0.10 0.14 0.68 0.00 0.02 0.06
#> TCGA.DH.5144.01 5 0.4040 0.5740 0.00 0.02 0.00 0.38 0.58 0.00 0.02 0.00
#> TCGA.HT.A615.01 1 0.3083 0.5179 0.66 0.00 0.34 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7874.01 1 0.0000 0.9349 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7471.01 5 0.4236 0.6970 0.00 0.02 0.00 0.04 0.72 0.00 0.18 0.04
#> TCGA.HT.A5R9.01 5 0.1275 0.7651 0.00 0.04 0.00 0.00 0.94 0.00 0.00 0.02
#> TCGA.CS.5396.01 6 0.0941 0.9325 0.00 0.00 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.DH.A7UR.01 5 0.2407 0.7679 0.00 0.06 0.00 0.08 0.86 0.00 0.00 0.00
#> TCGA.DU.6400.01 2 0.1557 0.8903 0.00 0.92 0.00 0.00 0.00 0.00 0.06 0.02
#> TCGA.DB.A75K.01 5 0.4540 0.7175 0.00 0.00 0.02 0.10 0.72 0.00 0.06 0.10
#> TCGA.DB.A64Q.01 6 0.1341 0.8902 0.08 0.00 0.00 0.00 0.00 0.92 0.00 0.00
#> TCGA.S9.A6WH.01 2 0.0000 0.8966 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64U.01 3 0.0808 0.6454 0.04 0.00 0.96 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64W.01 2 0.2224 0.8695 0.00 0.86 0.00 0.00 0.00 0.00 0.12 0.02
#> TCGA.R8.A6MO.01 5 0.3728 0.6911 0.00 0.02 0.00 0.28 0.68 0.00 0.02 0.00
#> TCGA.DU.5870.02 7 0.4321 0.6066 0.00 0.00 0.00 0.10 0.02 0.02 0.72 0.14
#> TCGA.CS.6668.01 7 0.4350 0.5877 0.00 0.00 0.00 0.30 0.00 0.06 0.62 0.02
#> TCGA.DU.5870.01 7 0.4907 0.5868 0.00 0.00 0.02 0.10 0.02 0.02 0.68 0.16
#> TCGA.E1.5318.01 2 0.1563 0.8291 0.00 0.90 0.00 0.00 0.10 0.00 0.00 0.00
#> TCGA.S9.A7J3.01 7 0.3714 0.4390 0.00 0.00 0.00 0.44 0.00 0.02 0.54 0.00
#> TCGA.TQ.A7RS.01 1 0.3879 0.6746 0.74 0.00 0.14 0.00 0.00 0.00 0.02 0.10
#> TCGA.RY.A83X.01 3 0.1804 0.6428 0.00 0.00 0.90 0.00 0.00 0.00 0.02 0.08
#> TCGA.HT.7607.01 1 0.0000 0.9349 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7009.01 3 0.3291 0.3980 0.00 0.00 0.70 0.00 0.00 0.00 0.02 0.28
#> TCGA.P5.A781.01 3 0.1765 0.5728 0.00 0.00 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.FG.8186.01 3 0.4898 0.0570 0.30 0.00 0.56 0.00 0.00 0.00 0.02 0.12
#> TCGA.S9.A6U2.01 3 0.4247 0.0453 0.10 0.00 0.62 0.00 0.00 0.00 0.00 0.28
#> TCGA.S9.A6WN.01 1 0.0000 0.9349 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64L.01 5 0.5172 0.6156 0.00 0.04 0.00 0.32 0.56 0.00 0.04 0.04
#> TCGA.QH.A65X.01 3 0.2981 0.5189 0.00 0.00 0.76 0.00 0.00 0.00 0.02 0.22
#> TCGA.TM.A84G.01 4 0.1408 0.8205 0.00 0.00 0.00 0.94 0.02 0.02 0.00 0.02
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0221. Child nodes: Node022111-leaf , Node022112-leaf , Node022113-leaf , Node022121 , Node022122-leaf , Node022123-leaf , Node022211-leaf , Node022212-leaf , Node022231-leaf , Node022232-leaf , Node022233-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["02211"]
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 46 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 0.873 0.895 0.960 0.2855 0.768 0.768
#> 3 3 1.000 0.965 0.988 0.9173 0.675 0.577
#> 4 4 0.837 0.804 0.924 0.0593 0.984 0.963
#> 5 5 0.870 0.844 0.945 0.0765 0.887 0.745
#> 6 6 0.882 0.794 0.915 0.0539 0.936 0.836
#> 7 7 0.796 0.746 0.889 0.0143 0.945 0.852
#> 8 8 0.798 0.805 0.901 0.0349 0.978 0.931
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.E1.5319.01 1 0.000 0.951 1.00 0.00
#> TCGA.HT.A74L.01 1 0.000 0.951 1.00 0.00
#> TCGA.HT.A4DV.01 1 0.000 0.951 1.00 0.00
#> TCGA.HT.8113.01 1 0.000 0.951 1.00 0.00
#> TCGA.FG.A710.01 1 0.999 0.150 0.52 0.48
#> TCGA.DU.A6S6.01 1 0.000 0.951 1.00 0.00
#> TCGA.HT.7877.01 1 0.000 0.951 1.00 0.00
#> TCGA.QH.A6CU.01 1 0.000 0.951 1.00 0.00
#> TCGA.HT.8010.01 1 0.000 0.951 1.00 0.00
#> TCGA.FG.7638.01 1 0.000 0.951 1.00 0.00
#> TCGA.FG.A6J1.01 1 0.000 0.951 1.00 0.00
#> TCGA.S9.A7QY.01 1 0.000 0.951 1.00 0.00
#> TCGA.P5.A77X.01 2 0.000 1.000 0.00 1.00
#> TCGA.P5.A5EX.01 2 0.000 1.000 0.00 1.00
#> TCGA.QH.A6X5.01 1 0.000 0.951 1.00 0.00
#> TCGA.FG.A60K.01 1 0.000 0.951 1.00 0.00
#> TCGA.DU.A7T6.01 2 0.000 1.000 0.00 1.00
#> TCGA.TM.A84O.01 1 0.000 0.951 1.00 0.00
#> TCGA.HT.A61A.01 1 0.000 0.951 1.00 0.00
#> TCGA.TQ.A7RQ.01 1 0.990 0.270 0.56 0.44
#> TCGA.HT.7681.01 1 0.000 0.951 1.00 0.00
#> TCGA.QH.A65V.01 1 0.000 0.951 1.00 0.00
#> TCGA.DU.A6S8.01 2 0.000 1.000 0.00 1.00
#> TCGA.DB.A64R.01 1 0.000 0.951 1.00 0.00
#> TCGA.HT.7695.01 1 0.000 0.951 1.00 0.00
#> TCGA.DU.A6S2.01 1 0.000 0.951 1.00 0.00
#> TCGA.HW.7495.01 1 0.000 0.951 1.00 0.00
#> TCGA.S9.A7IQ.01 1 0.000 0.951 1.00 0.00
#> TCGA.S9.A6WI.01 1 0.000 0.951 1.00 0.00
#> TCGA.TQ.A7RI.01 1 0.000 0.951 1.00 0.00
#> TCGA.FG.A713.01 1 0.000 0.951 1.00 0.00
#> TCGA.HT.A615.01 1 0.000 0.951 1.00 0.00
#> TCGA.HT.7874.01 1 0.000 0.951 1.00 0.00
#> TCGA.CS.5396.01 2 0.000 1.000 0.00 1.00
#> TCGA.DB.A64Q.01 2 0.000 1.000 0.00 1.00
#> TCGA.DB.A64U.01 1 0.000 0.951 1.00 0.00
#> TCGA.DU.5870.01 1 0.990 0.270 0.56 0.44
#> TCGA.TQ.A7RS.01 1 0.000 0.951 1.00 0.00
#> TCGA.RY.A83X.01 1 0.000 0.951 1.00 0.00
#> TCGA.HT.7607.01 1 0.000 0.951 1.00 0.00
#> TCGA.DU.7009.01 1 0.000 0.951 1.00 0.00
#> TCGA.P5.A781.01 1 0.000 0.951 1.00 0.00
#> TCGA.FG.8186.01 1 0.000 0.951 1.00 0.00
#> TCGA.S9.A6U2.01 1 0.000 0.951 1.00 0.00
#> TCGA.S9.A6WN.01 1 0.141 0.933 0.98 0.02
#> TCGA.QH.A65X.01 1 0.990 0.270 0.56 0.44
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.E1.5319.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.HT.A74L.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.HT.A4DV.01 3 0.000 0.923 0.00 0 1.00
#> TCGA.HT.8113.01 3 0.000 0.923 0.00 0 1.00
#> TCGA.FG.A710.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.DU.A6S6.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.HT.7877.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.QH.A6CU.01 3 0.480 0.658 0.22 0 0.78
#> TCGA.HT.8010.01 3 0.000 0.923 0.00 0 1.00
#> TCGA.FG.7638.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.FG.A6J1.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.S9.A7QY.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.P5.A77X.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.P5.A5EX.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.QH.A6X5.01 3 0.583 0.489 0.34 0 0.66
#> TCGA.FG.A60K.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.DU.A7T6.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.TM.A84O.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.HT.A61A.01 3 0.000 0.923 0.00 0 1.00
#> TCGA.TQ.A7RQ.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.HT.7681.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.QH.A65V.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.DU.A6S8.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DB.A64R.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.HT.7695.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.DU.A6S2.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.HW.7495.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.S9.A7IQ.01 3 0.000 0.923 0.00 0 1.00
#> TCGA.S9.A6WI.01 3 0.000 0.923 0.00 0 1.00
#> TCGA.TQ.A7RI.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.FG.A713.01 3 0.000 0.923 0.00 0 1.00
#> TCGA.HT.A615.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.HT.7874.01 3 0.000 0.923 0.00 0 1.00
#> TCGA.CS.5396.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DB.A64Q.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.DB.A64U.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.DU.5870.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.TQ.A7RS.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.RY.A83X.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.HT.7607.01 3 0.000 0.923 0.00 0 1.00
#> TCGA.DU.7009.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.P5.A781.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.FG.8186.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.S9.A6U2.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.S9.A6WN.01 3 0.000 0.923 0.00 0 1.00
#> TCGA.QH.A65X.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.E1.5319.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.HT.A74L.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.HT.A4DV.01 3 0.000 0.858 0.00 0.00 1.00 0.00
#> TCGA.HT.8113.01 3 0.000 0.858 0.00 0.00 1.00 0.00
#> TCGA.FG.A710.01 1 0.428 0.660 0.72 0.00 0.00 0.28
#> TCGA.DU.A6S6.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.HT.7877.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.QH.A6CU.01 3 0.462 0.376 0.34 0.00 0.66 0.00
#> TCGA.HT.8010.01 3 0.000 0.858 0.00 0.00 1.00 0.00
#> TCGA.FG.7638.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.FG.A6J1.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.S9.A7QY.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.P5.A77X.01 2 0.441 0.550 0.00 0.70 0.00 0.30
#> TCGA.P5.A5EX.01 4 0.498 -0.518 0.00 0.46 0.00 0.54
#> TCGA.QH.A6X5.01 3 0.471 0.349 0.36 0.00 0.64 0.00
#> TCGA.FG.A60K.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.DU.A7T6.01 2 0.000 0.749 0.00 1.00 0.00 0.00
#> TCGA.TM.A84O.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.HT.A61A.01 3 0.000 0.858 0.00 0.00 1.00 0.00
#> TCGA.TQ.A7RQ.01 1 0.428 0.660 0.72 0.00 0.00 0.28
#> TCGA.HT.7681.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.QH.A65V.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.DU.A6S8.01 2 0.000 0.749 0.00 1.00 0.00 0.00
#> TCGA.DB.A64R.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.HT.7695.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.DU.A6S2.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.HW.7495.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.S9.A7IQ.01 3 0.000 0.858 0.00 0.00 1.00 0.00
#> TCGA.S9.A6WI.01 3 0.000 0.858 0.00 0.00 1.00 0.00
#> TCGA.TQ.A7RI.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.FG.A713.01 3 0.000 0.858 0.00 0.00 1.00 0.00
#> TCGA.HT.A615.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.HT.7874.01 3 0.000 0.858 0.00 0.00 1.00 0.00
#> TCGA.CS.5396.01 2 0.000 0.749 0.00 1.00 0.00 0.00
#> TCGA.DB.A64Q.01 2 0.441 0.550 0.00 0.70 0.00 0.30
#> TCGA.DB.A64U.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.DU.5870.01 1 0.428 0.660 0.72 0.00 0.00 0.28
#> TCGA.TQ.A7RS.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.RY.A83X.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.HT.7607.01 3 0.000 0.858 0.00 0.00 1.00 0.00
#> TCGA.DU.7009.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.P5.A781.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.FG.8186.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.S9.A6U2.01 1 0.000 0.955 1.00 0.00 0.00 0.00
#> TCGA.S9.A6WN.01 4 0.452 0.120 0.00 0.00 0.32 0.68
#> TCGA.QH.A65X.01 1 0.428 0.660 0.72 0.00 0.00 0.28
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.E1.5319.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A74L.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A4DV.01 3 0.0000 0.831 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.8113.01 3 0.0000 0.831 0.00 0.00 1.00 0.00 0.00
#> TCGA.FG.A710.01 5 0.3274 0.705 0.22 0.00 0.00 0.00 0.78
#> TCGA.DU.A6S6.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7877.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CU.01 3 0.4287 0.220 0.46 0.00 0.54 0.00 0.00
#> TCGA.HT.8010.01 3 0.0000 0.831 0.00 0.00 1.00 0.00 0.00
#> TCGA.FG.7638.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A6J1.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7QY.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A77X.01 5 0.1043 0.554 0.00 0.00 0.00 0.04 0.96
#> TCGA.P5.A5EX.01 5 0.2012 0.529 0.00 0.02 0.00 0.06 0.92
#> TCGA.QH.A6X5.01 3 0.4227 0.265 0.42 0.00 0.58 0.00 0.00
#> TCGA.FG.A60K.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A7T6.01 2 0.1648 0.873 0.00 0.94 0.00 0.02 0.04
#> TCGA.TM.A84O.01 1 0.0609 0.975 0.98 0.00 0.00 0.00 0.02
#> TCGA.HT.A61A.01 3 0.0000 0.831 0.00 0.00 1.00 0.00 0.00
#> TCGA.TQ.A7RQ.01 5 0.3796 0.640 0.30 0.00 0.00 0.00 0.70
#> TCGA.HT.7681.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A65V.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A6S8.01 2 0.2873 0.880 0.00 0.86 0.00 0.02 0.12
#> TCGA.DB.A64R.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7695.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A6S2.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.HW.7495.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IQ.01 3 0.0000 0.831 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6WI.01 3 0.0000 0.831 0.00 0.00 1.00 0.00 0.00
#> TCGA.TQ.A7RI.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A713.01 3 0.0000 0.831 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.A615.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7874.01 3 0.0000 0.831 0.00 0.00 1.00 0.00 0.00
#> TCGA.CS.5396.01 2 0.1410 0.904 0.00 0.94 0.00 0.00 0.06
#> TCGA.DB.A64Q.01 5 0.3390 0.474 0.00 0.10 0.00 0.06 0.84
#> TCGA.DB.A64U.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5870.01 5 0.3274 0.705 0.22 0.00 0.00 0.00 0.78
#> TCGA.TQ.A7RS.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.RY.A83X.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7607.01 3 0.0000 0.831 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.7009.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A781.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8186.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6U2.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WN.01 4 0.1410 0.000 0.00 0.00 0.06 0.94 0.00
#> TCGA.QH.A65X.01 5 0.3684 0.665 0.28 0.00 0.00 0.00 0.72
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 0.9289 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A74L.01 1 0.0547 0.9255 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.HT.A4DV.01 3 0.0000 0.9566 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.8113.01 3 0.0000 0.9566 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.A710.01 5 0.0547 0.6598 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.DU.A6S6.01 1 0.0547 0.9255 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.HT.7877.01 1 0.0000 0.9289 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CU.01 1 0.6397 0.0280 0.44 0.00 0.26 0.00 0.02 0.28
#> TCGA.HT.8010.01 3 0.4326 0.5756 0.02 0.00 0.68 0.00 0.02 0.28
#> TCGA.FG.7638.01 1 0.0547 0.9255 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.FG.A6J1.01 1 0.0547 0.9255 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.S9.A7QY.01 1 0.0000 0.9289 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A77X.01 5 0.3711 0.5845 0.00 0.02 0.00 0.00 0.72 0.26
#> TCGA.P5.A5EX.01 5 0.4801 0.3552 0.00 0.02 0.00 0.02 0.50 0.46
#> TCGA.QH.A6X5.01 1 0.6449 -0.0233 0.42 0.00 0.28 0.00 0.02 0.28
#> TCGA.FG.A60K.01 1 0.0547 0.9255 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DU.A7T6.01 2 0.1865 0.8318 0.00 0.92 0.00 0.04 0.00 0.04
#> TCGA.TM.A84O.01 1 0.4393 0.6392 0.72 0.00 0.00 0.00 0.14 0.14
#> TCGA.HT.A61A.01 3 0.0000 0.9566 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RQ.01 5 0.2454 0.6145 0.16 0.00 0.00 0.00 0.84 0.00
#> TCGA.HT.7681.01 1 0.0000 0.9289 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A65V.01 1 0.0000 0.9289 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A6S8.01 2 0.2631 0.7689 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.DB.A64R.01 1 0.0547 0.9255 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.HT.7695.01 1 0.0000 0.9289 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A6S2.01 1 0.0000 0.9289 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HW.7495.01 1 0.0000 0.9289 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IQ.01 3 0.0000 0.9566 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6WI.01 3 0.0000 0.9566 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RI.01 1 0.0547 0.9255 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.FG.A713.01 3 0.0000 0.9566 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.A615.01 1 0.0000 0.9289 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7874.01 3 0.0000 0.9566 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CS.5396.01 2 0.0000 0.8578 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64Q.01 5 0.5406 0.4097 0.00 0.12 0.00 0.00 0.50 0.38
#> TCGA.DB.A64U.01 1 0.0000 0.9289 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5870.01 5 0.1807 0.6755 0.06 0.00 0.00 0.00 0.92 0.02
#> TCGA.TQ.A7RS.01 1 0.0547 0.9255 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.RY.A83X.01 1 0.0000 0.9289 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7607.01 3 0.0000 0.9566 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7009.01 1 0.1267 0.8928 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.P5.A781.01 1 0.0000 0.9289 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8186.01 1 0.0547 0.9255 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.S9.A6U2.01 1 0.0000 0.9289 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WN.01 4 0.0000 0.0000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.QH.A65X.01 5 0.2454 0.6145 0.16 0.00 0.00 0.00 0.84 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 1 0.0000 0.97084 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A74L.01 1 0.0000 0.97084 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A4DV.01 3 0.0504 0.90399 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.HT.8113.01 3 0.0000 0.92322 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A710.01 5 0.1433 0.58903 0.08 0.00 0.00 0.00 0.92 0.00 0.00
#> TCGA.DU.A6S6.01 1 0.0000 0.97084 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7877.01 1 0.0000 0.97084 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CU.01 7 0.5402 0.94120 0.28 0.00 0.24 0.00 0.00 0.00 0.48
#> TCGA.HT.8010.01 3 0.3558 -0.00975 0.00 0.00 0.52 0.00 0.00 0.00 0.48
#> TCGA.FG.7638.01 1 0.0000 0.97084 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A6J1.01 1 0.0000 0.97084 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7QY.01 1 0.0000 0.97084 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A77X.01 5 0.4638 -0.27872 0.00 0.00 0.00 0.00 0.54 0.38 0.08
#> TCGA.P5.A5EX.01 5 0.5995 -0.01921 0.00 0.02 0.00 0.02 0.48 0.16 0.32
#> TCGA.QH.A6X5.01 7 0.5410 0.94049 0.26 0.00 0.26 0.00 0.00 0.00 0.48
#> TCGA.FG.A60K.01 1 0.0000 0.97084 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A7T6.01 2 0.0000 0.46217 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84O.01 1 0.4742 0.18652 0.62 0.00 0.00 0.00 0.22 0.00 0.16
#> TCGA.HT.A61A.01 3 0.0000 0.92322 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RQ.01 5 0.2422 0.60805 0.18 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.HT.7681.01 1 0.0000 0.97084 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A65V.01 1 0.0504 0.94819 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DU.A6S8.01 6 0.2832 -0.31652 0.00 0.24 0.00 0.00 0.00 0.76 0.00
#> TCGA.DB.A64R.01 1 0.0000 0.97084 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7695.01 1 0.0000 0.97084 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A6S2.01 1 0.0000 0.97084 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HW.7495.01 1 0.0000 0.97084 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IQ.01 3 0.0000 0.92322 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WI.01 3 0.0000 0.92322 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RI.01 1 0.0000 0.97084 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A713.01 3 0.0000 0.92322 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A615.01 1 0.0504 0.94819 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.HT.7874.01 3 0.0000 0.92322 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.5396.01 2 0.4945 0.34947 0.00 0.52 0.00 0.00 0.00 0.36 0.12
#> TCGA.DB.A64Q.01 6 0.5709 0.09220 0.00 0.02 0.00 0.00 0.34 0.46 0.18
#> TCGA.DB.A64U.01 1 0.0000 0.97084 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5870.01 5 0.1886 0.61872 0.12 0.00 0.00 0.00 0.88 0.00 0.00
#> TCGA.TQ.A7RS.01 1 0.0000 0.97084 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RY.A83X.01 1 0.0000 0.97084 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7607.01 3 0.0000 0.92322 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7009.01 1 0.1433 0.86614 0.92 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.P5.A781.01 1 0.0000 0.97084 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8186.01 1 0.0000 0.97084 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6U2.01 1 0.0000 0.97084 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WN.01 4 0.0000 0.00000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.QH.A65X.01 5 0.2572 0.58677 0.20 0.00 0.00 0.00 0.80 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 1 0.0000 0.9486 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A74L.01 1 0.1341 0.9152 0.92 0.00 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.HT.A4DV.01 3 0.0471 0.9759 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.HT.8113.01 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A710.01 5 0.2591 0.8407 0.08 0.00 0.00 0.00 0.86 0.00 0.04 0.02
#> TCGA.DU.A6S6.01 1 0.1341 0.9152 0.92 0.00 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.HT.7877.01 1 0.0000 0.9486 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A6CU.01 7 0.3729 0.7371 0.18 0.00 0.10 0.00 0.00 0.00 0.72 0.00
#> TCGA.HT.8010.01 7 0.3198 0.5975 0.02 0.00 0.26 0.00 0.00 0.00 0.72 0.00
#> TCGA.FG.7638.01 1 0.0471 0.9427 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.FG.A6J1.01 1 0.0808 0.9375 0.96 0.00 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.S9.A7QY.01 1 0.0000 0.9486 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A77X.01 8 0.5801 0.4254 0.00 0.02 0.00 0.00 0.34 0.14 0.04 0.46
#> TCGA.P5.A5EX.01 8 0.7019 0.2892 0.00 0.14 0.00 0.02 0.28 0.04 0.12 0.40
#> TCGA.QH.A6X5.01 7 0.4061 0.7755 0.14 0.00 0.12 0.00 0.02 0.00 0.72 0.00
#> TCGA.FG.A60K.01 1 0.0808 0.9375 0.96 0.00 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.DU.A7T6.01 2 0.2114 0.0000 0.00 0.84 0.00 0.00 0.00 0.16 0.00 0.00
#> TCGA.TM.A84O.01 1 0.4841 -0.0439 0.50 0.00 0.00 0.00 0.16 0.00 0.34 0.00
#> TCGA.HT.A61A.01 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RQ.01 5 0.2224 0.8657 0.12 0.02 0.00 0.00 0.86 0.00 0.00 0.00
#> TCGA.HT.7681.01 1 0.0000 0.9486 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A65V.01 1 0.0000 0.9486 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A6S8.01 6 0.1887 0.5258 0.00 0.06 0.00 0.00 0.00 0.90 0.00 0.04
#> TCGA.DB.A64R.01 1 0.0808 0.9343 0.96 0.00 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.HT.7695.01 1 0.0000 0.9486 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A6S2.01 1 0.0000 0.9486 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HW.7495.01 1 0.0000 0.9486 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IQ.01 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WI.01 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RI.01 1 0.1341 0.9152 0.92 0.00 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.FG.A713.01 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A615.01 1 0.0000 0.9486 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7874.01 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.5396.01 6 0.3794 0.4582 0.00 0.18 0.00 0.00 0.00 0.74 0.04 0.04
#> TCGA.DB.A64Q.01 8 0.4245 0.3258 0.00 0.00 0.00 0.00 0.08 0.14 0.06 0.72
#> TCGA.DB.A64U.01 1 0.0000 0.9486 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5870.01 5 0.2547 0.8283 0.12 0.00 0.00 0.00 0.84 0.00 0.00 0.04
#> TCGA.TQ.A7RS.01 1 0.1341 0.9152 0.92 0.00 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.RY.A83X.01 1 0.0000 0.9486 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7607.01 3 0.0000 0.9966 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7009.01 1 0.1563 0.8969 0.90 0.00 0.00 0.00 0.10 0.00 0.00 0.00
#> TCGA.P5.A781.01 1 0.0808 0.9351 0.96 0.00 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.FG.8186.01 1 0.0000 0.9486 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6U2.01 1 0.0000 0.9486 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WN.01 4 0.0000 0.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A65X.01 5 0.2484 0.8861 0.10 0.02 0.00 0.00 0.86 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: Node0221. Child nodes: Node022111-leaf , Node022112-leaf , Node022113-leaf , Node022121 , Node022122-leaf , Node022123-leaf , Node022211-leaf , Node022212-leaf , Node022231-leaf , Node022232-leaf , Node022233-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 34 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.938 0.933 0.974 0.4930 0.513 0.513
#> 3 3 1.000 1.000 1.000 0.1903 0.836 0.699
#> 4 4 0.708 0.709 0.831 0.2021 0.861 0.664
#> 5 5 0.754 0.886 0.885 0.0921 0.852 0.528
#> 6 6 0.950 0.961 0.949 0.0549 0.979 0.896
#> 7 7 0.891 0.800 0.873 0.0312 0.968 0.841
#> 8 8 0.867 0.725 0.834 0.0331 0.925 0.600
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 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.A74K.01 2 0.000 0.987 0.00 1.00
#> TCGA.QH.A6X8.01 2 0.000 0.987 0.00 1.00
#> TCGA.P5.A72Z.01 2 0.000 0.987 0.00 1.00
#> TCGA.DU.8168.01 1 0.000 0.960 1.00 0.00
#> TCGA.EZ.7264.01 2 0.000 0.987 0.00 1.00
#> TCGA.DU.7298.01 1 0.000 0.960 1.00 0.00
#> TCGA.CS.5390.01 1 0.000 0.960 1.00 0.00
#> TCGA.DU.7294.01 1 0.958 0.402 0.62 0.38
#> TCGA.DB.5274.01 1 0.000 0.960 1.00 0.00
#> TCGA.HT.8012.01 1 0.000 0.960 1.00 0.00
#> TCGA.P5.A77W.01 1 0.000 0.960 1.00 0.00
#> TCGA.DU.7302.01 2 0.000 0.987 0.00 1.00
#> TCGA.QH.A65R.01 1 0.000 0.960 1.00 0.00
#> TCGA.DU.5874.01 1 0.000 0.960 1.00 0.00
#> TCGA.R8.A73M.01 1 0.000 0.960 1.00 0.00
#> TCGA.DB.A4XH.01 1 0.000 0.960 1.00 0.00
#> TCGA.VW.A7QS.01 2 0.000 0.987 0.00 1.00
#> TCGA.DU.7018.01 1 0.958 0.402 0.62 0.38
#> TCGA.DU.7300.01 2 0.584 0.825 0.14 0.86
#> TCGA.DH.5144.01 1 0.000 0.960 1.00 0.00
#> TCGA.HT.7471.01 1 0.000 0.960 1.00 0.00
#> TCGA.HT.A5R9.01 1 0.000 0.960 1.00 0.00
#> TCGA.DH.A7UR.01 1 0.000 0.960 1.00 0.00
#> TCGA.DU.6400.01 1 0.000 0.960 1.00 0.00
#> TCGA.DB.A75K.01 1 0.000 0.960 1.00 0.00
#> TCGA.S9.A6WH.01 1 0.000 0.960 1.00 0.00
#> TCGA.DB.A64W.01 2 0.000 0.987 0.00 1.00
#> TCGA.R8.A6MO.01 1 0.000 0.960 1.00 0.00
#> TCGA.DU.5870.02 2 0.000 0.987 0.00 1.00
#> TCGA.CS.6668.01 2 0.000 0.987 0.00 1.00
#> TCGA.E1.5318.01 1 0.000 0.960 1.00 0.00
#> TCGA.S9.A7J3.01 2 0.000 0.987 0.00 1.00
#> TCGA.DB.A64L.01 2 0.000 0.987 0.00 1.00
#> TCGA.TM.A84G.01 2 0.000 0.987 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.HT.A74K.01 3 0 1 0 0 1
#> TCGA.QH.A6X8.01 2 0 1 0 1 0
#> TCGA.P5.A72Z.01 3 0 1 0 0 1
#> TCGA.DU.8168.01 1 0 1 1 0 0
#> TCGA.EZ.7264.01 2 0 1 0 1 0
#> TCGA.DU.7298.01 1 0 1 1 0 0
#> TCGA.CS.5390.01 1 0 1 1 0 0
#> TCGA.DU.7294.01 2 0 1 0 1 0
#> TCGA.DB.5274.01 1 0 1 1 0 0
#> TCGA.HT.8012.01 1 0 1 1 0 0
#> TCGA.P5.A77W.01 1 0 1 1 0 0
#> TCGA.DU.7302.01 2 0 1 0 1 0
#> TCGA.QH.A65R.01 1 0 1 1 0 0
#> TCGA.DU.5874.01 1 0 1 1 0 0
#> TCGA.R8.A73M.01 1 0 1 1 0 0
#> TCGA.DB.A4XH.01 1 0 1 1 0 0
#> TCGA.VW.A7QS.01 2 0 1 0 1 0
#> TCGA.DU.7018.01 2 0 1 0 1 0
#> TCGA.DU.7300.01 2 0 1 0 1 0
#> TCGA.DH.5144.01 1 0 1 1 0 0
#> TCGA.HT.7471.01 1 0 1 1 0 0
#> TCGA.HT.A5R9.01 1 0 1 1 0 0
#> TCGA.DH.A7UR.01 1 0 1 1 0 0
#> TCGA.DU.6400.01 1 0 1 1 0 0
#> TCGA.DB.A75K.01 1 0 1 1 0 0
#> TCGA.S9.A6WH.01 1 0 1 1 0 0
#> TCGA.DB.A64W.01 2 0 1 0 1 0
#> TCGA.R8.A6MO.01 1 0 1 1 0 0
#> TCGA.DU.5870.02 3 0 1 0 0 1
#> TCGA.CS.6668.01 3 0 1 0 0 1
#> TCGA.E1.5318.01 1 0 1 1 0 0
#> TCGA.S9.A7J3.01 2 0 1 0 1 0
#> TCGA.DB.A64L.01 2 0 1 0 1 0
#> TCGA.TM.A84G.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.A74K.01 3 0.736 0.2331 0.00 0.32 0.50 0.18
#> TCGA.QH.A6X8.01 2 0.000 0.7224 0.00 1.00 0.00 0.00
#> TCGA.P5.A72Z.01 3 0.000 0.8314 0.00 0.00 1.00 0.00
#> TCGA.DU.8168.01 1 0.000 0.8545 1.00 0.00 0.00 0.00
#> TCGA.EZ.7264.01 2 0.480 0.6845 0.00 0.72 0.02 0.26
#> TCGA.DU.7298.01 4 0.462 0.9527 0.34 0.00 0.00 0.66
#> TCGA.CS.5390.01 4 0.428 0.9111 0.28 0.00 0.00 0.72
#> TCGA.DU.7294.01 2 0.495 0.5365 0.00 0.56 0.00 0.44
#> TCGA.DB.5274.01 1 0.452 0.2284 0.68 0.00 0.00 0.32
#> TCGA.HT.8012.01 1 0.000 0.8545 1.00 0.00 0.00 0.00
#> TCGA.P5.A77W.01 1 0.000 0.8545 1.00 0.00 0.00 0.00
#> TCGA.DU.7302.01 2 0.000 0.7224 0.00 1.00 0.00 0.00
#> TCGA.QH.A65R.01 1 0.000 0.8545 1.00 0.00 0.00 0.00
#> TCGA.DU.5874.01 1 0.000 0.8545 1.00 0.00 0.00 0.00
#> TCGA.R8.A73M.01 4 0.428 0.9111 0.28 0.00 0.00 0.72
#> TCGA.DB.A4XH.01 1 0.000 0.8545 1.00 0.00 0.00 0.00
#> TCGA.VW.A7QS.01 2 0.480 0.6845 0.00 0.72 0.02 0.26
#> TCGA.DU.7018.01 2 0.495 0.5365 0.00 0.56 0.00 0.44
#> TCGA.DU.7300.01 2 0.495 0.5365 0.00 0.56 0.00 0.44
#> TCGA.DH.5144.01 4 0.462 0.9527 0.34 0.00 0.00 0.66
#> TCGA.HT.7471.01 1 0.471 0.0731 0.64 0.00 0.00 0.36
#> TCGA.HT.A5R9.01 1 0.000 0.8545 1.00 0.00 0.00 0.00
#> TCGA.DH.A7UR.01 1 0.000 0.8545 1.00 0.00 0.00 0.00
#> TCGA.DU.6400.01 4 0.462 0.9527 0.34 0.00 0.00 0.66
#> TCGA.DB.A75K.01 4 0.462 0.9527 0.34 0.00 0.00 0.66
#> TCGA.S9.A6WH.01 1 0.000 0.8545 1.00 0.00 0.00 0.00
#> TCGA.DB.A64W.01 2 0.000 0.7224 0.00 1.00 0.00 0.00
#> TCGA.R8.A6MO.01 1 0.495 -0.3216 0.56 0.00 0.00 0.44
#> TCGA.DU.5870.02 3 0.000 0.8314 0.00 0.00 1.00 0.00
#> TCGA.CS.6668.01 3 0.000 0.8314 0.00 0.00 1.00 0.00
#> TCGA.E1.5318.01 1 0.000 0.8545 1.00 0.00 0.00 0.00
#> TCGA.S9.A7J3.01 2 0.000 0.7224 0.00 1.00 0.00 0.00
#> TCGA.DB.A64L.01 2 0.480 0.6845 0.00 0.72 0.02 0.26
#> TCGA.TM.A84G.01 2 0.494 0.6713 0.00 0.70 0.02 0.28
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.HT.A74K.01 5 0.327 0.653 0.00 0.0 0.22 0.00 0.78
#> TCGA.QH.A6X8.01 2 0.000 0.842 0.00 1.0 0.00 0.00 0.00
#> TCGA.P5.A72Z.01 3 0.000 1.000 0.00 0.0 1.00 0.00 0.00
#> TCGA.DU.8168.01 1 0.173 0.941 0.92 0.0 0.00 0.00 0.08
#> TCGA.EZ.7264.01 5 0.202 0.912 0.00 0.1 0.00 0.00 0.90
#> TCGA.DU.7298.01 4 0.369 0.891 0.20 0.0 0.00 0.78 0.02
#> TCGA.CS.5390.01 4 0.173 0.799 0.08 0.0 0.00 0.92 0.00
#> TCGA.DU.7294.01 2 0.505 0.769 0.00 0.7 0.00 0.18 0.12
#> TCGA.DB.5274.01 4 0.543 0.727 0.32 0.0 0.00 0.60 0.08
#> TCGA.HT.8012.01 1 0.141 0.951 0.94 0.0 0.00 0.00 0.06
#> TCGA.P5.A77W.01 1 0.173 0.941 0.92 0.0 0.00 0.00 0.08
#> TCGA.DU.7302.01 2 0.000 0.842 0.00 1.0 0.00 0.00 0.00
#> TCGA.QH.A65R.01 1 0.000 0.968 1.00 0.0 0.00 0.00 0.00
#> TCGA.DU.5874.01 1 0.000 0.968 1.00 0.0 0.00 0.00 0.00
#> TCGA.R8.A73M.01 4 0.233 0.797 0.08 0.0 0.00 0.90 0.02
#> TCGA.DB.A4XH.01 1 0.000 0.968 1.00 0.0 0.00 0.00 0.00
#> TCGA.VW.A7QS.01 5 0.202 0.912 0.00 0.1 0.00 0.00 0.90
#> TCGA.DU.7018.01 2 0.505 0.769 0.00 0.7 0.00 0.18 0.12
#> TCGA.DU.7300.01 2 0.505 0.769 0.00 0.7 0.00 0.18 0.12
#> TCGA.DH.5144.01 4 0.369 0.894 0.20 0.0 0.00 0.78 0.02
#> TCGA.HT.7471.01 4 0.514 0.825 0.26 0.0 0.00 0.66 0.08
#> TCGA.HT.A5R9.01 1 0.000 0.968 1.00 0.0 0.00 0.00 0.00
#> TCGA.DH.A7UR.01 1 0.000 0.968 1.00 0.0 0.00 0.00 0.00
#> TCGA.DU.6400.01 4 0.311 0.893 0.20 0.0 0.00 0.80 0.00
#> TCGA.DB.A75K.01 4 0.369 0.894 0.20 0.0 0.00 0.78 0.02
#> TCGA.S9.A6WH.01 1 0.141 0.951 0.94 0.0 0.00 0.00 0.06
#> TCGA.DB.A64W.01 2 0.000 0.842 0.00 1.0 0.00 0.00 0.00
#> TCGA.R8.A6MO.01 4 0.356 0.861 0.26 0.0 0.00 0.74 0.00
#> TCGA.DU.5870.02 3 0.000 1.000 0.00 0.0 1.00 0.00 0.00
#> TCGA.CS.6668.01 3 0.000 1.000 0.00 0.0 1.00 0.00 0.00
#> TCGA.E1.5318.01 1 0.000 0.968 1.00 0.0 0.00 0.00 0.00
#> TCGA.S9.A7J3.01 2 0.000 0.842 0.00 1.0 0.00 0.00 0.00
#> TCGA.DB.A64L.01 5 0.202 0.912 0.00 0.1 0.00 0.00 0.90
#> TCGA.TM.A84G.01 5 0.370 0.875 0.00 0.1 0.00 0.08 0.82
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.HT.A74K.01 5 0.2020 0.911 0.00 0.00 0.04 0.02 0.92 0.02
#> TCGA.QH.A6X8.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A72Z.01 3 0.0000 0.984 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.8168.01 1 0.0937 0.974 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.EZ.7264.01 5 0.0000 0.962 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.7298.01 4 0.1480 0.939 0.04 0.00 0.00 0.94 0.00 0.02
#> TCGA.CS.5390.01 4 0.0937 0.915 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.DU.7294.01 6 0.3688 0.979 0.00 0.14 0.00 0.02 0.04 0.80
#> TCGA.DB.5274.01 4 0.3045 0.875 0.10 0.00 0.00 0.84 0.00 0.06
#> TCGA.HT.8012.01 1 0.0937 0.974 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.P5.A77W.01 1 0.0937 0.974 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.DU.7302.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QH.A65R.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.5874.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.R8.A73M.01 4 0.1556 0.913 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.DB.A4XH.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VW.A7QS.01 5 0.0000 0.962 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.7018.01 6 0.3688 0.979 0.00 0.14 0.00 0.02 0.04 0.80
#> TCGA.DU.7300.01 6 0.4162 0.959 0.00 0.12 0.00 0.04 0.06 0.78
#> TCGA.DH.5144.01 4 0.1865 0.940 0.04 0.00 0.00 0.92 0.00 0.04
#> TCGA.HT.7471.01 4 0.2794 0.916 0.06 0.00 0.00 0.86 0.00 0.08
#> TCGA.HT.A5R9.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A7UR.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6400.01 4 0.0937 0.943 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.DB.A75K.01 4 0.1865 0.940 0.04 0.00 0.00 0.92 0.00 0.04
#> TCGA.S9.A6WH.01 1 0.0937 0.974 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.DB.A64W.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.R8.A6MO.01 4 0.1807 0.934 0.06 0.00 0.00 0.92 0.00 0.02
#> TCGA.DU.5870.02 3 0.0000 0.984 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CS.6668.01 3 0.1092 0.967 0.00 0.00 0.96 0.02 0.00 0.02
#> TCGA.E1.5318.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7J3.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64L.01 5 0.0000 0.962 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.TM.A84G.01 5 0.1556 0.923 0.00 0.00 0.00 0.00 0.92 0.08
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.HT.A74K.01 5 0.1006 0.933 0.00 0.00 0.02 0.00 0.96 0.00 0.02
#> TCGA.QH.A6X8.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A72Z.01 3 0.0000 0.991 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.8168.01 1 0.0863 0.753 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.EZ.7264.01 5 0.0504 0.949 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DU.7298.01 4 0.3841 0.708 0.04 0.00 0.00 0.68 0.00 0.28 0.00
#> TCGA.CS.5390.01 4 0.4278 0.412 0.00 0.00 0.00 0.50 0.00 0.46 0.04
#> TCGA.DU.7294.01 7 0.1006 0.880 0.00 0.02 0.00 0.02 0.00 0.00 0.96
#> TCGA.DB.5274.01 1 0.5115 -0.310 0.48 0.00 0.00 0.38 0.00 0.14 0.00
#> TCGA.HT.8012.01 1 0.0000 0.768 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A77W.01 1 0.0863 0.753 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.DU.7302.01 2 0.0863 0.965 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.QH.A65R.01 1 0.2832 0.817 0.76 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.DU.5874.01 1 0.2832 0.817 0.76 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.R8.A73M.01 4 0.1928 0.754 0.00 0.00 0.00 0.90 0.00 0.02 0.08
#> TCGA.DB.A4XH.01 1 0.2832 0.817 0.76 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.VW.A7QS.01 5 0.0504 0.949 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DU.7018.01 7 0.1006 0.880 0.00 0.02 0.00 0.02 0.00 0.00 0.96
#> TCGA.DU.7300.01 7 0.3984 0.750 0.00 0.02 0.00 0.02 0.00 0.28 0.68
#> TCGA.DH.5144.01 4 0.2016 0.790 0.06 0.00 0.00 0.90 0.00 0.04 0.00
#> TCGA.HT.7471.01 4 0.3927 0.585 0.30 0.00 0.00 0.66 0.00 0.04 0.00
#> TCGA.HT.A5R9.01 1 0.2832 0.817 0.76 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.DH.A7UR.01 1 0.2832 0.817 0.76 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.DU.6400.01 4 0.2278 0.803 0.04 0.00 0.00 0.88 0.00 0.08 0.00
#> TCGA.DB.A75K.01 4 0.0863 0.800 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.S9.A6WH.01 1 0.0504 0.761 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DB.A64W.01 2 0.0863 0.947 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.R8.A6MO.01 4 0.2803 0.792 0.06 0.00 0.00 0.84 0.00 0.10 0.00
#> TCGA.DU.5870.02 3 0.0000 0.991 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6668.01 3 0.0504 0.983 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.E1.5318.01 1 0.2832 0.817 0.76 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.S9.A7J3.01 2 0.0863 0.965 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.DB.A64L.01 5 0.0504 0.949 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.TM.A84G.01 5 0.2745 0.826 0.00 0.00 0.00 0.00 0.82 0.16 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.A74K.01 5 0.1887 0.8639 0.04 0.00 0.0 0.00 0.90 0.00 0.00 0.06
#> TCGA.QH.A6X8.01 2 0.0000 0.9302 0.00 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A72Z.01 3 0.0000 0.9544 0.00 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.8168.01 6 0.1557 0.5747 0.06 0.00 0.0 0.02 0.00 0.92 0.00 0.00
#> TCGA.EZ.7264.01 5 0.0000 0.9151 0.00 0.00 0.0 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7298.01 8 0.6292 0.2334 0.10 0.00 0.0 0.30 0.00 0.26 0.00 0.34
#> TCGA.CS.5390.01 8 0.3015 0.3061 0.00 0.00 0.0 0.32 0.00 0.00 0.00 0.68
#> TCGA.DU.7294.01 7 0.0000 0.7695 0.00 0.00 0.0 0.00 0.00 0.00 1.00 0.00
#> TCGA.DB.5274.01 6 0.4394 0.0603 0.06 0.00 0.0 0.16 0.00 0.70 0.00 0.08
#> TCGA.HT.8012.01 6 0.2938 0.1205 0.30 0.00 0.0 0.00 0.00 0.70 0.00 0.00
#> TCGA.P5.A77W.01 6 0.0471 0.5821 0.00 0.00 0.0 0.02 0.00 0.98 0.00 0.00
#> TCGA.DU.7302.01 2 0.1091 0.9367 0.00 0.94 0.0 0.00 0.00 0.00 0.06 0.00
#> TCGA.QH.A65R.01 1 0.3193 1.0000 0.62 0.00 0.0 0.00 0.00 0.38 0.00 0.00
#> TCGA.DU.5874.01 1 0.3193 1.0000 0.62 0.00 0.0 0.00 0.00 0.38 0.00 0.00
#> TCGA.R8.A73M.01 4 0.1275 0.6773 0.00 0.00 0.0 0.94 0.00 0.00 0.04 0.02
#> TCGA.DB.A4XH.01 1 0.3193 1.0000 0.62 0.00 0.0 0.00 0.00 0.38 0.00 0.00
#> TCGA.VW.A7QS.01 5 0.0000 0.9151 0.00 0.00 0.0 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.7018.01 7 0.0000 0.7695 0.00 0.00 0.0 0.00 0.00 0.00 1.00 0.00
#> TCGA.DU.7300.01 7 0.3318 0.4312 0.00 0.00 0.0 0.00 0.00 0.00 0.54 0.46
#> TCGA.DH.5144.01 4 0.1091 0.7104 0.00 0.00 0.0 0.94 0.00 0.06 0.00 0.00
#> TCGA.HT.7471.01 4 0.3015 0.4045 0.00 0.00 0.0 0.68 0.00 0.32 0.00 0.00
#> TCGA.HT.A5R9.01 1 0.3193 1.0000 0.62 0.00 0.0 0.00 0.00 0.38 0.00 0.00
#> TCGA.DH.A7UR.01 1 0.3193 1.0000 0.62 0.00 0.0 0.00 0.00 0.38 0.00 0.00
#> TCGA.DU.6400.01 4 0.2020 0.7009 0.06 0.00 0.0 0.90 0.00 0.02 0.00 0.02
#> TCGA.DB.A75K.01 4 0.0471 0.7202 0.00 0.00 0.0 0.98 0.00 0.00 0.00 0.02
#> TCGA.S9.A6WH.01 6 0.3198 0.2773 0.26 0.00 0.0 0.02 0.00 0.72 0.00 0.00
#> TCGA.DB.A64W.01 2 0.1887 0.8854 0.04 0.90 0.0 0.00 0.00 0.00 0.00 0.06
#> TCGA.R8.A6MO.01 4 0.4079 0.4902 0.06 0.00 0.0 0.74 0.00 0.12 0.00 0.08
#> TCGA.DU.5870.02 3 0.0000 0.9544 0.00 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.CS.6668.01 3 0.1887 0.9071 0.04 0.00 0.9 0.00 0.00 0.00 0.00 0.06
#> TCGA.E1.5318.01 1 0.3193 1.0000 0.62 0.00 0.0 0.00 0.00 0.38 0.00 0.00
#> TCGA.S9.A7J3.01 2 0.1091 0.9367 0.00 0.94 0.0 0.00 0.00 0.00 0.06 0.00
#> TCGA.DB.A64L.01 5 0.0000 0.9151 0.00 0.00 0.0 0.00 1.00 0.00 0.00 0.00
#> TCGA.TM.A84G.01 5 0.3657 0.7244 0.20 0.00 0.0 0.00 0.72 0.00 0.00 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: Node02212. Child nodes: Node0221211-leaf , Node0221212-leaf , Node0221213-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["022121"]
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 7.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.327 0.711 0.795 0.4730 0.474 0.474
#> 3 3 1.000 0.989 0.992 0.3834 0.789 0.591
#> 4 4 0.737 0.420 0.675 0.1440 0.778 0.465
#> 5 5 0.807 0.947 0.928 0.0932 0.836 0.451
#> 6 6 0.912 0.872 0.899 0.0443 1.000 1.000
#> 7 7 0.906 0.681 0.783 0.0284 0.959 0.759
#> 8 8 0.877 0.752 0.814 0.0206 0.947 0.609
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 7
#> attr(,"optional")
#> [1] 3
There is also optional best \(k\) = 3 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.DU.8168.01 1 0.000 0.830 1.00 0.00
#> TCGA.DU.7298.01 2 0.990 0.715 0.44 0.56
#> TCGA.CS.5390.01 1 0.827 0.679 0.74 0.26
#> TCGA.DB.5274.01 1 0.000 0.830 1.00 0.00
#> TCGA.HT.8012.01 2 0.943 0.722 0.36 0.64
#> TCGA.P5.A77W.01 2 1.000 0.648 0.50 0.50
#> TCGA.QH.A65R.01 2 0.327 0.525 0.06 0.94
#> TCGA.DU.5874.01 1 0.000 0.830 1.00 0.00
#> TCGA.R8.A73M.01 2 0.990 0.715 0.44 0.56
#> TCGA.DB.A4XH.01 1 0.827 0.679 0.74 0.26
#> TCGA.DH.5144.01 1 0.141 0.804 0.98 0.02
#> TCGA.HT.7471.01 2 0.990 0.715 0.44 0.56
#> TCGA.HT.A5R9.01 2 0.000 0.557 0.00 1.00
#> TCGA.DH.A7UR.01 2 0.000 0.557 0.00 1.00
#> TCGA.DU.6400.01 1 0.000 0.830 1.00 0.00
#> TCGA.DB.A75K.01 2 0.943 0.722 0.36 0.64
#> TCGA.S9.A6WH.01 1 0.000 0.830 1.00 0.00
#> TCGA.R8.A6MO.01 2 1.000 0.648 0.50 0.50
#> TCGA.E1.5318.01 1 0.827 0.679 0.74 0.26
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.DU.8168.01 1 0.0892 0.990 0.98 0.02 0.00
#> TCGA.DU.7298.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.CS.5390.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.DB.5274.01 1 0.0892 0.990 0.98 0.02 0.00
#> TCGA.HT.8012.01 2 0.0892 0.980 0.00 0.98 0.02
#> TCGA.P5.A77W.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.QH.A65R.01 3 0.0892 0.983 0.02 0.00 0.98
#> TCGA.DU.5874.01 1 0.0892 0.990 0.98 0.02 0.00
#> TCGA.R8.A73M.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DB.A4XH.01 1 0.0000 0.983 1.00 0.00 0.00
#> TCGA.DH.5144.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.HT.7471.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.HT.A5R9.01 3 0.0000 0.991 0.00 0.00 1.00
#> TCGA.DH.A7UR.01 3 0.0000 0.991 0.00 0.00 1.00
#> TCGA.DU.6400.01 1 0.0892 0.990 0.98 0.02 0.00
#> TCGA.DB.A75K.01 2 0.0892 0.980 0.00 0.98 0.02
#> TCGA.S9.A6WH.01 1 0.0892 0.990 0.98 0.02 0.00
#> TCGA.R8.A6MO.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.E1.5318.01 1 0.0000 0.983 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.DU.8168.01 1 0.0000 0.827 1.00 0.00 0.0 0.0
#> TCGA.DU.7298.01 2 0.0000 0.680 0.00 1.00 0.0 0.0
#> TCGA.CS.5390.01 4 0.5000 -0.242 0.50 0.00 0.0 0.5
#> TCGA.DB.5274.01 2 0.4713 0.263 0.36 0.64 0.0 0.0
#> TCGA.HT.8012.01 2 0.5000 0.473 0.00 0.50 0.0 0.5
#> TCGA.P5.A77W.01 2 0.0000 0.680 0.00 1.00 0.0 0.0
#> TCGA.QH.A65R.01 4 0.5000 -0.372 0.00 0.00 0.5 0.5
#> TCGA.DU.5874.01 1 0.0000 0.827 1.00 0.00 0.0 0.0
#> TCGA.R8.A73M.01 2 0.5000 0.473 0.00 0.50 0.0 0.5
#> TCGA.DB.A4XH.01 1 0.5000 -0.208 0.50 0.00 0.0 0.5
#> TCGA.DH.5144.01 2 0.0707 0.670 0.02 0.98 0.0 0.0
#> TCGA.HT.7471.01 4 0.5000 -0.654 0.00 0.50 0.0 0.5
#> TCGA.HT.A5R9.01 3 0.0000 1.000 0.00 0.00 1.0 0.0
#> TCGA.DH.A7UR.01 3 0.0000 1.000 0.00 0.00 1.0 0.0
#> TCGA.DU.6400.01 1 0.0000 0.827 1.00 0.00 0.0 0.0
#> TCGA.DB.A75K.01 2 0.5000 0.473 0.00 0.50 0.0 0.5
#> TCGA.S9.A6WH.01 1 0.0000 0.827 1.00 0.00 0.0 0.0
#> TCGA.R8.A6MO.01 2 0.0000 0.680 0.00 1.00 0.0 0.0
#> TCGA.E1.5318.01 4 0.5000 -0.242 0.50 0.00 0.0 0.5
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.DU.8168.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7298.01 2 0.0609 0.968 0.00 0.98 0.00 0.00 0.02
#> TCGA.CS.5390.01 4 0.3878 0.903 0.12 0.02 0.00 0.82 0.04
#> TCGA.DB.5274.01 2 0.2012 0.903 0.06 0.92 0.00 0.02 0.00
#> TCGA.HT.8012.01 5 0.3946 0.932 0.00 0.08 0.00 0.12 0.80
#> TCGA.P5.A77W.01 2 0.0609 0.968 0.00 0.98 0.00 0.00 0.02
#> TCGA.QH.A65R.01 4 0.4527 0.770 0.00 0.02 0.12 0.78 0.08
#> TCGA.DU.5874.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.R8.A73M.01 5 0.1732 0.932 0.00 0.08 0.00 0.00 0.92
#> TCGA.DB.A4XH.01 4 0.2280 0.912 0.12 0.00 0.00 0.88 0.00
#> TCGA.DH.5144.01 2 0.0609 0.960 0.02 0.98 0.00 0.00 0.00
#> TCGA.HT.7471.01 5 0.1732 0.932 0.00 0.08 0.00 0.00 0.92
#> TCGA.HT.A5R9.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.DH.A7UR.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.DU.6400.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A75K.01 5 0.3946 0.932 0.00 0.08 0.00 0.12 0.80
#> TCGA.S9.A6WH.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.R8.A6MO.01 2 0.0609 0.968 0.00 0.98 0.00 0.00 0.02
#> TCGA.E1.5318.01 4 0.2280 0.912 0.12 0.00 0.00 0.88 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 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7298.01 6 0.2793 0.818 0 0.20 0.00 0.00 0.00 0.80
#> TCGA.CS.5390.01 4 0.3499 0.793 0 0.32 0.00 0.68 0.00 0.00
#> TCGA.DB.5274.01 6 0.0547 0.863 0 0.00 0.00 0.02 0.00 0.98
#> TCGA.HT.8012.01 5 0.3819 0.824 0 0.28 0.00 0.00 0.70 0.02
#> TCGA.P5.A77W.01 6 0.0000 0.873 0 0.00 0.00 0.00 0.00 1.00
#> TCGA.QH.A65R.01 4 0.3647 0.777 0 0.36 0.00 0.64 0.00 0.00
#> TCGA.DU.5874.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.R8.A73M.01 5 0.0547 0.826 0 0.00 0.00 0.00 0.98 0.02
#> TCGA.DB.A4XH.01 4 0.0000 0.799 0 0.00 0.00 1.00 0.00 0.00
#> TCGA.DH.5144.01 6 0.3647 0.714 0 0.36 0.00 0.00 0.00 0.64
#> TCGA.HT.7471.01 5 0.1480 0.810 0 0.04 0.00 0.00 0.94 0.02
#> TCGA.HT.A5R9.01 3 0.0000 0.987 0 0.00 1.00 0.00 0.00 0.00
#> TCGA.DH.A7UR.01 3 0.0547 0.987 0 0.00 0.98 0.00 0.02 0.00
#> TCGA.DU.6400.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A75K.01 5 0.3711 0.831 0 0.26 0.00 0.00 0.72 0.02
#> TCGA.S9.A6WH.01 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.R8.A6MO.01 6 0.0000 0.873 0 0.00 0.00 0.00 0.00 1.00
#> TCGA.E1.5318.01 4 0.0000 0.799 0 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.DU.8168.01 1 0.0000 0.989 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7298.01 6 0.5055 0.627 0.00 0.00 0.00 0.18 0.00 0.56 0.26
#> TCGA.CS.5390.01 4 0.4692 0.841 0.00 0.42 0.00 0.50 0.00 0.00 0.08
#> TCGA.DB.5274.01 6 0.0000 0.756 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.8012.01 7 0.3558 0.000 0.00 0.00 0.00 0.00 0.48 0.00 0.52
#> TCGA.P5.A77W.01 6 0.1166 0.753 0.00 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.QH.A65R.01 4 0.3413 0.847 0.00 0.38 0.00 0.62 0.00 0.00 0.00
#> TCGA.DU.5874.01 1 0.0000 0.989 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.R8.A73M.01 5 0.0000 0.473 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DB.A4XH.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.5144.01 6 0.5579 0.472 0.00 0.00 0.00 0.36 0.00 0.38 0.26
#> TCGA.HT.7471.01 5 0.1006 0.473 0.00 0.00 0.00 0.02 0.96 0.00 0.02
#> TCGA.HT.A5R9.01 3 0.0000 0.972 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A7UR.01 3 0.0863 0.972 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.DU.6400.01 1 0.0000 0.989 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A75K.01 5 0.3558 -0.926 0.00 0.00 0.00 0.00 0.52 0.00 0.48
#> TCGA.S9.A6WH.01 1 0.0863 0.966 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.R8.A6MO.01 6 0.0000 0.756 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.E1.5318.01 2 0.0000 1.000 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.DU.8168.01 1 0.0000 0.954 1.00 0.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7298.01 6 0.0000 0.150 0.00 0.00 0.0 0.00 0.00 1.00 0.00 0.00
#> TCGA.CS.5390.01 4 0.4559 0.873 0.00 0.30 0.0 0.60 0.00 0.00 0.08 0.02
#> TCGA.DB.5274.01 8 0.3329 1.000 0.00 0.00 0.0 0.00 0.00 0.48 0.00 0.52
#> TCGA.HT.8012.01 7 0.2534 0.720 0.00 0.00 0.0 0.00 0.22 0.00 0.78 0.00
#> TCGA.P5.A77W.01 6 0.3299 -0.874 0.00 0.00 0.0 0.00 0.00 0.56 0.00 0.44
#> TCGA.QH.A65R.01 4 0.2852 0.875 0.00 0.28 0.0 0.72 0.00 0.00 0.00 0.00
#> TCGA.DU.5874.01 1 0.0471 0.947 0.98 0.00 0.0 0.00 0.00 0.00 0.02 0.00
#> TCGA.R8.A73M.01 5 0.0000 1.000 0.00 0.00 0.0 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.A4XH.01 2 0.0000 1.000 0.00 1.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.5144.01 6 0.4050 0.258 0.00 0.00 0.0 0.06 0.00 0.60 0.00 0.34
#> TCGA.HT.7471.01 5 0.0000 1.000 0.00 0.00 0.0 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.A5R9.01 3 0.0000 0.924 0.00 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A7UR.01 3 0.1887 0.924 0.00 0.00 0.9 0.00 0.00 0.00 0.06 0.04
#> TCGA.DU.6400.01 1 0.0000 0.954 1.00 0.00 0.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A75K.01 7 0.5647 0.709 0.00 0.00 0.0 0.18 0.26 0.00 0.50 0.06
#> TCGA.S9.A6WH.01 1 0.2674 0.872 0.86 0.00 0.0 0.04 0.00 0.00 0.06 0.04
#> TCGA.R8.A6MO.01 8 0.3329 1.000 0.00 0.00 0.0 0.00 0.00 0.48 0.00 0.52
#> TCGA.E1.5318.01 2 0.0000 1.000 0.00 1.00 0.0 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node022. Child nodes: Node01211-leaf , Node01212-leaf , Node01213-leaf , Node02211 , Node02212 , Node02221 , Node02222-leaf , Node02223 , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02321-leaf , Node02322-leaf , Node02323-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 100 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 0.982 0.993 0.4998 0.500 0.500
#> 3 3 0.955 0.961 0.980 0.2938 0.649 0.418
#> 4 4 0.714 0.828 0.903 0.1367 0.759 0.439
#> 5 5 0.736 0.638 0.812 0.0788 0.913 0.685
#> 6 6 0.749 0.674 0.795 0.0411 0.900 0.573
#> 7 7 0.791 0.667 0.816 0.0271 0.954 0.755
#> 8 8 0.791 0.584 0.781 0.0231 0.967 0.806
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 2 0.000 0.9966 0.00 1.00
#> TCGA.S9.A6TX.01 1 0.999 0.0669 0.52 0.48
#> TCGA.DB.A4XA.01 2 0.000 0.9966 0.00 1.00
#> TCGA.E1.5311.01 1 0.000 0.9890 1.00 0.00
#> TCGA.HT.7620.01 2 0.000 0.9966 0.00 1.00
#> TCGA.HT.7480.01 1 0.000 0.9890 1.00 0.00
#> TCGA.HT.8109.01 2 0.680 0.7765 0.18 0.82
#> TCGA.S9.A7R1.01 1 0.000 0.9890 1.00 0.00
#> TCGA.HW.7486.01 2 0.000 0.9966 0.00 1.00
#> TCGA.FG.7634.01 2 0.000 0.9966 0.00 1.00
#> TCGA.HT.7605.01 2 0.000 0.9966 0.00 1.00
#> TCGA.HT.7608.01 2 0.000 0.9966 0.00 1.00
#> TCGA.W9.A837.01 2 0.000 0.9966 0.00 1.00
#> TCGA.TM.A7C5.01 1 0.000 0.9890 1.00 0.00
#> TCGA.P5.A5ET.01 2 0.000 0.9966 0.00 1.00
#> TCGA.FG.A6IZ.01 1 0.000 0.9890 1.00 0.00
#> TCGA.KT.A74X.01 2 0.000 0.9966 0.00 1.00
#> TCGA.E1.A7YO.01 1 0.000 0.9890 1.00 0.00
#> TCGA.TQ.A7RG.01 2 0.000 0.9966 0.00 1.00
#> TCGA.RY.A847.01 2 0.000 0.9966 0.00 1.00
#> TCGA.VM.A8CA.01 2 0.000 0.9966 0.00 1.00
#> TCGA.DB.A4XG.01 1 0.000 0.9890 1.00 0.00
#> TCGA.HT.7856.01 2 0.000 0.9966 0.00 1.00
#> TCGA.S9.A6TY.01 1 0.000 0.9890 1.00 0.00
#> TCGA.IK.8125.01 1 0.000 0.9890 1.00 0.00
#> TCGA.HT.7467.01 2 0.000 0.9966 0.00 1.00
#> TCGA.TQ.A7RN.01 2 0.000 0.9966 0.00 1.00
#> TCGA.DH.5141.01 2 0.000 0.9966 0.00 1.00
#> TCGA.S9.A6WP.01 1 0.000 0.9890 1.00 0.00
#> TCGA.DB.5278.01 2 0.000 0.9966 0.00 1.00
#> TCGA.E1.A7YS.01 1 0.000 0.9890 1.00 0.00
#> TCGA.HT.7881.01 2 0.000 0.9966 0.00 1.00
#> TCGA.FG.7637.01 2 0.000 0.9966 0.00 1.00
#> TCGA.VM.A8CE.01 2 0.000 0.9966 0.00 1.00
#> TCGA.S9.A6U5.01 2 0.000 0.9966 0.00 1.00
#> TCGA.HW.7487.01 2 0.000 0.9966 0.00 1.00
#> TCGA.HW.7491.01 1 0.000 0.9890 1.00 0.00
#> TCGA.TM.A84R.01 2 0.000 0.9966 0.00 1.00
#> TCGA.FG.8187.01 2 0.000 0.9966 0.00 1.00
#> TCGA.S9.A7QZ.01 1 0.000 0.9890 1.00 0.00
#> TCGA.QH.A6X4.01 2 0.000 0.9966 0.00 1.00
#> TCGA.DU.A7TG.01 2 0.000 0.9966 0.00 1.00
#> TCGA.S9.A6TW.01 2 0.000 0.9966 0.00 1.00
#> TCGA.HT.7481.01 2 0.000 0.9966 0.00 1.00
#> TCGA.HT.7875.01 2 0.000 0.9966 0.00 1.00
#> TCGA.DU.6394.01 1 0.000 0.9890 1.00 0.00
#> TCGA.S9.A6WD.01 1 0.000 0.9890 1.00 0.00
#> TCGA.TQ.A7RU.01 1 0.000 0.9890 1.00 0.00
#> TCGA.S9.A6WE.01 2 0.000 0.9966 0.00 1.00
#> TCGA.R8.A6MK.01 2 0.000 0.9966 0.00 1.00
#> TCGA.QH.A6CY.01 2 0.000 0.9966 0.00 1.00
#> TCGA.S9.A7J1.01 2 0.000 0.9966 0.00 1.00
#> TCGA.P5.A5F0.01 2 0.000 0.9966 0.00 1.00
#> TCGA.DU.A6S3.01 1 0.000 0.9890 1.00 0.00
#> TCGA.DU.8164.01 1 0.000 0.9890 1.00 0.00
#> TCGA.DU.5849.01 2 0.000 0.9966 0.00 1.00
#> TCGA.HT.7468.01 1 0.000 0.9890 1.00 0.00
#> TCGA.DB.5279.01 1 0.000 0.9890 1.00 0.00
#> TCGA.HT.7677.01 1 0.000 0.9890 1.00 0.00
#> TCGA.HT.7694.01 2 0.000 0.9966 0.00 1.00
#> TCGA.TM.A84M.01 1 0.000 0.9890 1.00 0.00
#> TCGA.F6.A8O3.01 2 0.000 0.9966 0.00 1.00
#> TCGA.QH.A86X.01 2 0.000 0.9966 0.00 1.00
#> TCGA.DU.A76R.01 2 0.000 0.9966 0.00 1.00
#> TCGA.DB.A64V.01 2 0.000 0.9966 0.00 1.00
#> TCGA.RY.A840.01 1 0.000 0.9890 1.00 0.00
#> TCGA.HW.A5KJ.01 1 0.000 0.9890 1.00 0.00
#> TCGA.HT.8105.01 1 0.000 0.9890 1.00 0.00
#> TCGA.HT.A619.01 1 0.000 0.9890 1.00 0.00
#> TCGA.FG.5964.01 2 0.000 0.9966 0.00 1.00
#> TCGA.S9.A6WL.01 1 0.000 0.9890 1.00 0.00
#> TCGA.P5.A737.01 1 0.000 0.9890 1.00 0.00
#> TCGA.HT.7616.01 1 0.000 0.9890 1.00 0.00
#> TCGA.RY.A83Y.01 1 0.000 0.9890 1.00 0.00
#> TCGA.HW.8322.01 2 0.000 0.9966 0.00 1.00
#> TCGA.HT.7692.01 2 0.000 0.9966 0.00 1.00
#> TCGA.R8.A6ML.01 1 0.000 0.9890 1.00 0.00
#> TCGA.DU.6410.01 1 0.000 0.9890 1.00 0.00
#> TCGA.TQ.A7RO.01 2 0.000 0.9966 0.00 1.00
#> TCGA.TM.A84S.01 2 0.000 0.9966 0.00 1.00
#> TCGA.QH.A65Z.01 1 0.000 0.9890 1.00 0.00
#> TCGA.P5.A730.01 2 0.000 0.9966 0.00 1.00
#> TCGA.S9.A6UB.01 1 0.000 0.9890 1.00 0.00
#> TCGA.DH.A66F.01 1 0.000 0.9890 1.00 0.00
#> TCGA.DU.6393.01 1 0.000 0.9890 1.00 0.00
#> TCGA.S9.A7IY.01 2 0.000 0.9966 0.00 1.00
#> TCGA.FG.7641.01 2 0.000 0.9966 0.00 1.00
#> TCGA.DH.A7US.01 2 0.000 0.9966 0.00 1.00
#> TCGA.VV.A829.01 1 0.000 0.9890 1.00 0.00
#> TCGA.DU.6397.02 1 0.000 0.9890 1.00 0.00
#> TCGA.DU.6397.01 2 0.000 0.9966 0.00 1.00
#> TCGA.CS.6670.01 2 0.000 0.9966 0.00 1.00
#> TCGA.DB.A64P.01 1 0.000 0.9890 1.00 0.00
#> TCGA.QH.A6CZ.01 2 0.000 0.9966 0.00 1.00
#> TCGA.DH.A669.02 1 0.000 0.9890 1.00 0.00
#> TCGA.DH.A669.01 1 0.000 0.9890 1.00 0.00
#> TCGA.VM.A8CB.01 2 0.000 0.9966 0.00 1.00
#> TCGA.HT.7687.01 1 0.000 0.9890 1.00 0.00
#> TCGA.CS.5394.01 1 0.000 0.9890 1.00 0.00
#> TCGA.FG.5962.01 1 0.000 0.9890 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 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.S9.A6TX.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.DB.A4XA.01 3 0.0000 0.976 0.00 0.00 1.00
#> TCGA.E1.5311.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.HT.7620.01 3 0.0000 0.976 0.00 0.00 1.00
#> TCGA.HT.7480.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.HT.8109.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.S9.A7R1.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.HW.7486.01 3 0.0000 0.976 0.00 0.00 1.00
#> TCGA.FG.7634.01 3 0.0000 0.976 0.00 0.00 1.00
#> TCGA.HT.7605.01 3 0.0000 0.976 0.00 0.00 1.00
#> TCGA.HT.7608.01 2 0.0892 0.949 0.00 0.98 0.02
#> TCGA.W9.A837.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.TM.A7C5.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.P5.A5ET.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.FG.A6IZ.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.KT.A74X.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.E1.A7YO.01 2 0.4796 0.752 0.22 0.78 0.00
#> TCGA.TQ.A7RG.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.RY.A847.01 3 0.0000 0.976 0.00 0.00 1.00
#> TCGA.VM.A8CA.01 3 0.3686 0.861 0.00 0.14 0.86
#> TCGA.DB.A4XG.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.HT.7856.01 3 0.0000 0.976 0.00 0.00 1.00
#> TCGA.S9.A6TY.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.IK.8125.01 2 0.3686 0.846 0.14 0.86 0.00
#> TCGA.HT.7467.01 3 0.0000 0.976 0.00 0.00 1.00
#> TCGA.TQ.A7RN.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.DH.5141.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.S9.A6WP.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.DB.5278.01 3 0.0000 0.976 0.00 0.00 1.00
#> TCGA.E1.A7YS.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.HT.7881.01 3 0.0000 0.976 0.00 0.00 1.00
#> TCGA.FG.7637.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.VM.A8CE.01 3 0.0000 0.976 0.00 0.00 1.00
#> TCGA.S9.A6U5.01 3 0.0000 0.976 0.00 0.00 1.00
#> TCGA.HW.7487.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.HW.7491.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.TM.A84R.01 3 0.0000 0.976 0.00 0.00 1.00
#> TCGA.FG.8187.01 3 0.0000 0.976 0.00 0.00 1.00
#> TCGA.S9.A7QZ.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.QH.A6X4.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.DU.A7TG.01 3 0.0000 0.976 0.00 0.00 1.00
#> TCGA.S9.A6TW.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.HT.7481.01 3 0.0000 0.976 0.00 0.00 1.00
#> TCGA.HT.7875.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.DU.6394.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.S9.A6WD.01 2 0.4796 0.752 0.22 0.78 0.00
#> TCGA.TQ.A7RU.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.S9.A6WE.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.R8.A6MK.01 3 0.2066 0.939 0.00 0.06 0.94
#> TCGA.QH.A6CY.01 3 0.0000 0.976 0.00 0.00 1.00
#> TCGA.S9.A7J1.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.P5.A5F0.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.DU.A6S3.01 2 0.4555 0.777 0.20 0.80 0.00
#> TCGA.DU.8164.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.DU.5849.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.HT.7468.01 2 0.0892 0.951 0.02 0.98 0.00
#> TCGA.DB.5279.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.HT.7677.01 2 0.5016 0.724 0.24 0.76 0.00
#> TCGA.HT.7694.01 3 0.2537 0.925 0.00 0.08 0.92
#> TCGA.TM.A84M.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.F6.A8O3.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.QH.A86X.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.DU.A76R.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.DB.A64V.01 3 0.2537 0.925 0.00 0.08 0.92
#> TCGA.RY.A840.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.HW.A5KJ.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.HT.8105.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.HT.A619.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.FG.5964.01 3 0.2537 0.925 0.00 0.08 0.92
#> TCGA.S9.A6WL.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.P5.A737.01 2 0.4002 0.824 0.16 0.84 0.00
#> TCGA.HT.7616.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.RY.A83Y.01 2 0.5016 0.724 0.24 0.76 0.00
#> TCGA.HW.8322.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.HT.7692.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.R8.A6ML.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.DU.6410.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.TQ.A7RO.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.TM.A84S.01 3 0.0000 0.976 0.00 0.00 1.00
#> TCGA.QH.A65Z.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.P5.A730.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.S9.A6UB.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.DH.A66F.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.DU.6393.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.S9.A7IY.01 3 0.0000 0.976 0.00 0.00 1.00
#> TCGA.FG.7641.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.DH.A7US.01 3 0.2537 0.925 0.00 0.08 0.92
#> TCGA.VV.A829.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.DU.6397.02 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.DU.6397.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.CS.6670.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.DB.A64P.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.QH.A6CZ.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.DH.A669.02 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.DH.A669.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.VM.A8CB.01 2 0.0000 0.966 0.00 1.00 0.00
#> TCGA.HT.7687.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.CS.5394.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.FG.5962.01 2 0.0000 0.966 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.A7J2.01 2 0.164 0.830 0.00 0.94 0.00 0.06
#> TCGA.S9.A6TX.01 4 0.485 0.122 0.00 0.40 0.00 0.60
#> TCGA.DB.A4XA.01 3 0.361 0.857 0.00 0.20 0.80 0.00
#> TCGA.E1.5311.01 4 0.000 0.865 0.00 0.00 0.00 1.00
#> TCGA.HT.7620.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.HT.7480.01 4 0.317 0.713 0.00 0.16 0.00 0.84
#> TCGA.HT.8109.01 4 0.413 0.527 0.00 0.26 0.00 0.74
#> TCGA.S9.A7R1.01 4 0.000 0.865 0.00 0.00 0.00 1.00
#> TCGA.HW.7486.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.FG.7634.01 3 0.361 0.857 0.00 0.20 0.80 0.00
#> TCGA.HT.7605.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.HT.7608.01 2 0.000 0.816 0.00 1.00 0.00 0.00
#> TCGA.W9.A837.01 2 0.000 0.816 0.00 1.00 0.00 0.00
#> TCGA.TM.A7C5.01 4 0.292 0.798 0.14 0.00 0.00 0.86
#> TCGA.P5.A5ET.01 2 0.000 0.816 0.00 1.00 0.00 0.00
#> TCGA.FG.A6IZ.01 1 0.000 0.983 1.00 0.00 0.00 0.00
#> TCGA.KT.A74X.01 2 0.380 0.816 0.00 0.78 0.00 0.22
#> TCGA.E1.A7YO.01 4 0.000 0.865 0.00 0.00 0.00 1.00
#> TCGA.TQ.A7RG.01 2 0.000 0.816 0.00 1.00 0.00 0.00
#> TCGA.RY.A847.01 3 0.380 0.837 0.00 0.22 0.78 0.00
#> TCGA.VM.A8CA.01 2 0.000 0.816 0.00 1.00 0.00 0.00
#> TCGA.DB.A4XG.01 4 0.380 0.723 0.22 0.00 0.00 0.78
#> TCGA.HT.7856.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.S9.A6TY.01 4 0.317 0.781 0.16 0.00 0.00 0.84
#> TCGA.IK.8125.01 4 0.000 0.865 0.00 0.00 0.00 1.00
#> TCGA.HT.7467.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.TQ.A7RN.01 2 0.000 0.816 0.00 1.00 0.00 0.00
#> TCGA.DH.5141.01 2 0.265 0.834 0.00 0.88 0.00 0.12
#> TCGA.S9.A6WP.01 4 0.380 0.723 0.22 0.00 0.00 0.78
#> TCGA.DB.5278.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.E1.A7YS.01 1 0.000 0.983 1.00 0.00 0.00 0.00
#> TCGA.HT.7881.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.FG.7637.01 2 0.380 0.816 0.00 0.78 0.00 0.22
#> TCGA.VM.A8CE.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.S9.A6U5.01 3 0.361 0.857 0.00 0.20 0.80 0.00
#> TCGA.HW.7487.01 2 0.398 0.796 0.00 0.76 0.00 0.24
#> TCGA.HW.7491.01 4 0.265 0.812 0.12 0.00 0.00 0.88
#> TCGA.TM.A84R.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.FG.8187.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.S9.A7QZ.01 4 0.380 0.723 0.22 0.00 0.00 0.78
#> TCGA.QH.A6X4.01 2 0.361 0.830 0.00 0.80 0.00 0.20
#> TCGA.DU.A7TG.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.S9.A6TW.01 2 0.000 0.816 0.00 1.00 0.00 0.00
#> TCGA.HT.7481.01 3 0.000 0.922 0.00 0.00 1.00 0.00
#> TCGA.HT.7875.01 2 0.361 0.830 0.00 0.80 0.00 0.20
#> TCGA.DU.6394.01 1 0.000 0.983 1.00 0.00 0.00 0.00
#> TCGA.S9.A6WD.01 4 0.000 0.865 0.00 0.00 0.00 1.00
#> TCGA.TQ.A7RU.01 1 0.265 0.860 0.88 0.00 0.00 0.12
#> TCGA.S9.A6WE.01 2 0.000 0.816 0.00 1.00 0.00 0.00
#> TCGA.R8.A6MK.01 2 0.234 0.724 0.00 0.90 0.10 0.00
#> TCGA.QH.A6CY.01 3 0.340 0.868 0.00 0.18 0.82 0.00
#> TCGA.S9.A7J1.01 2 0.000 0.816 0.00 1.00 0.00 0.00
#> TCGA.P5.A5F0.01 2 0.361 0.830 0.00 0.80 0.00 0.20
#> TCGA.DU.A6S3.01 4 0.000 0.865 0.00 0.00 0.00 1.00
#> TCGA.DU.8164.01 1 0.000 0.983 1.00 0.00 0.00 0.00
#> TCGA.DU.5849.01 2 0.000 0.816 0.00 1.00 0.00 0.00
#> TCGA.HT.7468.01 4 0.000 0.865 0.00 0.00 0.00 1.00
#> TCGA.DB.5279.01 4 0.380 0.723 0.22 0.00 0.00 0.78
#> TCGA.HT.7677.01 4 0.000 0.865 0.00 0.00 0.00 1.00
#> TCGA.HT.7694.01 2 0.471 0.236 0.00 0.64 0.36 0.00
#> TCGA.TM.A84M.01 4 0.201 0.836 0.08 0.00 0.00 0.92
#> TCGA.F6.A8O3.01 2 0.380 0.816 0.00 0.78 0.00 0.22
#> TCGA.QH.A86X.01 2 0.000 0.816 0.00 1.00 0.00 0.00
#> TCGA.DU.A76R.01 2 0.361 0.830 0.00 0.80 0.00 0.20
#> TCGA.DB.A64V.01 2 0.441 0.395 0.00 0.70 0.30 0.00
#> TCGA.RY.A840.01 4 0.265 0.761 0.00 0.12 0.00 0.88
#> TCGA.HW.A5KJ.01 1 0.000 0.983 1.00 0.00 0.00 0.00
#> TCGA.HT.8105.01 1 0.000 0.983 1.00 0.00 0.00 0.00
#> TCGA.HT.A619.01 1 0.000 0.983 1.00 0.00 0.00 0.00
#> TCGA.FG.5964.01 2 0.471 0.236 0.00 0.64 0.36 0.00
#> TCGA.S9.A6WL.01 1 0.000 0.983 1.00 0.00 0.00 0.00
#> TCGA.P5.A737.01 4 0.000 0.865 0.00 0.00 0.00 1.00
#> TCGA.HT.7616.01 4 0.380 0.723 0.22 0.00 0.00 0.78
#> TCGA.RY.A83Y.01 4 0.000 0.865 0.00 0.00 0.00 1.00
#> TCGA.HW.8322.01 2 0.361 0.830 0.00 0.80 0.00 0.20
#> TCGA.HT.7692.01 2 0.361 0.830 0.00 0.80 0.00 0.20
#> TCGA.R8.A6ML.01 4 0.201 0.836 0.08 0.00 0.00 0.92
#> TCGA.DU.6410.01 1 0.000 0.983 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RO.01 2 0.361 0.830 0.00 0.80 0.00 0.20
#> TCGA.TM.A84S.01 3 0.361 0.857 0.00 0.20 0.80 0.00
#> TCGA.QH.A65Z.01 1 0.265 0.860 0.88 0.00 0.00 0.12
#> TCGA.P5.A730.01 2 0.380 0.816 0.00 0.78 0.00 0.22
#> TCGA.S9.A6UB.01 1 0.000 0.983 1.00 0.00 0.00 0.00
#> TCGA.DH.A66F.01 4 0.000 0.865 0.00 0.00 0.00 1.00
#> TCGA.DU.6393.01 1 0.000 0.983 1.00 0.00 0.00 0.00
#> TCGA.S9.A7IY.01 3 0.340 0.868 0.00 0.18 0.82 0.00
#> TCGA.FG.7641.01 2 0.361 0.830 0.00 0.80 0.00 0.20
#> TCGA.DH.A7US.01 2 0.380 0.555 0.00 0.78 0.22 0.00
#> TCGA.VV.A829.01 4 0.380 0.723 0.22 0.00 0.00 0.78
#> TCGA.DU.6397.02 4 0.340 0.682 0.00 0.18 0.00 0.82
#> TCGA.DU.6397.01 2 0.361 0.830 0.00 0.80 0.00 0.20
#> TCGA.CS.6670.01 2 0.361 0.830 0.00 0.80 0.00 0.20
#> TCGA.DB.A64P.01 4 0.000 0.865 0.00 0.00 0.00 1.00
#> TCGA.QH.A6CZ.01 2 0.361 0.830 0.00 0.80 0.00 0.20
#> TCGA.DH.A669.02 1 0.000 0.983 1.00 0.00 0.00 0.00
#> TCGA.DH.A669.01 1 0.000 0.983 1.00 0.00 0.00 0.00
#> TCGA.VM.A8CB.01 2 0.380 0.816 0.00 0.78 0.00 0.22
#> TCGA.HT.7687.01 1 0.000 0.983 1.00 0.00 0.00 0.00
#> TCGA.CS.5394.01 1 0.000 0.983 1.00 0.00 0.00 0.00
#> TCGA.FG.5962.01 4 0.000 0.865 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 2 0.104 0.7180 0.00 0.96 0.00 0.04 0.00
#> TCGA.S9.A6TX.01 4 0.635 0.2952 0.00 0.16 0.00 0.42 0.42
#> TCGA.DB.A4XA.01 5 0.518 -0.2558 0.00 0.04 0.48 0.00 0.48
#> TCGA.E1.5311.01 4 0.454 0.6221 0.00 0.02 0.00 0.64 0.34
#> TCGA.HT.7620.01 3 0.000 0.8786 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7480.01 4 0.620 0.3679 0.00 0.16 0.00 0.52 0.32
#> TCGA.HT.8109.01 5 0.454 -0.0951 0.00 0.02 0.00 0.34 0.64
#> TCGA.S9.A7R1.01 4 0.202 0.8270 0.00 0.00 0.00 0.90 0.10
#> TCGA.HW.7486.01 3 0.000 0.8786 0.00 0.00 1.00 0.00 0.00
#> TCGA.FG.7634.01 3 0.453 0.6895 0.00 0.04 0.70 0.00 0.26
#> TCGA.HT.7605.01 3 0.104 0.8652 0.00 0.00 0.96 0.00 0.04
#> TCGA.HT.7608.01 5 0.431 0.2291 0.00 0.50 0.00 0.00 0.50
#> TCGA.W9.A837.01 5 0.429 0.2578 0.00 0.46 0.00 0.00 0.54
#> TCGA.TM.A7C5.01 4 0.104 0.8295 0.04 0.00 0.00 0.96 0.00
#> TCGA.P5.A5ET.01 2 0.000 0.6961 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.A6IZ.01 1 0.000 0.9508 1.00 0.00 0.00 0.00 0.00
#> TCGA.KT.A74X.01 2 0.485 0.6077 0.00 0.68 0.00 0.06 0.26
#> TCGA.E1.A7YO.01 4 0.202 0.8270 0.00 0.00 0.00 0.90 0.10
#> TCGA.TQ.A7RG.01 2 0.104 0.6568 0.00 0.96 0.00 0.00 0.04
#> TCGA.RY.A847.01 5 0.618 0.0207 0.00 0.14 0.38 0.00 0.48
#> TCGA.VM.A8CA.01 2 0.431 -0.3074 0.00 0.50 0.00 0.00 0.50
#> TCGA.DB.A4XG.01 4 0.275 0.8049 0.08 0.00 0.00 0.88 0.04
#> TCGA.HT.7856.01 3 0.000 0.8786 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6TY.01 4 0.141 0.8243 0.06 0.00 0.00 0.94 0.00
#> TCGA.IK.8125.01 4 0.311 0.8202 0.00 0.00 0.00 0.80 0.20
#> TCGA.HT.7467.01 3 0.000 0.8786 0.00 0.00 1.00 0.00 0.00
#> TCGA.TQ.A7RN.01 2 0.000 0.6961 0.00 1.00 0.00 0.00 0.00
#> TCGA.DH.5141.01 5 0.483 -0.1923 0.00 0.48 0.00 0.02 0.50
#> TCGA.S9.A6WP.01 4 0.141 0.8243 0.06 0.00 0.00 0.94 0.00
#> TCGA.DB.5278.01 3 0.000 0.8786 0.00 0.00 1.00 0.00 0.00
#> TCGA.E1.A7YS.01 1 0.000 0.9508 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7881.01 3 0.000 0.8786 0.00 0.00 1.00 0.00 0.00
#> TCGA.FG.7637.01 2 0.426 0.6551 0.00 0.76 0.00 0.06 0.18
#> TCGA.VM.A8CE.01 3 0.000 0.8786 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6U5.01 3 0.440 0.7111 0.00 0.04 0.72 0.00 0.24
#> TCGA.HW.7487.01 5 0.573 0.1318 0.00 0.22 0.00 0.16 0.62
#> TCGA.HW.7491.01 4 0.104 0.8295 0.04 0.00 0.00 0.96 0.00
#> TCGA.TM.A84R.01 3 0.000 0.8786 0.00 0.00 1.00 0.00 0.00
#> TCGA.FG.8187.01 3 0.252 0.8140 0.00 0.00 0.86 0.00 0.14
#> TCGA.S9.A7QZ.01 4 0.201 0.8216 0.06 0.00 0.00 0.92 0.02
#> TCGA.QH.A6X4.01 2 0.104 0.7180 0.00 0.96 0.00 0.04 0.00
#> TCGA.DU.A7TG.01 3 0.000 0.8786 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6TW.01 5 0.400 0.3020 0.00 0.24 0.00 0.02 0.74
#> TCGA.HT.7481.01 3 0.000 0.8786 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.7875.01 2 0.104 0.7180 0.00 0.96 0.00 0.04 0.00
#> TCGA.DU.6394.01 1 0.000 0.9508 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WD.01 4 0.293 0.8188 0.00 0.00 0.00 0.82 0.18
#> TCGA.TQ.A7RU.01 1 0.398 0.5569 0.66 0.00 0.00 0.34 0.00
#> TCGA.S9.A6WE.01 2 0.141 0.6283 0.00 0.94 0.00 0.00 0.06
#> TCGA.R8.A6MK.01 5 0.518 0.2735 0.00 0.48 0.04 0.00 0.48
#> TCGA.QH.A6CY.01 3 0.453 0.6895 0.00 0.04 0.70 0.00 0.26
#> TCGA.S9.A7J1.01 2 0.426 -0.1976 0.00 0.56 0.00 0.00 0.44
#> TCGA.P5.A5F0.01 5 0.483 -0.1923 0.00 0.48 0.00 0.02 0.50
#> TCGA.DU.A6S3.01 4 0.293 0.8188 0.00 0.00 0.00 0.82 0.18
#> TCGA.DU.8164.01 1 0.141 0.9054 0.94 0.00 0.00 0.06 0.00
#> TCGA.DU.5849.01 5 0.400 0.3020 0.00 0.24 0.00 0.02 0.74
#> TCGA.HT.7468.01 4 0.293 0.8187 0.00 0.00 0.00 0.82 0.18
#> TCGA.DB.5279.01 4 0.364 0.8012 0.06 0.00 0.00 0.82 0.12
#> TCGA.HT.7677.01 4 0.173 0.8315 0.00 0.00 0.00 0.92 0.08
#> TCGA.HT.7694.01 5 0.597 0.2747 0.00 0.14 0.30 0.00 0.56
#> TCGA.TM.A84M.01 4 0.262 0.8146 0.02 0.00 0.00 0.88 0.10
#> TCGA.F6.A8O3.01 2 0.485 0.6077 0.00 0.68 0.00 0.06 0.26
#> TCGA.QH.A86X.01 2 0.104 0.6568 0.00 0.96 0.00 0.00 0.04
#> TCGA.DU.A76R.01 5 0.483 -0.1923 0.00 0.48 0.00 0.02 0.50
#> TCGA.DB.A64V.01 5 0.620 0.3107 0.00 0.18 0.28 0.00 0.54
#> TCGA.RY.A840.01 4 0.550 0.5517 0.00 0.08 0.00 0.58 0.34
#> TCGA.HW.A5KJ.01 1 0.000 0.9508 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8105.01 1 0.000 0.9508 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A619.01 1 0.000 0.9508 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.5964.01 5 0.613 0.2692 0.00 0.16 0.30 0.00 0.54
#> TCGA.S9.A6WL.01 1 0.000 0.9508 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A737.01 4 0.141 0.8238 0.00 0.00 0.00 0.94 0.06
#> TCGA.HT.7616.01 4 0.280 0.8217 0.06 0.00 0.00 0.88 0.06
#> TCGA.RY.A83Y.01 4 0.202 0.8326 0.00 0.00 0.00 0.90 0.10
#> TCGA.HW.8322.01 2 0.104 0.7180 0.00 0.96 0.00 0.04 0.00
#> TCGA.HT.7692.01 2 0.104 0.7180 0.00 0.96 0.00 0.04 0.00
#> TCGA.R8.A6ML.01 4 0.208 0.8230 0.04 0.00 0.00 0.92 0.04
#> TCGA.DU.6410.01 1 0.000 0.9508 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RO.01 2 0.473 0.6186 0.00 0.70 0.00 0.06 0.24
#> TCGA.TM.A84S.01 3 0.453 0.6895 0.00 0.04 0.70 0.00 0.26
#> TCGA.QH.A65Z.01 1 0.398 0.5569 0.66 0.00 0.00 0.34 0.00
#> TCGA.P5.A730.01 2 0.485 0.6077 0.00 0.68 0.00 0.06 0.26
#> TCGA.S9.A6UB.01 1 0.000 0.9508 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A66F.01 4 0.287 0.8107 0.00 0.02 0.00 0.86 0.12
#> TCGA.DU.6393.01 1 0.000 0.9508 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IY.01 3 0.440 0.7111 0.00 0.04 0.72 0.00 0.24
#> TCGA.FG.7641.01 2 0.454 0.5049 0.00 0.64 0.00 0.02 0.34
#> TCGA.DH.A7US.01 5 0.569 0.3190 0.00 0.44 0.08 0.00 0.48
#> TCGA.VV.A829.01 4 0.364 0.8012 0.06 0.00 0.00 0.82 0.12
#> TCGA.DU.6397.02 5 0.606 -0.4344 0.00 0.12 0.00 0.42 0.46
#> TCGA.DU.6397.01 2 0.453 0.6056 0.00 0.70 0.00 0.04 0.26
#> TCGA.CS.6670.01 2 0.443 0.6477 0.00 0.74 0.00 0.06 0.20
#> TCGA.DB.A64P.01 4 0.413 0.6814 0.00 0.02 0.00 0.72 0.26
#> TCGA.QH.A6CZ.01 2 0.104 0.7180 0.00 0.96 0.00 0.04 0.00
#> TCGA.DH.A669.02 1 0.000 0.9508 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A669.01 1 0.000 0.9508 1.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8CB.01 2 0.392 0.6690 0.00 0.78 0.00 0.04 0.18
#> TCGA.HT.7687.01 1 0.000 0.9508 1.00 0.00 0.00 0.00 0.00
#> TCGA.CS.5394.01 1 0.000 0.9508 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.5962.01 4 0.293 0.8188 0.00 0.00 0.00 0.82 0.18
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.S9.A7J2.01 2 0.0000 0.876 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TX.01 6 0.4361 0.575 0.00 0.04 0.00 0.14 0.06 0.76
#> TCGA.DB.A4XA.01 5 0.4002 0.287 0.00 0.02 0.32 0.00 0.66 0.00
#> TCGA.E1.5311.01 6 0.3706 0.165 0.00 0.00 0.00 0.38 0.00 0.62
#> TCGA.HT.7620.01 3 0.0000 0.797 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7480.01 6 0.4834 0.468 0.00 0.10 0.00 0.26 0.00 0.64
#> TCGA.HT.8109.01 6 0.4667 0.549 0.00 0.04 0.00 0.10 0.12 0.74
#> TCGA.S9.A7R1.01 4 0.2941 0.726 0.00 0.00 0.00 0.78 0.00 0.22
#> TCGA.HW.7486.01 3 0.0000 0.797 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.7634.01 3 0.3851 0.348 0.00 0.00 0.54 0.00 0.46 0.00
#> TCGA.HT.7605.01 3 0.3198 0.629 0.00 0.00 0.74 0.00 0.26 0.00
#> TCGA.HT.7608.01 5 0.3499 0.602 0.00 0.32 0.00 0.00 0.68 0.00
#> TCGA.W9.A837.01 5 0.5628 0.514 0.00 0.22 0.00 0.00 0.54 0.24
#> TCGA.TM.A7C5.01 4 0.1807 0.794 0.00 0.00 0.00 0.92 0.06 0.02
#> TCGA.P5.A5ET.01 2 0.0547 0.869 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.FG.A6IZ.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KT.A74X.01 6 0.3797 0.456 0.00 0.42 0.00 0.00 0.00 0.58
#> TCGA.E1.A7YO.01 4 0.2260 0.786 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.TQ.A7RG.01 2 0.1267 0.840 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.RY.A847.01 5 0.4462 0.369 0.00 0.06 0.28 0.00 0.66 0.00
#> TCGA.VM.A8CA.01 5 0.3499 0.602 0.00 0.32 0.00 0.00 0.68 0.00
#> TCGA.DB.A4XG.01 4 0.3324 0.778 0.02 0.00 0.00 0.84 0.08 0.06
#> TCGA.HT.7856.01 3 0.0000 0.797 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6TY.01 4 0.1092 0.802 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.IK.8125.01 4 0.3787 0.772 0.00 0.00 0.00 0.78 0.10 0.12
#> TCGA.HT.7467.01 3 0.0000 0.797 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RN.01 2 0.0547 0.869 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.DH.5141.01 6 0.5173 0.537 0.00 0.20 0.00 0.00 0.18 0.62
#> TCGA.S9.A6WP.01 4 0.1480 0.802 0.02 0.00 0.00 0.94 0.04 0.00
#> TCGA.DB.5278.01 3 0.0000 0.797 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YS.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7881.01 3 0.0000 0.797 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.7637.01 2 0.2941 0.598 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.VM.A8CE.01 3 0.0000 0.797 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6U5.01 3 0.3828 0.394 0.00 0.00 0.56 0.00 0.44 0.00
#> TCGA.HW.7487.01 6 0.4733 0.562 0.00 0.06 0.00 0.08 0.12 0.74
#> TCGA.HW.7491.01 4 0.1865 0.795 0.00 0.00 0.00 0.92 0.04 0.04
#> TCGA.TM.A84R.01 3 0.0000 0.797 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FG.8187.01 3 0.3647 0.516 0.00 0.00 0.64 0.00 0.36 0.00
#> TCGA.S9.A7QZ.01 4 0.2629 0.803 0.02 0.00 0.00 0.88 0.08 0.02
#> TCGA.QH.A6X4.01 2 0.0000 0.876 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A7TG.01 3 0.0000 0.797 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6TW.01 5 0.5110 0.202 0.00 0.08 0.00 0.00 0.48 0.44
#> TCGA.HT.7481.01 3 0.0000 0.797 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7875.01 2 0.0000 0.876 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6394.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WD.01 4 0.3163 0.787 0.00 0.00 0.00 0.82 0.04 0.14
#> TCGA.TQ.A7RU.01 4 0.5049 0.471 0.30 0.00 0.00 0.62 0.06 0.02
#> TCGA.S9.A6WE.01 2 0.1267 0.840 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.R8.A6MK.01 5 0.3499 0.602 0.00 0.32 0.00 0.00 0.68 0.00
#> TCGA.QH.A6CY.01 3 0.3864 0.295 0.00 0.00 0.52 0.00 0.48 0.00
#> TCGA.S9.A7J1.01 5 0.5692 0.517 0.00 0.32 0.00 0.00 0.50 0.18
#> TCGA.P5.A5F0.01 6 0.5173 0.537 0.00 0.20 0.00 0.00 0.18 0.62
#> TCGA.DU.A6S3.01 4 0.3523 0.775 0.00 0.00 0.00 0.78 0.04 0.18
#> TCGA.DU.8164.01 1 0.2020 0.944 0.92 0.00 0.00 0.02 0.04 0.02
#> TCGA.DU.5849.01 5 0.5295 0.148 0.00 0.10 0.00 0.00 0.46 0.44
#> TCGA.HT.7468.01 4 0.4723 0.723 0.00 0.00 0.00 0.68 0.14 0.18
#> TCGA.DB.5279.01 4 0.5027 0.681 0.00 0.00 0.00 0.64 0.20 0.16
#> TCGA.HT.7677.01 4 0.1267 0.804 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.HT.7694.01 5 0.5855 0.621 0.00 0.06 0.14 0.00 0.62 0.18
#> TCGA.TM.A84M.01 4 0.4566 0.702 0.00 0.00 0.00 0.70 0.16 0.14
#> TCGA.F6.A8O3.01 6 0.3756 0.473 0.00 0.40 0.00 0.00 0.00 0.60
#> TCGA.QH.A86X.01 2 0.1556 0.821 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.DU.A76R.01 6 0.5173 0.537 0.00 0.20 0.00 0.00 0.18 0.62
#> TCGA.DB.A64V.01 5 0.5855 0.621 0.00 0.06 0.14 0.00 0.62 0.18
#> TCGA.RY.A840.01 6 0.5996 0.371 0.00 0.10 0.00 0.16 0.12 0.62
#> TCGA.HW.A5KJ.01 1 0.0547 0.980 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.HT.8105.01 1 0.0547 0.980 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.HT.A619.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.5964.01 5 0.5855 0.621 0.00 0.06 0.14 0.00 0.62 0.18
#> TCGA.S9.A6WL.01 1 0.1480 0.960 0.94 0.00 0.00 0.02 0.04 0.00
#> TCGA.P5.A737.01 4 0.2794 0.793 0.00 0.00 0.00 0.86 0.06 0.08
#> TCGA.HT.7616.01 4 0.3697 0.799 0.04 0.00 0.00 0.82 0.08 0.06
#> TCGA.RY.A83Y.01 4 0.2260 0.786 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.HW.8322.01 2 0.0000 0.876 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7692.01 2 0.0000 0.876 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.R8.A6ML.01 4 0.1865 0.803 0.00 0.00 0.00 0.92 0.04 0.04
#> TCGA.DU.6410.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RO.01 6 0.3828 0.415 0.00 0.44 0.00 0.00 0.00 0.56
#> TCGA.TM.A84S.01 5 0.3828 -0.133 0.00 0.00 0.44 0.00 0.56 0.00
#> TCGA.QH.A65Z.01 4 0.5208 0.502 0.28 0.00 0.00 0.62 0.08 0.02
#> TCGA.P5.A730.01 6 0.3756 0.473 0.00 0.40 0.00 0.00 0.00 0.60
#> TCGA.S9.A6UB.01 1 0.0937 0.973 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.DH.A66F.01 4 0.4326 0.603 0.00 0.02 0.00 0.68 0.02 0.28
#> TCGA.DU.6393.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IY.01 3 0.3828 0.394 0.00 0.00 0.56 0.00 0.44 0.00
#> TCGA.FG.7641.01 6 0.4631 0.549 0.00 0.32 0.00 0.00 0.06 0.62
#> TCGA.DH.A7US.01 5 0.4172 0.627 0.00 0.28 0.04 0.00 0.68 0.00
#> TCGA.VV.A829.01 4 0.5027 0.681 0.00 0.00 0.00 0.64 0.20 0.16
#> TCGA.DU.6397.02 6 0.6265 0.400 0.00 0.10 0.00 0.12 0.20 0.58
#> TCGA.DU.6397.01 6 0.4873 0.431 0.00 0.42 0.00 0.00 0.06 0.52
#> TCGA.CS.6670.01 2 0.3864 -0.337 0.00 0.52 0.00 0.00 0.00 0.48
#> TCGA.DB.A64P.01 4 0.4282 0.310 0.00 0.02 0.00 0.56 0.00 0.42
#> TCGA.QH.A6CZ.01 2 0.0000 0.876 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A669.02 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A669.01 1 0.0000 0.983 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8CB.01 2 0.2454 0.703 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.HT.7687.01 1 0.0937 0.973 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.CS.5394.01 1 0.0547 0.980 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.FG.5962.01 4 0.3985 0.771 0.00 0.00 0.00 0.76 0.10 0.14
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 2 0.0504 0.8539 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.S9.A6TX.01 6 0.2654 0.4496 0.00 0.00 0.00 0.02 0.02 0.86 0.10
#> TCGA.DB.A4XA.01 5 0.2376 0.7094 0.00 0.00 0.12 0.00 0.86 0.00 0.02
#> TCGA.E1.5311.01 6 0.5234 -0.1006 0.00 0.00 0.00 0.30 0.02 0.56 0.12
#> TCGA.HT.7620.01 3 0.0000 0.9680 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7480.01 6 0.5617 -0.0526 0.00 0.06 0.00 0.22 0.00 0.58 0.14
#> TCGA.HT.8109.01 6 0.1718 0.5168 0.00 0.00 0.00 0.00 0.04 0.92 0.04
#> TCGA.S9.A7R1.01 4 0.3985 0.6034 0.00 0.00 0.00 0.72 0.00 0.10 0.18
#> TCGA.HW.7486.01 3 0.2163 0.8583 0.00 0.00 0.88 0.00 0.10 0.00 0.02
#> TCGA.FG.7634.01 5 0.3517 0.6116 0.00 0.00 0.28 0.00 0.70 0.00 0.02
#> TCGA.HT.7605.01 5 0.3985 0.2615 0.00 0.00 0.46 0.00 0.52 0.00 0.02
#> TCGA.HT.7608.01 5 0.3914 0.6358 0.00 0.10 0.00 0.00 0.78 0.06 0.06
#> TCGA.W9.A837.01 6 0.5429 -0.1080 0.00 0.06 0.00 0.00 0.40 0.48 0.06
#> TCGA.TM.A7C5.01 4 0.1006 0.7274 0.00 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.P5.A5ET.01 2 0.1433 0.8415 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.FG.A6IZ.01 1 0.0000 0.9632 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KT.A74X.01 6 0.4264 0.3624 0.00 0.32 0.00 0.00 0.00 0.62 0.06
#> TCGA.E1.A7YO.01 4 0.2572 0.7168 0.00 0.00 0.00 0.86 0.00 0.06 0.08
#> TCGA.TQ.A7RG.01 2 0.2313 0.8161 0.00 0.88 0.00 0.00 0.06 0.00 0.06
#> TCGA.RY.A847.01 5 0.2163 0.7134 0.00 0.00 0.10 0.00 0.88 0.02 0.00
#> TCGA.VM.A8CA.01 5 0.3404 0.6597 0.00 0.08 0.00 0.00 0.82 0.04 0.06
#> TCGA.DB.A4XG.01 4 0.2213 0.7141 0.00 0.00 0.00 0.90 0.04 0.02 0.04
#> TCGA.HT.7856.01 3 0.0000 0.9680 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TY.01 4 0.0504 0.7292 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.IK.8125.01 4 0.3991 0.6829 0.00 0.00 0.00 0.72 0.02 0.04 0.22
#> TCGA.HT.7467.01 3 0.0000 0.9680 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RN.01 2 0.2278 0.8349 0.00 0.88 0.00 0.00 0.00 0.04 0.08
#> TCGA.DH.5141.01 6 0.1363 0.5544 0.00 0.02 0.00 0.00 0.04 0.94 0.00
#> TCGA.S9.A6WP.01 4 0.1664 0.7177 0.00 0.00 0.00 0.92 0.06 0.00 0.02
#> TCGA.DB.5278.01 3 0.0000 0.9680 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YS.01 1 0.0000 0.9632 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7881.01 3 0.0000 0.9680 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7637.01 2 0.4340 0.6330 0.00 0.72 0.00 0.00 0.02 0.14 0.12
#> TCGA.VM.A8CE.01 3 0.0000 0.9680 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6U5.01 5 0.3221 0.5719 0.00 0.00 0.32 0.00 0.68 0.00 0.00
#> TCGA.HW.7487.01 6 0.1718 0.5168 0.00 0.00 0.00 0.00 0.04 0.92 0.04
#> TCGA.HW.7491.01 4 0.0504 0.7292 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.TM.A84R.01 3 0.0000 0.9680 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8187.01 5 0.3294 0.5398 0.00 0.00 0.34 0.00 0.66 0.00 0.00
#> TCGA.S9.A7QZ.01 4 0.2016 0.7193 0.00 0.00 0.00 0.90 0.06 0.00 0.04
#> TCGA.QH.A6X4.01 2 0.0863 0.8510 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.DU.A7TG.01 3 0.0000 0.9680 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TW.01 6 0.3417 0.4162 0.00 0.02 0.00 0.00 0.26 0.72 0.00
#> TCGA.HT.7481.01 3 0.2163 0.8583 0.00 0.00 0.88 0.00 0.10 0.00 0.02
#> TCGA.HT.7875.01 2 0.1166 0.8440 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.DU.6394.01 1 0.0000 0.9632 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WD.01 4 0.3566 0.7085 0.00 0.00 0.00 0.78 0.02 0.04 0.16
#> TCGA.TQ.A7RU.01 4 0.4431 0.4524 0.24 0.00 0.00 0.68 0.04 0.00 0.04
#> TCGA.S9.A6WE.01 2 0.2313 0.8161 0.00 0.88 0.00 0.00 0.06 0.00 0.06
#> TCGA.R8.A6MK.01 5 0.3404 0.6597 0.00 0.08 0.00 0.00 0.82 0.04 0.06
#> TCGA.QH.A6CY.01 5 0.3417 0.6299 0.00 0.00 0.26 0.00 0.72 0.00 0.02
#> TCGA.S9.A7J1.01 5 0.5776 0.2508 0.00 0.10 0.00 0.00 0.46 0.38 0.06
#> TCGA.P5.A5F0.01 6 0.1363 0.5544 0.00 0.02 0.00 0.00 0.04 0.94 0.00
#> TCGA.DU.A6S3.01 4 0.3744 0.6966 0.00 0.00 0.00 0.78 0.02 0.08 0.12
#> TCGA.DU.8164.01 1 0.2804 0.8817 0.86 0.00 0.00 0.06 0.06 0.00 0.02
#> TCGA.DU.5849.01 6 0.3307 0.4350 0.00 0.02 0.00 0.00 0.24 0.74 0.00
#> TCGA.HT.7468.01 4 0.4461 0.5029 0.00 0.00 0.00 0.54 0.00 0.06 0.40
#> TCGA.DB.5279.01 4 0.3943 0.4403 0.00 0.00 0.00 0.56 0.02 0.00 0.42
#> TCGA.HT.7677.01 4 0.2313 0.7263 0.00 0.00 0.00 0.88 0.00 0.06 0.06
#> TCGA.HT.7694.01 5 0.4127 0.4690 0.00 0.00 0.04 0.00 0.60 0.36 0.00
#> TCGA.TM.A84M.01 4 0.3525 0.4273 0.00 0.00 0.00 0.56 0.00 0.00 0.44
#> TCGA.F6.A8O3.01 6 0.4795 0.3700 0.00 0.28 0.00 0.00 0.02 0.62 0.08
#> TCGA.QH.A86X.01 2 0.2313 0.8161 0.00 0.88 0.00 0.00 0.06 0.00 0.06
#> TCGA.DU.A76R.01 6 0.2159 0.5470 0.00 0.02 0.00 0.00 0.06 0.90 0.02
#> TCGA.DB.A64V.01 5 0.4070 0.4979 0.00 0.00 0.04 0.00 0.62 0.34 0.00
#> TCGA.RY.A840.01 7 0.5399 0.8569 0.00 0.10 0.00 0.08 0.00 0.20 0.62
#> TCGA.HW.A5KJ.01 1 0.1166 0.9562 0.94 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.HT.8105.01 1 0.1166 0.9562 0.94 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.HT.A619.01 1 0.0000 0.9632 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.5964.01 5 0.4127 0.4690 0.00 0.00 0.04 0.00 0.60 0.36 0.00
#> TCGA.S9.A6WL.01 1 0.1664 0.9426 0.92 0.00 0.00 0.02 0.06 0.00 0.00
#> TCGA.P5.A737.01 4 0.3667 0.6938 0.00 0.00 0.00 0.74 0.00 0.06 0.20
#> TCGA.HT.7616.01 4 0.2829 0.7201 0.00 0.00 0.00 0.84 0.08 0.00 0.08
#> TCGA.RY.A83Y.01 4 0.2572 0.7168 0.00 0.00 0.00 0.86 0.00 0.06 0.08
#> TCGA.HW.8322.01 2 0.0504 0.8539 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.HT.7692.01 2 0.0863 0.8508 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.R8.A6ML.01 4 0.1433 0.7335 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.DU.6410.01 1 0.0000 0.9632 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RO.01 6 0.4264 0.3624 0.00 0.32 0.00 0.00 0.00 0.62 0.06
#> TCGA.TM.A84S.01 5 0.2081 0.7031 0.00 0.00 0.14 0.00 0.86 0.00 0.00
#> TCGA.QH.A65Z.01 4 0.4318 0.4836 0.22 0.00 0.00 0.70 0.04 0.00 0.04
#> TCGA.P5.A730.01 6 0.4795 0.3700 0.00 0.28 0.00 0.00 0.02 0.62 0.08
#> TCGA.S9.A6UB.01 1 0.1166 0.9562 0.94 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.DH.A66F.01 4 0.5086 0.3972 0.00 0.02 0.00 0.62 0.00 0.20 0.16
#> TCGA.DU.6393.01 1 0.0000 0.9632 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IY.01 5 0.3221 0.5719 0.00 0.00 0.32 0.00 0.68 0.00 0.00
#> TCGA.FG.7641.01 6 0.2769 0.5325 0.00 0.08 0.00 0.00 0.02 0.86 0.04
#> TCGA.DH.A7US.01 5 0.2509 0.6937 0.00 0.06 0.02 0.00 0.88 0.04 0.00
#> TCGA.VV.A829.01 4 0.3525 0.4273 0.00 0.00 0.00 0.56 0.00 0.00 0.44
#> TCGA.DU.6397.02 7 0.4928 0.8523 0.00 0.08 0.00 0.04 0.00 0.24 0.64
#> TCGA.DU.6397.01 6 0.5589 -0.1000 0.00 0.32 0.00 0.00 0.00 0.40 0.28
#> TCGA.CS.6670.01 2 0.3968 0.0416 0.00 0.54 0.00 0.00 0.00 0.44 0.02
#> TCGA.DB.A64P.01 4 0.5047 0.0966 0.00 0.00 0.00 0.52 0.00 0.34 0.14
#> TCGA.QH.A6CZ.01 2 0.0000 0.8542 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A669.02 1 0.0000 0.9632 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A669.01 1 0.0000 0.9632 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8CB.01 2 0.3404 0.7837 0.00 0.82 0.00 0.00 0.04 0.06 0.08
#> TCGA.HT.7687.01 1 0.1166 0.9562 0.94 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.CS.5394.01 1 0.1166 0.9562 0.94 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.FG.5962.01 4 0.3991 0.6829 0.00 0.00 0.00 0.72 0.02 0.04 0.22
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 2 0.0941 0.8319 0.00 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.S9.A6TX.01 6 0.3744 0.5309 0.00 0.00 0.00 0.18 0.00 0.74 0.06 0.02
#> TCGA.DB.A4XA.01 5 0.0000 0.7887 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.5311.01 6 0.5273 0.1922 0.00 0.00 0.00 0.42 0.00 0.44 0.06 0.08
#> TCGA.HT.7620.01 3 0.0000 0.9439 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7480.01 6 0.5659 0.2472 0.00 0.02 0.00 0.40 0.00 0.44 0.06 0.08
#> TCGA.HT.8109.01 6 0.3320 0.5425 0.00 0.00 0.00 0.12 0.00 0.80 0.04 0.04
#> TCGA.S9.A7R1.01 4 0.2399 0.4342 0.00 0.00 0.00 0.88 0.00 0.04 0.04 0.04
#> TCGA.HW.7486.01 3 0.2534 0.7443 0.00 0.00 0.78 0.00 0.22 0.00 0.00 0.00
#> TCGA.FG.7634.01 5 0.2547 0.7457 0.00 0.00 0.12 0.00 0.84 0.00 0.00 0.04
#> TCGA.HT.7605.01 5 0.2534 0.6467 0.00 0.00 0.22 0.00 0.78 0.00 0.00 0.00
#> TCGA.HT.7608.01 5 0.3169 0.7142 0.00 0.00 0.00 0.00 0.78 0.02 0.02 0.18
#> TCGA.W9.A837.01 6 0.4686 0.2863 0.00 0.00 0.00 0.00 0.28 0.56 0.00 0.16
#> TCGA.TM.A7C5.01 4 0.3658 -0.4006 0.00 0.00 0.00 0.58 0.00 0.00 0.02 0.40
#> TCGA.P5.A5ET.01 2 0.2350 0.8114 0.00 0.86 0.00 0.00 0.00 0.00 0.04 0.10
#> TCGA.FG.A6IZ.01 1 0.0000 0.9495 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KT.A74X.01 6 0.5371 0.4853 0.00 0.22 0.00 0.02 0.00 0.60 0.06 0.10
#> TCGA.E1.A7YO.01 4 0.0471 0.4378 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.TQ.A7RG.01 2 0.2807 0.8026 0.00 0.84 0.00 0.00 0.02 0.00 0.04 0.10
#> TCGA.RY.A847.01 5 0.0471 0.7875 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.VM.A8CA.01 5 0.2404 0.7507 0.00 0.00 0.00 0.00 0.84 0.00 0.02 0.14
#> TCGA.DB.A4XG.01 8 0.3318 0.7458 0.00 0.00 0.00 0.46 0.00 0.00 0.00 0.54
#> TCGA.HT.7856.01 3 0.0000 0.9439 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TY.01 4 0.2938 -0.1619 0.00 0.00 0.00 0.70 0.00 0.00 0.00 0.30
#> TCGA.IK.8125.01 4 0.3551 0.4037 0.00 0.00 0.00 0.72 0.00 0.06 0.22 0.00
#> TCGA.HT.7467.01 3 0.0000 0.9439 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RN.01 2 0.1804 0.8258 0.00 0.90 0.00 0.00 0.00 0.00 0.02 0.08
#> TCGA.DH.5141.01 6 0.1275 0.6192 0.00 0.00 0.00 0.00 0.04 0.94 0.00 0.02
#> TCGA.S9.A6WP.01 4 0.3142 -0.3891 0.00 0.00 0.00 0.64 0.00 0.00 0.00 0.36
#> TCGA.DB.5278.01 3 0.0000 0.9439 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YS.01 1 0.0000 0.9495 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7881.01 3 0.0000 0.9439 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.7637.01 2 0.5433 0.3994 0.00 0.60 0.00 0.02 0.00 0.20 0.06 0.12
#> TCGA.VM.A8CE.01 3 0.0000 0.9439 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6U5.01 5 0.2725 0.7290 0.00 0.00 0.14 0.00 0.82 0.00 0.00 0.04
#> TCGA.HW.7487.01 6 0.1887 0.5903 0.00 0.00 0.00 0.06 0.00 0.90 0.04 0.00
#> TCGA.HW.7491.01 4 0.3237 -0.4030 0.00 0.00 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.TM.A84R.01 3 0.0000 0.9439 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8187.01 5 0.2114 0.7201 0.00 0.00 0.16 0.00 0.84 0.00 0.00 0.00
#> TCGA.S9.A7QZ.01 4 0.3943 -0.4795 0.00 0.00 0.00 0.56 0.00 0.00 0.04 0.40
#> TCGA.QH.A6X4.01 2 0.1275 0.8237 0.00 0.94 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.DU.A7TG.01 3 0.0000 0.9439 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TW.01 6 0.3657 0.4886 0.00 0.00 0.00 0.00 0.20 0.72 0.00 0.08
#> TCGA.HT.7481.01 3 0.2534 0.7443 0.00 0.00 0.78 0.00 0.22 0.00 0.00 0.00
#> TCGA.HT.7875.01 2 0.1275 0.8224 0.00 0.94 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.DU.6394.01 1 0.0000 0.9495 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6WD.01 4 0.3154 0.4592 0.00 0.00 0.00 0.78 0.00 0.06 0.16 0.00
#> TCGA.TQ.A7RU.01 8 0.4340 0.8343 0.08 0.00 0.00 0.38 0.00 0.00 0.00 0.54
#> TCGA.S9.A6WE.01 2 0.2807 0.8026 0.00 0.84 0.00 0.00 0.02 0.00 0.04 0.10
#> TCGA.R8.A6MK.01 5 0.2404 0.7596 0.00 0.00 0.00 0.00 0.84 0.00 0.02 0.14
#> TCGA.QH.A6CY.01 5 0.1765 0.7525 0.00 0.00 0.12 0.00 0.88 0.00 0.00 0.00
#> TCGA.S9.A7J1.01 6 0.6188 0.2194 0.00 0.04 0.00 0.00 0.26 0.46 0.04 0.20
#> TCGA.P5.A5F0.01 6 0.0471 0.6180 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.DU.A6S3.01 4 0.3434 0.4301 0.00 0.00 0.00 0.76 0.00 0.14 0.10 0.00
#> TCGA.DU.8164.01 1 0.2406 0.8113 0.80 0.00 0.00 0.00 0.00 0.00 0.00 0.20
#> TCGA.DU.5849.01 6 0.3528 0.5152 0.00 0.00 0.00 0.00 0.18 0.74 0.00 0.08
#> TCGA.HT.7468.01 4 0.4680 -0.1016 0.00 0.00 0.00 0.48 0.00 0.00 0.40 0.12
#> TCGA.DB.5279.01 7 0.5055 0.3683 0.00 0.00 0.00 0.28 0.00 0.00 0.48 0.24
#> TCGA.HT.7677.01 4 0.1765 0.3430 0.00 0.00 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.HT.7694.01 5 0.4318 0.4713 0.00 0.00 0.00 0.00 0.60 0.30 0.00 0.10
#> TCGA.TM.A84M.01 7 0.5158 0.2792 0.00 0.00 0.00 0.26 0.00 0.00 0.44 0.30
#> TCGA.F6.A8O3.01 6 0.5577 0.4737 0.00 0.22 0.00 0.02 0.00 0.58 0.08 0.10
#> TCGA.QH.A86X.01 2 0.2807 0.8026 0.00 0.84 0.00 0.00 0.02 0.00 0.04 0.10
#> TCGA.DU.A76R.01 6 0.3131 0.5886 0.00 0.00 0.00 0.02 0.04 0.84 0.04 0.06
#> TCGA.DB.A64V.01 5 0.4318 0.4713 0.00 0.00 0.00 0.00 0.60 0.30 0.00 0.10
#> TCGA.RY.A840.01 7 0.6079 0.1723 0.00 0.04 0.00 0.28 0.00 0.10 0.50 0.08
#> TCGA.HW.A5KJ.01 1 0.1341 0.9398 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.HT.8105.01 1 0.1341 0.9398 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.HT.A619.01 1 0.0000 0.9495 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.5964.01 5 0.4318 0.4713 0.00 0.00 0.00 0.00 0.60 0.30 0.00 0.10
#> TCGA.S9.A6WL.01 1 0.1563 0.9258 0.90 0.00 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.P5.A737.01 4 0.4342 0.2437 0.00 0.00 0.00 0.64 0.00 0.00 0.18 0.18
#> TCGA.HT.7616.01 4 0.5037 -0.1231 0.00 0.00 0.00 0.54 0.00 0.02 0.14 0.30
#> TCGA.RY.A83Y.01 4 0.0471 0.4479 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.HW.8322.01 2 0.0471 0.8313 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.HT.7692.01 2 0.0941 0.8274 0.00 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.R8.A6ML.01 4 0.4557 -0.0197 0.00 0.00 0.00 0.58 0.00 0.00 0.14 0.28
#> TCGA.DU.6410.01 1 0.0000 0.9495 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TQ.A7RO.01 6 0.5130 0.4892 0.00 0.22 0.00 0.02 0.00 0.62 0.04 0.10
#> TCGA.TM.A84S.01 5 0.0000 0.7887 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.QH.A65Z.01 8 0.4174 0.8630 0.06 0.00 0.00 0.40 0.00 0.00 0.00 0.54
#> TCGA.P5.A730.01 6 0.5577 0.4737 0.00 0.22 0.00 0.02 0.00 0.58 0.08 0.10
#> TCGA.S9.A6UB.01 1 0.1341 0.9398 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.DH.A66F.01 4 0.4503 0.3156 0.00 0.00 0.00 0.70 0.00 0.10 0.08 0.12
#> TCGA.DU.6393.01 1 0.0000 0.9495 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IY.01 5 0.1947 0.7388 0.00 0.00 0.14 0.00 0.86 0.00 0.00 0.00
#> TCGA.FG.7641.01 6 0.3871 0.5958 0.00 0.08 0.00 0.02 0.00 0.78 0.04 0.08
#> TCGA.DH.A7US.01 5 0.2025 0.7658 0.00 0.00 0.00 0.00 0.88 0.00 0.02 0.10
#> TCGA.VV.A829.01 7 0.5055 0.3683 0.00 0.00 0.00 0.28 0.00 0.00 0.48 0.24
#> TCGA.DU.6397.02 7 0.3227 0.3393 0.00 0.00 0.00 0.14 0.00 0.08 0.78 0.00
#> TCGA.DU.6397.01 6 0.5178 0.2870 0.00 0.24 0.00 0.00 0.00 0.40 0.36 0.00
#> TCGA.CS.6670.01 2 0.5098 -0.1835 0.00 0.44 0.00 0.00 0.00 0.44 0.06 0.06
#> TCGA.DB.A64P.01 4 0.4971 0.1897 0.00 0.00 0.00 0.62 0.00 0.22 0.08 0.08
#> TCGA.QH.A6CZ.01 2 0.0000 0.8323 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A669.02 1 0.0000 0.9495 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A669.01 1 0.0000 0.9495 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VM.A8CB.01 2 0.4022 0.7082 0.00 0.74 0.00 0.00 0.00 0.04 0.10 0.12
#> TCGA.HT.7687.01 1 0.1341 0.9398 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.CS.5394.01 1 0.1341 0.9398 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.FG.5962.01 4 0.3551 0.4037 0.00 0.00 0.00 0.72 0.00 0.06 0.22 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: Node022111-leaf , Node022112-leaf , Node022113-leaf , Node022121 , Node022122-leaf , Node022123-leaf , Node022211-leaf , Node022212-leaf , Node022231-leaf , Node022232-leaf , Node022233-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 28 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 8.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.923 0.965 0.983 0.4037 0.611 0.611
#> 3 3 0.810 0.847 0.928 0.5338 0.741 0.576
#> 4 4 0.732 0.914 0.902 0.1789 0.746 0.396
#> 5 5 0.812 0.890 0.923 0.0600 0.979 0.910
#> 6 6 0.806 0.810 0.899 0.0200 0.987 0.939
#> 7 7 0.889 0.853 0.931 0.0285 0.989 0.949
#> 8 8 0.929 0.702 0.881 0.0281 0.963 0.816
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
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.TM.A7C5.01 1 0.000 0.976 1.00 0.00
#> TCGA.FG.A6IZ.01 1 0.000 0.976 1.00 0.00
#> TCGA.DB.A4XG.01 1 0.000 0.976 1.00 0.00
#> TCGA.S9.A6TY.01 1 0.000 0.976 1.00 0.00
#> TCGA.S9.A6WP.01 1 0.000 0.976 1.00 0.00
#> TCGA.E1.A7YS.01 2 0.000 1.000 0.00 1.00
#> TCGA.HW.7491.01 1 0.000 0.976 1.00 0.00
#> TCGA.S9.A7QZ.01 1 0.000 0.976 1.00 0.00
#> TCGA.DU.6394.01 1 0.680 0.802 0.82 0.18
#> TCGA.TQ.A7RU.01 1 0.000 0.976 1.00 0.00
#> TCGA.DU.8164.01 1 0.000 0.976 1.00 0.00
#> TCGA.DB.5279.01 2 0.000 1.000 0.00 1.00
#> TCGA.TM.A84M.01 2 0.000 1.000 0.00 1.00
#> TCGA.HW.A5KJ.01 1 0.529 0.869 0.88 0.12
#> TCGA.HT.8105.01 1 0.000 0.976 1.00 0.00
#> TCGA.HT.A619.01 1 0.000 0.976 1.00 0.00
#> TCGA.S9.A6WL.01 1 0.000 0.976 1.00 0.00
#> TCGA.HT.7616.01 2 0.000 1.000 0.00 1.00
#> TCGA.R8.A6ML.01 1 0.000 0.976 1.00 0.00
#> TCGA.DU.6410.01 1 0.680 0.802 0.82 0.18
#> TCGA.QH.A65Z.01 1 0.000 0.976 1.00 0.00
#> TCGA.S9.A6UB.01 1 0.000 0.976 1.00 0.00
#> TCGA.DU.6393.01 1 0.000 0.976 1.00 0.00
#> TCGA.VV.A829.01 2 0.000 1.000 0.00 1.00
#> TCGA.DH.A669.02 2 0.000 1.000 0.00 1.00
#> TCGA.DH.A669.01 2 0.000 1.000 0.00 1.00
#> TCGA.HT.7687.01 1 0.000 0.976 1.00 0.00
#> TCGA.CS.5394.01 1 0.000 0.976 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.TM.A7C5.01 1 0.0000 0.998 1.00 0.0 0.00
#> TCGA.FG.A6IZ.01 3 0.6126 0.532 0.40 0.0 0.60
#> TCGA.DB.A4XG.01 1 0.0000 0.998 1.00 0.0 0.00
#> TCGA.S9.A6TY.01 3 0.6126 0.532 0.40 0.0 0.60
#> TCGA.S9.A6WP.01 1 0.0000 0.998 1.00 0.0 0.00
#> TCGA.E1.A7YS.01 2 0.0000 0.867 0.00 1.0 0.00
#> TCGA.HW.7491.01 1 0.0000 0.998 1.00 0.0 0.00
#> TCGA.S9.A7QZ.01 1 0.0000 0.998 1.00 0.0 0.00
#> TCGA.DU.6394.01 3 0.0000 0.671 0.00 0.0 1.00
#> TCGA.TQ.A7RU.01 1 0.0000 0.998 1.00 0.0 0.00
#> TCGA.DU.8164.01 1 0.0000 0.998 1.00 0.0 0.00
#> TCGA.DB.5279.01 2 0.0000 0.867 0.00 1.0 0.00
#> TCGA.TM.A84M.01 2 0.6126 0.572 0.00 0.6 0.40
#> TCGA.HW.A5KJ.01 3 0.0000 0.671 0.00 0.0 1.00
#> TCGA.HT.8105.01 1 0.0000 0.998 1.00 0.0 0.00
#> TCGA.HT.A619.01 3 0.0000 0.671 0.00 0.0 1.00
#> TCGA.S9.A6WL.01 1 0.0892 0.974 0.98 0.0 0.02
#> TCGA.HT.7616.01 2 0.6126 0.572 0.00 0.6 0.40
#> TCGA.R8.A6ML.01 1 0.0000 0.998 1.00 0.0 0.00
#> TCGA.DU.6410.01 3 0.0000 0.671 0.00 0.0 1.00
#> TCGA.QH.A65Z.01 1 0.0000 0.998 1.00 0.0 0.00
#> TCGA.S9.A6UB.01 1 0.0000 0.998 1.00 0.0 0.00
#> TCGA.DU.6393.01 1 0.0000 0.998 1.00 0.0 0.00
#> TCGA.VV.A829.01 2 0.0000 0.867 0.00 1.0 0.00
#> TCGA.DH.A669.02 2 0.0000 0.867 0.00 1.0 0.00
#> TCGA.DH.A669.01 2 0.0000 0.867 0.00 1.0 0.00
#> TCGA.HT.7687.01 3 0.6126 0.532 0.40 0.0 0.60
#> TCGA.CS.5394.01 1 0.0000 0.998 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.TM.A7C5.01 1 0.3172 1.000 0.84 0.00 0.00 0.16
#> TCGA.FG.A6IZ.01 4 0.0000 0.849 0.00 0.00 0.00 1.00
#> TCGA.DB.A4XG.01 4 0.3801 0.778 0.22 0.00 0.00 0.78
#> TCGA.S9.A6TY.01 4 0.0000 0.849 0.00 0.00 0.00 1.00
#> TCGA.S9.A6WP.01 4 0.3801 0.778 0.22 0.00 0.00 0.78
#> TCGA.E1.A7YS.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.HW.7491.01 1 0.3172 1.000 0.84 0.00 0.00 0.16
#> TCGA.S9.A7QZ.01 4 0.0707 0.848 0.02 0.00 0.00 0.98
#> TCGA.DU.6394.01 3 0.0000 0.923 0.00 0.00 1.00 0.00
#> TCGA.TQ.A7RU.01 1 0.3172 1.000 0.84 0.00 0.00 0.16
#> TCGA.DU.8164.01 1 0.3172 1.000 0.84 0.00 0.00 0.16
#> TCGA.DB.5279.01 2 0.0000 0.982 0.00 1.00 0.00 0.00
#> TCGA.TM.A84M.01 3 0.1211 0.919 0.04 0.00 0.96 0.00
#> TCGA.HW.A5KJ.01 3 0.1411 0.920 0.02 0.00 0.96 0.02
#> TCGA.HT.8105.01 1 0.3172 1.000 0.84 0.00 0.00 0.16
#> TCGA.HT.A619.01 3 0.5327 0.740 0.06 0.00 0.72 0.22
#> TCGA.S9.A6WL.01 4 0.0000 0.849 0.00 0.00 0.00 1.00
#> TCGA.HT.7616.01 3 0.1211 0.919 0.04 0.00 0.96 0.00
#> TCGA.R8.A6ML.01 4 0.3801 0.778 0.22 0.00 0.00 0.78
#> TCGA.DU.6410.01 3 0.1637 0.913 0.06 0.00 0.94 0.00
#> TCGA.QH.A65Z.01 1 0.3172 1.000 0.84 0.00 0.00 0.16
#> TCGA.S9.A6UB.01 4 0.3801 0.778 0.22 0.00 0.00 0.78
#> TCGA.DU.6393.01 1 0.3172 1.000 0.84 0.00 0.00 0.16
#> TCGA.VV.A829.01 2 0.0707 0.975 0.02 0.98 0.00 0.00
#> TCGA.DH.A669.02 2 0.1211 0.977 0.04 0.96 0.00 0.00
#> TCGA.DH.A669.01 2 0.1211 0.977 0.04 0.96 0.00 0.00
#> TCGA.HT.7687.01 4 0.0000 0.849 0.00 0.00 0.00 1.00
#> TCGA.CS.5394.01 1 0.3172 1.000 0.84 0.00 0.00 0.16
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.TM.A7C5.01 1 0.1043 1.000 0.96 0.00 0.00 0.04 0.00
#> TCGA.FG.A6IZ.01 4 0.0000 0.910 0.00 0.00 0.00 1.00 0.00
#> TCGA.DB.A4XG.01 4 0.2873 0.903 0.12 0.00 0.00 0.86 0.02
#> TCGA.S9.A6TY.01 4 0.0609 0.909 0.00 0.00 0.00 0.98 0.02
#> TCGA.S9.A6WP.01 4 0.2873 0.903 0.12 0.00 0.00 0.86 0.02
#> TCGA.E1.A7YS.01 2 0.0609 0.954 0.02 0.98 0.00 0.00 0.00
#> TCGA.HW.7491.01 1 0.1043 1.000 0.96 0.00 0.00 0.04 0.00
#> TCGA.S9.A7QZ.01 4 0.0609 0.919 0.02 0.00 0.00 0.98 0.00
#> TCGA.DU.6394.01 3 0.3895 0.552 0.00 0.00 0.68 0.00 0.32
#> TCGA.TQ.A7RU.01 1 0.1043 1.000 0.96 0.00 0.00 0.04 0.00
#> TCGA.DU.8164.01 1 0.1043 1.000 0.96 0.00 0.00 0.04 0.00
#> TCGA.DB.5279.01 2 0.0000 0.956 0.00 1.00 0.00 0.00 0.00
#> TCGA.TM.A84M.01 3 0.0000 0.678 0.00 0.00 1.00 0.00 0.00
#> TCGA.HW.A5KJ.01 3 0.4726 0.392 0.00 0.00 0.58 0.02 0.40
#> TCGA.HT.8105.01 1 0.1043 1.000 0.96 0.00 0.00 0.04 0.00
#> TCGA.HT.A619.01 5 0.3110 0.851 0.00 0.00 0.06 0.08 0.86
#> TCGA.S9.A6WL.01 4 0.1216 0.918 0.02 0.00 0.00 0.96 0.02
#> TCGA.HT.7616.01 3 0.0000 0.678 0.00 0.00 1.00 0.00 0.00
#> TCGA.R8.A6ML.01 4 0.2280 0.904 0.12 0.00 0.00 0.88 0.00
#> TCGA.DU.6410.01 5 0.2873 0.841 0.00 0.00 0.12 0.02 0.86
#> TCGA.QH.A65Z.01 1 0.1043 1.000 0.96 0.00 0.00 0.04 0.00
#> TCGA.S9.A6UB.01 4 0.2280 0.904 0.12 0.00 0.00 0.88 0.00
#> TCGA.DU.6393.01 1 0.1043 1.000 0.96 0.00 0.00 0.04 0.00
#> TCGA.VV.A829.01 2 0.0000 0.956 0.00 1.00 0.00 0.00 0.00
#> TCGA.DH.A669.02 2 0.2331 0.938 0.02 0.90 0.00 0.00 0.08
#> TCGA.DH.A669.01 2 0.2331 0.938 0.02 0.90 0.00 0.00 0.08
#> TCGA.HT.7687.01 4 0.0000 0.910 0.00 0.00 0.00 1.00 0.00
#> TCGA.CS.5394.01 1 0.1043 1.000 0.96 0.00 0.00 0.04 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.TM.A7C5.01 1 0.0937 1.000 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.FG.A6IZ.01 4 0.0937 0.866 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.DB.A4XG.01 4 0.3544 0.853 0.12 0.00 0.00 0.80 0.00 0.08
#> TCGA.S9.A6TY.01 4 0.2048 0.860 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.S9.A6WP.01 4 0.3544 0.853 0.12 0.00 0.00 0.80 0.00 0.08
#> TCGA.E1.A7YS.01 2 0.0000 0.884 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HW.7491.01 1 0.0937 1.000 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.S9.A7QZ.01 4 0.0547 0.876 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.DU.6394.01 3 0.4078 0.312 0.00 0.00 0.64 0.00 0.34 0.02
#> TCGA.TQ.A7RU.01 1 0.0937 1.000 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.DU.8164.01 1 0.0937 1.000 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.DB.5279.01 2 0.0000 0.884 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84M.01 3 0.0000 0.766 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HW.A5KJ.01 5 0.4105 0.455 0.00 0.00 0.24 0.02 0.72 0.02
#> TCGA.HT.8105.01 1 0.0937 1.000 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.HT.A619.01 6 0.4078 0.000 0.00 0.00 0.00 0.02 0.34 0.64
#> TCGA.S9.A6WL.01 4 0.2048 0.860 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.HT.7616.01 3 0.0000 0.766 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.R8.A6ML.01 4 0.2048 0.859 0.12 0.00 0.00 0.88 0.00 0.00
#> TCGA.DU.6410.01 5 0.1480 0.331 0.02 0.00 0.00 0.00 0.94 0.04
#> TCGA.QH.A65Z.01 1 0.0937 1.000 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.S9.A6UB.01 4 0.2048 0.859 0.12 0.00 0.00 0.88 0.00 0.00
#> TCGA.DU.6393.01 1 0.0937 1.000 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.VV.A829.01 2 0.0000 0.884 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A669.02 2 0.3460 0.818 0.02 0.76 0.00 0.00 0.00 0.22
#> TCGA.DH.A669.01 2 0.3460 0.818 0.02 0.76 0.00 0.00 0.00 0.22
#> TCGA.HT.7687.01 4 0.0937 0.866 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.CS.5394.01 1 0.0937 1.000 0.96 0.00 0.00 0.04 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.TM.A7C5.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.A6IZ.01 4 0.2081 0.879 0.00 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.DB.A4XG.01 4 0.2159 0.891 0.02 0.00 0.00 0.90 0.00 0.02 0.06
#> TCGA.S9.A6TY.01 4 0.2906 0.862 0.00 0.00 0.00 0.80 0.00 0.02 0.18
#> TCGA.S9.A6WP.01 4 0.2706 0.879 0.02 0.00 0.00 0.88 0.02 0.04 0.04
#> TCGA.E1.A7YS.01 2 0.0504 0.920 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.HW.7491.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7QZ.01 4 0.0000 0.897 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.6394.01 5 0.2422 0.722 0.00 0.00 0.18 0.00 0.82 0.00 0.00
#> TCGA.TQ.A7RU.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.8164.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5279.01 2 0.0000 0.928 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.TM.A84M.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HW.A5KJ.01 5 0.0504 0.687 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.HT.8105.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A619.01 6 0.0863 0.000 0.00 0.00 0.00 0.00 0.04 0.96 0.00
#> TCGA.S9.A6WL.01 4 0.3566 0.862 0.00 0.00 0.00 0.78 0.02 0.04 0.16
#> TCGA.HT.7616.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.R8.A6ML.01 4 0.1006 0.888 0.02 0.00 0.00 0.96 0.00 0.00 0.02
#> TCGA.DU.6410.01 7 0.3755 0.000 0.00 0.00 0.00 0.00 0.34 0.02 0.64
#> TCGA.QH.A65Z.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6UB.01 4 0.2003 0.884 0.02 0.00 0.00 0.92 0.02 0.02 0.02
#> TCGA.DU.6393.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VV.A829.01 2 0.0000 0.928 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A669.02 2 0.2081 0.896 0.00 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.DH.A669.01 2 0.2081 0.896 0.00 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.HT.7687.01 4 0.1886 0.878 0.00 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.CS.5394.01 1 0.0000 1.000 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.TM.A7C5.01 1 0.0000 1.000 1.00 0.0 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.FG.A6IZ.01 4 0.3943 -0.381 0.00 0.0 0.00 0.56 0.00 0 0.04 0.40
#> TCGA.DB.A4XG.01 4 0.2407 0.657 0.08 0.0 0.00 0.86 0.00 0 0.00 0.06
#> TCGA.S9.A6TY.01 8 0.3015 0.898 0.00 0.0 0.00 0.32 0.00 0 0.00 0.68
#> TCGA.S9.A6WP.01 4 0.2648 0.648 0.08 0.0 0.00 0.84 0.00 0 0.00 0.08
#> TCGA.E1.A7YS.01 2 0.4415 0.770 0.00 0.6 0.00 0.02 0.32 0 0.00 0.06
#> TCGA.HW.7491.01 1 0.0000 1.000 1.00 0.0 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.S9.A7QZ.01 4 0.0471 0.627 0.02 0.0 0.00 0.98 0.00 0 0.00 0.00
#> TCGA.DU.6394.01 5 0.5435 0.823 0.00 0.0 0.14 0.00 0.58 0 0.10 0.18
#> TCGA.TQ.A7RU.01 1 0.0000 1.000 1.00 0.0 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.DU.8164.01 1 0.0000 1.000 1.00 0.0 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.DB.5279.01 2 0.3237 0.782 0.00 0.6 0.00 0.00 0.40 0 0.00 0.00
#> TCGA.TM.A84M.01 3 0.0000 1.000 0.00 0.0 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.HW.A5KJ.01 5 0.5189 0.817 0.00 0.0 0.04 0.00 0.56 0 0.14 0.26
#> TCGA.HT.8105.01 1 0.0000 1.000 1.00 0.0 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.HT.A619.01 6 0.0000 0.000 0.00 0.0 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.S9.A6WL.01 8 0.3083 0.894 0.00 0.0 0.00 0.34 0.00 0 0.00 0.66
#> TCGA.HT.7616.01 3 0.0000 1.000 0.00 0.0 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.R8.A6ML.01 4 0.1341 0.670 0.08 0.0 0.00 0.92 0.00 0 0.00 0.00
#> TCGA.DU.6410.01 7 0.0808 0.000 0.00 0.0 0.00 0.00 0.04 0 0.96 0.00
#> TCGA.QH.A65Z.01 1 0.0000 1.000 1.00 0.0 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.S9.A6UB.01 4 0.1804 0.669 0.08 0.0 0.00 0.90 0.00 0 0.00 0.02
#> TCGA.DU.6393.01 1 0.0000 1.000 1.00 0.0 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.VV.A829.01 2 0.3237 0.782 0.00 0.6 0.00 0.00 0.40 0 0.00 0.00
#> TCGA.DH.A669.02 2 0.0000 0.684 0.00 1.0 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.DH.A669.01 2 0.0000 0.684 0.00 1.0 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.HT.7687.01 4 0.3943 -0.381 0.00 0.0 0.00 0.56 0.00 0 0.04 0.40
#> TCGA.CS.5394.01 1 0.0000 1.000 1.00 0.0 0.00 0.00 0.00 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: Node0222. Child nodes: Node022111-leaf , Node022112-leaf , Node022113-leaf , Node022121 , Node022122-leaf , Node022123-leaf , Node022211-leaf , Node022212-leaf , Node022231-leaf , Node022232-leaf , Node022233-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["02223"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 25 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.780 0.930 0.964 0.4766 0.500 0.500
#> 3 3 1.000 1.000 1.000 0.4276 0.687 0.447
#> 4 4 0.710 0.632 0.841 0.0869 0.973 0.917
#> 5 5 0.731 0.554 0.751 0.0734 0.827 0.480
#> 6 6 0.759 0.620 0.813 0.0290 0.863 0.461
#> 7 7 0.768 0.576 0.806 0.0338 0.907 0.576
#> 8 8 0.787 0.620 0.778 0.0315 0.950 0.717
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.DB.A4XA.01 2 0.000 1.000 0.0 1.0
#> TCGA.HT.7620.01 1 0.000 0.895 1.0 0.0
#> TCGA.HW.7486.01 1 0.881 0.667 0.7 0.3
#> TCGA.FG.7634.01 2 0.000 1.000 0.0 1.0
#> TCGA.HT.7605.01 2 0.000 1.000 0.0 1.0
#> TCGA.RY.A847.01 2 0.000 1.000 0.0 1.0
#> TCGA.VM.A8CA.01 2 0.000 1.000 0.0 1.0
#> TCGA.HT.7856.01 1 0.000 0.895 1.0 0.0
#> TCGA.HT.7467.01 1 0.000 0.895 1.0 0.0
#> TCGA.DB.5278.01 2 0.000 1.000 0.0 1.0
#> TCGA.HT.7881.01 1 0.000 0.895 1.0 0.0
#> TCGA.VM.A8CE.01 2 0.000 1.000 0.0 1.0
#> TCGA.S9.A6U5.01 2 0.000 1.000 0.0 1.0
#> TCGA.TM.A84R.01 1 0.000 0.895 1.0 0.0
#> TCGA.FG.8187.01 2 0.000 1.000 0.0 1.0
#> TCGA.DU.A7TG.01 1 0.000 0.895 1.0 0.0
#> TCGA.HT.7481.01 1 0.881 0.667 0.7 0.3
#> TCGA.R8.A6MK.01 2 0.000 1.000 0.0 1.0
#> TCGA.QH.A6CY.01 2 0.000 1.000 0.0 1.0
#> TCGA.HT.7694.01 1 0.000 0.895 1.0 0.0
#> TCGA.DB.A64V.01 1 0.881 0.667 0.7 0.3
#> TCGA.FG.5964.01 2 0.000 1.000 0.0 1.0
#> TCGA.TM.A84S.01 2 0.000 1.000 0.0 1.0
#> TCGA.S9.A7IY.01 2 0.000 1.000 0.0 1.0
#> TCGA.DH.A7US.01 2 0.000 1.000 0.0 1.0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.DB.A4XA.01 2 0 1 0 1 0
#> TCGA.HT.7620.01 1 0 1 1 0 0
#> TCGA.HW.7486.01 3 0 1 0 0 1
#> TCGA.FG.7634.01 2 0 1 0 1 0
#> TCGA.HT.7605.01 3 0 1 0 0 1
#> TCGA.RY.A847.01 2 0 1 0 1 0
#> TCGA.VM.A8CA.01 2 0 1 0 1 0
#> TCGA.HT.7856.01 1 0 1 1 0 0
#> TCGA.HT.7467.01 1 0 1 1 0 0
#> TCGA.DB.5278.01 3 0 1 0 0 1
#> TCGA.HT.7881.01 1 0 1 1 0 0
#> TCGA.VM.A8CE.01 3 0 1 0 0 1
#> TCGA.S9.A6U5.01 2 0 1 0 1 0
#> TCGA.TM.A84R.01 1 0 1 1 0 0
#> TCGA.FG.8187.01 2 0 1 0 1 0
#> TCGA.DU.A7TG.01 1 0 1 1 0 0
#> TCGA.HT.7481.01 3 0 1 0 0 1
#> TCGA.R8.A6MK.01 2 0 1 0 1 0
#> TCGA.QH.A6CY.01 3 0 1 0 0 1
#> TCGA.HT.7694.01 3 0 1 0 0 1
#> TCGA.DB.A64V.01 3 0 1 0 0 1
#> TCGA.FG.5964.01 3 0 1 0 0 1
#> TCGA.TM.A84S.01 2 0 1 0 1 0
#> TCGA.S9.A7IY.01 2 0 1 0 1 0
#> TCGA.DH.A7US.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.DB.A4XA.01 2 0.506 0.481 0.00 0.68 0.02 0.30
#> TCGA.HT.7620.01 1 0.712 0.548 0.54 0.00 0.30 0.16
#> TCGA.HW.7486.01 3 0.000 0.594 0.00 0.00 1.00 0.00
#> TCGA.FG.7634.01 2 0.000 0.846 0.00 1.00 0.00 0.00
#> TCGA.HT.7605.01 3 0.441 0.261 0.00 0.00 0.70 0.30
#> TCGA.RY.A847.01 2 0.340 0.823 0.00 0.82 0.00 0.18
#> TCGA.VM.A8CA.01 2 0.340 0.823 0.00 0.82 0.00 0.18
#> TCGA.HT.7856.01 1 0.000 0.845 1.00 0.00 0.00 0.00
#> TCGA.HT.7467.01 1 0.000 0.845 1.00 0.00 0.00 0.00
#> TCGA.DB.5278.01 4 0.485 0.000 0.00 0.00 0.40 0.60
#> TCGA.HT.7881.01 1 0.632 0.673 0.66 0.00 0.18 0.16
#> TCGA.VM.A8CE.01 3 0.441 0.261 0.00 0.00 0.70 0.30
#> TCGA.S9.A6U5.01 2 0.398 0.798 0.00 0.76 0.00 0.24
#> TCGA.TM.A84R.01 1 0.000 0.845 1.00 0.00 0.00 0.00
#> TCGA.FG.8187.01 2 0.361 0.680 0.00 0.80 0.00 0.20
#> TCGA.DU.A7TG.01 1 0.000 0.845 1.00 0.00 0.00 0.00
#> TCGA.HT.7481.01 3 0.000 0.594 0.00 0.00 1.00 0.00
#> TCGA.R8.A6MK.01 2 0.398 0.798 0.00 0.76 0.00 0.24
#> TCGA.QH.A6CY.01 3 0.441 0.261 0.00 0.00 0.70 0.30
#> TCGA.HT.7694.01 3 0.317 0.394 0.00 0.00 0.84 0.16
#> TCGA.DB.A64V.01 3 0.000 0.594 0.00 0.00 1.00 0.00
#> TCGA.FG.5964.01 3 0.340 0.463 0.00 0.00 0.82 0.18
#> TCGA.TM.A84S.01 2 0.000 0.846 0.00 1.00 0.00 0.00
#> TCGA.S9.A7IY.01 2 0.000 0.846 0.00 1.00 0.00 0.00
#> TCGA.DH.A7US.01 2 0.000 0.846 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.DB.A4XA.01 2 0.4287 0.176 0.00 0.54 0.00 0.46 0.00
#> TCGA.HT.7620.01 3 0.5700 0.428 0.28 0.00 0.60 0.00 0.12
#> TCGA.HW.7486.01 3 0.4182 0.570 0.00 0.00 0.60 0.40 0.00
#> TCGA.FG.7634.01 2 0.1043 0.508 0.00 0.96 0.00 0.00 0.04
#> TCGA.HT.7605.01 4 0.0000 0.771 0.00 0.00 0.00 1.00 0.00
#> TCGA.RY.A847.01 2 0.4126 -0.522 0.00 0.62 0.00 0.00 0.38
#> TCGA.VM.A8CA.01 2 0.4126 -0.522 0.00 0.62 0.00 0.00 0.38
#> TCGA.HT.7856.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7467.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5278.01 4 0.6610 0.342 0.00 0.00 0.28 0.46 0.26
#> TCGA.HT.7881.01 3 0.5864 0.363 0.32 0.00 0.56 0.00 0.12
#> TCGA.VM.A8CE.01 4 0.0000 0.771 0.00 0.00 0.00 1.00 0.00
#> TCGA.S9.A6U5.01 5 0.4227 1.000 0.00 0.42 0.00 0.00 0.58
#> TCGA.TM.A84R.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8187.01 2 0.4126 0.330 0.00 0.62 0.00 0.38 0.00
#> TCGA.DU.A7TG.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7481.01 3 0.4182 0.570 0.00 0.00 0.60 0.40 0.00
#> TCGA.R8.A6MK.01 5 0.4227 1.000 0.00 0.42 0.00 0.00 0.58
#> TCGA.QH.A6CY.01 4 0.0609 0.765 0.00 0.00 0.02 0.98 0.00
#> TCGA.HT.7694.01 3 0.5700 0.581 0.00 0.00 0.60 0.28 0.12
#> TCGA.DB.A64V.01 3 0.4182 0.570 0.00 0.00 0.60 0.40 0.00
#> TCGA.FG.5964.01 4 0.2732 0.602 0.00 0.00 0.16 0.84 0.00
#> TCGA.TM.A84S.01 2 0.0000 0.518 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A7IY.01 2 0.0000 0.518 0.00 1.00 0.00 0.00 0.00
#> TCGA.DH.A7US.01 2 0.0000 0.518 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.DB.A4XA.01 2 0.327 0.432 0.00 0.82 0.00 0.12 0.06 0.00
#> TCGA.HT.7620.01 3 0.156 0.895 0.08 0.00 0.92 0.00 0.00 0.00
#> TCGA.HW.7486.01 4 0.331 0.518 0.00 0.00 0.28 0.72 0.00 0.00
#> TCGA.FG.7634.01 2 0.569 0.429 0.00 0.56 0.08 0.00 0.32 0.04
#> TCGA.HT.7605.01 4 0.331 0.565 0.00 0.28 0.00 0.72 0.00 0.00
#> TCGA.RY.A847.01 5 0.331 0.553 0.00 0.28 0.00 0.00 0.72 0.00
#> TCGA.VM.A8CA.01 5 0.331 0.553 0.00 0.28 0.00 0.00 0.72 0.00
#> TCGA.HT.7856.01 1 0.000 0.943 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7467.01 1 0.148 0.911 0.94 0.02 0.00 0.00 0.00 0.04
#> TCGA.DB.5278.01 6 0.219 0.000 0.00 0.06 0.00 0.04 0.00 0.90
#> TCGA.HT.7881.01 3 0.301 0.881 0.08 0.02 0.86 0.00 0.00 0.04
#> TCGA.VM.A8CE.01 4 0.331 0.565 0.00 0.28 0.00 0.72 0.00 0.00
#> TCGA.S9.A6U5.01 5 0.000 0.680 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.TM.A84R.01 1 0.148 0.948 0.94 0.04 0.00 0.00 0.00 0.02
#> TCGA.FG.8187.01 2 0.251 0.474 0.00 0.88 0.00 0.06 0.06 0.00
#> TCGA.DU.A7TG.01 1 0.148 0.948 0.94 0.04 0.00 0.00 0.00 0.02
#> TCGA.HT.7481.01 4 0.331 0.518 0.00 0.00 0.28 0.72 0.00 0.00
#> TCGA.R8.A6MK.01 5 0.000 0.680 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.QH.A6CY.01 4 0.331 0.565 0.00 0.28 0.00 0.72 0.00 0.00
#> TCGA.HT.7694.01 3 0.156 0.836 0.00 0.00 0.92 0.08 0.00 0.00
#> TCGA.DB.A64V.01 4 0.331 0.518 0.00 0.00 0.28 0.72 0.00 0.00
#> TCGA.FG.5964.01 4 0.000 0.589 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.TM.A84S.01 2 0.380 0.493 0.00 0.58 0.00 0.00 0.42 0.00
#> TCGA.S9.A7IY.01 2 0.380 0.493 0.00 0.58 0.00 0.00 0.42 0.00
#> TCGA.DH.A7US.01 2 0.376 0.513 0.00 0.60 0.00 0.00 0.40 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.DB.A4XA.01 4 0.3985 -0.214 0.00 0.46 0.00 0.52 0.00 0.02 0.00
#> TCGA.HT.7620.01 3 0.0000 0.944 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HW.7486.01 4 0.7193 0.382 0.00 0.00 0.28 0.36 0.20 0.02 0.14
#> TCGA.FG.7634.01 7 0.3221 0.000 0.00 0.32 0.00 0.00 0.00 0.00 0.68
#> TCGA.HT.7605.01 4 0.0000 0.431 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.RY.A847.01 2 0.3047 0.482 0.00 0.72 0.00 0.00 0.28 0.00 0.00
#> TCGA.VM.A8CA.01 2 0.3047 0.482 0.00 0.72 0.00 0.00 0.28 0.00 0.00
#> TCGA.HT.7856.01 1 0.2016 0.909 0.90 0.00 0.00 0.00 0.00 0.06 0.04
#> TCGA.HT.7467.01 1 0.3011 0.867 0.82 0.00 0.00 0.00 0.00 0.06 0.12
#> TCGA.DB.5278.01 6 0.1886 0.000 0.00 0.00 0.00 0.12 0.00 0.88 0.00
#> TCGA.HT.7881.01 3 0.1886 0.886 0.00 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.VM.A8CE.01 4 0.0504 0.436 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.S9.A6U5.01 5 0.2572 0.983 0.00 0.20 0.00 0.00 0.80 0.00 0.00
#> TCGA.TM.A84R.01 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FG.8187.01 2 0.3863 0.380 0.00 0.74 0.00 0.20 0.00 0.04 0.02
#> TCGA.DU.A7TG.01 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7481.01 4 0.7193 0.382 0.00 0.00 0.28 0.36 0.20 0.02 0.14
#> TCGA.R8.A6MK.01 5 0.3052 0.983 0.00 0.20 0.00 0.00 0.78 0.02 0.00
#> TCGA.QH.A6CY.01 4 0.0504 0.432 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.HT.7694.01 3 0.0000 0.944 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64V.01 4 0.7193 0.382 0.00 0.00 0.28 0.36 0.20 0.02 0.14
#> TCGA.FG.5964.01 4 0.4963 0.435 0.00 0.00 0.00 0.64 0.18 0.02 0.16
#> TCGA.TM.A84S.01 2 0.0000 0.692 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7IY.01 2 0.0000 0.692 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DH.A7US.01 2 0.1363 0.663 0.00 0.94 0.00 0.00 0.00 0.04 0.02
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.DB.A4XA.01 4 0.5116 -0.00604 0.00 0.28 0.00 0.46 0.00 0 0.00 0.26
#> TCGA.HT.7620.01 3 0.0000 0.97109 0.00 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.HW.7486.01 8 0.4998 1.00000 0.00 0.00 0.26 0.24 0.00 0 0.00 0.50
#> TCGA.FG.7634.01 7 0.2114 0.00000 0.00 0.16 0.00 0.00 0.00 0 0.84 0.00
#> TCGA.HT.7605.01 4 0.0000 0.61205 0.00 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.RY.A847.01 2 0.3015 0.38051 0.00 0.68 0.00 0.00 0.32 0 0.00 0.00
#> TCGA.VM.A8CA.01 2 0.3015 0.38051 0.00 0.68 0.00 0.00 0.32 0 0.00 0.00
#> TCGA.HT.7856.01 1 0.0000 0.82675 1.00 0.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.HT.7467.01 1 0.0941 0.80876 0.96 0.00 0.00 0.00 0.02 0 0.02 0.00
#> TCGA.DB.5278.01 6 0.0000 0.00000 0.00 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.HT.7881.01 3 0.1275 0.94152 0.00 0.00 0.94 0.00 0.02 0 0.04 0.00
#> TCGA.VM.A8CE.01 4 0.0000 0.61205 0.00 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.S9.A6U5.01 5 0.1563 1.00000 0.00 0.10 0.00 0.00 0.90 0 0.00 0.00
#> TCGA.TM.A84R.01 1 0.3817 0.83429 0.76 0.00 0.00 0.00 0.08 0 0.04 0.12
#> TCGA.FG.8187.01 2 0.4921 0.18112 0.00 0.52 0.00 0.22 0.00 0 0.00 0.26
#> TCGA.DU.A7TG.01 1 0.3817 0.83429 0.76 0.00 0.00 0.00 0.08 0 0.04 0.12
#> TCGA.HT.7481.01 8 0.4998 1.00000 0.00 0.00 0.26 0.24 0.00 0 0.00 0.50
#> TCGA.R8.A6MK.01 5 0.1563 1.00000 0.00 0.10 0.00 0.00 0.90 0 0.00 0.00
#> TCGA.QH.A6CY.01 4 0.2407 0.56414 0.00 0.00 0.00 0.86 0.00 0 0.06 0.08
#> TCGA.HT.7694.01 3 0.0000 0.97109 0.00 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.DB.A64V.01 8 0.4998 1.00000 0.00 0.00 0.26 0.24 0.00 0 0.00 0.50
#> TCGA.FG.5964.01 4 0.4403 -0.20689 0.00 0.00 0.00 0.48 0.00 0 0.08 0.44
#> TCGA.TM.A84S.01 2 0.0000 0.62777 0.00 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.S9.A7IY.01 2 0.0000 0.62777 0.00 1.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.DH.A7US.01 2 0.2267 0.54487 0.00 0.82 0.00 0.00 0.00 0 0.00 0.18
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: Node0121 , Node0122-leaf , Node0123-leaf , Node0211-leaf , Node0212-leaf , Node0213-leaf , Node0221 , Node0222 , Node0231 , Node0232 .
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 37 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.987 0.994 0.4865 0.517 0.517
#> 3 3 0.754 0.875 0.938 0.3411 0.788 0.599
#> 4 4 0.703 0.868 0.876 0.1201 0.898 0.706
#> 5 5 0.827 0.898 0.864 0.0797 0.937 0.760
#> 6 6 0.835 0.869 0.884 0.0347 0.970 0.850
#> 7 7 0.773 0.763 0.848 0.0237 0.994 0.965
#> 8 8 0.854 0.673 0.839 0.0299 0.983 0.901
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.CS.6665.01 1 0.000 1.000 1.00 0.00
#> TCGA.FG.A6J3.01 1 0.000 1.000 1.00 0.00
#> TCGA.E1.A7YI.01 1 0.000 1.000 1.00 0.00
#> TCGA.HT.7689.01 2 0.000 0.990 0.00 1.00
#> TCGA.E1.A7YE.01 1 0.000 1.000 1.00 0.00
#> TCGA.S9.A7J0.01 2 0.000 0.990 0.00 1.00
#> TCGA.DU.6407.02 1 0.000 1.000 1.00 0.00
#> TCGA.E1.A7YU.01 2 0.000 0.990 0.00 1.00
#> TCGA.IK.7675.01 2 0.000 0.990 0.00 1.00
#> TCGA.HT.8563.01 2 0.000 0.990 0.00 1.00
#> TCGA.S9.A7IS.01 1 0.000 1.000 1.00 0.00
#> TCGA.S9.A89Z.01 2 0.000 0.990 0.00 1.00
#> TCGA.HT.A618.01 2 0.000 0.990 0.00 1.00
#> TCGA.RY.A83Z.01 1 0.000 1.000 1.00 0.00
#> TCGA.P5.A5EU.01 1 0.000 1.000 1.00 0.00
#> TCGA.DB.A64X.01 2 0.000 0.990 0.00 1.00
#> TCGA.HT.7477.01 2 0.000 0.990 0.00 1.00
#> TCGA.DU.7304.02 2 0.680 0.785 0.18 0.82
#> TCGA.S9.A6TS.01 2 0.000 0.990 0.00 1.00
#> TCGA.E1.A7YV.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.7007.01 2 0.000 0.990 0.00 1.00
#> TCGA.DB.5277.01 2 0.000 0.990 0.00 1.00
#> TCGA.HT.7606.01 2 0.000 0.990 0.00 1.00
#> TCGA.E1.A7YK.01 2 0.000 0.990 0.00 1.00
#> TCGA.S9.A6TV.01 2 0.000 0.990 0.00 1.00
#> TCGA.HW.8319.01 2 0.000 0.990 0.00 1.00
#> TCGA.DU.A5TU.01 2 0.000 0.990 0.00 1.00
#> TCGA.HT.7686.01 2 0.000 0.990 0.00 1.00
#> TCGA.TQ.A7RM.01 1 0.000 1.000 1.00 0.00
#> TCGA.E1.5304.01 2 0.242 0.953 0.04 0.96
#> TCGA.HT.7470.01 2 0.000 0.990 0.00 1.00
#> TCGA.DU.7010.01 1 0.000 1.000 1.00 0.00
#> TCGA.DU.6396.01 2 0.000 0.990 0.00 1.00
#> TCGA.FG.A87N.01 1 0.000 1.000 1.00 0.00
#> TCGA.FG.5965.02 1 0.000 1.000 1.00 0.00
#> TCGA.DH.A7UU.01 2 0.000 0.990 0.00 1.00
#> TCGA.TM.A84I.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.CS.6665.01 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.FG.A6J3.01 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.E1.A7YI.01 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.HT.7689.01 2 0.0000 0.930 0.0 1.00 0.00
#> TCGA.E1.A7YE.01 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.S9.A7J0.01 2 0.0000 0.930 0.0 1.00 0.00
#> TCGA.DU.6407.02 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.E1.A7YU.01 2 0.0000 0.930 0.0 1.00 0.00
#> TCGA.IK.7675.01 2 0.0892 0.918 0.0 0.98 0.02
#> TCGA.HT.8563.01 3 0.5948 0.587 0.0 0.36 0.64
#> TCGA.S9.A7IS.01 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.S9.A89Z.01 2 0.0000 0.930 0.0 1.00 0.00
#> TCGA.HT.A618.01 3 0.5948 0.587 0.0 0.36 0.64
#> TCGA.RY.A83Z.01 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.P5.A5EU.01 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.DB.A64X.01 2 0.0000 0.930 0.0 1.00 0.00
#> TCGA.HT.7477.01 3 0.0000 0.767 0.0 0.00 1.00
#> TCGA.DU.7304.02 3 0.0000 0.767 0.0 0.00 1.00
#> TCGA.S9.A6TS.01 2 0.0000 0.930 0.0 1.00 0.00
#> TCGA.E1.A7YV.01 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.DU.7007.01 2 0.0000 0.930 0.0 1.00 0.00
#> TCGA.DB.5277.01 2 0.3686 0.823 0.0 0.86 0.14
#> TCGA.HT.7606.01 3 0.0000 0.767 0.0 0.00 1.00
#> TCGA.E1.A7YK.01 2 0.4555 0.744 0.0 0.80 0.20
#> TCGA.S9.A6TV.01 2 0.0000 0.930 0.0 1.00 0.00
#> TCGA.HW.8319.01 3 0.5948 0.587 0.0 0.36 0.64
#> TCGA.DU.A5TU.01 2 0.0000 0.930 0.0 1.00 0.00
#> TCGA.HT.7686.01 3 0.5948 0.587 0.0 0.36 0.64
#> TCGA.TQ.A7RM.01 3 0.2959 0.697 0.1 0.00 0.90
#> TCGA.E1.5304.01 3 0.0000 0.767 0.0 0.00 1.00
#> TCGA.HT.7470.01 2 0.4555 0.744 0.0 0.80 0.20
#> TCGA.DU.7010.01 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.DU.6396.01 2 0.4555 0.744 0.0 0.80 0.20
#> TCGA.FG.A87N.01 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.FG.5965.02 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.DH.A7UU.01 2 0.0000 0.930 0.0 1.00 0.00
#> TCGA.TM.A84I.01 1 0.0000 1.000 1.0 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.CS.6665.01 1 0.000 0.866 1.00 0.00 0.00 0.00
#> TCGA.FG.A6J3.01 1 0.398 0.888 0.76 0.00 0.00 0.24
#> TCGA.E1.A7YI.01 1 0.398 0.888 0.76 0.00 0.00 0.24
#> TCGA.HT.7689.01 2 0.340 0.761 0.00 0.82 0.00 0.18
#> TCGA.E1.A7YE.01 1 0.398 0.888 0.76 0.00 0.00 0.24
#> TCGA.S9.A7J0.01 2 0.000 0.884 0.00 1.00 0.00 0.00
#> TCGA.DU.6407.02 1 0.000 0.866 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YU.01 2 0.340 0.761 0.00 0.82 0.00 0.18
#> TCGA.IK.7675.01 2 0.361 0.801 0.00 0.80 0.00 0.20
#> TCGA.HT.8563.01 4 0.590 0.880 0.00 0.14 0.16 0.70
#> TCGA.S9.A7IS.01 1 0.000 0.866 1.00 0.00 0.00 0.00
#> TCGA.S9.A89Z.01 2 0.121 0.873 0.00 0.96 0.00 0.04
#> TCGA.HT.A618.01 4 0.590 0.880 0.00 0.14 0.16 0.70
#> TCGA.RY.A83Z.01 1 0.398 0.888 0.76 0.00 0.00 0.24
#> TCGA.P5.A5EU.01 1 0.000 0.866 1.00 0.00 0.00 0.00
#> TCGA.DB.A64X.01 2 0.000 0.884 0.00 1.00 0.00 0.00
#> TCGA.HT.7477.01 3 0.000 0.969 0.00 0.00 1.00 0.00
#> TCGA.DU.7304.02 3 0.000 0.969 0.00 0.00 1.00 0.00
#> TCGA.S9.A6TS.01 2 0.340 0.809 0.00 0.82 0.00 0.18
#> TCGA.E1.A7YV.01 1 0.398 0.888 0.76 0.00 0.00 0.24
#> TCGA.DU.7007.01 2 0.000 0.884 0.00 1.00 0.00 0.00
#> TCGA.DB.5277.01 2 0.529 0.702 0.00 0.74 0.18 0.08
#> TCGA.HT.7606.01 3 0.000 0.969 0.00 0.00 1.00 0.00
#> TCGA.E1.A7YK.01 4 0.441 0.816 0.00 0.30 0.00 0.70
#> TCGA.S9.A6TV.01 2 0.000 0.884 0.00 1.00 0.00 0.00
#> TCGA.HW.8319.01 4 0.590 0.880 0.00 0.14 0.16 0.70
#> TCGA.DU.A5TU.01 2 0.000 0.884 0.00 1.00 0.00 0.00
#> TCGA.HT.7686.01 4 0.590 0.880 0.00 0.14 0.16 0.70
#> TCGA.TQ.A7RM.01 3 0.234 0.878 0.10 0.00 0.90 0.00
#> TCGA.E1.5304.01 3 0.000 0.969 0.00 0.00 1.00 0.00
#> TCGA.HT.7470.01 4 0.441 0.816 0.00 0.30 0.00 0.70
#> TCGA.DU.7010.01 1 0.398 0.888 0.76 0.00 0.00 0.24
#> TCGA.DU.6396.01 4 0.441 0.816 0.00 0.30 0.00 0.70
#> TCGA.FG.A87N.01 1 0.000 0.866 1.00 0.00 0.00 0.00
#> TCGA.FG.5965.02 1 0.000 0.866 1.00 0.00 0.00 0.00
#> TCGA.DH.A7UU.01 2 0.121 0.873 0.00 0.96 0.00 0.04
#> TCGA.TM.A84I.01 1 0.398 0.888 0.76 0.00 0.00 0.24
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CS.6665.01 5 0.406 0.986 0.36 0.00 0.00 0.00 0.64
#> TCGA.FG.A6J3.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YI.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7689.01 2 0.400 0.694 0.00 0.74 0.00 0.24 0.02
#> TCGA.E1.A7YE.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7J0.01 2 0.000 0.833 0.00 1.00 0.00 0.00 0.00
#> TCGA.DU.6407.02 5 0.406 0.986 0.36 0.00 0.00 0.00 0.64
#> TCGA.E1.A7YU.01 2 0.400 0.694 0.00 0.74 0.00 0.24 0.02
#> TCGA.IK.7675.01 2 0.605 0.665 0.00 0.56 0.00 0.16 0.28
#> TCGA.HT.8563.01 4 0.201 0.949 0.00 0.02 0.06 0.92 0.00
#> TCGA.S9.A7IS.01 5 0.406 0.986 0.36 0.00 0.00 0.00 0.64
#> TCGA.S9.A89Z.01 2 0.311 0.810 0.00 0.84 0.00 0.02 0.14
#> TCGA.HT.A618.01 4 0.201 0.949 0.00 0.02 0.06 0.92 0.00
#> TCGA.RY.A83Z.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A5EU.01 5 0.406 0.986 0.36 0.00 0.00 0.00 0.64
#> TCGA.DB.A64X.01 2 0.000 0.833 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7477.01 3 0.165 0.947 0.00 0.00 0.94 0.02 0.04
#> TCGA.DU.7304.02 3 0.000 0.955 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6TS.01 2 0.526 0.730 0.00 0.68 0.00 0.18 0.14
#> TCGA.E1.A7YV.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7007.01 2 0.000 0.833 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.5277.01 2 0.715 0.496 0.00 0.48 0.18 0.04 0.30
#> TCGA.HT.7606.01 3 0.000 0.955 0.00 0.00 1.00 0.00 0.00
#> TCGA.E1.A7YK.01 4 0.201 0.932 0.00 0.06 0.00 0.92 0.02
#> TCGA.S9.A6TV.01 2 0.000 0.833 0.00 1.00 0.00 0.00 0.00
#> TCGA.HW.8319.01 4 0.201 0.949 0.00 0.02 0.06 0.92 0.00
#> TCGA.DU.A5TU.01 2 0.000 0.833 0.00 1.00 0.00 0.00 0.00
#> TCGA.HT.7686.01 4 0.201 0.949 0.00 0.02 0.06 0.92 0.00
#> TCGA.TQ.A7RM.01 3 0.141 0.915 0.00 0.00 0.94 0.00 0.06
#> TCGA.E1.5304.01 3 0.233 0.934 0.00 0.00 0.90 0.02 0.08
#> TCGA.HT.7470.01 4 0.201 0.932 0.00 0.06 0.00 0.92 0.02
#> TCGA.DU.7010.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6396.01 4 0.201 0.932 0.00 0.06 0.00 0.92 0.02
#> TCGA.FG.A87N.01 5 0.492 0.931 0.34 0.00 0.00 0.04 0.62
#> TCGA.FG.5965.02 5 0.406 0.986 0.36 0.00 0.00 0.00 0.64
#> TCGA.DH.A7UU.01 2 0.228 0.811 0.00 0.88 0.00 0.00 0.12
#> TCGA.TM.A84I.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.CS.6665.01 5 0.3198 0.957 0.26 0.00 0.00 0.00 0.74 0.00
#> TCGA.FG.A6J3.01 1 0.0547 0.986 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.E1.A7YI.01 1 0.0000 0.989 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7689.01 2 0.4460 0.544 0.00 0.70 0.00 0.24 0.04 0.02
#> TCGA.E1.A7YE.01 1 0.0000 0.989 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A7J0.01 2 0.0000 0.821 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6407.02 5 0.3409 0.958 0.30 0.00 0.00 0.00 0.70 0.00
#> TCGA.E1.A7YU.01 2 0.3483 0.698 0.00 0.82 0.00 0.12 0.04 0.02
#> TCGA.IK.7675.01 6 0.4067 0.782 0.00 0.26 0.00 0.00 0.04 0.70
#> TCGA.HT.8563.01 4 0.0000 0.948 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A7IS.01 5 0.3409 0.958 0.30 0.00 0.00 0.00 0.70 0.00
#> TCGA.S9.A89Z.01 2 0.2260 0.739 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.HT.A618.01 4 0.0937 0.937 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.RY.A83Z.01 1 0.0000 0.989 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.P5.A5EU.01 5 0.3198 0.957 0.26 0.00 0.00 0.00 0.74 0.00
#> TCGA.DB.A64X.01 2 0.0000 0.821 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7477.01 3 0.2981 0.801 0.00 0.00 0.82 0.00 0.02 0.16
#> TCGA.DU.7304.02 3 0.0000 0.866 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A6TS.01 2 0.5825 0.461 0.00 0.60 0.00 0.22 0.04 0.14
#> TCGA.E1.A7YV.01 1 0.0000 0.989 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7007.01 2 0.0000 0.821 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5277.01 6 0.2790 0.797 0.00 0.14 0.02 0.00 0.00 0.84
#> TCGA.HT.7606.01 3 0.0000 0.866 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YK.01 4 0.1480 0.940 0.00 0.00 0.00 0.94 0.04 0.02
#> TCGA.S9.A6TV.01 2 0.0000 0.821 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HW.8319.01 4 0.0937 0.937 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.DU.A5TU.01 2 0.0000 0.821 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7686.01 4 0.0547 0.946 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.TQ.A7RM.01 3 0.0937 0.851 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.E1.5304.01 3 0.5524 0.660 0.00 0.00 0.62 0.02 0.16 0.20
#> TCGA.HT.7470.01 4 0.1480 0.940 0.00 0.00 0.00 0.94 0.04 0.02
#> TCGA.DU.7010.01 1 0.0547 0.986 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DU.6396.01 4 0.1480 0.940 0.00 0.00 0.00 0.94 0.04 0.02
#> TCGA.FG.A87N.01 5 0.4711 0.923 0.28 0.00 0.00 0.00 0.64 0.08
#> TCGA.FG.5965.02 5 0.3309 0.963 0.28 0.00 0.00 0.00 0.72 0.00
#> TCGA.DH.A7UU.01 2 0.2048 0.746 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.TM.A84I.01 1 0.0547 0.986 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.CS.6665.01 5 0.1664 0.907 0.00 0.00 0.00 0.00 0.92 0.02 0.06
#> TCGA.FG.A6J3.01 1 0.4193 0.917 0.72 0.00 0.00 0.00 0.20 0.04 0.04
#> TCGA.E1.A7YI.01 1 0.2572 0.937 0.80 0.00 0.00 0.00 0.20 0.00 0.00
#> TCGA.HT.7689.01 2 0.4356 0.398 0.02 0.56 0.00 0.40 0.00 0.02 0.00
#> TCGA.E1.A7YE.01 1 0.2572 0.937 0.80 0.00 0.00 0.00 0.20 0.00 0.00
#> TCGA.S9.A7J0.01 2 0.0000 0.744 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6407.02 5 0.0863 0.903 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.E1.A7YU.01 2 0.4212 0.468 0.02 0.62 0.00 0.34 0.00 0.02 0.00
#> TCGA.IK.7675.01 6 0.3370 0.843 0.06 0.16 0.00 0.00 0.00 0.78 0.00
#> TCGA.HT.8563.01 4 0.3058 0.865 0.10 0.00 0.00 0.82 0.00 0.00 0.08
#> TCGA.S9.A7IS.01 5 0.0863 0.903 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.S9.A89Z.01 2 0.2708 0.595 0.00 0.78 0.00 0.00 0.00 0.22 0.00
#> TCGA.HT.A618.01 4 0.3284 0.863 0.10 0.00 0.00 0.80 0.00 0.00 0.10
#> TCGA.RY.A83Z.01 1 0.2572 0.937 0.80 0.00 0.00 0.00 0.20 0.00 0.00
#> TCGA.P5.A5EU.01 5 0.1664 0.907 0.00 0.00 0.00 0.00 0.92 0.02 0.06
#> TCGA.DB.A64X.01 2 0.0000 0.744 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7477.01 3 0.3667 0.433 0.00 0.00 0.74 0.00 0.00 0.20 0.06
#> TCGA.DU.7304.02 3 0.0000 0.806 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TS.01 2 0.5756 0.313 0.02 0.48 0.00 0.28 0.00 0.22 0.00
#> TCGA.E1.A7YV.01 1 0.2572 0.937 0.80 0.00 0.00 0.00 0.20 0.00 0.00
#> TCGA.DU.7007.01 2 0.0000 0.744 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5277.01 6 0.2163 0.833 0.02 0.10 0.00 0.00 0.00 0.88 0.00
#> TCGA.HT.7606.01 3 0.0000 0.806 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YK.01 4 0.0504 0.828 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.S9.A6TV.01 2 0.0000 0.744 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HW.8319.01 4 0.3284 0.863 0.10 0.00 0.00 0.80 0.00 0.00 0.10
#> TCGA.DU.A5TU.01 2 0.0000 0.744 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7686.01 4 0.3284 0.863 0.10 0.00 0.00 0.80 0.00 0.00 0.10
#> TCGA.TQ.A7RM.01 3 0.2016 0.738 0.00 0.00 0.90 0.00 0.00 0.04 0.06
#> TCGA.E1.5304.01 7 0.4938 0.000 0.00 0.00 0.32 0.02 0.00 0.08 0.58
#> TCGA.HT.7470.01 4 0.0504 0.828 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.DU.7010.01 1 0.4533 0.883 0.66 0.00 0.00 0.00 0.26 0.04 0.04
#> TCGA.DU.6396.01 4 0.1006 0.813 0.02 0.00 0.00 0.96 0.00 0.02 0.00
#> TCGA.FG.A87N.01 5 0.2572 0.792 0.00 0.00 0.00 0.00 0.80 0.00 0.20
#> TCGA.FG.5965.02 5 0.0863 0.912 0.00 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.DH.A7UU.01 2 0.2572 0.605 0.00 0.80 0.00 0.00 0.00 0.20 0.00
#> TCGA.TM.A84I.01 1 0.4533 0.883 0.66 0.00 0.00 0.00 0.26 0.04 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.CS.6665.01 5 0.1765 0.86126 0.00 0.00 0.00 0.12 0.88 0.00 0.00 0.00
#> TCGA.FG.A6J3.01 1 0.3385 0.88539 0.76 0.00 0.00 0.16 0.08 0.00 0.00 0.00
#> TCGA.E1.A7YI.01 1 0.1341 0.91623 0.92 0.00 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.HT.7689.01 2 0.5089 0.27616 0.00 0.52 0.00 0.32 0.00 0.02 0.00 0.14
#> TCGA.E1.A7YE.01 1 0.1341 0.91623 0.92 0.00 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.S9.A7J0.01 2 0.0000 0.70472 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.6407.02 5 0.0000 0.89613 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.E1.A7YU.01 2 0.4415 0.37623 0.00 0.60 0.00 0.32 0.00 0.02 0.00 0.06
#> TCGA.IK.7675.01 6 0.4604 0.43623 0.06 0.04 0.00 0.12 0.00 0.72 0.06 0.00
#> TCGA.HT.8563.01 8 0.0000 0.82943 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.S9.A7IS.01 5 0.0000 0.89613 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.S9.A89Z.01 2 0.4004 0.00482 0.00 0.50 0.00 0.04 0.00 0.46 0.00 0.00
#> TCGA.HT.A618.01 8 0.0808 0.82476 0.00 0.00 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.RY.A83Z.01 1 0.1341 0.91623 0.92 0.00 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.P5.A5EU.01 5 0.1563 0.86824 0.00 0.00 0.00 0.10 0.90 0.00 0.00 0.00
#> TCGA.DB.A64X.01 2 0.0000 0.70472 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7477.01 3 0.5838 0.32922 0.02 0.00 0.54 0.10 0.00 0.24 0.10 0.00
#> TCGA.DU.7304.02 3 0.0000 0.79395 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TS.01 6 0.5922 0.09865 0.00 0.26 0.00 0.20 0.00 0.46 0.00 0.08
#> TCGA.E1.A7YV.01 1 0.1341 0.91623 0.92 0.00 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.DU.7007.01 2 0.0000 0.70472 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5277.01 6 0.1408 0.38634 0.02 0.00 0.00 0.02 0.00 0.94 0.02 0.00
#> TCGA.HT.7606.01 3 0.0000 0.79395 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.A7YK.01 8 0.2650 0.78639 0.00 0.00 0.00 0.24 0.00 0.00 0.00 0.76
#> TCGA.S9.A6TV.01 2 0.0000 0.70472 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HW.8319.01 8 0.0808 0.82476 0.00 0.00 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.DU.A5TU.01 2 0.0000 0.70472 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.7686.01 8 0.0808 0.82476 0.00 0.00 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.TQ.A7RM.01 3 0.1341 0.77634 0.00 0.00 0.92 0.08 0.00 0.00 0.00 0.00
#> TCGA.E1.5304.01 7 0.2547 0.00000 0.00 0.00 0.12 0.00 0.00 0.04 0.84 0.00
#> TCGA.HT.7470.01 8 0.2650 0.78639 0.00 0.00 0.00 0.24 0.00 0.00 0.00 0.76
#> TCGA.DU.7010.01 1 0.3528 0.87811 0.74 0.00 0.00 0.18 0.08 0.00 0.00 0.00
#> TCGA.DU.6396.01 8 0.2650 0.78639 0.00 0.00 0.00 0.24 0.00 0.00 0.00 0.76
#> TCGA.FG.A87N.01 5 0.3970 0.61709 0.00 0.00 0.00 0.22 0.68 0.00 0.10 0.00
#> TCGA.FG.5965.02 5 0.0000 0.89613 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DH.A7UU.01 2 0.3299 0.11165 0.00 0.56 0.00 0.00 0.00 0.44 0.00 0.00
#> TCGA.TM.A84I.01 1 0.3528 0.87811 0.74 0.00 0.00 0.18 0.08 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node023. Child nodes: Node01211-leaf , Node01212-leaf , Node01213-leaf , Node02211 , Node02212 , Node02221 , Node02222-leaf , Node02223 , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02321-leaf , Node02322-leaf , Node02323-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 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 0.4401 0.560 0.560
#> 3 3 1.000 1.000 1.000 0.3991 0.824 0.686
#> 4 4 0.802 0.872 0.953 0.1279 0.923 0.800
#> 5 5 0.824 0.766 0.926 0.0784 0.967 0.893
#> 6 6 0.813 0.781 0.929 0.1082 0.868 0.520
#> 7 7 0.934 0.725 0.974 0.0501 0.978 0.846
#> 8 8 0.879 0.625 0.914 0.0254 1.000 1.000
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.CS.6665.01 1 0 1 1 0
#> TCGA.FG.A6J3.01 1 0 1 1 0
#> TCGA.E1.A7YI.01 2 0 1 0 1
#> TCGA.E1.A7YE.01 1 0 1 1 0
#> TCGA.DU.6407.02 1 0 1 1 0
#> TCGA.S9.A7IS.01 2 0 1 0 1
#> TCGA.RY.A83Z.01 1 0 1 1 0
#> TCGA.P5.A5EU.01 1 0 1 1 0
#> TCGA.E1.A7YV.01 1 0 1 1 0
#> TCGA.TQ.A7RM.01 1 0 1 1 0
#> TCGA.DU.7010.01 1 0 1 1 0
#> TCGA.FG.A87N.01 2 0 1 0 1
#> TCGA.FG.5965.02 2 0 1 0 1
#> TCGA.TM.A84I.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CS.6665.01 1 0 1 1 0 0
#> TCGA.FG.A6J3.01 1 0 1 1 0 0
#> TCGA.E1.A7YI.01 2 0 1 0 1 0
#> TCGA.E1.A7YE.01 1 0 1 1 0 0
#> TCGA.DU.6407.02 1 0 1 1 0 0
#> TCGA.S9.A7IS.01 2 0 1 0 1 0
#> TCGA.RY.A83Z.01 1 0 1 1 0 0
#> TCGA.P5.A5EU.01 3 0 1 0 0 1
#> TCGA.E1.A7YV.01 1 0 1 1 0 0
#> TCGA.TQ.A7RM.01 1 0 1 1 0 0
#> TCGA.DU.7010.01 1 0 1 1 0 0
#> TCGA.FG.A87N.01 2 0 1 0 1 0
#> TCGA.FG.5965.02 2 0 1 0 1 0
#> TCGA.TM.A84I.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.CS.6665.01 1 0.283 0.912 0.90 0.00 0.04 0.06
#> TCGA.FG.A6J3.01 1 0.283 0.912 0.90 0.00 0.04 0.06
#> TCGA.E1.A7YI.01 2 0.000 0.952 0.00 1.00 0.00 0.00
#> TCGA.E1.A7YE.01 1 0.000 0.941 1.00 0.00 0.00 0.00
#> TCGA.DU.6407.02 1 0.000 0.941 1.00 0.00 0.00 0.00
#> TCGA.S9.A7IS.01 2 0.000 0.952 0.00 1.00 0.00 0.00
#> TCGA.RY.A83Z.01 1 0.000 0.941 1.00 0.00 0.00 0.00
#> TCGA.P5.A5EU.01 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.E1.A7YV.01 1 0.000 0.941 1.00 0.00 0.00 0.00
#> TCGA.TQ.A7RM.01 4 0.380 0.000 0.22 0.00 0.00 0.78
#> TCGA.DU.7010.01 1 0.234 0.922 0.92 0.00 0.02 0.06
#> TCGA.FG.A87N.01 2 0.317 0.847 0.00 0.84 0.00 0.16
#> TCGA.FG.5965.02 2 0.000 0.952 0.00 1.00 0.00 0.00
#> TCGA.TM.A84I.01 3 0.000 1.000 0.00 0.00 1.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CS.6665.01 1 0.356 0.790 0.74 0.00 0 0.26 0.00
#> TCGA.FG.A6J3.01 1 0.356 0.790 0.74 0.00 0 0.26 0.00
#> TCGA.E1.A7YI.01 2 0.000 1.000 0.00 1.00 0 0.00 0.00
#> TCGA.E1.A7YE.01 1 0.000 0.837 1.00 0.00 0 0.00 0.00
#> TCGA.DU.6407.02 1 0.000 0.837 1.00 0.00 0 0.00 0.00
#> TCGA.S9.A7IS.01 2 0.000 1.000 0.00 1.00 0 0.00 0.00
#> TCGA.RY.A83Z.01 1 0.000 0.837 1.00 0.00 0 0.00 0.00
#> TCGA.P5.A5EU.01 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.E1.A7YV.01 1 0.000 0.837 1.00 0.00 0 0.00 0.00
#> TCGA.TQ.A7RM.01 4 0.443 0.000 0.20 0.00 0 0.74 0.06
#> TCGA.DU.7010.01 1 0.356 0.790 0.74 0.00 0 0.26 0.00
#> TCGA.FG.A87N.01 5 0.141 0.000 0.00 0.06 0 0.00 0.94
#> TCGA.FG.5965.02 2 0.000 1.000 0.00 1.00 0 0.00 0.00
#> TCGA.TM.A84I.01 3 0.000 1.000 0.00 0.00 1 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.CS.6665.01 6 0.3198 0.828 0.26 0.00 0 0 0 0.74
#> TCGA.FG.A6J3.01 6 0.3756 0.693 0.40 0.00 0 0 0 0.60
#> TCGA.E1.A7YI.01 2 0.2454 0.850 0.00 0.84 0 0 0 0.16
#> TCGA.E1.A7YE.01 1 0.0000 0.990 1.00 0.00 0 0 0 0.00
#> TCGA.DU.6407.02 1 0.0547 0.970 0.98 0.00 0 0 0 0.02
#> TCGA.S9.A7IS.01 2 0.0000 0.928 0.00 1.00 0 0 0 0.00
#> TCGA.RY.A83Z.01 1 0.0000 0.990 1.00 0.00 0 0 0 0.00
#> TCGA.P5.A5EU.01 3 0.0000 1.000 0.00 0.00 1 0 0 0.00
#> TCGA.E1.A7YV.01 1 0.0000 0.990 1.00 0.00 0 0 0 0.00
#> TCGA.TQ.A7RM.01 4 0.0000 0.000 0.00 0.00 0 1 0 0.00
#> TCGA.DU.7010.01 6 0.2454 0.772 0.16 0.00 0 0 0 0.84
#> TCGA.FG.A87N.01 5 0.0000 0.000 0.00 0.00 0 0 1 0.00
#> TCGA.FG.5965.02 2 0.0000 0.928 0.00 1.00 0 0 0 0.00
#> TCGA.TM.A84I.01 3 0.0000 1.000 0.00 0.00 1 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.CS.6665.01 6 0.0504 0.783 0.02 0.00 0 0 0 0.98 0.00
#> TCGA.FG.A6J3.01 6 0.3139 0.590 0.30 0.00 0 0 0 0.70 0.00
#> TCGA.E1.A7YI.01 7 0.0504 0.000 0.00 0.02 0 0 0 0.00 0.98
#> TCGA.E1.A7YE.01 1 0.0000 1.000 1.00 0.00 0 0 0 0.00 0.00
#> TCGA.DU.6407.02 1 0.0000 1.000 1.00 0.00 0 0 0 0.00 0.00
#> TCGA.S9.A7IS.01 2 0.0000 1.000 0.00 1.00 0 0 0 0.00 0.00
#> TCGA.RY.A83Z.01 1 0.0000 1.000 1.00 0.00 0 0 0 0.00 0.00
#> TCGA.P5.A5EU.01 3 0.0000 1.000 0.00 0.00 1 0 0 0.00 0.00
#> TCGA.E1.A7YV.01 1 0.0000 1.000 1.00 0.00 0 0 0 0.00 0.00
#> TCGA.TQ.A7RM.01 4 0.0000 0.000 0.00 0.00 0 1 0 0.00 0.00
#> TCGA.DU.7010.01 6 0.0504 0.771 0.00 0.00 0 0 0 0.98 0.02
#> TCGA.FG.A87N.01 5 0.0000 0.000 0.00 0.00 0 0 1 0.00 0.00
#> TCGA.FG.5965.02 2 0.0000 1.000 0.00 1.00 0 0 0 0.00 0.00
#> TCGA.TM.A84I.01 3 0.0000 1.000 0.00 0.00 1 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.CS.6665.01 6 0.0000 0.707 0.00 0 0.00 0 0 1.00 0 0.00
#> TCGA.FG.A6J3.01 6 0.3934 0.584 0.14 0 0.00 0 0 0.70 0 0.16
#> TCGA.E1.A7YI.01 7 0.0000 0.000 0.00 0 0.00 0 0 0.00 1 0.00
#> TCGA.E1.A7YE.01 8 0.0471 0.951 0.02 0 0.00 0 0 0.00 0 0.98
#> TCGA.DU.6407.02 8 0.2224 0.876 0.12 0 0.00 0 0 0.02 0 0.86
#> TCGA.S9.A7IS.01 2 0.0000 1.000 0.00 1 0.00 0 0 0.00 0 0.00
#> TCGA.RY.A83Z.01 8 0.0000 0.953 0.00 0 0.00 0 0 0.00 0 1.00
#> TCGA.P5.A5EU.01 3 0.0000 0.549 0.00 0 1.00 0 0 0.00 0 0.00
#> TCGA.E1.A7YV.01 8 0.0000 0.953 0.00 0 0.00 0 0 0.00 0 1.00
#> TCGA.TQ.A7RM.01 4 0.0000 0.000 0.00 0 0.00 1 0 0.00 0 0.00
#> TCGA.DU.7010.01 6 0.2756 0.629 0.26 0 0.00 0 0 0.74 0 0.00
#> TCGA.FG.A87N.01 5 0.0000 0.000 0.00 0 0.00 0 1 0.00 0 0.00
#> TCGA.FG.5965.02 2 0.0000 1.000 0.00 1 0.00 0 0 0.00 0 0.00
#> TCGA.TM.A84I.01 3 0.3329 0.549 0.48 0 0.52 0 0 0.00 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: Node023. Child nodes: Node01211-leaf , Node01212-leaf , Node01213-leaf , Node02211 , Node02212 , Node02221 , Node02222-leaf , Node02223 , Node02311-leaf , Node02312-leaf , Node02313-leaf , Node02321-leaf , Node02322-leaf , Node02323-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0232"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 23 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.973 0.989 0.5164 0.486 0.486
#> 3 3 1.000 1.000 1.000 0.3096 0.806 0.614
#> 4 4 0.753 0.828 0.868 0.0878 1.000 1.000
#> 5 5 0.719 0.693 0.811 0.0548 0.984 0.951
#> 6 6 0.738 0.623 0.700 0.0475 0.818 0.425
#> 7 7 0.714 0.707 0.737 0.0278 0.976 0.842
#> 8 8 0.738 0.758 0.810 0.0417 0.945 0.622
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.HT.7689.01 1 0.000 0.978 1.00 0.00
#> TCGA.S9.A7J0.01 2 0.000 1.000 0.00 1.00
#> TCGA.E1.A7YU.01 1 0.000 0.978 1.00 0.00
#> TCGA.IK.7675.01 2 0.000 1.000 0.00 1.00
#> TCGA.HT.8563.01 1 0.000 0.978 1.00 0.00
#> TCGA.S9.A89Z.01 2 0.000 1.000 0.00 1.00
#> TCGA.HT.A618.01 1 0.000 0.978 1.00 0.00
#> TCGA.DB.A64X.01 1 0.827 0.649 0.74 0.26
#> TCGA.HT.7477.01 2 0.000 1.000 0.00 1.00
#> TCGA.DU.7304.02 2 0.000 1.000 0.00 1.00
#> TCGA.S9.A6TS.01 2 0.000 1.000 0.00 1.00
#> TCGA.DU.7007.01 1 0.000 0.978 1.00 0.00
#> TCGA.DB.5277.01 2 0.000 1.000 0.00 1.00
#> TCGA.HT.7606.01 2 0.000 1.000 0.00 1.00
#> TCGA.E1.A7YK.01 1 0.000 0.978 1.00 0.00
#> TCGA.S9.A6TV.01 1 0.000 0.978 1.00 0.00
#> TCGA.HW.8319.01 1 0.000 0.978 1.00 0.00
#> TCGA.DU.A5TU.01 1 0.000 0.978 1.00 0.00
#> TCGA.HT.7686.01 1 0.000 0.978 1.00 0.00
#> TCGA.E1.5304.01 2 0.000 1.000 0.00 1.00
#> TCGA.HT.7470.01 1 0.000 0.978 1.00 0.00
#> TCGA.DU.6396.01 1 0.000 0.978 1.00 0.00
#> TCGA.DH.A7UU.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.HT.7689.01 1 0 1 1 0 0
#> TCGA.S9.A7J0.01 2 0 1 0 1 0
#> TCGA.E1.A7YU.01 1 0 1 1 0 0
#> TCGA.IK.7675.01 2 0 1 0 1 0
#> TCGA.HT.8563.01 1 0 1 1 0 0
#> TCGA.S9.A89Z.01 2 0 1 0 1 0
#> TCGA.HT.A618.01 1 0 1 1 0 0
#> TCGA.DB.A64X.01 3 0 1 0 0 1
#> TCGA.HT.7477.01 2 0 1 0 1 0
#> TCGA.DU.7304.02 2 0 1 0 1 0
#> TCGA.S9.A6TS.01 2 0 1 0 1 0
#> TCGA.DU.7007.01 3 0 1 0 0 1
#> TCGA.DB.5277.01 2 0 1 0 1 0
#> TCGA.HT.7606.01 2 0 1 0 1 0
#> TCGA.E1.A7YK.01 1 0 1 1 0 0
#> TCGA.S9.A6TV.01 3 0 1 0 0 1
#> TCGA.HW.8319.01 1 0 1 1 0 0
#> TCGA.DU.A5TU.01 3 0 1 0 0 1
#> TCGA.HT.7686.01 1 0 1 1 0 0
#> TCGA.E1.5304.01 3 0 1 0 0 1
#> TCGA.HT.7470.01 1 0 1 1 0 0
#> TCGA.DU.6396.01 1 0 1 1 0 0
#> TCGA.DH.A7UU.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 1 0.361 0.852 0.80 0.00 0.20 0.00
#> TCGA.S9.A7J0.01 2 0.452 0.813 0.00 0.68 0.32 0.00
#> TCGA.E1.A7YU.01 1 0.361 0.852 0.80 0.00 0.20 0.00
#> TCGA.IK.7675.01 2 0.292 0.749 0.00 0.86 0.14 0.00
#> TCGA.HT.8563.01 1 0.164 0.890 0.94 0.00 0.06 0.00
#> TCGA.S9.A89Z.01 2 0.380 0.843 0.00 0.78 0.22 0.00
#> TCGA.HT.A618.01 1 0.201 0.882 0.92 0.00 0.08 0.00
#> TCGA.DB.A64X.01 4 0.000 0.880 0.00 0.00 0.00 1.00
#> TCGA.HT.7477.01 2 0.292 0.749 0.00 0.86 0.14 0.00
#> TCGA.DU.7304.02 2 0.380 0.843 0.00 0.78 0.22 0.00
#> TCGA.S9.A6TS.01 2 0.234 0.777 0.00 0.90 0.10 0.00
#> TCGA.DU.7007.01 4 0.000 0.880 0.00 0.00 0.00 1.00
#> TCGA.DB.5277.01 2 0.413 0.837 0.00 0.74 0.26 0.00
#> TCGA.HT.7606.01 2 0.121 0.802 0.00 0.96 0.04 0.00
#> TCGA.E1.A7YK.01 1 0.121 0.887 0.96 0.00 0.04 0.00
#> TCGA.S9.A6TV.01 4 0.000 0.880 0.00 0.00 0.00 1.00
#> TCGA.HW.8319.01 1 0.201 0.882 0.92 0.00 0.08 0.00
#> TCGA.DU.A5TU.01 4 0.121 0.864 0.00 0.00 0.04 0.96
#> TCGA.HT.7686.01 1 0.201 0.882 0.92 0.00 0.08 0.00
#> TCGA.E1.5304.01 4 0.760 0.424 0.00 0.20 0.38 0.42
#> TCGA.HT.7470.01 1 0.121 0.887 0.96 0.00 0.04 0.00
#> TCGA.DU.6396.01 1 0.361 0.852 0.80 0.00 0.20 0.00
#> TCGA.DH.A7UU.01 2 0.380 0.843 0.00 0.78 0.22 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.HT.7689.01 1 0.5232 0.670 0.60 0.34 0.00 0.00 0.06
#> TCGA.S9.A7J0.01 3 0.4254 0.617 0.00 0.22 0.74 0.00 0.04
#> TCGA.E1.A7YU.01 1 0.5232 0.670 0.60 0.34 0.00 0.00 0.06
#> TCGA.IK.7675.01 3 0.5673 0.508 0.00 0.42 0.50 0.00 0.08
#> TCGA.HT.8563.01 1 0.3106 0.765 0.84 0.14 0.00 0.00 0.02
#> TCGA.S9.A89Z.01 3 0.0000 0.730 0.00 0.00 1.00 0.00 0.00
#> TCGA.HT.A618.01 1 0.2280 0.747 0.88 0.00 0.00 0.00 0.12
#> TCGA.DB.A64X.01 4 0.0000 0.939 0.00 0.00 0.00 1.00 0.00
#> TCGA.HT.7477.01 3 0.5673 0.508 0.00 0.42 0.50 0.00 0.08
#> TCGA.DU.7304.02 3 0.0000 0.730 0.00 0.00 1.00 0.00 0.00
#> TCGA.S9.A6TS.01 3 0.5157 0.549 0.00 0.44 0.52 0.00 0.04
#> TCGA.DU.7007.01 4 0.0000 0.939 0.00 0.00 0.00 1.00 0.00
#> TCGA.DB.5277.01 3 0.1410 0.714 0.00 0.06 0.94 0.00 0.00
#> TCGA.HT.7606.01 3 0.4540 0.642 0.00 0.34 0.64 0.00 0.02
#> TCGA.E1.A7YK.01 1 0.2020 0.761 0.90 0.00 0.00 0.00 0.10
#> TCGA.S9.A6TV.01 4 0.0609 0.930 0.00 0.02 0.00 0.98 0.00
#> TCGA.HW.8319.01 1 0.2280 0.747 0.88 0.00 0.00 0.00 0.12
#> TCGA.DU.A5TU.01 4 0.2020 0.838 0.00 0.00 0.00 0.90 0.10
#> TCGA.HT.7686.01 1 0.2280 0.747 0.88 0.00 0.00 0.00 0.12
#> TCGA.E1.5304.01 5 0.5382 0.000 0.00 0.10 0.00 0.26 0.64
#> TCGA.HT.7470.01 1 0.2020 0.761 0.90 0.00 0.00 0.00 0.10
#> TCGA.DU.6396.01 1 0.5355 0.696 0.66 0.22 0.00 0.00 0.12
#> TCGA.DH.A7UU.01 3 0.0000 0.730 0.00 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.HT.7689.01 6 0.3706 0.8735 0.38 0.00 0.00 0.00 0.00 0.62
#> TCGA.S9.A7J0.01 5 0.6618 0.0843 0.00 0.20 0.20 0.00 0.52 0.08
#> TCGA.E1.A7YU.01 6 0.3706 0.8735 0.38 0.00 0.00 0.00 0.00 0.62
#> TCGA.IK.7675.01 2 0.0000 0.6324 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8563.01 1 0.3409 -0.1588 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.S9.A89Z.01 3 0.3797 0.9861 0.00 0.42 0.58 0.00 0.00 0.00
#> TCGA.HT.A618.01 1 0.0000 0.7040 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64X.01 4 0.0547 0.9147 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.HT.7477.01 2 0.0000 0.6324 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DU.7304.02 3 0.3797 0.9861 0.00 0.42 0.58 0.00 0.00 0.00
#> TCGA.S9.A6TS.01 5 0.5235 -0.0817 0.00 0.38 0.10 0.00 0.52 0.00
#> TCGA.DU.7007.01 4 0.0000 0.9170 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DB.5277.01 3 0.3828 0.9576 0.00 0.44 0.56 0.00 0.00 0.00
#> TCGA.HT.7606.01 2 0.5235 -0.0664 0.00 0.52 0.10 0.00 0.38 0.00
#> TCGA.E1.A7YK.01 1 0.4495 0.5739 0.72 0.00 0.02 0.00 0.20 0.06
#> TCGA.S9.A6TV.01 4 0.1267 0.9005 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.HW.8319.01 1 0.0000 0.7040 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TU.01 4 0.2454 0.8130 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.HT.7686.01 1 0.0000 0.7040 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5304.01 5 0.8501 0.0984 0.00 0.12 0.16 0.12 0.32 0.28
#> TCGA.HT.7470.01 1 0.4495 0.5739 0.72 0.00 0.02 0.00 0.20 0.06
#> TCGA.DU.6396.01 6 0.6152 0.7313 0.40 0.00 0.16 0.00 0.02 0.42
#> TCGA.DH.A7UU.01 3 0.3797 0.9861 0.00 0.42 0.58 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.HT.7689.01 6 0.3221 0.852 0.32 0.00 0.00 0.00 0.00 0.68 0.00
#> TCGA.S9.A7J0.01 5 0.1166 0.453 0.00 0.06 0.00 0.00 0.94 0.00 0.00
#> TCGA.E1.A7YU.01 6 0.3221 0.852 0.32 0.00 0.00 0.00 0.00 0.68 0.00
#> TCGA.IK.7675.01 2 0.0000 0.925 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.8563.01 1 0.3780 0.296 0.72 0.00 0.02 0.00 0.00 0.24 0.02
#> TCGA.S9.A89Z.01 3 0.5378 0.944 0.00 0.22 0.48 0.00 0.30 0.00 0.00
#> TCGA.HT.A618.01 1 0.0000 0.674 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DB.A64X.01 4 0.0504 0.886 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.HT.7477.01 2 0.1664 0.925 0.00 0.92 0.02 0.00 0.00 0.06 0.00
#> TCGA.DU.7304.02 3 0.5378 0.944 0.00 0.22 0.48 0.00 0.30 0.00 0.00
#> TCGA.S9.A6TS.01 5 0.6177 0.649 0.00 0.22 0.02 0.00 0.52 0.20 0.04
#> TCGA.DU.7007.01 4 0.0000 0.888 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DB.5277.01 3 0.5233 0.833 0.00 0.28 0.52 0.00 0.20 0.00 0.00
#> TCGA.HT.7606.01 5 0.6046 0.592 0.00 0.32 0.00 0.00 0.44 0.20 0.04
#> TCGA.E1.A7YK.01 1 0.4718 0.479 0.60 0.00 0.32 0.00 0.00 0.06 0.02
#> TCGA.S9.A6TV.01 4 0.2857 0.821 0.00 0.00 0.04 0.86 0.04 0.06 0.00
#> TCGA.HW.8319.01 1 0.0000 0.674 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DU.A5TU.01 4 0.2376 0.802 0.00 0.00 0.12 0.86 0.00 0.00 0.02
#> TCGA.HT.7686.01 1 0.0000 0.674 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.E1.5304.01 7 0.1664 0.000 0.00 0.00 0.00 0.06 0.02 0.00 0.92
#> TCGA.HT.7470.01 1 0.4718 0.479 0.60 0.00 0.32 0.00 0.00 0.06 0.02
#> TCGA.DU.6396.01 6 0.6324 0.668 0.36 0.00 0.12 0.00 0.02 0.44 0.06
#> TCGA.DH.A7UU.01 3 0.5378 0.944 0.00 0.22 0.48 0.00 0.30 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.7689.01 6 0.1947 0.679 0.00 0.00 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.S9.A7J0.01 5 0.6043 0.474 0.28 0.10 0.18 0.00 0.44 0.00 0.00 0.00
#> TCGA.E1.A7YU.01 6 0.2404 0.679 0.00 0.00 0.00 0.00 0.02 0.84 0.00 0.14
#> TCGA.IK.7675.01 2 0.3729 0.908 0.00 0.72 0.10 0.00 0.18 0.00 0.00 0.00
#> TCGA.HT.8563.01 6 0.5593 -0.109 0.26 0.02 0.00 0.00 0.00 0.38 0.00 0.34
#> TCGA.S9.A89Z.01 3 0.0000 0.984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HT.A618.01 1 0.3992 1.000 0.52 0.00 0.00 0.00 0.00 0.04 0.00 0.44
#> TCGA.DB.A64X.01 4 0.0471 0.815 0.00 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.HT.7477.01 2 0.5452 0.908 0.02 0.62 0.10 0.00 0.20 0.04 0.02 0.00
#> TCGA.DU.7304.02 3 0.0000 0.984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.S9.A6TS.01 5 0.1563 0.719 0.00 0.00 0.10 0.00 0.90 0.00 0.00 0.00
#> TCGA.DU.7007.01 4 0.0000 0.816 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DB.5277.01 3 0.0941 0.952 0.00 0.00 0.96 0.00 0.02 0.00 0.02 0.00
#> TCGA.HT.7606.01 5 0.2025 0.712 0.00 0.02 0.10 0.00 0.88 0.00 0.00 0.00
#> TCGA.E1.A7YK.01 8 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.S9.A6TV.01 4 0.4988 0.625 0.06 0.14 0.00 0.68 0.04 0.08 0.00 0.00
#> TCGA.HW.8319.01 1 0.3992 1.000 0.52 0.00 0.00 0.00 0.00 0.04 0.00 0.44
#> TCGA.DU.A5TU.01 4 0.2267 0.717 0.00 0.00 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.HT.7686.01 1 0.3992 1.000 0.52 0.00 0.00 0.00 0.00 0.04 0.00 0.44
#> TCGA.E1.5304.01 7 0.1887 0.000 0.00 0.00 0.00 0.04 0.06 0.00 0.90 0.00
#> TCGA.HT.7470.01 8 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DU.6396.01 6 0.6057 0.586 0.20 0.02 0.00 0.00 0.02 0.56 0.08 0.12
#> TCGA.DH.A7UU.01 3 0.0000 0.984 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
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